Fixes#7159
When activating extensions in external views, the --ignore-conflicts
option was being ignored. In this particular issue the conflict was
for the duplicate __init__ file for multiple python packages in the
same namespace, but in general any conflict for extensions would
cause an error whether or not --ignore-conflicts was set.
This also renames the 'force' option of do_activate to
'with_dependencies' and updates views to call do_activate with this
set to False (since it traverses the dependency dag anyway). This
isn't strictly required, it just avoids redundant calls.
This reorganizes most sections and rewords a significant portion of
the content (including all introductions) but keeps all the examples.
* Remove section 'What happens at subscript time' from tutorial:
it is too detailed for a tutorial
* Move the 'Extra query parameters' and 'Attach attributes to other
packages' sections into a separate grouping 'Other packaging topics'
* move the 'Set variables at build time yourself' section after
'Set environment variables in dependents' section since the latter
is more motivating
* start the 'set environment variables at build-time for yourself'
section with qt as an example
* renamed section 'specs build interface' to 'retrieving library
information' and updated section introduction
* renamed section 'a motivating example' to 'accessing library
dependencies'; split out the material which deals with implementing
.libs for netlib-lapack into a separate section called 'providing
libraries to dependents'. consolidated in material from the section
'single package providing multiple virtual specs' since
netlib-lapack is an example of this (this removes the material
about intel-parallel studio)
* Allow dashes in command names and fix command name handling
- Command should allow dashes in their names like the reest of spack,
e.g. `spack log-parse`
- It might be too late for `spack build-cache` (since it is already
called `spack buildcache`), but we should try a bit to avoid
inconsistencies in naming conventions
- The code was inconsistent about where commands should be called by
their python module name (e.g. `log_parse`) and where the actual
command name should be used (e.g. `log-parse`).
- This made it hard to make a command with a dash in the name, and it
made `SpackCommand` fail to recognize commands with dashes.
- The code now uses the user-facing name with dashes for function
parameters, then converts that the module name when needed.
* Improve performance of log parsing
- A number of regular expressions from ctest_log_parser have really poor
performance, most due to untethered expressions with * or + (i.e., they
don't start with ^, so the repetition has to be checked for every
position in the string with Python's backtracking regex implementation)
- I can't verify that CTest's regexes work with an added ^, so I don't
really want to touch them. I tried adding this and found that it
caused some tests to break.
- Instead of using only "efficient" regular expressions, Added a
prefilter() class that allows the parser to quickly check a
precondition before evaluating any of the expensive regexes.
- Preconditions do things like check whether the string contains "error"
or "warning" (linear time things) before evaluating regexes that would
require them. It's sad that Python doesn't use Thompson string
matching (see https://swtch.com/~rsc/regexp/regexp1.html)
- Even with Python's slow implementation, this makes the parser ~200x
faster on the input we tried it on.
* Add `spack log-parse` command and improve the display of parsed logs
- Add better coloring and line wrapping to the log parse output. This
makes nasty build output look better with the line numbers.
- `spack log-parse` allows the log parsing logic used at the end of
builds to be executed on arbitrary files, which is handy even outside
of spack.
- Also provides a profile option -- we can profile arbitrary files and
show which regular expressions in the magic CTest parser take the most
time.
* Parallelize log parsing
- Log parsing now uses multiple threads for long logs
- Lines from logs are divided into chnks and farmed out to <ncpus>
- Add -j option to `spack log-parse`
* libdwarf: fix linker flags
* libdwarf: fix header install names
* libdwarf: add zlib dependency
Prior to this commit, libdwarf was linked to the system zlib. This
commit links it to spack-installed zlib.
* libdwarf: fix dynamic library suffix for Darwin
* Adding support for the Accelerate library on OS X
* Fixed guard on variable and added another depends_on statement to make sure that openblas gets selected even when openmp_blas variant is not turned on.
* Added a package for the MDAnalysis toolkit.
* Added some flags to fix the build RPATHs and OpenMP for LBANN on OS X.
* Fixed Hydrogen branch of Elemental to find OpenMP on OS X.
* Marking database tests as slow
* Marking url command tests as slow
* Marking every test that uses database as slow
* Marking tests that import files as slow
* Marking gpg tests as slow
* Marking all versions and one list tests as slow
* Added more markers to unit tests + cli option to skip slow tests
Following a discussion with Axel, the generic 'slowtest' marker has been
split into 'db', 'network' and 'maybeslow'. A brief description of the
meaning of each marker has been added to pytest.ini.
A command line option to run only fast tests has been added to
'spack test'
* Don't use classes to group tests together
Reverted grouping tests under a class, as required in the review
* Minor style changes
This attempts to address one of the complaints at #5996 (comment):
> Repo currently caches package instances by Spec, and those Package instances have a Spec.
> This is unnecessary and causes confusion. I think I thought that we'd need to cache instances
> after loading package classes, but really just caching the classes is fine.
With this update, Repo's package cache is removed and Specs cache the package reference themselves. One consequence is that Specs which compare as equal will store separate instances of a Package class (not doing this creates issues for #4595 (comment)).
There were several references to Spec.package that could be replaced with Spec.package_class without any additional modifications. There are still a couple remaining references to Spec.package in Spec that would require adding functionality before replacing (e.g. calling Package.provides and Package.installed).
Note this makes it difficult to mock fetchers for tests which invokes code that reconstructs specs. test_packaging was one example of this where the updates caused a failure (in that case the error was avoided by not making an unnecessary call).
Details:
* Replace instances of spec.package with spec.package_class where a class method is being called
* Remove instances of Repo.get where Spec.package_class can be used in its place
* remove Repo.get caching instances of Package class for specs
* remove redundant check (which is also incorrect now that each spec stores its own copy of its package)
* avoid creating mirror with specs because it copies specs and those copies dont refer to the mocked fetcher (and it is also not required for the test)
* remove checks that are no longer necessary since repo doesn't cache specs
* Cleaned up JUnit report generation on install
The generation of a JUnit report was previously part of the install
command. This commit factors the logic into its own module, and uses
a template for the generation of the report.
It also improves report generation, that now can deal with multiple
specs installed at once. Finally, extending the list of supported
formats is much easier than before, as it entails just writing a
new template.
* Polished report generation + added tests for failures and errors
The generation of a JUnit report has been polished, so that the
stacktrace is correctly displayed with Jenkins JUnit plugin. Standard
error is still not used.
Added unit tests to cover for installation failures and installation
errors.
* libtool: fix linking of libtool on darwin
* binutils, libtool: fix conflicts w/ BSD tools, v2
Fix namespace conflicts with BSD tools in a more elegant fashion,
using a program prefix, similar to Homebrew.
* Tell R's configure about tcltk config
Add configure arguments that specify the location of
the tcl and tk config scripts.
Fixes#7072
* Flake8 cleanup
Looking at build logs, it seems that prior to this commit bzip2 was
using 'cc', and relying on the PATH to be set correctly to find Spack
wrappers. This commit improves the robustness of the recipe, by using
the absolute path of the wrapper.
Avoid adding an "outside" (local home's) python user site directory
during python package installs.
Implements #6611
Fixes packages with auto-find side effects such as `py-setuptools`
that cause `py-matplotlib` to fail to build #6558
On Darwin and other BSD systems, the system 'libtool' and 'libtoolize'
are BSD libtool and libtoolize, respectively. Some build systems
require the GNU versions of these commands, so BSD package systems
tend to name the GNU versions 'glibtool' and 'glibtoolize',
respectively, to avoid namespace collisions.
A problem with the current libtool package is that it installs the GNU
libtool commands as 'libtool' and 'libtoolize', respectively, but
build systems on BSD platforms will attempt to run 'glibtool' and
'glibtoolize'. The expedient solution to this problem is to symlink
'libtool' to 'glibtool' and 'libtoolize' to 'glibtoolize', because
attempting to patch the detection logic one build system at a time
seems impractical.
* Added new link line flag
* Refactored some of the common components out of the different
version's build commands. Also corrected the when commands to
properly capture non-numeric names such as local.
* Added support to the Elemental package for the Hydrogen branch.
* Turning off default Qt support. Restricting Qt version to <= 4.9 else geant4 won't build
* Making vecgeom optional
* Differentiating between cxx11 and cxx14 support
* Making vecgeom optional. Part 2. forgot to move usolids option
* Adding explicit CXX11 and CXX14 support
* Adding more clhep version to support newer GEANT4 versions
* Adding GEANT4 versions 10.03.p03 and 10.04
* Checkpoint. Adding opengl and x11 variant. Lead up to more changes to enable X11 support
* Adding dependency on fixesproto for newer versions
* Making the X11 dependent pieces work without requiring X11 on the system
* Adding motif
This provides options for hardware and software rendering with the
gl API and updates the vtk package to make use of those options:
* Create new "gl" virtual package, provided by mesa
* Add external-only "opengl" package, which represents a system
install that provides gl
* For vtk: prefer system gl implementation by default to get speed
up from hardware rendering. When software rendering is specifically
requested (+osmesa), try to use the llvmpipe approach, as it is
much faster.
* Make qt dependency optional for vtk
* Add basic support for VTK on osx
* qt: Depend on virtual gl package, rather than mesa impl
* visit: add version 2.12.3
* visit: add version 2.13.0
* visit: enable building with hdf5+mpi
* visit: add qwt dependency
Building VisIt requires Qwt, which is not part of Qt. Prior to this
commit, this dependency was not included in the VisIt spack package,
resulting in a configure-time bug with an error message indicating a
missing Qwt dependency.
This commit fixes this bug by adding Qwt dependency information.
* Revert "Travis: use --concurrency=multiprocessing only on build tests (#6872)"
This reverts commit 596d463714.
* Removing 'coverage combine' in test script
According to what was discovered in #6887, one of the problems is
calling 'coverage combine' twice without the '-a' flag. This removes
the first call within our test scripts.
Update the qt4 CoreWLAN patch to apply to macOS/OS X 10.12 and 10.13,
which both still use the CoreWLAN framework in their SDKs (although
it's apparently deprecated?!). Without this patch update, `spack
install qt@4.8.6` fails on macOS/OS X 10.12 because the linker
cannot find headers from the CoreWLAN framework.
Apple removed support for Objective-C garbage collection in binaries
in XCode 5.1, but VTK 6.1.0 and earlier set flags for garbage
collection, resulting in a compile-time bug when compiling VTK using
any recent version of XCode (i.e., Apple Clang).
This commit fixes this bug by removing the garbage collection flags
via setting the variable `VTK_REQUIRED_OBJCXX_FLAGS` to the empty
string. This variable has the same value (i.e., the empty string) in
the root-level CMakeLists.txt file for VTK 6.2.0 and later.
VTK 6.1.0 and earlier do not use paths stored in `NETCDF_CXX_ROOT` to
detect the presence of NetCDF C++ headers and libraries. Consequently,
VTK 6.1.0 does not build.
This commit fixes this bug by setting the advanced variables
`NETCDF_CXX_INCLUDE_DIR` and `NETCDF_CXX_LIBRARY` at the command line
to specify the directory containing headers and the full library path
for the NetCDF C++ bindings.
The flag_handlers method was being set as a bound method, but when
reset in the package.py file it was being set as an unbound method
(all python2 issues). This gets the underlying function information,
which is the same in either case.
The bug was uncovered for parmetis in #6858. This is a partial fix.
Included are changes to the parmetis package.py file to make use of
flag_handlers.
This makes use of the new flag_handler logic from 28d8784a to set
compiler flags for ipopt by passing them as arguments to the build
system rather than injecting them into the compiler wrappers. This
avoids conflicts between flags that are chosen by the build system
and flags that are set by the user.
The feature added in #4611 is currently broken. This commit fixes the
behavior of the command and adds unit tests to ensure the basic semantic
is maintained.
It also changes slightly the behavior of Spec.concretized to avoid
copying caches before the concretization (as this may result in a
wrong hash computation for the DAG).
- Generating the HTML from for >2300 packages from RST in Sphinx seems to
take forever.
- Add an option to `spack list` to generate straight HTML instead.
- This reduces the doc build time to about a minute (from 5 minutes on a mac laptop).
* Vendor ordereddict for python2.6 only
This commit substitutes the custom module 'ordereddict_backport' with
the more known 'ordereddict' and vendors it only for python 2.6. Other
supported versions of python will use 'collections.OrderedDict'.
* Use absolute imports also for python 2.6
See PEP-328 for more information on the subject
* Added provenance of vendored ordereddict
* ruby: fix +openssl & +readline variants
Fix "unqualified variable spec['openssl']" error in the ruby package
that arises when trying to install the `+openssl` variant by
referencing the `spec` field in the `Ruby` class. A similar error
arises when trying to install the `+readline` variant; this error is
also fixed by this patch.
* ruby: make +openssl variant default to on
Ruby's gem command will fetch gems from HTTPS resources by default
(e.g., gem install bundler). Without openssl, request to fetch gems
bounce back with the error
```
ERROR: While executing gem ... (Gem::Exception)
Unable to require openssl, install OpenSSL and rebuild ruby (preferred) or use non-HTTPS sources
```
Without the ability to install gems -- required for some spack
packages -- the ruby installation has limited utility for many users.
* ruby: update rubygems ssl cert to fix ssl errors
The SSL certificate bundled with Ruby 2.2.0 is outdated, so e.g., `gem
install erubis` will fail with an SSL certificate error. This commit
installs the updated SSL certificate to the proper directory so that
gems can be downloaded and installed from RubyGems.
The url in graphviz has been fixed and its version has been
updated to the latest available (2.40.1). Added variants for
expat, qt, gtk+ and ghostscript.
* py-fparser: parser for Fortran 77..2003 code
* py-fparser: guard against external pytest.ini
* py-fparser: define 'develop' version as latest master branch
* py-fparser: fetch tagged versions from git repo
* py-fparser: add latest release 0.0.6
* py-fparser: whitespace adjustments for flake8
* py-fparser: inherit python dependency from PythonPackage
* py-fparser: rely on spack to resolve sub-dependencies
* py-fparser: try type='test' for py-pytest
* py-fparser: fetch release tarballs instead of git commits
* py-fparser: test deptype is available, remove comment
* py-fparser: limit versions that use py-six
* py-fparser: version ranges do not need a lower bound
* qt: move licence acceptance from qt3krell.patch to qt3accept.patch
* qt: ensure that ptrdiff_t is defined for qt@3.3.8b
* qt: disable webglplugin for qt@5.10~opengl
* qt: depend on libxext (for qt@3 and @4)
* qt: avoid X dependencies on darwin platforms
* Revert "qt: avoid X dependencies on darwin platforms"
This reverts commit 05ce08de94.
* qt: limit range of versions depending on libxext
See #6794
This fixes cases where test-only dependencies were omitted from
consideration when modifying the environment at build time. This
includes an update to the python package definition to add
testing-related python extensions to its specialized environment
setup.
* coinhsl: add version 2014.01.10 (stable)
* coinhsl: make 2014.01.10 preferred version
Make Harwell Subroutines Library for IPOPT version 2014.01.10 the
preferred version because it is the latest stable version released.
* coinhsl: add option to link w/ BLAS libraries
This updates the conflict-checking logic to require that the conflict
spec matches exactly and that all fields mentioned in the conflict
spec are present in the concretized spec in order to report a
conflict. This will automatically skip all conflict checks for
dependencies of externals (since externals strip dependencies). This
will not affect non-external packages since all fields and
dependencies are fully specified for such packages.
According to Travis docs the exit code of after_success doesn't affect
the build result. Instead, uploading the coverage data as the last step
of the script will cause the job to fail if the command exits with
non-zero.
https://docs.travis-ci.com/user/customizing-the-build/#Breaking-the-Build
* Keep track of source and versions for external libraries
* Note source of more obscure libraries
* We aren't upgrading jsonschema after all
* Add note on modifications made to pytest
On a local workstation, it seems that tracking multiple processes during
coverage may result in malformed coverage reports for unit tests and not
for build tests.
Given that multiple processes make a difference in coverage mainly for
build tests, try to disable the tracking for unit tests to see if we get
more stable coverage results.
Building emacs on darwin throws an error when trying to build an Emacs
app in the nextstep/Emacs.app path of the build tree. For now, disable
building this app.
It's possible to enable building the app also; Homebrew offers options
to this effect, and also adds Mac-specific options for starting the
emacs daemon. However, for the sake of simplicity and getting a
workable up-to-date emacs installation on my machine as quickly as
possible, this commit focuses on a minimal viable modification.
* Add a new package: unblur.
* Add a new package: unblur.
* Add a new package: unblur.
* Add a new package: unblur.
Conflicts:
var/spack/repos/builtin/packages/unblur/package.py
* Add a new package: unblur.
* Fix git on ubuntu, first cut
Spack needs to pass information about where the linker
can find `libintl`. We're currently using `LDFLAGS` to do so.
The `LDFLAGS` info is pasted into the command line upstream
of the a file (`libgit.a`) that includes unresolved symbols that
need that library. This fails on Ubuntu, although it seems to
work on CentOS (see #6841).
This change allows git to build on a Ubuntu 16.04.3 droplet.
TODO: test on other platforms...
* Add a bit of useful commentary
* Upgrade recipe for parmetis to be a CMakePackage
+ Eliminate `install` method (use the one from CMakePackage).
+ Move configure options to new method `cmake_args`
+ Move special install instructions for DarwinOS to a `run_after` method.
* Fix run_after section; Remove variant +debug.
Control the find_package of the PNG variant explicitly.
This avoids picking up an "external" PNGwriter install in
case `~png` is picked by changing the default "AUTO" search
to explicit "ON" (required) of "OFF" (ignore if exists).
* py-psyclone: Code generation for the PSyKAl framework from the GungHo project
* py-psyclone: add installation tests based on py.test
* py-psyclone: define 'develop' version as latest master branch
* py-psyclone: extract tagged version 1.5.1 from git repo
* py-psyclone: whitespace adjustments for flake8
* py-psyclone: use compatible versions of py-fparser
* py-psyclone: use type='test' for selected dependencies
* Updating OpenFAST to use explicit lapack and blas libraries from Spack.
* Simplifying openfast blas lib logic and fixes flake8 errors.
* Changing order of blas and lapack libs in openfast package.
* py-pybedtools: Create new package
* py-pybedtools: add py-six requirement
* py-pybedtools: remove py-cython dependency for release version
* py-pybedtools: include minimum version of py-pysam
* Provide build_type variant for Metis.
+ Ideally, we would make Metis a CMakePackage, but `metis@:5` doesn't use CMake.
+ For now, provide a `build_type=` variant similar what is found in
CMakePackage.
+ There is a potential for duplicate specification of `CMAKE_BUILD_TYPE` if both
variants `+debug` and `build_type=` are specified. I am looking for advice on
how this can be resolved.
* Update metis recipe in response to flake8 and user comments.
+ Wrap comment lines that used more than 80 columns.
+ Change `+debug` variant to avoid potential for multiple `-DCMAKE_BUID_TYPE=`
arguments provided to cmake. Specifying this variant no longer appends this
configure option. However, if `+debug` is specified, require
`build_type=Debug` to maintain expected behavior.
* For metis, remove +debug variant; use build_type= instead.
+ Update recipe for metis@4 to extract `build_type=` values and set `OPTFLAGS`
accordingly.
+ For metis@5:, the behavior from the previously supported variant `+debug` can
be obtained with the options `+gdb build_type=Debug`
* Conflicts added for metis@4 when build_type != Release|Debug.
* Use spack function conflicts instead of 'raise InstallError'.
* Create a symbolic link for MotionCor2.
* Create a symbolic link for MotionCor2.
* Create a symbolic link for MotionCor2.
* Create a symbolic link for MotionCor2.
* Adding NEURON package widely used in computational neuroscience community
* flake8 fixes
* Add rx3d variant
* Addressed review comments from Adam
* Addressed 2nd review comments
* Added check for +mpi on bg-q
* Filter spack compiler wrappers in NEURON scripts
Add gcc march=native flag to make front-end build robust
* Make develop as preferred version due to bug in long filename handlings in <= v7.4
* Avoid use of gcc in cross compiling environment
Use arch specific options on cray and bg-q arch
* Simplify cross compiling build:
- v7.5 added and no longer need develop as preferred version
- legacy cray related options removed
- cross compiling args reduced
- python arguments reduced as neuron finds proper libraries
* Simplify bg-q configurations
* Cleanup and unify arch options
* Make sure to add commonly available packages as dependency
* Arch path added to dependent_environment as nrniv needed at runtime
* Support for Power 8 architecture
* Fix python3 on OS X
* flake8 fix
* remove unnecessary conflcist directives
* Added a package for the MDAnalysis toolkit.
* Added a patch file to get rid of compiler warnings with intel compiler
and inlining. Added checksum values for other versions of protobuf.
* Added dependency on Intel compiler for intel patch
* added variant examples to paraview package.py
* qt: added libxt dependency
* add variant to use external hdf5, this is needed when compiling with gcc@4.8.5
* paraview: added python dependecies to PYTHONPATH
* Start adding Nek5000 package
* Add tools to install: genmap, prenek, postnek
* Address comments by @davydden
* Use install_tree (thanks @junghans) and polish
* Update url
* Fix flake formatting errors
* Change F77 and CC compilers
Apparently spack compilers can't be called outside spack and we
have an underscore test in our Nek5000/core/makenek.inc file which
calls F77 compiler.
* Add support for visit and profiling options
* Fix a typo
* Fix a typo
* Remove the C check
* Add visit variant
* Update the install of int_tp tool
* Let MAXNEL to be set during installation
* Added magma package
* Incorporated Serban's change
* Remove deleted files
* argparse.py
* Sync forked Spack repo in github
* Add spectrum-mpi lib path to LD_LIBRAY_PATH in spack_env.
As a result of supporting alternate installation directories, spectrum-mpi does
not use rpath anymore, so we need to set LD_LIBRARY_PATH in spack_env to allow
MPI programs to run during dependent package configuration.
* Fix flake8 error (blank line at EOF)
* xios: XML-IO-SERVER library for IO management of climate models
* xios: install to prefix directory
* xios: add a test case
* xios: define versions to use cache and mirror directories
* xios: use proper svn URL for version 910
* xios: package url must be defined, otherwise uninstall fails
* xios: add trunk version to allow building latest revision
* xios: enable parallel build
* xios: allow installation with mpif90 compiler wrappers
* xios: use mpi variants of dependencies
* xios: allow user to specify MPI launcher via MPIRUN environment variable
* xios: prefer spack versions of blitz and boost (needed for gcc@7)
* xios: enable builds with clang+gfortran on OSX
* xios: use numeric versions for releases, @develop for trunk
* xios: different patches required for @1.0 and @develop
* xios: patch function for clang works across revisions
* xios: link blitz library
* xios: workaround bug 17782 in llvm
* xios: whitespace adjustments for flake8
* xios: avoid bare except clause
* xios: netcdf-fortran inherits ^netcdf+mpi from xios dependencies
* combine all patches for 1612 into a single file, with additional
comments to explain the rational.
* Add kahip decomposition variant.
* Add support for ARM64 architecture.
* filter instead of patching etc/config.*/settings. This eliminates
patch files for 1706, perhaps for the future as well.
* URLs at or before version 1612 have a different structure, so
provide a url_for_version implementation to handle this
* singularity - added master branch as this has latest fixes - 2.4 does not compile on centos 6 without use of this branch
* renamed to develop
* added master branch properly
* add OctavePackage
1. remove import CudaPackage which is not needed anymore
2. mention CudaPackage and OctavePackage in packaging guide
3. adjust OctavePackageTemplate
4. add clue file for Octave build
5. sanity check on self.prefix
* use setup_environment
* esmf: put .mod files in the spack compiler search path
* esmf: allow building with Cray mpi
* esmf: create run-path dependent libraries on osx
* esmf: link fortran interface libraries when building with mpich
* Fix detection of blas and lapack: provide libraries/includes as
arguments to CMake rather than using CMake's auto-detection.
This includes a patch to QMCPACK's CMake files to refer to
Spack-built blas/lapack implementations. This also includes
special-case logic for the intel-mkl implementation of blas/lapack
* Break up unit tests and short tests. Only hard failure if the unit
tests fail, if short tests fail issue a warning only.
* Add QMCPACK 3.3.0, get rid of 3.0.0
* Only specify a file as needing relocation if it contains the spack
root as a text string (this constraint also applies to binaries)
* Don't fail if there is an error retrieving RPATH information from a
binary (even if it is specified as requiring relocation)
This adds the ability for packages to apply compiler flags in one of
three ways: by injecting them into the compiler wrapper calls (the
default in this PR and previously the only automated choice);
exporting environment variable definitions for variables with
corresponding names (e.g. CPPFLAGS=...); providing them as arguments
to the build system (e.g. configure).
When applying compiler flags using build system arguments, a package
must implement the 'flags_to_build_system_args" function. This is
provided for CMake and autotools packages, so for packages which
subclass those build systems, they need only update their flag
handler method specify which compiler flags should be specified as
arguments to the build system.
Convenience methods are provided to specify that all flags be applied
in one of the 3 available ways, so a custom implementation is only
required if more than one method of applying compiler flags is
needed.
This also removes redundant build system definitions from tutorial
examples
- define MPICH_SKIP_MPICXX, link libmpich instead of libmpi
(as per disussion in PR #4990)
ENH: more flexible editing/patching of openfoam env files
CONFIG: comment out requirement for openmpi+thread_multiple
- was originally slated for the 1712 release and beyond, but there are
reportedly unstable version/network combinations.
Leave as comment for future reference, since it may be arise again.
STYLE: renamed openfoam-site.patch as 1706-site.patch (and reformatted)
- to preserve against impending changes in the layout of
config.{csh,sh}/settings
Fixes#5940
This PR changes the option '--restage' of 'spack install' to
'--dont-restage', inverting its meaning and the default behavior
of the command.
* fix post install method for py3 in mercurial
* Update package.py
* Update package.py
* use print_str instead of manual print detection
* Update package.py
* use only depends_on
* Update package.py
* Update package.py
State py3 compatibility for @4.3: according to setup.py from the 4.3.tar.gz from pypi
Fixes#6200
For compilers that successfully run a version detection script but
don't actually return a version, Spack was keeping track of the
empty version and then failing when attempting to construct a
compiler spec. This skips any attempt to add a compiler entry when
no version is reported (but logs when a compiler fails to report
a version).
* Support pruning of vars with Env from_sourcing_file (issue #6501)
- Blacklist string literals or regular expressions of environment
variables that are to be removed from consideration as being affect
by the sourcing of the file. Conversely, whitelist modifications
that should not ignored. Whitelisted variables have priority over
blacklisting.
Eg,
EnvironmentModifications.from_sourcing_file
(
bashrc
blacklist=['JUNK_ENV', 'OPTIONAL_.*'],
whitelist=['OPTIONAL_REQUIRED.*']
)
This modification can be used to eliminate environment variables that
are not generalized for modules (eg, user-specific variables).
* BUG: module prepend-path in wrong order (fixes#6501)
* STYLE: module variables in sorted order (issue #6501)
- looks nicer and also helps when comparing the contents of different
module files.
* ENH: remove duplicates from env paths when creating modules (issue #6501)
- this makes for a cleaner module environment and helps avoid some
unnecessary changes to the environment that are only provoked by
redundancies in the PATH.
eg,
before PATH=/usr/bin
after PATH=/usr/bin:/usr/bin:/my/application/bin
should only result in /my/application/bin being added to the PATH
and not /usr/bin:/my/application/bin
Activate via the 'clean' flag (default: False):
EnvironmentModifications.from_sourcing_file(bashrc, clean=True,..
Add preferred version 2.0.3. Added beta version. Added conflict with
gcc versions >= 5 when building with cuda@8 (which is currently the
only supported cuda version). Added cuda architecture variant. Added
comment about current lack of cuda@9 support.
Fixes#6522
Patch psxevars.sh and psxevars.csh only when year > 2016.
pxevars.csh does not exist for versions before 2017. psxevars.sh
does not appear to require this patch for versions before 2017.
Fixes#2440
The "Getting started" guide should be short and sweet. This commit
simplifies the "Environment-Modules" section pruning:
- outdated / wrong suggestions as noted in #2440
- uncommon setups that are better treated in a reference guide
Fixes#6521.
Bazel's build system filters environment variables, including those
set by Spack for use by its compiler wrapper. This updates the patch
to include the SPACK_DEBUG_LOG_ID variable added in #5837.
* optional path to use spacks py-site-pkgs, install host-cfg for provenance
* add more comments and address review requests
* only use st-pkgs-dir when +python
* ascent does not need doxygen
* capture mpiexec if it exists
* added missing import
* flake8 fix
* default adios variant to False
* ascent develop now reqs conduit master
* optional path to use spacks py-site-pkgs, install host-cfg for provenance
* add more comments and address review requests
* only use st-pkgs-dir when +python
* ascent does not need doxygen
* capture mpiexec if it exists
* added missing import
* flake8 fix
* default adios variant to False
* ascent develop now reqs conduit master
* conduit: use hdf5 1.8 for wider output compat
* Add: Py-Plotly
The requirements of py-plotlit are rather strict fixed to specific
versions, so I did not add an "upper versions" `:` to the constrains.
See
https://github.com/plotly/plotly.py/blob/master/requirements.txt
* Py-Requests, Py-Six, Py-Pytz: Older Versions
Add two older versions of requests, pytz and six for plotly.
- depends on GTK+ with X enabled
(btw, non-X backends are deprecated/removed in GTK+)
- patch for 3.0.1-3.0.2: missing include caused multiple
`error: call of overloaded ‘abs(XYPOSITION)’ is ambiguous`
(seen in GCC 6.3.0); fixed in 3.0.3+
According to the documentation here:
http://www.sphinx-doc.org/en/stable/ext/autodoc.html
"For module data members and class attributes, documentation can either
be put into a comment with special formatting (using a #: to start the
comment instead of just #), or in a docstring after the definition."
* Update CGNS to be able to be used in Trilinos.
* Updating Trilinos to be able to use CGNS.
* Fixing wrong cmake defines in trilinos for enabling cgns and cleaning up cgns package.
* Changing cgns parallel variant to mpi. Removing explicit dependence on parallel-netcdf in trilinos.
Add additional transform libraries to ADIOS.
Also modifies existing transforms to the versions they were
introduced (otherwise this was resulting in unknown configure flags).
* Updated function which checks if a binary file needs relocation.
Previously this was incorrectly identifying ELF binaries as symbolic
links (so they were being excluded from relocation). Added test to
check that ELF binaries are not considered symlinks.
* relocate_text was not replacing paths in text files. Added test to
check that text files are relocated properly (i.e. paths in the file
are converted to the new prefix).
* Exclude backup files created by filter_file when installing from
binary cache.
* Update write_buildinfo_file method signature to distinguish between
the spec prefix and the working directory for the binary cache
package.
"spack spec" was providing helpful error information about conflicts
that was missing from "spack install", this updates "spack install"
to provide the same information.
The original docstring had confusing wording re: what is going to
symlinked and where when using the `extend` directive, and how exactly
the symlinking is performed (not automatically on install, but using
`spack activate`). See #5559.
Showing "Normalize" on output doesn't give users additional information,
as this step is essentially an implementation detail of concretization.
This PR skips it and shows just the input spec and the concretized one.
Printing partial hashes for input spec has been disabled.
* xsdk: Added MFEM rc package.
* xsdk: add version entry for xsdk-0.3.0-rc1 - and set it as preferred version
* xsdk: remove 'xsdk' from version - recommended by Todd.
Now the usage is:
'spack install xsdk@0.3.0-rc1'
instead of the previous usage:
'spack install xsdk@xsdk-0.2.0'
* xsdk: add petsc@3.8.0 as a dependency for xsdk-0.3.0-rc1
* mfem: fix dependency to use the corrected xsdk version
* Updated the mfem version tags.
* mfem: fix merge
* fix flake8 warning
* Modified xSDK scripts
* fixing the default package.yaml
* fix bad revert
* revert changes to superlu-dist so that the 5.2.1 update can be merged
* update xsdk to use superlu-dist-5.2.1
* update alquimia for xsdk
* fix whitespace
* update hypre for xsdk
* update sundials for xsdk
* update sundials for xsdk
* Fix checking for MKL and extend range of GCC versions
* pflotran: update to release branch
* plasma: fix spec -> self.spec
* Changes to enable mfem hooks into hypre, superlu-dist, and petsc. Sundials hooks may come in the future.
* adding plasma with comment
* Bumped the version of mfem up to handle integration with sundials3.0.0. Also enabled hypre in sundials.
* Turn on the plasma package definition for testing
* Fix conflict declaration to obey ordering rules
* xsdk: udate superlu-dist dependency to v5.2.2
* plasma: change gcc dependency to workarround potential spack bug #5778
* trilinos: update hdf5 dependency to use 'hdf5+hl'
Without this change - I get the following error [triggered by 161dca6d5c9810f808 changes]
$ ./bin/spack install trilinos+hdf5
==> Error: An unsatisfiable variant constraint has been detected for spec:
hdf5@1.10.1%gcc@7~cxx~debug~fortran~hl+mpi+pic+shared~szip~threadsafe arch=linux-fedora27-x86_64
while trying to concretize the partial spec:
netcdf+mpi
^m4
^mpich@3.3a2%gcc@7 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-fedora27-x86_64
^zlib@1.2.11%gcc@7+optimize+pic+shared arch=linux-fedora27-x86_64
netcdf requires hdf5 variant +hl, but spec asked for ~hl
* plasma: add in -lm dependency per #6046
* update sundials version to 3.0.0
* Add fixes to support Netlib LAPACK
* mfem does not use cmake for builds [anymore] - so remove code corresponding to this dependency.
This enables mfem build on OSX [with xcode/clang compilers]
* mfem: update to v3.3.2-rc4
* add patch for building sundials on mac
* xsdk: enable plasma for gcc-4.9+ - same as what plasma/package.py does.
* magma: Fix for cuda-9.0 as it does not support sm20
nvcc fatal : Unsupported gpu architecture 'compute_20'
* add in code for 'spack install xsdk+cuda' - which installs magma
* fix flake8 warning
* fix flake8 warnings
* Updated to the latest MFEM RC.
* alquimia: fix to use petsc-3.8.0+ versions
* petsc: update to version 3.8.1
* petsc: add in conflict between petsc-3.8.0 & mkl
* xsdk: update petsc to 3.8.1 to get MKL build fix
* petsc: fix superlu_dist dependency
* petsc: when hdf5 depends on zlib - petsc+hdf5 should also be configured with zlib
* petsc: fix dependency [of zlib to be on hdf5 - and not on petsc]
* petsc: fix pkgconfig error - with incorrect library link order that can break mfem examples with static build
* petsc: use the fact that hdf5/package.py has a hard dependency on zlib [so no need to check for this dependency in code]
recommended-by: @davydden
* petsc: change hdf5 dependency to 'hdf5+hl' as petsc configure is looing for -lhdf5_hl
https://github.com/spack/spack/issues/5846
* plasma: also detect -lgfortran
* update sundials version to 3.1.0
* alquimia: xsdk-0.3.0-rc -> xsdk-0.3.0
* petsc: update to version 3.8.2
Includes pkgconfig fix [for mfem static build failure]
* Revert "petsc: fix pkgconfig error - with incorrect library link order that can break mfem examples with static build"
This reverts commit d1afa8c20d.
* xsdk: update to use petsc-3.8.2
* Fixed a problem with MFEM trying to use mpicxx instead of the spack defined compiler.
* Minor changes to the mfem build and pointing at mfem's release branch that is currently undergoing internal testing.
* Enabling shared build for Plasma
* plasma: do not look for libgfortran on cray - spack finds the wrong one from the frontend
'-L/usr/lib64/gcc/x86_64-suse-linux/4.3 -L/usr/lib64 -lgfortran'
* Some changes to the mfem package that are in the process of being pulled into spack/develop.
* xsdk: switch from 0.3.0-rc1 to 0.3.0
* fix flake8 warnings
* plasma: extract plasma changes from xsdk-0.3.0
* plasma: cleanup per review
- netlib-lapack: add support for spec['lapack:c'].libs, spec['blas:c'].libs
- add getblaslapacklibs() to eliminate duplicate code in edit() and build_targets()
- eliminate string manipulation of ld_flags
- remove gfortran check (will check later)
- remove build() (will check later)
* netlib-lapack: fix tuple per review
* netlib-lapack: use spec[lapack:c,fortran]
* Adding version 2.4.3 to ViennaRNA
* Replaced tab indent with spaces
Flake8 error correction
* no swig for viennarna v2.4.3 only
* correcting version/argument conditional syntax error
libtool is also needed for linking, otherwise downstream
dependencies such as clfft will fail linking against pocl's
libOpenCL.so with errors such as:
```
>> 182 /usr/bin/ld: warning: libltdl.so.7, needed by /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pocl-0.14-rwo73qzkcxfupndxoz3pcl2s34o5pt6i/lib/libOpenCL.so, not found (try using -rpath or -rpath-link)
>> 183 /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pocl-0.14-rwo73qzkcxfupndxoz3pcl2s34o5pt6i/lib/libOpenCL.so: undefined reference to `lt_dlinit'
>> 184 /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pocl-0.14-rwo73qzkcxfupndxoz3pcl2s34o5pt6i/lib/libOpenCL.so: undefined reference to `lt_dlerror'
>> 185 /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pocl-0.14-rwo73qzkcxfupndxoz3pcl2s34o5pt6i/lib/libOpenCL.so: undefined reference to `lt_dlopen'
>> 186 /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pocl-0.14-rwo73qzkcxfupndxoz3pcl2s34o5pt6i/lib/libOpenCL.so: undefined reference to `lt_dlsym'
>> 187 collect2: error: ld returned 1 exit status
```
* Reduce the calls to the python interpreter during initialization
This should reduce the delay the users experience when sourcing the
setup file to activate shell support. It works by generating at once
all the commands that needs to evaluated (they are stored in
a string and later `eval`ed by the shell).
* setup_env.sh: changed `read` with an equivalent magic
For some reason `read` breaks when sourced from a running script.
Change the incantation we use to construct the unique python command
that will be evaluated.
* setup_env.sh: python command now constructed with `printf` for portability
This recovers the support for `zsh` that was broken in previous commits.
* py-petsc4py: Update version to 3.8.0 and add dependencies
- Added explicit dependency on python and numpy
* Kept old version - and corrected minimal python version
* Update to 3.8.1
- Previously variant values had to be a tuple or a callable predicate.
- This allows 'any' as shorthand for `lambda x: True` and type objects
as shorthand for "any value of this type".
- Makes variant definitions more readable, keeps lambdas out of
packages for common cases.
* First draft for SC17 build systems portion
Added tutorial_buildsystems.rst file as well as example files under
the tutorial/ directory.
* Remove floating `
* Add requested changes, and examples of subclasses
Added in the requested changes to the documentation. Also added in
information about the subclasses and the defaults that they provide.
Also fixed some phrasing issues, formatting and punctuation.
* Flake8 fixes and new files for classes
Made flake8 fixes to pass tests and also added files to demonstrate code
in the classes.
* Minor edits
Edits in formatting and made some sentence changes
* Flake8 fixes
More flake8 fixes
* Flake8 fix
* Change section order on tutorial and minor edits
Placed the section at the appropriate section for the tutorial and then
added some minor edits that were requested.
* Add requested changes and more details
Added more details to Cmake, Makefile and Python Packages.
* Fixed formatting and minor edits
* Fix doc build error
* Allow types and 'any' in variant definitions.
- Previously variant values had to be a tuple or a callable predicate.
- This allows 'any' as shorthand for `lambda x: True` and type objects
as shorthand for "any value of this type".
- Makes variant definitions more readable, keeps lambdas out of
packages for common cases.
* Update packaging tutorial
* Fix bad file reference in packaging tutorial
* First draft of the advanced packaging tutorial
* advanced packaging tutorial: improved phrasing
Thanks Denis and Hartzell!
* Fixed typos + reworded a couple of sentences
* Reworked module file tutorial section
First draft for the SC17 update. This includes:
- adding an introduction on module files + Spack's module
generation blueprints
- adding a set-up section and provide a docker image for easy set-up
- updating all the relevant snippets
- extending a bit some of the concepts that were already touched
* Added reference to #5582 + committed Dockerfiles
Also fixed a couple of typos spotted by Denis.
* module file tutorial: added section on template customization
* module file tutorial: fixed minor typos + rephrased a sentence
* module file tutorial: made explicit that Docker image comes with software
* module file tutorial: improved phrasing and layout.
Thanks Hartzell!
* module file tutorial: added vim and nano to editors
* module file tutorial: fixed typo
* Fixed typos
Thanks Adam!
* module file tutorial: updated Dockerfile + minor changes in introduction
* add ascent package and and deps
* proper use of site_packages_dir prop
* flake8
* add maitain, small updates
* flake8
* flake8
* fixs for docstrings for sphinx
Fixes#6154
For compiler options which set values using the syntax "-flag value"
(with a space between the flag and the flag's value) the flag and
value were treated as separate and reordered. This updates Spack's
logic to treat the flag and value as a single unit, even if there is
a space between them. It assumes that all flags are prefixed with
"-" and that all flag values are not.
We're adopting the contributor covenant for now. This isn't something we've needed to use yet, but it is good to have in case we actually do have a problem.
* petsc: when hdf5 depends on zlib - petsc+hdf5 should also be configured with zlib
* petsc: fix dependency [of zlib to be on hdf5 - and not on petsc]
* petsc: use the fact that hdf5/package.py has a hard dependency on zlib [so no need to check for this dependency in code]
recommended-by: @davydden
* petsc: change hdf5 dependency to 'hdf5+hl' as petsc configure is looing for -lhdf5_hl
https://github.com/spack/spack/issues/5846
* Skip rewriting files that are links (this also avoids issues with parsing
the output of the 'file' command for symlinks)
* Fail rather than warn for several gpg signing issues (e.g. if there is no
key available to sign with)
* Installation with 'buildcache install' only retrieves link and run
dependencies (this matches 'buildcache create' which only creates tarballs
of link/run dependencies)
* Don't rewrite RPATHs for a binary if the binary cached package was created
with relative RPATHs
* Refactor relocate_binary to operate on multiple binaries (given as a
collection of paths). This was likewise done for relocate_text and
make_binary_relative
* Added missing deps to libffs
* SOSflow spack package pointing to sos_flow feature/spack branch
* Using tag for spack build
* Change url to spack/spack
nghttp2 depends on python, and requires the install directory to exist,
and contain the python module directory which it will eventually
install the python modules into.
- This isn't one of those autogenerated SVGs from a drawing program!
- This is a completely re-traced, minimalist SVG file with clearly
delineated pieces so that your favorite renderer can draw a Spack logo
at whatever resolution you want.
- Included versions with text, as well.
* trilinos: update hdf5 dependency to use 'hdf5+hl'
Without this change - I get the following error [triggered by 161dca6d5c9810f808 changes]
$ ./bin/spack install trilinos+hdf5
==> Error: An unsatisfiable variant constraint has been detected for spec:
hdf5@1.10.1%gcc@7~cxx~debug~fortran~hl+mpi+pic+shared~szip~threadsafe arch=linux-fedora27-x86_64
while trying to concretize the partial spec:
netcdf+mpi
^m4
^mpich@3.3a2%gcc@7 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-fedora27-x86_64
^zlib@1.2.11%gcc@7+optimize+pic+shared arch=linux-fedora27-x86_64
netcdf requires hdf5 variant +hl, but spec asked for ~hl
* fix flake8 warning
Fixes#6126#3183 removed the print_help function from the "modules" module.
This adds it back so that if a user invokes 'spack load foo' without
having sourced an environment setup script, they will be prompted
to do so. This also improves the placeholder message to tell the
user to invoke 'spack' as shell function rather than as an executable.
* added relion v 2.1
* relion 2.1 - misssed comma
* relion now pulling from master branch - removed 2.03 - added cuda 8 as dependency given 9 does not yet work with relion per https://github.com/3dem/relion/issues/296
* r-igraph: find old packages in the archive
Fixes#6104.
* r-irlba: find old packages in the archive
Fixes#6101.
* r-lazyeval: find old packages in the archive
Fixes#6102.
* packages: set list_url for all packages hosted on CRAN
* packages: consistently use the CRAN archive URLs
Part of the resource staging process is to place downloaded/expanded
files in the root stage. This was not happening when a resource stage
was restaged.
Aspell compiles in the paths it looks for rather than looking relative
to its binary location. There are also no environment variables to
redirect it other than changing the path to the configuration file it
looks at.
Fixes#5778.
Spack uses 'gcc -dumpversion' to determine the full version of gcc.
'gcc -dumpversion' no longer gives the full version on gcc 7.2.0.
'gcc -dumpfullversion' is required instead. This PR detects when
'gcc -dumpversion' gives a truncated version of '7' and in that
case retrieves the full version with 'gcc -dumpfullversion'
- hdf5's +hl variant is required because the build uses libhdf5_hl.
- sz is only compatible up to version 1.4.10 because the library has
been renamed to libSZ in 1.4.11.
The name of the debug log written by the cc compiler wrapper was given
by Spec.short_spec, which includes the architecture. Somewhere along
the line Spec.format started adding spaces around the architecture
property so the filename started including spaces; the cc wrapper
script appears to ignore this, so files like spack-cc-bzip2-....in.log
(which record the wrapped compiler invocations) were not being
generated. This uses a different format string from the spec to
generate the wrapper log file names (which does not include spaces).
* when a user-provided spec refers to an already-installed package, packages with patches applied were causing validation errors based on the recorded variants in the package's class
* avoid checks on all reserved variants (not just 'patches')
* Fixed the datatype flag in the LBANN package.
Fixed where the datatype flag should be set.
* Added variant to OpenCV to disable building DNN support
* Fixed a bug in how the elemental package tries to find its Fortran
library. The current method does not work with Intel compilers.
* Added necessary paths for cuDNN and CUB.
* Addressed flake8 issues in Elemental package.
* Fixed several flake8 errors. Added variant to build with or without
support for arbitrary-precision floating point arithmetic.
* Added the proper CMake flag when MPFR support is disabled.
* Fixed a bug in how the cudnn path was being set when there was no
cudnn requested. Also requested that OpenCV is built without eigen
support.
* Fixed another bug where a dependency may not be there and thus should
not be always checked.
* Added a package for the MDAnalysis toolkit.
* Changed dependency for the eigen library to not include support for
multiple-precision (arbitrary-precision) floating point arithmetic,
since OpenCV does not support these data types.
* Fixed incorrect implementation
* dockbook: remove update to dependent environment
Remove override of setup_dependent_environment in both docbook-xml
and docbook-xsl, which seems to generate a warning from spack about
"Suspicious requests to set or unset 'XML_CATLOG_FILES' found."
* flux: update version/dependencies to 0.8.0
Update flux-core to v0.8.0. Clean up dependencies and remove unneeded
extra invocation of ./autogen.sh when building from @master.
* flux: modify environment for Lua tests
Modify Spack environment to add `./?.lua` to LUA_PATH so that
fluxometer.lua can be found by tests during `make check` run
from `spack install --tests all flux`
* flux: fix broken flux version when on master
When building @master with spack, the flux version test from
`make check` fails because spack is using a shallow clone. Add
a setup section for @master that calls git pull --depth=50 --tags
to pull down tags and (hopefully) enough information for git-describe
to work properly.
A recent update (#5907) to htslib added a different URL for an old
version of htslib.
Now the package is using that URL as the pattern for the newer
versions too.
I have a vague memory of running into this before, that it's a known
issue.
This fixes it by adding an explicit `url_for_version` routine.
* basic functionality to install spec from a binary cache when it's available; this spiders each cache for each package and could likely be more efficient by caching the results of the first check
* add spec to db after installing from binary cache
* cache (in memory) spec listings retrieved from binary caches
* print a warning vs. failing when no mirrors are configured to retrieve pre-built Spack packages
* make automatic retrieval of pre-built spack packages from mirrors optional
* no code was using the links stored in the dictionary returned by get_specs, so this simplifies the logic to return only a set of specs
* print package prefix after installing from binary cache
* provide more information to user on install progress
* Add bowtie2@2.3.0, fix dependencies and sbangs
Add support for bowtie2@2.3.0
- digest
- a patch for 2.3.0 that parallels the existing package. Truth be
told it builds (for me) without this, but I'm assuming that they're
there for a reason...).
- tune up dependencies
- need tbb
- don't need readline or zlib
Several things were installed with sbang's that use `/usr/bin/env` to
fine perl or python. Fix the dependency and clean up the sbang lines.
* Fix python exe name, avoid path banging
I'd cut and pasted the python bit from the perl bit and missed one
reference to perl.
While I'm there, use the cleaner `spec['perl'].command` instead of
banging together the path from its bits.
* Fix up the "when" constraints on the dependencies
Get the edge cases right.
- 2.2.5 doesn't need tbb, 2.3.[01] do.
- 2.3.1 needs readline and zlib.
The go team released 1.9.2 which includes fixes for some things
that 1.9.1 broke:
> ... include fixes to the compiler, linker, runtime, documentation, go command, and the crypto/x509, database/sql, log, and net/smtp packages. They include a fix to a bug introduced in Go 1.9.1 and Go 1.8.4 that broke "go get" of non-Git repositories under certain conditions.
This updates the logic for Package.extends so that if the spec
associated with the package is not concrete, it will report true if
the package *could extend* the given spec; generally speaking a
package could extend a spec as long as none of the details associated
with its extendee spec conflict with the given spec. When the spec
associated with the package is concrete, this function will only
report whether the package *does extend* the given spec. When both
the specs are concrete, the semantics are the same as before.
* Exodus: skip the -G "Unix Makefiles" part
The problem is that spack passes -G "Unix Makefiles" into cmake, which normally
works. But in the Exodus package, it is being passed into a bash wrapper
script. In there, the $@ then loses the information about "Unix Makefiles"
being just one argument, and in effect passes -G Unix Makefiles into the cmake
(without quotes), and so cmake only sees -G Unix, and then fails. This is a
known problem with bash with no simple solutions. As a workaround, this patch
skips the first two arguments, i.e., -G and "Unix Makefiles". This makes it
work.
Fixes#5895.
* Port exodusii to cmake
The cmake options were taken from the cmake-exodus bash script and ported to
spack directly.
* Use variant forwarding to forward the 'mpi'
Now instead of
spack install exodusii~mpi^netcdf~mpi^hdf5~mpi
one can just use
spack install exodusii~mpi
* When creating a tar of a package for a build cache, symlinks are
preserved (the corresponding path in the newly-created tarfile will
be a symlink rather than a copy of the file)
* Dont add external packages to a build cache
* When installing from binary cache, don't create install prefix until
verification is complete
* sw4lite: fix build errors and add variants
* sw4lite: change linking against blas and lapack
* change order of blas and lapack
* satisfy flake8 requirements
* Update package.py
* Add the custom paraview lib directory structure to the library paths in the paraview module file.
* Fixing flake8 issues.
* Checking if lib64 exists for paraview module file generation, else use lib.
* Fixing more flake8 problems I introduced.
Since LLVM 3.9 Clang can use the libc++ library by default using the
CLANG_DEFAULT_CXX_STDLIB cmake configuration variable, without having to
specify the -stdlib=libc++ option on the clang++ command line.
This commit makes clang++ use libc++ by default for LLVM 3.9 and later if the
libcxx variant is on.
Fixes#5942.
* Fixes#5754
Previously when RepoPath.repo_for_pkg was invoked with a string,
it did not check if the string included a namespace. Any
namespace-qualified package provided as a string would not be found
(at which point the behavior was to return the highest-precedence
repository).
* handle nested namespaces for packages specified as strings in repo_for_pkg
* add preliminary repository tests
* add test which replicates #5754
* refactor repo tests with fixtures
* define repo_path equivalent at test-level scope for repo tests
* add tests for unknown namespace/package
* rename fixture function (no longer prefixed with 'test_')
Internally we work against a branch named 'llnl/develop', which
mirrors the public repository's `develop` branch.
It's useful to be able to run flake8 on our changes, using
`llnl/develop` as the base branch instead of `develop`.
Internally the flake8 subcommand generates the list of changes files
using a hardcoded range of `develop...`.
This makes the base of that range a command line option, with a
default of `develop`.
That lets us do this:
```
spack flake8 --base llnl/develop
```
which uses a range of `llnl/develop...`.
Chasing a performance regression has lead me to this change, going from default optimization gives a significant performance win. The sweet spot for zlib is apparently `-O2`, both `-Ofast` and `-O3` are slightly worse (regression is about 3% compared with `-O2) in my testing.
Happy to share my methodology with people so we can benchmark on a wider variety of systems.
* Add package for scalpel@0.5.3
Scalpel's a bit of a mess, it expects it's users to just unpack the
tarball, build it in the resulting directory and install that
directory onto their PATH. My install step recapitulates this into
prefix.bin. The alternative was rewiring their scripts (perl), which
use `FindBin` and expect things to be located in the same dir that the
script itself is.
Sigh.
Lightly tested on CentOS 7.
* Flake8 cleanup
* Additional flake8 cleanup
* Added procedure to edit sbangs of the parallel perl scripts.
* Specify the types of perl dependency
Adding ", type=('build', 'run')" to the dependency declaration to clarify when and how perl is required
* flake8 cleanup
The problem was that the configure script was not using spack's compiler
wrappers. We now pass the proper compiler wrapper using the CC argument
explicitly.
Fixes#5892.
'spack install' can now reinstall a spec even if it has dependents, via
the --overwrite option. This option moves the current installation in a
temporary directory. If the reinstallation is successful the temporary
is removed, otherwise a rollback is performed.
* r-a4: Add r dependency and update url.
* r-a4base: Add r dependency and update url.
* r-a4classif: update url and add r dependency.
* r-a4core: Update url and add r dependency.
* r-a4preproc: Update url and add r dependency.
* r-a4reporting: Update url and add r dependency.
* r-abaenrichment: Update url and add r dependency.
* r-absseq: Update url and add r dependency.
* r-acgh: Update url and add r dependency.
* r-acme: Update url and add r dependency.
* r-adsplit: Update url and add r dependency.
* r-affxparser: Update url and add r dependency.
* r-affycomp: Update url and add r dependency.
* r-affycompatible: Update url and add r dependency.
* r-affycontam: Update url and add r dependency.
* r-annaffy: Update url and add r dependency.
* r-annotate: Update url and add r dependency.
* r-annotate: Update url and add r dependency.
* r-annotationdbi: Update url and add r dependency.
* r-genefilter: Update url and add r dependency.
* r-mlinterfaces: Update url and add r dependency.
* r-limma: Update url and add r dependency.
* r-multtest: Update url and add r dependency.
* r-a4classif: Correct format.
* r-affycomp: Correct error.
- new E741 flake8 checks disallow 'l', 'O', and 'I' as variable names
- rework parts of the code that use this, to be compliant
- we could add exceptions for this, but we're trying to mostly keep up
with PEP8 and we already have more than a few exceptions.
- When you don't use wildcards, flake8 will find places where you used an
undefined name.
- This commit has all the bugfixes resulting from this static check.
There are now separate flake8 configs for core vs. packages:
- core has a smaller set of flake8 exceptions
- packages allow `from spack import *` and module globals
- Allows core to take advantage of static checking for undefined names
- Allows packages to keep using Spack tricks like `from spack import *`
and dependencies setting globals for dependents.
Jansson builds only a static library by default, which is probably
not what most users want. Add Cmake args required to build a shared
library and enable those via a default 'shared' variant of the
package.
* new package: hpgmg
* removed build and changed extend() to append()
* changes based on comments
* pep8 compliant
* addressed rest of comments
* trigger checks
* changed from fe_fv to two boolean variants
* fixed compilation issues
* cleared up ambiguities in solver variants
* removed +mpi condition
* changes based on review
* Update Getting Started docs to clarify that full Xcode suite is required for qt
* Better error message when only the command-line tools are installed
#5776 cleaned up the way the the current working directory is
managed (less magic state).
bcl2fastq is packaged like a russian doll, rather than an archive file
that contains the source, there's a zip file that contains a tar.gz
file that contains the source. The package definition has a bit of
extra code that unpacks the inner tarball.
That extra bit of code now needs to explicitly arrange to be in the
correct directory before it does its work.
* py-mpi4py: Add develop version and dependencies
- Add cython dependency for develop version
- Add explicit python dependency
* py-mpi4py: Specify 2.0.1 instead of develop for conditional dep
Perl installs a couple of config files that need to be munged so that
they don't refer to the spack compiler. These files are installed
read-only. Behind the scenes 'filter_file' moves its file to a safe
place, and tries to create a working file that is both O_WRONLY and
has the perms of the original file. On an NFSv4 filesystem, the
combination of 'r--r--r--' and O_WRONLY throws a permissions error.
This commit adds a simple context manager that temporarily makes the
files writable.
I'm tracking down a problem with the perl package that's been
generating this error:
```
OSError: OSError: [Errno 2] No such file or directory: '/blah/blah/blah/lib/5.24.1/x86_64-linux/Config.pm~'
```
The real problem is upstream, but it's being masked by an exception
raised in `filter_file`s finally block.
In my case, `backup` is `False`.
The backup is created around line 127, the `re.sub()` calls
fails (working on that), the `except` block fires and moves the backup
file back, then the finally block tries to remove the non-existent
backup file.
This change just avoids trying to remove the non-existent file.
* Add a new +clanglibcpp option for Boost
Currently, the compile of boost with clang will use the stdlibc++. This patch adds an optional flag to use clangs included libc++ instead.
* Linting
Fix long lines and white space errors
- The shell script uses arrays and hence only works on sophisticated shells and not the default `sh`. For clarity the shebang `#!/bin/bash` has been used instead.
- This fakes out GitFetchStrategy to try code paths for different git
versions.
- This allows us to test code paths for old versions using a newer git
version.
- Tests use a session-scoped mock stage directory so as not to interfere
with the real install.
- Every test is forced to clean up after itself with an additional check.
We now automatically assert that no new files have been added to
`spack.stage_path` during each test.
- This means that tests that fail installs now need to clean up their
stages, but in all other cases the check is useful.
- Be explicit about stage creation during the install process.
- This avoids accidental creation of stages
- e.g., during `spack install --fake`, stages were erroneously recreated
after being destroyed
- This prevents the main spack install from being clusttered by
invocations of `spack test`.
- This uses a session-scoped stage fixture to ensure tests don't
interfere.
- Spack's core package interface was previously overly stateful, in that
calling methods like `do_stage()` could change your working directory.
- This removes Stage's `chdir` and `chdir_to_source` methods and replaces
their usages with `with working_dir(stage.path)` and `with
working_dir(stage.source_path)`, respectively. These ensure the
original working directory is preserved.
- This not only makes the API more usable, it makes the tests more
deterministic, as previously a test could leave the current working
directory in a bad state and cause subsequent tests to fail
mysteriously.
1.64 had issues serialization (make_array and others) when built with
+mpi+python. It appears that those issues are fixed in 1.65.1
so we can remove preferred tag from 1.63.
* initial update of sundials package
* fix bugs in initial sundials update
* add xsdk cmake setup, fix generic math option, add cuda/raja Makefiles to install fixes
* Fix lapack install bug, add new conflicts, clean up formatting
* Address pull requeset comments and make fomatting style consistent
Remove blas variant as blas is only needed when used by an external
linear solver. Set related CMake blas variables as needed depending
enabled external linear solvers.
Add minimum required CMake version.
Additional conflicts and dependencies for external libraries based
on mpi, indextype, and precision.
Fix SuperLU_MT logic to check which threading type SuperLU_MT was
configured with.
Add maintaiers.
Change Sundials solver options to use an array of values.
Consistently use % for formatting.
* change triple-single quotes to single quotes
* Change indextype option to a single int64 option
- Assertion would search for root through all possible paths.
- It's also really slow.
- This isn't needed anymore. We're pretty good at ensuring single-rooted
DAGs, and this assertion has never been thrown.
- This shaves another 6 seconds off r-rminer concretization
- This reduces concretization time for r-rminer from over 1 minute to
only 16 seconds.
- OrderedDict ends up taking a *lot* of time to compare larger specs.
- An OrderedDict isn't actually needed here. It's actually not possible
to find duplicates, and we end up sorting the contents of the
OrderedDict anyway.
- This is an optimization to the way traverse_edges iterates over
successors.
- Previous version called dependencies_dict(), which involved a lot of
redundant work (creating dicts and calling caonical_deptype)
- Spack ends up constructing compilers frequently from YAML data.
- This caches the result of parsing the compiler config
- The logic in compilers/__init__.py could use a bigger cleanup, but this
makes concretization much faster for now.
- on macOS, this also ensures that xcrun is called only twice, as opposed
to every time a new compiler object is constructed.
This adds a workflow section on how to use spack on Docker.
It provides an example on the best-practices I collected over the
last months and circumvents the common pitfalls I tapped in.
Works with MPI, CUDA, Modules, execution as root, etc.
Background: Developed initially for PIConGPU.
* Make --trusted default when running spack gpg list
Currently running `spack gpg list` with no arguments returns nothing. You must supply either the `--trusted` or the `--signing` options. The idea here is to return some initial data to the user when the command is run. The alternative is to return an error, telling the user to select one of the two options.
* Add an extra test case for the empty list command
Fixes the issue with code coverage
This isn't a rework of the concretizer but it speeds things up a LOT.
The main culprits were:
1. Variant code, `provider_index`, and `concretize.py` were calling
`spec.package` when they could use `spec.package_class`
- `spec.package` looks up a package instance by `Spec`, which requires a
(fast-ish but not that fast) DAG compare.
- `spec.package_class` just looks up the package's class by name, and you
should use this when all you need is metadata (most of the time).
- not really clear that the current way packages are looked up is
necessary -- we can consider refactoring that in the future.
2. `Repository.repo_for_pkg` parses a `str` argument into a `Spec` when
called with one, via `@_autospec`, but this is not needed.
- Add some faster code to handle strings directly and avoid parsing
This speeds up concretization 3-9x in my limited tests. Still not super
fast but much more bearable:
Before:
- `spack spec xsdk` took 33.6s
- `spack spec dealii` took 1m39s
After:
- `spack spec xsdk` takes 6.8s
- `spack spec dealii` takes 10.8s
* Do not call setup_package for fake installs
- setup package could fail if ``setup_dependent_environment`` or other
routines expected to use executables from dependencies
- xpetsc and boost try to get python config variables in
`setup_dependent_package`; this would cause them not to be
fake-installable
* Remove vestigial deptype_query argument to Spec.traverse()
- The `deptype_query` argument isn't used anymore -- it's only passed
around and causes confusion when calling traverse.
- Get rid of it and just keep the `deptypes` argument
* Don't print redundant messages when installing dependencies
- `do_install()` was originally depth-first recursive, and printed "<pkg>
already installed in ..." multiple times for packages as recursive
calls encountered them.
- For much cleaner output, use spec.traverse(order='post') to install
dependencies instead
* Add dmlc/mxnet packags.
* Build mxnet+cuda+opencv with GCC-4.8.5 and GCC-5.4.0.
* Build mxnet version 0.10.0, 0.10.0.post1 and 0.10.0.post2.
* Add component version constrain for mxnet 0.10.0.x .
* Go through flake8.
* Replace commit hash with commit date as package version.
* Go throught Travis-CI.
* Update submodule version for 0.10.0.post2.
* Add openmp variant for dmlc-core and mxnet.
* Refine variant handling.
* Fix filter_file for dmlc-core.
* Cut long strings into multiple lies due to PEP8 requirements.
* Fix for PEP8.
* Add CUB_INCLUDE.
* Add py-mxnet: Python binding for MXNet.
* Remove distutils.dir_util.
* Add the profiler variant for mxnet.
* Add a shared variant for nnvm.
* Set USE_OPENMP to OFF by default.
* Fix flake8 errors.
* Fix flake8 issues.
* flake8 issues again.
closes#5506
The application of patches to upstream executables has been reworked
according to the suggestions of the main developer in #5506. In
particular we are not maintaining a dictionary that maps plumed
versions to the versions of patchable executables, and we are using a
non-interactive command to patch applications.
All the comments on substituting plumed at run-time do not apply here,
since we use RPATH and we want to maintain a 1:1 relationship between
the DAG hash and the plumed library used.
* Add package for aspell and ass't dictionaries
Add a package definition for aspell.
Add a handful of dictionaries to convince myself that the support for
a bunch of dictionaries works.
* Flake8 cleanup
* Use six's version of urlparse
`urlparse` is not python3 friendly. This works around it (stolen from
`.../cmd/md5.py`).
* Fix incorrect trimming regexp
* Clean up dictionary build
- more parsimonious use of `which` (`make()` has already been made)
- use `sh` instead of `bash`
* Use a helper method to generate info for variants
I figured out my issues with static methods. I *think* that it this
is pythonic.
* Convert aspell to an extendable package
Convert aspell to be extendable and rework the dictionaries to be
extensions.
As it stands, there's a great deal of cut and paste in the
dictionaries, I'll abstract that out next.
The {de,}activate methods copy a great deal of code out of
package.py. Perhaps there's a better way....
* Create AspellDictPackage and use it for the dictionaries
Reduce the repeated code, pull it into a base class.
I'm confused about why 'from spack import *' wasn't more useful in the
base class.
* Oops, -de & -es should be AspellDictPackages too
* Typo: pakcage -> package
* Address some commentary
* Update copyright dates, 2016->2017
* spec and spec.package.spec can refer to different objects in the
database. When these two instances of spec differ in terms of
the value of the 'concrete' property, Spec._mark_concrete can
fail when checking Spec.package.installed (which requires
package.spec to be concrete). This skips the check for
spec.package.installed when _mark_concrete is called with
'True' (in other words, when the database is marking all specs
as being concrete).
* add test to confirm this fixes#5293
This is a simple package that drops their shell wrapper into
prefix.bin and their jar files into prefix.lib.
The approach comes from the picard package.
* Updating ag to the latest version
* Pretty by request
* Restore url to previous value
There *is* an https version available, but I've also been told
to not just update the url when adding new version. I'm following
the latter advice and trusting security to the digest.
* Adding maven v3.5.0
Updating package file to include later version of maven but still signifying a preference for the older
* removing specific preference flag
* ncl: Fix temp directory
Currently, ncl is configured using a transient temp directory. This
leads to warnings such as this when executing ncl later on:
warning:"/tmp/ncl_ncar_xxxxxx" tmp dir does not exist or is not writable:
NCL functionality may be limited -- check TMPDIR environment variable
As this also breaks some functionality, use the system temp directory
instead (typically /tmp).
* ncl: Depend on esmf
esmf is required for some ncl scripts (such as ESMF_regridding.ncl).
* Add link dependency on xproto to xau
The libxcb build was failing like so:
```
1 error found in build log:
[ ... ]
131 checking whether to build developer documentation... yes
132 checking for doxygen... /usr/bin/doxygen
133 checking for dot... /usr/bin/dot
134 checking for CHECK... no
135 checking for XCBPROTO... yes
136 checking for NEEDED... no
>> 137 configure: error: Package requirements (pthread-stubs xau >= 0.99.2) were not met:
138
139 Package 'xproto', required by 'xau', not found
140
141 Consider adjusting the PKG_CONFIG_PATH environment variable if you
142 installed software in a non-standard prefix.
143
```
This adds a link dependency on libxproto that allows the libxcb build to
succeed.
* Change more build deps to build, link
These were also necessary for emacs+X to build.
* Fix flake8 complaint
* edits to address issues where spack concretization attempts to set properties on already-installed specs
* most added checks only need to check if the spec is concrete; they dont also need to check if the package is installed
* add test to ensure that patches are not applied to an installed spec
* add test to ensure that an error is detected when a dependent requests a dependency constraint which conflicts with a requested installed dependency
Fixes#5455
All methods within setup_package use an EnvironmentModifications object
to control the environment. Those modifications are applied at the end
of setup_package. Module loads for the build environment need to be
done after the rest of the environment modifications are applied, as
otherwise Spack may unset variables set by those modules (for example
LD_LIBRARY_PATH).
closes#2884closes#4684
In #1848 we decided to use `Spec.format` to expand certain tokens in
the module file naming scheme or in the environment variable name.
Not all the tokens that are allowed in `Spec.format` make sense in
module file generation. This PR restricts the set of tokens that can
be used, and adds tests to check that the intended behavior is respected.
Additionally, the names of environment variables set/modified by module
files were, up to now, always uppercase. There are packages though that
require case sensitive variable names to honor certain behaviors (e.g.
OpenMPI). This PR restricts the uppercase transformation in variable
names to `Spec.format` tokens.
fixes#5587
In trying to preserve patch ordering, #5476 made equality inconsistent
for the added 'patches' variant. This commit maintains the original
weak ordering of patch applications while preserving consistency of
comparisons. The ordering DOES NOT enter the hashing mechanism. It's
supposed to be a hotfix, while we think of a cleaner and more-permanent
solution.
* Add package for multitail@6.4.2
Lightly tested on CentOS 7.
* Responde to feedback/comments
Use `install_targets` to specify PREFIX= and DESTDIR= instead of
hacking away at the Makefile. Expand commentary about "Why?".
Use `headers.include_flags` and `libs.ld_flags` to avoid explicitly
setting `-L` and `-I` when hacking away at the Makefile.
* Added exasp2 spackage
Added spackage for exasp2 proxy app
* Fixed MPI in ExaSP2
Explicitly disabled MPI when not enabled.
Set MPI variant to default as per Spack standards
* Generalized BML Passing for ExaSP2
* Modified to follow spack rules on blas
Fortunately was able to modify exasp2 build system to support spack
model for blas and lapack requirements. No guarantee is made for support
of anything other than originally supported libraries
* Fixed flake8 error
explicitly set the zlib path for libpng configure.
fixes:
```
[ ... ]
92 checking for memset... yes
93 checking for pow... no
94 checking for pow in -lm... yes
95 checking for clock_gettime... yes
96 checking for zlibVersion in -lz... no
97 checking for z_zlibVersion in -lz... no
>> 98 configure: error: zlib not installed
```
This is a partial fix for #5564.
This package used to trust that `configure` would discover `gmp` from
its environment.
It's safer to tell it where to find `gmp` explicitly.
This does that by adding a configure_args() that provides a
`--with-gmp=...` argument for configure.
* Added support for BML+mpi variant
Added support for BML+mpi variant. Currently restricted to master
(develop) branch pending release of next bml tag
* Update package.py
Removing redundant statement
* Update package.py
Added explicit disabling of MPI when not requested
- This steals the magic regular expressions that CTest uses to parse log
files and addds them to Spack. See here:
https://github.com/Kitware/CMake/blob/master/Source/CTest/cmCTestBuildHandler.cxx
These are BSD licensed, so the port is in `externa/ctest_log_parser.py`
- We currently use these to do better filtering of errors from build
output. Plan is to use them to generate good CDash output.
- A package can depend on a special patched version of its dependencies.
- The `Spec` YAML (and therefore the hash) now includes the sha256 of
the patch in the `Spec` YAML, which changes its hash.
- The special patched version will be built separately from a "vanilla"
version of the same package.
- This allows packages to maintain patches on their dependencies
without affecting either the dependency package or its dependents.
This could previously be accomplished with special variants, but
having to add variants means the hash of the dependency changes
frequently when it really doesn't need to. This commit allows the
hash to change *just* for dependencies that need patches.
- Patching dependencies shouldn't be the common case, but some packages
(qmcpack, hpctoolkit, openspeedshop) do this kind of thing and it
makes the code structure mirror maintenance responsibilities.
- Note that this commit means that adding or changing a patch on a
package will change its hash. This is probably what *should* happen,
but we haven't done it so far.
- Only applies to `patch()` directives; `package.py` files (and their
`patch()` functions) are not hashed, but we'd like to do that in the
future.
- The interface looks like this: `depends_on()` can optionally take a
patch directive or a list of them:
depends_on(<spec>,
patches=patch(..., when=<cond>),
when=<cond>)
# or
depends_on(<spec>,
patches=[patch(..., when=<cond>),
patch(..., when=<cond>)],
when=<cond>)
- Previously, the `patch()` directive only took an `md5` parameter. Now
it only takes a `sha256` parameter. We restrict this because we want
to be consistent about which hash is used in the `Spec`.
- A side effect of hashing patches is that *compressed* patches fetched
from URLs now need *two* checksums: one for the downloaded archive and
one for the content of the patch itself. Patches fetched uncompressed
only need a checksum for the patch. Rationale:
- we include the content of the *patch* in the spec hash, as that is
the checksum we can do consistently for patches included in Spack's
source and patches fetched remotely, both compressed and
uncompressed.
- we *still* need the patch of the downloaded archive, because we want
to verify the download *before* handing it off to tar, unzip, or
another decompressor. Not doing so is a security risk and leaves
users exposed to any arbitrary code execution vulnerabilities in
compression tools.
- Functions returned by directives were all called `_execute`, which made
reading stack traces hard because you couldn't tell what directive a
frame came from.
- renamed them all to `_execute_<directive>`
- Exceptions in directives were only really used in one or two places --
get rid of the boilerplate init functions and let the callsite specify
the message.
- move `spack.cmd.checksum.get_checksums` to `spack.util.web.spider_checksums`
- move `spack.error.NoNetworkError` to `spack.util.web.NoNetworkError` since
it is only used there.
- Previously, dependencies and dependency_types were stored as separate
dicts on Package.
- This means a package can only depend on another in one specific way,
which is usually but not always true.
- Prior code unioned dependency types statically across dependencies on
the same package.
- New code stores dependency relationships as their own object, with a
spec constraint and a set of dependency types per relationship.
- Dependency types are now more precise
- There is now room to add more information to dependency relationships.
- New Dependency class lives in dependency.py, along with deptype
definitions that used to live in spack.spec.
Move deptype definitions to spack.dependency
* Add '--test=all' and '--test=root' options to test either the root or the root and all dependencies.
* add a test dependency type that is only used when --test is enabled.
* test dependencies are not added to the spec, but they are provided in the test environment.
closes#5473
Prior to this PR we were not exiting early for external packages, which
caused the `configure_options` property of the contexts to fail with
e.g. a key error because the DAG gets truncated for them. More
importantly Spack configure options don't make any sense for externals.
Now we exit early, and leave a message in the module file clarifying
that this package has been installed outside of Spack.
+ Count, or compute differences of, physical lines of source code in the
given files (may be archives such as compressed tarballs or zip files)
and/or recursively below the given directories.
* Autodock vina: spec
* Adding comment to patch. The implemnetation of boost is version dependent on older boost replacing depecrated function of boost.
* Adding in boost version dependency
* Update the krell institute products to use the latest features of spack for building on cluster platforms.
* Address travis error messages and resubmit the pull request.
* Update the contents of openspeedshop package.py so it passes the flake8 tests.
* Fix flake8 error-whitespack issue in mrnet package.py file.
* Add updates based on spack reviewer feedback.
* More fixes based on comments from reviewers. Switch using extend to using append, remove additional setting of PATH and LD_LIBRARY_PATH that should not be required due to RPATH.
* More review related changes. Update MPIOption.append lines and take out xercesc references.
* Create a base options function for common openspeedshop base cmake options to reduce redundencies.
* Add libxml2+python depends on to get around issues with the libxml2 package file.
* Using boost over 1.60.0 causes compile errors. This is a known boost bug. Also, dyninst-9.2.0 is set to be the vesrion of dyninst to use with OSS, as of now. The newer version fails to build.
* Fix bad syntax in specifying the boost version range.
* Update the version numbers for the krell institute components and tools: cbtf and openspeedshop.
* Do not build glib for qt3, it is not needed and causes build problems at this time anyway.
* A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set.
* Update the fix for qt3 build by setting LD_LIBRARY_PATH instead of checking for whether it is set or not per Adams comment that spack clears LD_LIBRARY_PATH.
* A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set.
* Trim comments to fit more concisely.
* Fix tabs versus spaces and swap if and else clause check from a negative to a positive check.
* Add ability to build llvm-openmp-ompt alone, with gnu compilers and use the resulting ompt interface in cbtf-krell and openspeedshop to gather openmp specific performance information.
* Fix flake8 errors.
* Fix flake8 errors - stage 2.
* Fixes based on reviewer suggestions and comments.
* Use build_type variant to set the build type and allow changing of the type.
* Fix missing comma in cmake_arg list, found on another test machine.
* r-glmnet: Create New Package.
* pr-quantities: add version & py-numpy conflict (#5307)
* r-glmnet: Update version to 2.0-13
* r-matrix: Update version to 1.2-11
* r-lattice: Update version to 0.20-35.
The default implementation of Package.fetch_remote_versions will take
a URL like https://github.com/google/protobuf/archive/ and automatically
search https://github.com/google/protobuf/releases/ for new package
versions. In the case of protobuf the release/ path contains release
artifacts for a version and the archive/ path contains the desired
source. Since both are associated with the version, and
Package.fetch_remote_versions only stores one URL for a given version,
the two paths are in conflict; previously the URL returned for a
given version was arbitrarily chosen between the two paths. This
updates the definition for the Protobuf package to always search for
URLs in https://github.com/google/protobuf/archive/
closes#5201
Currently, if a user sets an external package to have a prefix that is
one of the system paths (like '/usr') the module files that are
generated will prepend '/usr/bin' to 'PATH', etc. This is particularly
nasty at the time when a module file is unloaded, and e.g. paths like
'/usr/bin' will be discarded from PATH.
This PR solves the issue skipping system paths when a prefix inspection
is made to generate module files.
* blas_lapack: add multithreading variant
* elemental: update
* intel-mkl: extend to macOS
* rename multithreading to threads
* intel-mkl: avoid long lines
* intel-mkl: make one install error a conflict
* openblas: fix a minor bug in the test
Update the git package to git@2.14.1.
This requires a pcre that has been built with `--enable-jit`, so this
adds a variant to pcre to support that and arranges so that git versions
before 2.14 depend on pcre and git 2.14 and after depend on pcre+jit.
Due to the logic in configure.ac, we may be using both the system
linker (LD_RO='ld -r -o') and the linker tied to the compiler (LD=$CXX).
This may produce weird link-time errors when the two executables are
not the same.
The PR works around the issue disabling 'ld -r'
Open MPI has been relying on versions of PMIx since the 2.0.0
release. Although the embedded version can be used, it makes
more sense long term for Spack to know about the PMIx package,
and to build Open MPI against PMIx as an external package.
There are other software components that may eventually be
reliant on PMIx including MPICH, GASNet, the OpenSHMEM reference
implementation, etc.
This is also partly motivated by the desire to have ECP ST
projects to be released through Spack.
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
* Make texlive untrusted
TeXLive updates their installer without changing its name. We've been
playing keep-up with them, but I'm proposing it's not worth it.
I seem to end up installing it '--no-checksum' anyway.
This commit updates the package to make that approach official,
removing the checksum, adding a note to the description and a bigger
note/comment inthe package body.
* Pull installer from stable source (packages are still *live*)
This pulls the installer script from the "historic" repository. It
appears to be stable, so that we can use a checksum with it (one
hopes, time will tell).
The installer still pulls the packages from the live repos so
installations aren't reproducible.
Add r-biobase package. Remove explicit R dependency from r-biocgenerics
package (since it is an instance of RPackage). Update version for
r-biocgenerics and remove github versions.
* First draft package for sambamba
Depends on the ldc package (#5279) that alalazo's working on.
It requires a patch to the Makefile because one of ldc's library
functions mentions dlopen. I *think* that ldc should be handling
this. See the discusssion in #5279.
It also requires a "static" ldc. Again, see #5279.
Finally, it needs "undeaD" as a resource, but I'm guessing at the
appropriate release. See
https://github.com/lomereiter/sambamba/issues/312.
* alalazo renamed the shared_libs variant, keep up...
+ The recipe for cgns seems to be wrong. CMake complains about variables set but
not used (`HDF5_NEEDS_ZLIB`, `HDF5_NEEDS_MPI` and `HDF5_NEEDS_SZIP`) and fails
to find HDF5.
+ This change set removes these variables from the cmake configure line,
replacing them with `'-DHDF5_DIR=%s' % spec['hdf5'].prefix`
+ cgns also has trouble with parallel make, so I set `parallel = False`.
* fixes#967
* Version bump to 0.9.1
- Bugfixes for spack find
- 0.9.1 can read specs from current develop.
* Don't assume spack is in the path when building docs.
* fixing build issues for gcc on osx
* reverting inadvertent change on develop
* fixing typesetting of bsws description
* very minor update to RTD docs footer to ref github contributors
* Revert "very minor update to RTD docs footer to ref github contributors"
This reverts commit c40d75da7f.
* switch fastmath to depend_on arpack_ng; remove arpack/parpack
* Module files now are generated using a template engine refers #2902#3173
jinja2 has been hooked into Spack.
The python module `modules.py` has been splitted into several modules
under the python package `spack/modules`. Unit tests stressing module
file generation have been refactored accordingly.
The module file generator for Lmod has been extended to multi-providers
and deeper hierarchies.
* Improved the support for templates in module files.
Added an entry in `config.yaml` (`template_dirs`) to list all the
directories where Spack could find templates for `jinja2`.
Module file generators have a simple override mechanism to override
template selection ('modules.yaml' beats 'package.py' beats 'default').
* Added jinja2 and MarkupSafe to vendored packages.
* Spec.concretize() sets mutual spec-package references
The correct place to set the mutual references between spec and package
objects at the end of concretization. After a call to concretize we
should now be ensured that spec is the same object as spec.package.spec.
Code in `build_environment.py` that was performing the same operation
has been turned into an assertion to be defensive on the new behavior.
* Improved code and data layout for modules and related tests.
Common fixtures related to module file generation have been extracted
in `conftest.py`. All the mock configurations for module files have been
extracted from python code and have been put into their own yaml file.
Added a `context_property` decorator for the template engine, to make
it easy to define dictionaries out of properties.
The default for `verbose` in `modules.yaml` is now False instead of True.
* Extendable module file contexts + short description from docstring
The contexts that are used in conjunction with `jinja2` templates to
generate module files can now be extended from package.py and
modules.yaml.
Module files generators now infer the short description from package.py
docstring (and as you may expect it's the first paragraph)
* 'module refresh' regenerates all modules by default
`module refresh` without `--module-type` specified tries to
regenerate all known module types. The same holds true for `module rm`
Configure options used at build time are extracted and written into the
module files where possible.
* Fixed python3 compatibility, tests for Lmod and Tcl.
Added test for exceptional paths of execution when generating Lmod
module files.
Fixed a few compatibility issues with python3.
Fixed a bug in Tcl with naming_scheme and autoload + unit tests
* Updated module file tutorial docs. Fixed a few typos in docstrings.
The reference section for module files has been reorganized. The idea is
to have only three topics at the highest level:
- shell support + spack load/unload use/unuse
- module file generation (a.k.a. APIs + modules.yaml)
- module file maintenance (spack module refresh/rm)
Module file generation will cover the entries in modules.yaml
Also:
- Licenses have been updated to include NOTICE and extended to 2017
- docstrings have been reformatted according to Google style
* Removed redundant arguments to RPackage and WafPackage.
All the callbacks in `RPackage` and `WafPackage` that are not build
phases have been modified not to accept a `spec` and a `prefix`
argument. This permits to leverage the common `configure_args` signature
to insert by default the configuration arguments into the generated
module files. I think it's preferable to handling those packages
differently than `AutotoolsPackage`. Besides only one package seems
to override one of these methods.
* Fixed broken indentation + improved resiliency of refresh
Fixed broken indentation in `spack module refresh` (probably a rebase
gone silently wrong?). Filter the writers for blacklisted specs before
searching for name clashes. An error with a single writer will not
stop regeneration, but instead will print a warning and continue
the command.
* Add --with-mpi=spec['mpi'].name at configure step to avoid error when finding 2 MPI implementations
* Improve scorep package with different compilers and mpi providers
Merge work from multiple contributors on the mesa package. This
includes the following changes and decisions:
* Added in mesa +hwrender support
* make +swrender the default selection since this represents a very
common usage case (ie, cluster usage)
* leave ~llvm as the default, since inadvertently building this package
could take a very long time. May need to revisit this assumption in
the future since the performance difference can be quite substantial.
* build libGLESv1+2 and libGL for all variants
* avoid dependence on dri/libdrm when ~hwrender
* disable gallium drivers if none are requested
- converted `log_path` and `env_path` to properties of PackageBase.
- InstallErrors in build_environment are now annotated with the package
that caused them, in the 'pkg' attribute.
- Add `--show-log-on-error` option to `spack install` that catches
InstallErrors and prints the log to stderr if it exists.
Note that adding a reference to the Pakcage allows a lot of stuff
currently handled by do_install() and build_environment to be handled
externally.
- '\b' in regular expression needs to be in a raw string (r'\b')
- Regression test that would've caught this was unintentionally disabled
- This fixes the string and the test
Fixes a problem in ymake-filter: The line buffer is currently hardcoded to be
2048 bytes large but some Makefiles contain lines longer than that. This
caused the Makefiles to sometimes not be generated, consequently failing parts
of the build.
setup-env.sh adds the 'module' command to the user's environment
if it is not defined and if there is a Spack installation of
environment-modules available. This commit updates that logic to
perform these checks and updates quietly.
The correct place to set the mutual references between spec and
package objects is at the end of concretization. After a call to
concretize we should now be ensured that spec is the same object
as spec.package.spec.
Code in `build_environment.py` that was performing the same
operation has been turned into an assertion to be defensive on
the new behavior.
- Fixes bugs where concretization would fail due to an erroneously cached
_concrete attribute.
- Ripped out a bunch of code in spec.py that isn't needed/valid anymore:
- The various concrete() methods on different types of Specs would
attempt to statically compute whether the Spec was concrete.
- This dates back to when DAGs were simpler and there were no optional
dependencies. It's actually NOT possible to compute statically
whether a Spec is concrete now. The ONLY way you know is if it goes
through concretization and is marked concrete once that completes.
- This commit removes all simple concreteness checks and relies only on
the _concrete attribute. This should make thinking about
concreteness simpler.
- Fixed a couple places where Specs need to be marked concrete explicitly.
- Specs read from files and Specs that are destructively copied from
concrete Specs now need to be marked concrete explicitly.
- These spots may previously have "worked", but they were brittle and
should be explcitly marked anyway.
- Dependencies in concrete specs did not previously have their cache
fields (_concrete, _normal, etc.) preserved.
- _dup and _dup_deps weren't passing each other enough information to
preserve concreteness properly, so only the root was properly
preserved.
- cached concreteness is now preserved properly for the entire DAG, not
just the root.
- added method docs.
Fixes#4112
This commit extends the support of the AutotoolsPackage methods
`with_or_without` and `enable_or_disable` to bool-valued variants. It
also defines for those functions a convenience short-cut if the
activation parameter is the prefix of a spec (like in
`--with-{pkg}={prefix}`).
This commit also includes:
* Updates to viennarna and adios accordingly: they have been modified to
use `enable_or_disable` and `with_or_without`
* Improved docstrings in `autotools.py`. Raise `KeyError` if name is
not a variant.
These were discovered with bash 4.1.2.
Add quotations around a variable to prevent the destruction of a
newline. Without this fix a conditional doesn't work properly.
Remove square brackets around a conditional meant to be evaluated based
on the return code of a command. This wasn't working properly with an
old bash.
Fix a typo.
* fix armadillo macro expansions
- most compilers `#define linux 1`
- armadillo does raw pasting of include directories in code
- this means macro expansion of `linux-x86_64` -> `1-x86_64`
- new version, previous download url seems broken
- lib64 instead of lib?
- needs verification, was required for intel, works for others
* flake8: two spaces is modules, one for classes
* add some explanation of how the patch works
* use p1 patch file with -U0 to prepend undef linux
* armadillo v8.100.1
* Improve PDToolkit support for different compilers
PDT dependency of TAU profiler doesn't use CC, CXX eb variables and needs command line arguments for compiler identification. If we don't pass compiler id then it uses gcc and result in link time errors while building TAU. This patch fixes it; tested with PGI and Intel compilers.
Renames the existing bootstrap command to 'clone'. Repurposes
'spack bootstrap' to install packages that are useful to the
operation of Spack (for now this is just environment-modules).
For bash and ksh users running setup-env.sh, if a Spack-installed
instance of environment-modules is detected and environment modules
and dotkit are not externally available, Spack will define the
'module' command in the user's shell to use the environment-modules
built by Spack.
First, quote the environment variable values. Second, export the
variables. sorry, this is bourn-shell syntax. Happy to consider a
shell-independent way to do this, but spack is already using sh-like
"env=value"
* Added support to query packages by tags.
- The querying commands `spack list`, `spack find` and `spack info` have
been modified to support querying by tags. Tests have been added to
check that the feature is working correctly under what should be the
most frequent use cases.
* Refactored Repo class to make insertion of new file caches easier.
- Added the class FastPackageChecker. This class is a Mapping from
package names to stat info, that gets memoized for faster access.
- Extracted the creation of a ProviderIndex to its own factory function.
* Added a cache file for tags.
- Following what was done for providers, a TagIndex class has been added.
This class can serialize and deserialize objects from json. Repo and
RepoPath have a new method 'packages_with_tags', that uses the TagIndex
to compute a list of package names that have all the tags passed as
arguments.
On Ubuntu 14.04 the effect if the cache reduces the time for spack list
from ~3sec. to ~0.3sec. after the cache has been built.
* Fixed colorization of `spack info`
This command broke after #5109. It was using the default value for the
"dirty" argument in `setup_package`. Now it adopts the same logic as
in `spack install`. Changed help for '--clean' and '--dirty'.
Improved coverage of spack env.
The private method `Spec._dup` was missing a line (when setting compiler
flags the parent spec was not set to `self`). This resulted in
an inconsistent state of the duplicated Spec. This problem has been
fixed here. The docstring of `Spec._dup` has been updated.
This change is done to avoid inconsistencies during refactoring. The rationale is that functions at different levels in the call stack all define a default for the 'dirty' argument. This PR removes the default value for all the functions except the top-level one (`PackageBase.do_install`).
In this way not defining 'dirty' will result in an error, instead of the default value being used. This will reduce the risk of having an inconsistent behavior after a refactoring.
* Respect --insecure when fetching list_url.
* Ensure support for Python 2.6, and that urlopen works for python versions prior 2.7.9 and between 3.0 and 3.4.3.
pkgconf is a new pkg-config implementation with additional features and
no external dependencies.
For a detailed comparison, see: http://pkgconf.org/features.html
* Simplified Spec.__init__ signature by removing the *dep_like argument.
The `*dep_like` argument of `Spec.__init__` is used only for tests. This
PR removes it from the call signature and introduces an equivalent
fixture to be used in tests.
* Refactored ``spec_from_dict`` to be a static method of ``Spec``
The fixture ``spec_from_dict`` has been refactored to be a static method
of ``Spec``. Test code has been updated accordingly. Added tests for
exceptional paths.
* Renamed argument `unique` to `normal` + added LazySpecCache class
As requested in the review the argument `unique` of `Spec.from_literal`
has been renamed to `normal`. To avoid eager evaluations of
`Spec(spec_like)` expressions a subclass of `collections.defaultdict`
has been introduced.
* Spec object can be keys of the dictionary for a spec literal.
Added back the possibility use a spec directly as a key. This permits
to build DAGs that are partially normalized.
Adds a development version of boost, based on their github master
repo.
Git clones the submodules forever, but installs! :)
Useful for testing since boost tends to break complex software
dependencies quite often. This helps testing it before releases.
- Update handling of ChildError so that its output is capturable from a
SpackCommand
- Update cmd/install test to make sure Python and build log output is
being displayed properly.
- install and probably other commands were designed to run once, but now
we can to test them from within Spack with SpackCommand
- cmd/install.py assumed that it could modify do_install in PackageBase
and leave it that way; this makes the decorator temporary
- package.py didn't properly initialize its stage if the same package had
been built successfully before (and the stage removed).
- manage stage lifecycle better and remember when Package needs to
re-create the stage
- If a failure comes from an external command and NOT the Python code,
display errors highlighted with some context.
- Add some rudimentary support for parsing errors out of the build log
(not very sophisticated yet).
- Build errors in Python code will still display with Python context.
* Package 'cdo': removed obsolete version 1.6.9.
* Package 'cdo': updated urls.
* Package 'cdo': added version 1.9.0.
* Package 'cdo': no need to specify per version urls.
* Package 'cdo': switched from Package to AutotoolsPackage.
* Package 'cdo': added new variant 'openmp'.
* Package 'cdo': variants 'curl' and 'magics' by default.
Users can now add an optional custom message to the conflicts directive.
Layout on screen has been changed to improve readability and the long
spec is shown in tree format. Two conflicts in `espresso` have been
modified to showcase the feature.
- Python I/O would not properly interleave (or appear) with output from
subcommands.
- Add a flusing wrapper around sys.stdout and sys.stderr when
redirecting, so that Python output is synchronous with that of
subcommands.
- 'v' toggle was previously only good for the current install.
- subsequent installs needed user to press 'v' again.
- 'v' state is now preserved across dependency installs.
- Previously we would use `os._exit()` in to avoid Spack error handling
in the parent process when build processes failed. This isn't
necessary anymore since build processes propagate their exceptions to
the parent process.
- Use `sys.exit` instead of `os._exit`. This has the advantage of
automatically flushing output streams on quit, so output from child
processes is not lost when Spack exits.
- Simplify interface to log_output. New interface requires only one
context handler instead of two. Before:
with log_output('logfile.txt') as log_redirection:
with log_redirection:
# do things ... output will be logged
After:
with log_output('logfile.txt'):
# do things ... output will be logged
If you also want the output to be echoed to ``stdout``, use the
`echo` parameter::
with log_output('logfile.txt', echo=True):
# do things ... output will be logged and printed out
And, if you just want to echo *some* stuff from the parent, use
``force_echo``:
with log_output('logfile.txt', echo=False) as logger:
# do things ... output will be logged
with logger.force_echo():
# things here will be echoed *and* logged
A key difference between this and the previous implementation is that
*everything* in the context handler is logged. Previously, things like
`Executing phase 'configure'` would not be logged, only output to the
screen, so understanding phases in the build log was difficult.
- The implementation of `log_output()` is different in two major ways:
1. This implementation avoids race cases by using only one pipe (before
we had a multiprocessing pipe and a unix pipe). The logger daemon
stops naturally when the input stream is closed, which avoids a race
in the previous implementation where we'd miss some lines of output
because the parent would shut the daemon down before it was done
with all output.
2. Instead of turning output redirection on and off, which prevented
some things from being logged, this version uses control characters
in the output stream to enable/disable forced echoing. We're using
the time-honored xon and xoff codes, which tell the daemon to echo
anything between them AND write it to the log. This is how
`logger.force_echo()` works.
- Fix places where output could get stuck in buffers by flushing more
aggressively. This makes the output printed to the terminal the same
as that which would be printed through a pipe to `cat` or to a file.
Previously these could be weirdly different, and some output would be
missing when redirecting Spack to a file or pipe.
- Simplify input and color handling in both `build_environment.fork()`
and `llnl.util.tty.log.log_output()`. Neither requires an input_stream
parameter anymore; we assume stdin will be forwarded if possible.
- remove `llnl.util.lang.duplicate_stream()` and remove associated
monkey-patching in tests, as these aren't needed if you just check
whether stdin is a tty and has a fileno attribute.
- Fix issue with color formatting regular expression.
- _separators regex in spec.py could be constructed such that '^' came
first in the character matcher, e.g. '[^@#/]'. This inverts the match
and causes transient KeyErrors.
- Fixed to escape all characters in the constructed regex.
- This bug comes up in Python3 due to its more randomized hash iteration
order, but it could probably also happen in a Python 2 implementation.
- also clean up variable docstrings in spec.py
- This should speed-up Travis CI tests and refers to #5049
- Travis uses build-stages to group tests together
- The idea is to let fast tests fail first, then move to longer ones.
- Added external perl to avoid download failure from CPAN and reduce build time
- Disabling perl-dbi: continues to fail with (504 Gateway Time-out) on Travis
- We now cover all the build systems in tests:
- Add back `openblas` to Travis as a separate package.
- Switched `openblas` for `astyle` to build a simpler MakefilePackage.
- Added 'tut' (WafPackage)
- Added 'py-setuptools' (PythonPackage)
- Added 'perl-dbi' (PerlPackage)
- Added 'build_systems' directory to the ones for which we get a summary
- Added 'openjpeg' (CMakePackage)
- Added 'r-rcpp' (RPackage)
- Added comments to build tests to show the covered build system
- Mac OS X Sierra has no /usr/include by default
- Instead of assuming there's an include directory in /usr, mock up a directory that looks like we expect.
+ gitk (and possibly other tools) expect to find the Tk executable `wish`, so
add a symlink with this name that points to the the versioned filename.
+ Example: `wish --> wish8.6`
This adds sbang hook support for node-js and fixes the sbang filter
for lua (the character class exclusion was swallowing newlines and
reporting a false positive if lua was mentioned anywhere in the
file).
Previously, when +graph and +mpi were enabled, the graph library
was replaced with the graph_parallel library. This alters the
logic for +graph+mpi to build both libraries.
* Gaussian: Gaussian install
* Adding Patch to spack installed files
* Adding extra environment variables for gaussian at run time
* Adding provides linda
* Adding linda as a provided package
* Shortning vars and fixing flake8 indentation and spacings
* Docs: Travis-CI Workflow
Add a workflow how to use spack on Travis-CI.
Future Work:
depending if and how we can simplify 5101:
add a multi-compiler, multi-C++-standard, multi-software
build matrix example
* Fix Typos
* Colorize spack info. Adds prominence to preferred version. fixes#2708
This uses 'llnl.util.tty.color' to colorize the output of 'spack info'.
It also displays versions in the order the concretizer would choose
them and shows the preferred in a line on its own and in bold.
* Modified output according to Adam and Denis reviews.
Section titles are not bold + black, but bold + blue. Added a new
section named "Preferred version", which prints the preferred version
in bold characters.
* Further modifications according to Adam and Denis reviews.
After "Homepage:" we now have a single space. Removed newline after each
variant. Preferred version is not in bold fonts anymore. Added a simple
test that just runs the command.
this is a fix to an installation that failed due to
configure for some reason not finding the libiconv
shipped with glibc, but still trying to link against it
see http://xmlsoft.org/FAQ.html
* Improved error message for unsatisfiable specs. fixes#5066
This PR improves the error message for unsatisfiable specs by showing in tree format both the spec that cannot satisfy the constraint and the spec that asked for that constraint. After that follows a readable error message.
This PR allows additional unused properties at the top-level of the config.yaml file. Having these properties permits to use two different versions of Spack, one of which adds a new property, without receiving error messages due to the presence of this new property in a configuration cache stored in the user's home.
This fixes a syntax error in the index.html file generated by the
"spack buildcache" command when creating build caches. This also
fixes support for installing unsigned binaries.
* Refactor IntelInstaller into IntelPackage base class
* Move license attributes from __init__ to class-level
* Flake8 fixes: remove unused imports
* Fix logic that writes the silent.cfg file
* More specific version numbers for Intel MPI
* Rework logic that selects components to install
* Final changes necessary to get intel package working
* Various updates to intel-parallel-studio
* Add latest version of every Intel package
* Add environment variables for Intel packages
* Update env vars for intel package
* Finalize components for intel-parallel-studio package
Adds a +tbb variant to intel-parallel-studio.
The tbb package was renamed to intel-tbb.
Now both intel-tbb and intel-parallel-studio+tbb
provide tbb.
* Overhaul environment variables set by intel-parallel-studio
* Point dependent packages to the correct MPI wrappers
* Never default to intel-parallel-studio
* Gather env vars by sourcing setup scripts
* Use mpiicc instead of mpicc when using Intel compiler
* Undo change to ARCH
* Add changes from intel-mpi to intel-parallel-studio
* Add comment explaining mpicc vs mpiicc
* Prepend env vars containing 'PATH' or separators
* Flake8 fix
* Fix bugs in from_sourcing_file
* Indentation fix
* Prepend, not set if contains separator
* Fix license symlinking broken by changes to intel-parallel-studio
* Use comments instead of docstrings to document attributes
* Flake8 fixes
* Use a set instead of a list to prevent duplicate components
* Fix MKL and MPI library linking directories
* Remove +all variant from intel-parallel-studio
* It is not possible to build with MKL, GCC, and OpenMP at this time
* Found a workaround for locating GCC libraries
* Typos and variable names
* Fix initialization of empty LibraryList
* Added a package for the MDAnalysis toolkit.
* Openblas now builds with clang when using 0.2.20
* Fixed flake8 error
* Added a guard to fail for openblas+openmp when on OSX systems
* Changed the guard to look for Apple's build of clang and to improve
the error messages.
* Removed blank line.
`h5z-zfp` now builds zfp with correct bit stream word size; the syntax of the variant declaration did not work in previous versions of spack but does now
Adds the "buildcache" command to spack. The buildcache command is
used to create gpg signatures for archives of installed spack
packages; the signatures and archives are placed together in a
directory that can be added to a spack mirror. A user can retrieve
the archives from a mirror and verify their integrity using the
buildcache command. It is often the case that the user's Spack
instance is located in a different path compared to the Spack
instance used to generate the package archive and signature, so
this includes logic to relocate the RPATHs generated by Spack.
The action `CleanOrDirtyAction` has been added. It sets the default
value for `dest` to `spack.dirty`, and changes it according to the flags
passed via command line. Added unit tests to check that the arguments
are parsed correctly. Removed lines in `PackageBase` that were setting
the default value of dirty according to what was in the configuration.
Popen.communicate outputs a str object for python2 and a bytes
object for python3. This updates the Executable.__call__ function
to call .decode on the output of Popen.communicate only for python3.
This ensures that Executable.__call__ returns a str for python2 and
python3.
fixes#4236fixes#5002
When a package is defined in more than one repository,
RepoPath.dirname_for_package_name may return the path
to either definition. This sidesteps that ambiguity by
accessing the module associated with the package definition.
* py-networkx: adding older version py-networkx
* py-pypeflow: new package
* falcon: adding new package
pacbio-daligner: adding new package
pacbio-damasker: adding new package
pacbio-dazz-db: adding new package
pacbio-dextractor: adding new package
* py-networkx: modifying version order to be in line with convention
* falcon: tweaking py-networkx dependency to satisfy setuptools
py-pypeflow: adding missing dependency
* pacbio-dextractor: changing hdf5 dependency
* pacbio-daligner: adding gmake build dep
pacbio-damasker: adding gmake build dep
pacbio-dazz-db: adding gmake build dep
pacbio-dextractor: adding gmake build dep
* mpest: new package
* adding architecture env var and making more version-flexible
* fixing environment
* fixed build directory
* getting rid of duplicated code
* signalp: new package
* fixed homepage
* fixed url and phases
* refixed phase
* improved readability
* making path in execuatble adaptable to new versions
* fixes#967
* Version bump to 0.9.1
- Bugfixes for spack find
- 0.9.1 can read specs from current develop.
* Don't assume spack is in the path when building docs.
* adding mfem variants; do not assume build defaults
* adjusting format to clarify options
* fixing some build issues
* fixing mfem+sundials
* removing mesquite variant...turns out it is obsolete
* adding examples to mfem; fixing sundials darwin installs
* adding some additional variants and setting some configure flags by fiat
* switching most check_variants logic to conflicts() directives
* adding comment about cmake config
* fixing flake8 issues; thought I had already done that
* moving func def into install method
* switch yes_no to no_yes; fix miss-spelling of miniapps
* switching make target all to lib
* changing yes_no to function as requested; fix problem with same in sundials
* fix missing import sys directive
* adding master and develop versions to amrex
* Added a package for the MDAnalysis toolkit.
* Added additional packages that Elemental depends on.
* Changed LBANN to not ask for the scalapack variant in Elemental.
* Removed variant control on scalapack
* New package: qbox
* API changes
* Use install instead of shutil for comd
* Use any BLAS library
* Fix typo
* Python2 fix
* python2 + fix backslashes
* Modified to respond to ld_flags correctly
* Modified to use ld_flags
* Add ld_flags support
* Updated Changes
* Updated AMG with required MPI
* Updated AMG with Version ' changes'
* Fixed Issues with flag's and variant checks
* Updated with MPI Alone and Changes - NO Serial Variant
* Updated with MPI Alone and Changes - NO Serial Variant
* Fixed Flake 8 line length error
* Updated Spack Issues
* Update the krell institute products to use the latest features of spack for building on cluster platforms.
* Address travis error messages and resubmit the pull request.
* Update the contents of openspeedshop package.py so it passes the flake8 tests.
* Fix flake8 error-whitespack issue in mrnet package.py file.
* Add updates based on spack reviewer feedback.
* More fixes based on comments from reviewers. Switch using extend to using append, remove additional setting of PATH and LD_LIBRARY_PATH that should not be required due to RPATH.
* More review related changes. Update MPIOption.append lines and take out xercesc references.
* Create a base options function for common openspeedshop base cmake options to reduce redundencies.
* Add libxml2+python depends on to get around issues with the libxml2 package file.
* Using boost over 1.60.0 causes compile errors. This is a known boost bug. Also, dyninst-9.2.0 is set to be the vesrion of dyninst to use with OSS, as of now. The newer version fails to build.
* Fix bad syntax in specifying the boost version range.
* Update the version numbers for the krell institute components and tools: cbtf and openspeedshop.
* Do not build glib for qt3, it is not needed and causes build problems at this time anyway.
* A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set.
* Update the fix for qt3 build by setting LD_LIBRARY_PATH instead of checking for whether it is set or not per Adams comment that spack clears LD_LIBRARY_PATH.
* A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set.
* Trim comments to fit more concisely.
* Fix tabs versus spaces and swap if and else clause check from a negative to a positive check.
* Add new OpenSpeedShop gui package based on qt4/qt5 gui toolkit.
* Fix flake8 errors.
* Fix flake8 errors.
* Update bcl2fastq2 with info for 2.19.1.403
Heads up, the download location changed (domain name AND protocol).
* Flake8 fix
What's one space between friends?
* Adding lower bound to pnetcdf conflict in Trilinos to allow for use of develop and master branch.
* Using even lower bound for pnetcdf conflict in Trilinos.
* Added a package for the MDAnalysis toolkit.
* Changed cmake_options to args to be consistent with the rest of the
file and fix a cmake error about undefined errors. Additionally,
added guards for both png and zlib to not include their cmake options
when those variants are not specified.
* Merged 'purge' command with 'clean'. Deleted 'purge'. fixes#2942
'spack purge' has been merged with 'spack clean'. Documentation has been
updated accordingly. The 'clean' and 'purge' behavior are not mutually
exclusive, and they log brief information to tty while they go.
* Fixed a wrong reference to spack clean in the docs
* Added tests for 'spack clean'. Updated bash completion.
* Typo fixes in docstrings.
* Let OS classes know if the paths they get were explicitly specified by user.
* Fixed regexp for cray compiler version matching.
* Replaced LinuxDistro with CrayFrontend for the Cray platform's frontend.
* slurm: added initial recipe
* Modified variants following Adam comment.
The MV variant 'features' has been turned into a set of BV variants. The
dependency on 'readline' has been made optional.
* new package: cns-nospec
* made changes as suggested and added proxy-app tag
* updated edit()
* adjusted logic for '+debug'
* install readme and license
* install readme and license
* install readme and license; fix mpi version build issues
* fix build issues for ~mpi
* pep8 compliant
* new package: amr-exp-parabolic
* removed boilerplate and added tag
* install license and readme
* fix mpi build issues
* change access to include/lib directories and pep8 compliant now
* Update the krell institute products to use the latest features of spack for building on cluster platforms.
* Address travis error messages and resubmit the pull request.
* Update the contents of openspeedshop package.py so it passes the flake8 tests.
* Fix flake8 error-whitespack issue in mrnet package.py file.
* Add updates based on spack reviewer feedback.
* More fixes based on comments from reviewers. Switch using extend to using append, remove additional setting of PATH and LD_LIBRARY_PATH that should not be required due to RPATH.
* More review related changes. Update MPIOption.append lines and take out xercesc references.
* Create a base options function for common openspeedshop base cmake options to reduce redundencies.
* Add libxml2+python depends on to get around issues with the libxml2 package file.
* Using boost over 1.60.0 causes compile errors. This is a known boost bug. Also, dyninst-9.2.0 is set to be the vesrion of dyninst to use with OSS, as of now. The newer version fails to build.
* Fix bad syntax in specifying the boost version range.
* Update the version numbers for the krell institute components and tools: cbtf and openspeedshop.
* Do not build glib for qt3, it is not needed and causes build problems at this time anyway.
* A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set.
* Update the fix for qt3 build by setting LD_LIBRARY_PATH instead of checking for whether it is set or not per Adams comment that spack clears LD_LIBRARY_PATH.
* A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set.
* Trim comments to fit more concisely.
* Fix tabs versus spaces and swap if and else clause check from a negative to a positive check.
* Fix issues with the cbtf-argonavis build, update to use dyninst-9.3.2, fixes to openspeedshop package build.
* Fix issues with the cbtf-argonavis package.py files related to comments.
* Add changes for changing the krell packages from Package to CMakePackage.
* Add better changes for changing the krell packages from Package to CMakePackage.
* Add more modifications for changing the krell packages from Package to CMakePackage.
* Add additional modifications for changing the krell packages from Package to CMakePackage and fixing Travis erros
* Fix new travis errors.
* Fix new travis errors.
* Add more changes for PR 4765.
* Add more refinements to the conversion from Package to CMakePackage.
* Fix new travis errors.
* Add dependencies for MPI to be passed to cbtf-krell, so it can build the MPI collectors requested by the builder of openspeedshop.
* Remove extra unnecessary routine to adjust build arguments. Fix if-else clause issue.
* Fix more flake issues caused by last changes.
* Fix a bug where openspeedshop will not build when no mpi variants are specified. Also switch to a multiple level variant for building the gui(s). Use none, qt3, and qt4 as the variants with qt3 being the default.
* Add fix for spack issue #4843, where LTDL include files were not found.
* Add the build_type variant back into the openspeedshop package file.
* Add new package for the Argo Navis/Krell new graphical user support library: QtGraph.
* Revert "Add new package for the Argo Navis/Krell new graphical user support library: QtGraph."
This reverts commit f8883de446.
* Add new package for the Argo Navis/Krell new graphical user support library: qtgraph.
* Fix flake8 errors.
* Fix flake8 errors.
* Fix flake8 errors.
* Fix flake8 errors.
* Fix flake8 errors.
* Add changes to support QMakePackage class instead of Package class for qtgraph.
* Update change for suggested reviewer improvements.
* Fix flake8 errors.
* Fix flake8 errors.
* new package: VPFFT
* install readme and license
* misc
* changed version name to 'develop'
* removed the misplaced package file
* updated eigen path, fixed docstring, and updated 'docs' installation method
* pep8 compliant, changed installation of docs
IceT places its CMake module in the wrong directory,
which is not included in the default CMake search paths.
This fixes it for *directly* depending packages without the
need to add
```yaml
icet:
environment:
prepend_path:
CMAKE_PREFIX_PATH: '${PREFIX}/lib'
```
to the `modules.yaml` as a workaround.
* Molcas 8.2: Adding molcas spec file
* Molcas 8.2: Putting in patch file for molcas driver not to be installed in spack stage directory
* Molcas making changes
* Making changes in ordering
* transabyss: new package and dependencies
* fixed build deps in igraph and version conflict spec in abyss
* fixed versioning stuff and package structure
* fixed dep type
* fixing dep type for real this time
Build system "usually" autodetects mpi library but this is
not the case on many platforms. Provide mpi library name/version
as part for configure args.
* savanna: explicitly adding variant sz to adios since it is no longer enabled by default in adios
* savanna: removing +sz from adios as sz is now enabled in adios by default
* savanna: explicitly specifying adios variants required by savanna
* adios: conform to pep8
* adios: added versions 1.11.0 and 1.12.0
* adios: added variant no_mpi to explicitly disable mpi support
* adios: add new variant mxml
adios v1.12.0 onwards contains an xml library built within.
To build with an external mxml, a new variant must be used
* adios: new variant for sz transform
* adios: flexpath and dataspaces staging variants
Two new variants for staging: flexpath and dataspaces.
New variant 'staging' that will enable both
* adios: dependency on libtool:2.4.2 since adios does not build with newer libtool 2.4.6
* adios: better description for variant no-mpi
* adios: new variant for netcdf
as requested by @mamelara from LBL
* adios: renamed variant 'no_mpi' to 'serial'
* adios: removed variant mxml
* adios: corrected implementation of the mpi dependency, along with its relation with the 'serial' variant
Added conflicts between 'serial' and other variants
* adios: added 'else' clause when variants are not added
* adios: replaced variant 'serial' with 'mpi'
* adios: Added configure option to explicitly disable variants that are not enabled.
* adios: setting default zfp to true
* adios: fixed flake8 errors
* adios: removed some old comments
* adios: setting default sz to False.
It is recommended to set default to False when dependency is on develop (sz@develop).
* adios: removing dependency on develop for sz and setting default sz to true
* adios: updated url to latest release.
Just keeping it clean
* new package:SNAP
* removed boilerplate
* Delete .nfs00000000003a8b1700001358
* install another executable in bin and install readme
* added quotes around README.md
* moved readme to prefix
* Added a package for the MDAnalysis toolkit.
* Added a patch that allows Elemental to use cuBLAS internally.
* Added support for LBANN to use the new cuBLAS extension in Elemental.
* Added a proper variant for when LBANN does not want to use cuBLAS in
elemental.
* Added a package for the cnpy project and used it in the lbann package.
* Removed unnecessary comment lines.
* Removed blank lines
* Removed debug variant
* Add support for libjpeg-turbo
* Added additional variants for OpenCV features. Fixed bug when linking
in TIFF support, where libtiff used the regular JPEG library and
OpenCV used libjpeg-turbo. Now libtiff can use libjpeg-turbo.
* Removed the variant for getting Elemental to use the cublas variant.
Updated the requirements for OpenCV to add new options.
* Fixed a flake8 error in OpenCV and added a path to find cnpy in lbann.
* Fixed line too long flake8 error.
* Added a flag to specify the datatype size in lbann and fixed a flake8 error.
* Added a debug build variant using hte new build_type
* Fixed flake8
* Fixed how the debug build is pushed to Elemental
* Fixed a bug in the Elemental package where the blas search flags were
being overridden by the blas link flags. Changed how the sequential
initialization variant is implemented in LBANN.
* Added support via a variant to explicitly use mkl or openblas. This
helps work around variant forwarding problems.
* Updated package files to address pull request comments.
* new package: cns-nospec
* made changes as suggested and added proxy-app tag
* updated edit()
* adjusted logic for '+debug'
* install readme and license
* install readme and license
* new package: SMC
* removed template and added proxy-app tag
* added comp variant in edit()
* edited comp variant in edit()
* move executable and input file into bin and install readme and license
Fixes#4898
Constraints that were supposed to be conditionally activated for
specified values of a single-valued variant were being activated
unconditionally in the case that the variant was associated with
an implicit dependency. For example if X->Y->Z and Y places a
conditional constraint on Z for a given single-valued variant on
Y, then it would have been applied unconditionally when
concretizing X.
Earlier versions of boost had a fixed maximum number of jobs. 1.54
was 64, it bumped once or twice afterwards and in 1.59 [this
commit][commit] it became dynamic.
I need 1.54 for as a prereq for bcl2fastq but I can't build 1.54 on my
144 core build box.
This fixes that.
[commit]: 316e26ca71
* Fix cdefs macro to be compatible with gcc 4.8.x
See the discussion in #4945 (after the merge) for additional
background.
libbsd builds with gcc@5.4.0 on CentOS 7, but not with the system's
gcc@4.8.5. Others have reported problems with gcc@4.8.3 on Fedora 19.
The problem boils down to the lack of support for the clang extension
`__has_include_next`. The immediate symptom seems to be the
pre-processor using defining macro like this
```
```
then then tripping over an expansion of it like this:
```
blah.h:13:23: error: missing binary operator before token "("
```
This patch changes the macro definition to:
```
```
which swallows the arguments with which the macro is invoked.
The end result is that libbsd builds for me on CentOS 7 using the
system compiler.
* Apply this patch for any compiler version before 5
This includes subversions of 4, like 4.8.5.
* chlorop: new package
* chlorop: moving main script to bin and moving runtime tmp location.
* chlorop: fixing flake8 error.
* chlorop: cleaning up, removing CHLOROTMP, advising user to set it.
* chlorop: removing unused import
Adds ADIOS2, the C++ Exascale HPC I/O rewrite of ORNL's ADIOS
library.
Currently, many variants (especially for data transforms such as
compression) are not yet added. It already provides Python bindings.
* Changed every 'fpic' variant to 'pic'. fixes#2463
Every variant that activates compilation of position independent code
has been changed to 'pic'. Hardcoded compiler flags in packages have
been substituted with `self.compiler.pic_flag`.
* Changed literal uses of '-fpic' to 'self.compiler.pic_flag'
* Add a QMakePackage base class
* Fix sqlite linking bug in qt-creator
* Add latest version of qt-creator
* Add latest version of qwt
* Use raw strings for regular expressions
* Increase minimum required version of qt
* Add comment about specific version of sqlite required
* Fixes for latest version of qwt and qt-creator
* Older versions of Qwt only work with older versions of Qt
* SCR CMake package
* Fix dtcmp variant description and set pdsh deptypes to build/run
* added variants for system config file location
* add variants for several scr cmake options
* Added more variants for compile time options
* Added libyogrt and made corrosponding changes to scr package.
* Cleanup yogrt package now that Ive verified it works
* Added description for libyogrt
* upper case async api names
* Make use of mv variants
* fix pdsh package for scr
* added IBM BBAPI as async option
* update pdsh and scr to use static pdsh modules
* Add package for libbsd, add variant to expat for libbsd
The recent expat release requires a high quality source of randomness.
CentOS 7 does not seem to have one, but one is available in libbsd.
This commit adds a package for libbsd and adds a variant to expat to
use it (defaults to False).
* Make libbsd default for newer, conflict for older
Make the libbsd variant default to true.
Conflict if you're asking for libbsd and an older version of expat.
This means that in order to install an older version of expat you'll
need to specify `~libbsd`.
* Rework so that 2.2.0 and 2.2.2 work by default
Get rid of the conflicts and use better constraints/tests in the
`depends_on` and the `configure_args` bits.
* Fix crashes when running spack install under nohup
Fixes#4919
For reasons that I do not entire understand, duplicate_stream() throws
an '[Errno 22] Invalid argument' exception when it tries to
`os.fdopen()` the duplicated file descriptor generated by
`os.dup(original.fileno())`. See spack/llnl/util/lang.py, line
394-ish.
This happens when run under `nohup`, which supposedly has hooked
`stdin` to `/dev/null`.
It seems like opening and using `devnull` on the `input_stream` in
this situation is a reasonable way to handle the problem.
* Be more specific about error being handled.
Only catch the specific error that happens when trying to dup
the stdin that nohup provides.
Catching e as a StandardErorr and then
`type(e).__name__` tells me that it's an OSError.
Printing e.errno tells me that it's 22
Double checking tells me that 22 is EINVAL.
Phew.
* Add package for canu
There's a top-level perl script, which is touched up to use a
spack-built perl instead of `#!/usr/bin/env perl`. It's
self-contained, it uses `FindBin` to locate it's libaries.
* Add dependency on gnuplot
I noticed a hidden mention of the use of gnuplot in the docs.
This adds the dependency.
* Tighten dependencies, flake8 cleanup
gnuplot is a run dependency.
jdk is a run dependency.
perl is a run dependency.
Make flake8 happy.
* Protobuf: CMake
This rebuilds protobuf to be build with CMake,
so cmake config packages are created and installed, too.
Unfurtunately, this drops support for protobuf < 3.
* Protobuf CMake: Add .pc files
* libprotobuf.a: -fPIC
* Protobuf: Minor Updates
Updates from upstream review and planned patch inclusion.
- Remove `special_types` dict in spec.py, as only 'all' is still used
- Still allow 'all' to be used as a deptype
- Simplify `canonical_deptype` function
- Clean up args in spack graph
- Add tests
* Fix xsdk build broken by petsc and trilinos
See #4891 for details
* Fix version conflict in trilinos package
Trilinos version 11 may conflict with superlu-dist.
The version "xsdk-0.2.0" was conflicting with superlu-dist,
even though it shouldn't. I added a lower bound to the
comparison to fix this problem.
Thanks for the help @davydden!
For packages which contain a mix of versions with formats X.Y and
X.Y.Z, if the user entered an X.Y version as a preference in
packages.yaml, Spack would get confused and favor any version A.B.Z
where X=A and Y=B. In the case where there is a mix of these version
types, this commit updates preferences so Spack will favor an exact
match.
* Disable spec colorization when redirecting stdout and add command line flag to re-enable
* Add command line `--color` flag to control output colorization
* Add options to `llnl.util.tty.color` to allow color to be auto/always/never
* Add `Spec.cformat()` function to be used when `format()` should have auto-coloring
Adds the cppzmq library, adding a C++ API to ZeroMQ (libzmq). In order to find the autotools-build libzmq, this requires the upcoming cppzmq release (or development branch).
zsh's configure script fails if there's it tries to test for terminal
functionality if there's not a terminal (e.g. in a Jenkins build).
The configure script has a switch that asserts that tcsetpgrp works
and thereby avoids running that test.
This commit adds a variant that invokes that switch, defaulting to
True.
Adds a the latest version of gBenchmark, release 1.2.0.
This is the first gBenchmark version with proper
[CMake config package installs](https://github.com/google/benchmark/issues/363).
This is important for dependencies building against it, such as gRPC.
* Initial Spackage for qmd-progress library
PROGRESS is a library is focused on the development of general solvers
that are commonly used in quantum chemistry packages.
* Removed LA-CC from description to fix formatting
* Added Additional Formatting Requests
Added requested formatting changes and also ensured that graphlib and
mpi are disabled if not enabled
* New Pacakge: lcals
* added logic for arch detection and compiler choice.
* fixes for comments.
* addressed comments.
* removed LCALS_ARCH and added flags though spack.
* addressed comments.
* flake 8 fix.
* reerted the changes along with comments.
* Update the krell institute products to use the latest features of spack for building on cluster platforms.
* Address travis error messages and resubmit the pull request.
* Update the contents of openspeedshop package.py so it passes the flake8 tests.
* Fix flake8 error-whitespack issue in mrnet package.py file.
* Add updates based on spack reviewer feedback.
* More fixes based on comments from reviewers. Switch using extend to using append, remove additional setting of PATH and LD_LIBRARY_PATH that should not be required due to RPATH.
* More review related changes. Update MPIOption.append lines and take out xercesc references.
* Create a base options function for common openspeedshop base cmake options to reduce redundencies.
* Add libxml2+python depends on to get around issues with the libxml2 package file.
* Using boost over 1.60.0 causes compile errors. This is a known boost bug. Also, dyninst-9.2.0 is set to be the vesrion of dyninst to use with OSS, as of now. The newer version fails to build.
* Fix bad syntax in specifying the boost version range.
* Update the version numbers for the krell institute components and tools: cbtf and openspeedshop.
* Do not build glib for qt3, it is not needed and causes build problems at this time anyway.
* A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set.
* Update the fix for qt3 build by setting LD_LIBRARY_PATH instead of checking for whether it is set or not per Adams comment that spack clears LD_LIBRARY_PATH.
* A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set.
* Trim comments to fit more concisely.
* Fix tabs versus spaces and swap if and else clause check from a negative to a positive check.
* Fix issues with the cbtf-argonavis build, update to use dyninst-9.3.2, fixes to openspeedshop package build.
* Fix issues with the cbtf-argonavis package.py files related to comments.
* Add changes for changing the krell packages from Package to CMakePackage.
* Add better changes for changing the krell packages from Package to CMakePackage.
* Add more modifications for changing the krell packages from Package to CMakePackage.
* Add additional modifications for changing the krell packages from Package to CMakePackage and fixing Travis erros
* Fix new travis errors.
* Fix new travis errors.
* Add more changes for PR 4765.
* Add more refinements to the conversion from Package to CMakePackage.
* Fix new travis errors.
* Add dependencies for MPI to be passed to cbtf-krell, so it can build the MPI collectors requested by the builder of openspeedshop.
* Remove extra unnecessary routine to adjust build arguments. Fix if-else clause issue.
* Fix more flake issues caused by last changes.
* Fix a bug where openspeedshop will not build when no mpi variants are specified. Also switch to a multiple level variant for building the gui(s). Use none, qt3, and qt4 as the variants with qt3 being the default.
* Add fix for spack issue #4843, where LTDL include files were not found.
* Add the build_type variant back into the openspeedshop package file.
* removed the tags as per comment in PR# 4749
* addressed above comments
* changed fortran compiler.
* added proxy application tags.
* added tags by removing them from description.
* addressed comments
* used join_path instead of path concat.
* removed the tags as per comment in PR# 4749
* addressed above comments
* changed fortran compiler.
* added proxy application tags.
* added tags by removing them from description.
* addressed comments
* used join_path instead of path concat.
* added tags.
* changes to use MPI as depedency.
* removed MPI as variant.
* changed pointer to filtered makenek file.
* flake 8 fix.
* Add universal build_type variant to CMakePackage
* Override build_type in some packages with different possible values
* Remove reference to no longer existent debug variant
* Update CBTF packages with new build_type variant
* Keep note on build size of LLVM
* fixes#967
* Version bump to 0.9.1
- Bugfixes for spack find
- 0.9.1 can read specs from current develop.
* Don't assume spack is in the path when building docs.
* Remove PKG_CONFIG_PATH from tmux configure
* Change tmux to AutotoolsPackage
* Correct link to libtinfo in tmux
* Change version.up_to() to return Version() object
* Add unit tests for Version.up_to()
* Fix packages that expected up_to() to return a string
* Ensure that up_to() preserves separator characters
* Use version indexing instead of up_to
* Make all Version formatting properties return Version objects
* Update docs
* Tests need to test string representation
* perl: prepend default perl @INC path to support package activation
* perl: remove stray comma from list of configure arguments
* perl: final comma in configure arguments makes adding arguments safer
This reverts commit fdc10cd611f525ebc31ca1953e048095b1c75350.
* perl: add comment about modified @INC (thanks to George Hartzell)
* perl: use self.prefix.lib and self.prefix.bin for clarity
* perl: convert tabs added by editor to spaces for flake8
* perl: use new path syntax: prefix.lib.perl5
* perl: avoid line break before binary operator
* perl: use compact spack syntax for perl executable
* gBenchmark: Development Package
Add the development version (master branch) of `gBenchmark`
* gBenchmark: Remove Duplicate
Remove duplicate `gbenchmark` library
and keep its patch to remove the shipped
-Werror
Adds SpackCommand class allowing Spack commands to be easily in Python
Example usage:
from spack.main import SpackCommand
info = SpackCommand('info')
out, err = info('mpich')
print(info.returncode)
This allows easier testing of Spack commands.
Also:
* Simplify command tests
* Simplify mocking in command tests.
* Simplify module command test
* Simplify python command test
* Simplify uninstall command test
* Simplify url command test
* SpackCommand uses more compatible output redirection
Installing the stable version 0.5 through the checksummed tar.gz does not fetch the git submodule in the package.
The submodule appears as an empty directory.
Thus, clone the commit tagged as v0.5 using git to get around this issue
* savanna: modified adios dependency spec
* Replaced adios+staging with adios+flexpath+dataspaces
* savanna: Enabling fortran support in adios by default
* savanna: reverting to variant 'staging' for enabling all staging transports
- +swrender variant lets you compile an off-screen only version for
software rendering on clusters.
- +swrender+llvm for using llvm for the software pipe
- added newer versions (17.1 and 13.0) and corrected the url location
to use the canonical location.
* gtkorvo-atl: atl library from gtkorvo
* gtkorvo-dill: dill library from gtkorvo
* gtkorvo-cercs-env: cercs_env library from gtkorvo
* gtkorvo-enet: Enet networking library from gtkorvo
* libffs: FFS middleware communication library from GTKorvo
* libevpath: EVPath high performance communication library from GTKorvo
* gtkorvo-cercs-env: Added homepage and removed function configure_args
* gtkorvo-cercs-env: Re-add of accidental removal of cmake_args function in previous commit
* gtkorvo-enet: Removed configure_args since unused
* removed the tags as per comment in PR# 4749
* addressed above comments
* changed fortran compiler.
* added proxy application tags.
* added tags by removing them from description.
* addressed comments
* used join_path instead of path concat.
* addressed comments
* removed string formatting for LDFLAGS.
* Update the krell institute products to use the latest features of spack for building on cluster platforms.
* Address travis error messages and resubmit the pull request.
* Update the contents of openspeedshop package.py so it passes the flake8 tests.
* Fix flake8 error-whitespack issue in mrnet package.py file.
* Add updates based on spack reviewer feedback.
* More fixes based on comments from reviewers. Switch using extend to using append, remove additional setting of PATH and LD_LIBRARY_PATH that should not be required due to RPATH.
* More review related changes. Update MPIOption.append lines and take out xercesc references.
* Create a base options function for common openspeedshop base cmake options to reduce redundencies.
* Add libxml2+python depends on to get around issues with the libxml2 package file.
* Using boost over 1.60.0 causes compile errors. This is a known boost bug. Also, dyninst-9.2.0 is set to be the vesrion of dyninst to use with OSS, as of now. The newer version fails to build.
* Fix bad syntax in specifying the boost version range.
* Update the version numbers for the krell institute components and tools: cbtf and openspeedshop.
* Do not build glib for qt3, it is not needed and causes build problems at this time anyway.
* A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set.
* Update the fix for qt3 build by setting LD_LIBRARY_PATH instead of checking for whether it is set or not per Adams comment that spack clears LD_LIBRARY_PATH.
* A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set.
* Trim comments to fit more concisely.
* Fix tabs versus spaces and swap if and else clause check from a negative to a positive check.
* Fix issues with the cbtf-argonavis build, update to use dyninst-9.3.2, fixes to openspeedshop package build.
* Fix issues with the cbtf-argonavis package.py files related to comments.
* Add changes for changing the krell packages from Package to CMakePackage.
* Add better changes for changing the krell packages from Package to CMakePackage.
* Add more modifications for changing the krell packages from Package to CMakePackage.
* Add additional modifications for changing the krell packages from Package to CMakePackage and fixing Travis erros
* Fix new travis errors.
* Fix new travis errors.
* Add more changes for PR 4765.
* Add more refinements to the conversion from Package to CMakePackage.
* Fix new travis errors.
* Add dependencies for MPI to be passed to cbtf-krell, so it can build the MPI collectors requested by the builder of openspeedshop.
* Remove extra unnecessary routine to adjust build arguments. Fix if-else clause issue.
* Fix more flake issues caused by last changes.
* Initial work on flag trapping using functions called <flag>_handler and default_flag_handler
* Update packages so they do not obliterate flags
* Added append to EnvironmentModifications class
* changed EnvironmentModifications to have append_flags method
* changed flag_val to be a tuple
* Increased test coverage
* added documentation of flag handling
* removed the tags as per comment in PR# 4749
* addressed above comments
* changed fortran compiler.
* added proxy application tags.
* added tags by removing them from description.
* addressed comments
* used join_path instead of path concat.
* added tags and other minor changes.
* removed tags from description.
* new package: CLAMR
* changed from bool variants to single value variants and corresponding logic in build_type and cmake_args
* lowercase variant values
* updated conditionals for variants
* adjusted url and docstring
* new package to be added: NuT
* removed cmake_args() and made other changes as suggested
* Added setup_environment()
* PEP8 compliant
* edited version name, build_targets, and files/directories to install
* corrected executable directory
* compiler dependencies based on version
* Change path to CMakeLists.txt to be relative to root, not pwd
* Changes requested during code review
* Revert back to old naming of root_cmakelists_dir
* Make relative directory more clear in docs
* Revert change causing build_type AttributeError
* Fix forgotten abs_path var
* Update CLHEP with new relative path
* Update more packages with new root_cmakelists_dir syntax
somatic-sniper installs its own copy of samtools, which needs curses.
I'm not sure why I didn't stumble on this in my dev environment, but I
just stumbled over it in a standalone build.
The 4.X branches are now on the homepage, so we take the GitHub release
artifact (careful: take their upload, not the automatic tarball).
Adds a development version of ZeroMQ.
Requires a autogen run, as for all their unreleased versions,
and the pkg-config fix in #4736
Always sets the `pkg-config` environment hint for
autotools.
Required dependency for `autoreconf` of ZeroMQ when
build from source (e.g. v4.2.2) via autotools in `autogen.sh`
step for `autoreconf`.
* Add package for r-ada, update r-rpart version
Adds a package for r-ada.
Update the version for r-rpart because the previous version is
no longer at that URL. The previous version *is* in the Archive,
but list_url does not seem to be able to find it.
* Clean up FIXMEs (blush)
* savanna: Runtime framework for online workflow management from the ECP CODAR project
* savanna: added version 0.5
* savanna: Copying the package contents to prefix as part of installation
* savanna: Doing submodules=true for git checkout of develop version
* savanna: removed dependency on adios@develop. depends on adios
* Savanna: Converted package to MakefilePackage
* New Package: Pathfinder
* Added index for String format
* Changed to make Makefile edit more specific
* Make Flake8 Happy
* Removed unneeded conversion
* Add package for Sniffles
* Wire up a manual install step
The cmake infra doesn't install anything, so do it by hand.
The binaries land in a location that embeds the version...
* hybpiper: new package and spades dependency
* hybpiper: making flkae8 happy
* hybpiper: fixing dependency errors
* fixing python dep type
* removing cmake from spade dependencies
* libwebsockets: new versions
both new versions fix a nasty bug leading to a hanging
connection on connect.
* ISAAC Server: Fix libwebsockets
ISAAC server did hang in docker containers due to a bug
in libwebsockets.
* Add two python packages for editing mach-O headers. Much faster than calling otool and install_name_tool directly
* remove non-overriding function
* autopep8
* Adding OpenMP variant to Trilinos. Also building NetCDF with PNetCDF in Trilinos when necessary.
* Adding runtime error for PNetCDF variant in Trilinos when necessary. Omitting unnecessary openmp variant for Trilinos in Nalu.
* Changing variant checks to conflicts statements.
* Adding comments to Trilinos package.
Adds the `gearshifft` package, a benchmark suite for heterogeneous implementations of FFTs.
Adds clFFT, a software library containing FFT functions written in OpenCL.
see: https://github.com/clMathLibraries/clFFT
The vcftools package was installing its Perl libraries into a
directory in the staging directory named 'lib', instead of installing
them into `prefix.lib` where they should have been because the value
passed to the configure script was wrong.
The result was that any attempt to run one of the scripts in the
package failed with something like:
> Can't locate VcfStats.pm in @INC (you may need to install the
> VcfStats module) [...]
This fix provides the correct information in `configure_args`.
Tested lightly on CentOS 7.
* Dataspaces spack package, hard-wired for ubuntu VM
* Initial commit of dataspaces spack package
* Made changes and additions necessary to install on Cori and Titan
* Added temp 1.6.2.1 for testing
* Updated tar file for 1.6.2
* Fixed formatting
* Set the type of build dependencies
* Changed the way autogen.sh is called for compatibility
* Use append instead of extend to add configure flags
* Various syntax fixes
* Switched string checking to method for compatibility
Now using the six library for Python 3 compatibility. Thanks @adamjstewart
* Made MPI variant default
- Lock test can be run either as a node-local test or as an MPI test.
- Lock test is now parametrized by filesystem, so you can test the
locking capabilities of your NFS, Lustre, or GPFS filesystem. See docs
for details.
- renamed develop version from 'plus' to 'develop'
- patches now prefixed by corresponding OpenFOAM version number.
This makes it easier to sort and see what old/junk exists.
- remove MPI_BUFFER_SIZEk env variable (for all openfoam variants).
The OpenFOAM shell setup addresses this and there is no reason
to pollute the module environment at this stage.
* sabre initial commit, works but test does not
* removing test until I have time to fix it
* sabre: fixing flake8 errors
* sabre: changing to MakefilePackage
* mpifileutils: update to v0.7
* mpifileutils: disable --enable-experimental in v0.6 and earlier
* mpifileutils: list newest version first, avoid experimental switch unless at v0.7 or later
* * add mpii* wrappers for use with intel compilers
* in mumps package, scotch is compiled without metis option when
ptscotch variant is selected. This removes confusion over which
metis.h to use
* for intel mkl, add SPACK_COMPILER_EXTRA_RPATHS ending in 'intel64'
* scotch lib requires libz when compression is turned on. This
caused a link issue on some Ubuntu distributions (not
redhat). Change Scotch package to add -lz when needed
* * intel-mkl append to SPACK_COMPILER_EXTRA_RPATHS rather than setting
* use more concise method to obtain libz libraries for scotch
* remove changes to intel mpi
* remove commented out depends_on
* fix flake8 errors
* Add package for primer3
Built and mildly tested on CentOS 7.
* Convert to MakefilePackage
I always forget about this...
* Set build_directory the easy way
Life's not always complicated. Don't go out of my way
to make it so....
* Fix Flake8 issue
* added perl-star-fusion and perl-intervaltree
* added perl-star-fusion and all dependencies
* changes
* made changes as requested to perl-star-fusion dependencies
* changed perl-intervaltree dependency
* changes to star fusion
* now using perl properly
- Thanks to pointer from @adamjstewart - can avoid this either by
avoiding an external mxml dependency, or by making certain that they
both use consistent code generation.
The adios package uses '-fPIC' for python linkage and this seems to
require the same for mxml too. If the adios-internal version of mxml
is used, it has the same flags for both.
- The buggy flex-2.6.2 was blacklisted in the corresponding flex
package, but now also removed the md5sum to avoid suggesting that
this version should be revived.
The 2.6.3 has similar problems (at least for scotch), but 2.6.4
seems to work.
- Rejig flex restriction for scotch to exclude 2.6.2-2.6.3 only. Since
flex-2.6.4 appears to be okay again, we can remove the flex version
restriction that trickled through into the openfoam packages as a
consequent of an spack spec bug.
- Make flex a build dependency for the openfoam packages
(seems to have been an earlier oversight).
* mv variants: packages are now needed only during normalization
The relationship among different types of variants have been weakened,
in the sense that now it is permitted to compare MV, SV and BV among
each other. The mechanism that permits this is an implicit conversion
of the variant passed as argument to the type of the variant asking
to execute a constrain, satisfies, etc. operation.
* asbtract variant: added a new type of variant
An abstract variant is like a multi valued variant, but behaves
differently on "satisfies" requests, because it will reply "True"
to requests that **it could** satisfy eventually.
Tests have been modified to reflect the fact that abstract variants
are now what get parsed from expressions like `foo=bar` given by users.
* Removed 'concrete=' and 'normal=' kwargs from Spec.__init__
These two keyword arguments where only used in one test module to force
a Spec to 'appear' concrete. I suspect they are just a leftover from
another refactoring, as now there's the private method '_mark_concrete'
that does essentially the same job. Removed them to reduce a bit the
clutter in Spec.
* Moved yaml related functions from MultiValuedVariant to AbstractVariant.
This is to fix the erros that are occurring in epfl-scitas#73, and that
I can't reproduce locally.
* Remove unneeded patch lines which fail for the most recent CNTK version on the head of the git repo
* Really check for NVML/GDK
* Fix some violations
* gtkplus: set XDG_DATA_DIRS
* shared-mime-info: database of common MIME types
* gtkplus: needs shared-mime-info for correct handling of stock icons
* shared-mime-info: builds with newer intltool than provided by some platforms
* atk: set XDG_DATA_DIRS at run-time
* gdk-pixbuf: set XDG_DATA_DIRS at run-time
* gtkplus: set XDG_DATA_DIRS at run-time
* pango: set XDG_DATA_DIRS at run-time
* shared-mime-info: set XDG_DATA_DIRS at run-time
* enable some of the tools
do not make zoltan default
* modify moab package
add shared, debug options to cgm, too
build some tools by default (mbsize, mbconvert)
add hdf5, netcdf dependency
add pnetcdf variant (dependency), metis, parmetis, zoltan
add shared, debug, fortran options to moab
* few kinks for moab
zoltan should be built without fortran api, otherwise moab
complains (need to fix)
also, notice that when built with cgm, shared can't find
cgm libraries for the new tools/geometry execs
install in serial for the time being (because of example makefile
duplicate?)
for example, these builds are successful:
spack install moab+mpi+hdf5+zoltan ^mpich@3.2
spack install moab+mpi+hdf5+shared ^mpich@3.2
* force hdf5+mpi if both are specified
also, something like this works:
spack install moab+mpi+hdf5+cgm ^mpich@3.2 ^cgm+oce+mpi ^oce@0.17.2
use mpich32, and cgm built with oce 0.17.2
* forgot about irel, fbigeom, mbcoupler
* add meshkit package
simple build so far, moab and cgm deps only
also, an example of complex build for cgm
spack install moab+mpi+hdf5+cgm+irel+fbigeom ^mpich@3.2 ^cgm+oce+mpi ^oce@0.17.2
* for meshkit, moab needs to have irel, fbigeom
* forgot to self.spec
after building moab with cgm with oce 0.17.2, we can build
meshkit with something like this
spack install meshkit ^moab/tsb75zk
cgm depencency is found out from moab
moab has to be built with irel and fbigeom
* add netgen package and review
do not support yet older versions of meshkit
(which depend on lasso, etc)
add netgen package; tested with meshkit (netgen has to be built without
occ, for meshkit)
We are not enforcing that yet, we may have to test
* use conflicts where needed, suggested by review
remove release candidates
* flake8 alignment errors
* flake8
* reviews
flake8 alignment
explicit options, even for default variants
variant for netgen should be "gui", with the default ~gui (False)
FIXME: with-occ does not work right for netgen ; maybe it should be disabled?
also, with +gui, it should depend on a lot more, like tk, tcl?
* flake8 issues
whitespaces and a comment in netgen
* add more explicit options
--without-mpi needs fixing for cgm, moab and meshkit
add variable url for netgen (although we don''t know if other
versions will appear)
* flake8, trailing whitespace
* ninja-fortran: a Fortran-capable fork of ninja build tool
* Use url_for_version for clarity
* Clean ninja-fortran
* Cleanup in the original ninja package
* added py-tomopy package
* fixed dependencies and added import_modules
* edited deps for tomopy with import_modules and added py-olefile pkg
* changed module name
* changed dependency to python because it will not build with setuptools
* fixed dependency list for py-tomopy and py-dxchange
* added py-nose dependency
* fixed tests
* commented out dependency py-counter
* fixed dependency py-pybtex-docutils
* removed nose as a dependency
* fixed flake8 errors
* fixed import_modules
* fixed import_modules indent
* fixed various issues in tomopy and deps files
- paraview 5.2.1 -> 5.4.0 supports both Qt4 and Qt5, but the assumed
default version changes between versions. So explicitly define
which QT major version is being used.
* Parse modules in a way that works for both lmod and tcl
* added test and made method more robust
* refactoring for pythonic clarity
* Improved detection of 'module' shell function + refactored module utilities into spack.util.module_cmd
* Improved regex to reject nested parentheses we are not prepared to handle
* make tests backwards compatible with python 2.6
* Improved regex to account for sh being aliased to bash and used in bash module definition on some systems
* Improve test compatibility with lmod
* Added error for None module_cmd
* Add test for get_module_cmd_from_which()
Add test for get_module_cmd_from_which().
Add -c argument to Popen call to typeset -f module in get_module_cmd_from_bash().
* Increased detection options
Included BASH_FUNC_module() variable outside of typeset as a detection option
This should work on bash even in restricted_shell mode
Kept the typeset detection as an option in case the module function is not exported in bash
Also added try statements to tests, with environment recreation in finally blocks.
* More tests added; some hackiness
* increased test coverage for util/module_cmd
* Several improvements for the openfoam packages
--
Refactor openfoam packages by adding an OpenfoamArch class
Use separate configure, build, install phases.
Provide FOAM_PROJECT_DIR dependent env for openfoam packages
- easier way to locate
Eliminate intermediate installation directories
- unneeded clutter.
- makes it less than easy to find the etc/bashrc file
Add versioning for all openfoam patches
- no certainty which parts (if any) will be needed in future versions,
especially if we strive to ensure that the upstream version builds
well with spack to begin with.
Support build of develop branches
- helps track build regressions for future openfoam releases
STYLE: use common/ and assets/ to provide additional (build) resources ...
* - adjust OpenFOAM provider
Move openfoam-com up front since this is the one being used as a base
for the others
Added line in package.py to patch using ipopt_ppc_build.patch. The patch simply adds support in config.guess and Ipopt/config.guess to build ipopt on ppc64le.
* adding H5Z-ZFP; updating zfp to use choice variant for bit stream word size
* fixing homepage url
* removed fortran error message...just build fortran if can, otherwise ignore
* Added magma package
* Incorporated Serban's change
* fftw: patch configuration file to remove search for xlc_r compiler
when compiler not gcc
FFTW assumes there are only 2 compilers: gcc and IBM XL. When
building threaded fftw, the configuration file is looking for
the threaded IBM XL's xlc_r compiler when the compiler is not gcc.
The PGI compiler is not gcc.
* Include depends_on for gperf
Sometime around 2.12.2 fontconfig acquired a build-time
dependency on `gperf` (this commit, I think:
59fd9960bbb58fd6257adb13ec0f918882149332).
This adds the dependency.
`gperf` is called in the `src/Makefile`, see line 907 of
`src/Makefile.in`.
* Only depend_on gperf if @2.12.2:
The gperf dependency *seems* to only be required when @2.12.2:.
Earlier releases do not check the arg type of the gperf lookup
function (which requires gperf) and are able to use pre-generated
files so gperf is not required at build time.
* fixes#967
* Version bump to 0.9.1
- Bugfixes for spack find
- 0.9.1 can read specs from current develop.
* Don't assume spack is in the path when building docs.
* fixing Makefile override of PREFIX and install w/gcc-6
* Code changes to enable system config scope in /etc
Files will go in either /etc/spack or /etc/spack/<platform>
Required minor changes to conftest.
* Updated documentation to match new config scope
* oce changes for cgm
cgm can be configured with oce, but oce needs
to have X11 enabled, because some libraries
(like TKCAF in occ/oce) gets built only of X11 is NOT disabled
so introduce a variant +X11 for oce, which is needed when
configuring cgm with oce(+X11)
* follow up review
simplify by removing the patch and different url paths
use append instead of extend, when necessary
make mpi true by default
X11 dependency is still to be addressed; it pulls in some opengl
library (on laptop nvidia seem to work, on virtual linux machine
mesa was good enough)
- previous code called `which` on $EDITOR, but that doesn't work for
EDITORs like `emacs -nw` or `emacsclient -t -nw`.
- This patch just trusts EDITOR if it is set (same as previous
behavior), and only uses the defaults if it's not.
* issue 4492: added xfailing test, added owner to DependencyMap
* DependencyMap.concrete checks if we have unconditional dependencies
This fixes#4492 and #4107 using some heuristics to avoid an infinite
recursion among Spec.satisfies, Spec.concrete and DependencyMap.concrete
The idea, as suggested by @becker33, is to check just for unconditional
dependencies. This is not covering the whole space and a package with
just conditional dependencies can still fail in the same way. It should
cover though all the **real** packages we have in our repo so far.
* Check for CRAYPE_VERSION instead of path
Architecture tests would fail on Cray since it would not find
the expected path. To make the test correctly work on Cray search
for the CRAYPE version instead.
* Catch SystemExit error in case flake8 not in path
On shared systems having flake8 can involve starting own virtual env.
Skip the test if no flake8 is found to avoid failure reporting.
* Add compatibility to 1.5 svnadmin create
The flag added is needed to correctly create svn repos on NERSC systems.
This could be unnecessary for other sites. I'd like to see others
test before this change gets merged.
- invoke make with the correct TARGET for aarch64
- foforce PILERDRIVER as openblas cannot correctly detect CPU on aarch64
- update url to more recent version
- Skip spack flake8 test when flake8 is not installed.
- Fix parsing of dashes in specs broken by new help parser.
- use argparse.REMAINDER instead of narg='?'
- don't interpret parts of specs like -mpi as arguments.
* Fix tpetra-related xsdk errors
Recent changes to the trilinos package broke the xsdk build.
xSDK explicitly disables tpetra, but packages depending on it
(such as ifpack2 and amesos2) are explicitly enabled by default
in the trilinos package. This commit explicitly disables them
within the xsdk package.py.
* Disabled exodus in the xsdk build
See issue #4502 for details
- Introduce an opengl variant that is enabled by default. Disabling it
allows building qt for X forwarding etc.
- Depend on fontconfig and freetype to make use of system fonts.
Otherwise qt can not find any fonts.
- libx11 is required when libxcb is used.
- Set MAKEFLAGS to parallelize qmake compilation.
* Initial version of the namd package
* Modified charm to consider compile against intel/intel-mpi
* Correction of namd to compile with intel-mkl and intel compiler
* Adding inclue64 in the prefix
* adding property for the build directory
* removing useless function build
Fixes#4488. When compiling metis as a shared library, the package
used the syntax `-rpath=`, followed by a path. This syntax is
non-portable, so replace it using Spack's compiler rpath argument
property.
* During install, remove prior unfinished installs
If a user performs an installation which fails, in some cases the
install prefix is still present, and the stage path may also be
present. With this commit, unless the user specifies
'--keep-prefix', installs are guaranteed to begin with a clean
slate. The database is used to decide whether an install finished,
since a database record is not added until the end of the install
process.
* test updates
* repair_partial uses keep_prefix and keep_stage
* use of mock stage object to ensure that stage is destroyed when it should be destroyed (and otherwise not)
* add --restage option to 'install' command; when this option is not set, the default is to reuse a stage if it is found.
* espresso: fixed compilation for 6.1 (elpa) and added support for hdf5
* espresso: addressed items in @davydden review
* espresso: fixed behavior for espresso@:5.4.0
* New Package: lanl-bml
Added LANL's BML library as Spack Package as dependency for future
packages
* Adjusted lanl-bml versions
Specified current master as develop and added v1.1.0 tagged version
* Renamed lanlbml package to bml
* First draft package for mono
Mono's vendor'ed boringssl interacts badly with openssl, so
you need to use `cmake~openssl`.
Left to its own devices, it wants to refer to things in
`/usr/share/.mono`. This doesn't work for installs that don't run as
root, etc... This package includes a variant to redirect those paths
to `prefix.share`.
* Whitespace/Flake8
* Adding Nalu package.
* Fixing flake8 stuff.
* Fixing flake8 stuff.
* Reorganizing trilinos package file a little to make it less verbose.
* Reorganizing trilinos package file for more general use as well as use as a dependency of the Nalu package. Setting fpic as default for yaml-cpp and superlu.
* Explicitly stating fpic variants in dependent packages.
* Updating nalu and trilinos package files with suggested changes.
* Fixing formatting issues. Making suggested changes.
* Fixing formatting.
* Reducing amount of explicit variants in Nalu. Adding suggested changes to Trilinos package file.
* Making suggested changes to Nalu package.
* Turning off superlu-dist variant.
* Cleaning up yaml-cpp file.
* Fixing pnetcdf requirements in trilinos.
* Handle missing defn of __NR_memfd_create
Generally SYS_foo is defined to __NR_foo (in sys/syscall.h) which is
then defined to a syscall number (in asm/unistd_64.h). Certain CentOS
systems have SYS_memfd_create defined to __NR_memfd_create but are
missing the second definition. This is a belt and suspenders solution
to the problem.
See [this post][syscall] for a nice general description of how these
parts fit together.
[syscall]: https://www.uninformativ.de/blog/postings/2017-02-11/0/POSTING-en.html
* Avoid flake8 warning
* postgresql: Fix build with threadsafe and add variant.
* postgresql: Convert Package to AutotoolsPackage.
Also add explicit enable flag for +threadsafe variant.
* Add add'l output formats for graphviz
Add support for additional output formats to graphviz, including gif,
jpg, pdf, and png.
Graphviz calls its pango+cairo option *pangocairo* so I followed suit.
Libgd was missing jpeg/jpg support. None of the other supported
formats are conditionalized and there is no --with/--without support,
so I followed suit.
* Fix ghostscript plugin
When I installed thusly:
spack install graphviz+pangocairo+libgd^cairo+X^pango+X
the ghostscript plugin tripped over some variable names that had
changes in `gs@9.18:`. This fixes them.
* Remove wayward import of tty
* Need to help Makefile.PL find the expat bits
We need to provide Makefile.PL with a clue about where our
expat bits live. We had the dependency, but I suspect
that the lib was actually linking against a system version.
* Use prefix.lib instead of building path myself
Ditto with .include
I've had non-repeatable failures in my CI runs on all three clusters
at the bamutil's step. In each case there are .o or .so files that
are corrupt or truncated.
I suspect that the homebrewed bamutil Makefile scheme doesn't actually
support parallel builds.
* Tighten up graphviz package
The fun started when configure discovered a broken/partial
installation of `swig` in `/usr/local`, then auto-discovered my
system's python and ruby packages.
- SpackException doesn't seem to exist. Convert it to a SpackError
and call `.format(...)` on the error string to fill in the
placeholder.
- Pull swig out of the list of languages. It's something that can be
asked for explicitly and that is needed if *any* of the langagues
are enabled. It's disabled by default.
- Explicitly disable the languages that are in "untested_bindings"
list lest the configure script pick up things from the system.
* Touch up variant description string
* Clean up conditional statement
* Use InstallError, not SpackError
* Drop the swig variant
Get rid of the swig variant and drive that bit based on whether any
languages are enabled.
* Move perl to the untested list
That's not strictly accurate. I tested it and it doesn't work.
There's a missing depends_on(). When you add that you'll discover
that the language binding bit can't find Perl's 'EXTERN.h'. Then
you'll discover that graphviz's `configure` script doesn't have a good
way to include the paths to Perl's bits (looks like I'll have to
gather them for each language and then use them to build `CFLAGS` and
`CXXFLAGS` and `LDFLAGS`). While pondering that, you'll discover that
EXTERN.h is buried down here:
```
opt/spack/linux-centos7-x86_64/gcc-4.8.5/perl-5.24.1-35ejv4426dmzreum4ekdibu3ddmhquvi/lib/5.24.1/x86_64-linux/CORE/EXTERN.h
```
and decide that you wish you had never thought to actually test
`graphviz+perl`.
I could find that directory with a snippet like so:
```
perl -MConfig -e 'print "$Config{archlib}\n"'
```
but at this point I'm much, much further down this rabbit hole then I
ever wanted to go.
* Convince python that tested_bindings is a list
When I removed `+perl` and made `tested_bindings` a list of one
thing, I ended up with this:
```
==> Error: cannot concatenate 'str' and 'tuple' objects
```
* Flake8 cleanup
* Don't convert a string to a string
* rm unused () and clarify variable name
Feedback from @adamjstewart
- Get rid of some unnecessary parens.
- Clearer variable name and use.
* Further cleanup of language enabling loop
Now we don't need that pesky temporary variable.
* Add package for cctools
Add a package for cctools.
Requires the recently submitted "useshrplib" support in Perl (or some
other mechanism to enable -fPIC for perl).
* Delete extraneous import
* Perl's shared variant changed, adapt...
The name of the variant that perl uses to build a shared lib changed and
it now defaults to True. Use the new name and continue to be insistent
about using the shared variant.
* Flake8 cleanup
* Added magma package
* Incorporated Serban's change
* boost-pgi: Add support for PGI compiler
There are two patches required:
(1) general fixes required by PGI
(2) workaround for a bug in PGI 17.4
Conflicts:
var/spack/repos/builtin/packages/boost/package.py
* Add variant to build shared Perl lib
Add a variant that enables Perl's "useshrplib" feature, which builds a
shared perl library.
This addresses problems like so:
```
/usr/bin/ld: /blah/blah/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/perl-5.24.1-y43dp3p5w66v7qh5xkwgufxohyuodyew/lib/5.24.1/x86_64-linux/CORE/libperl.a(op.o): relocation R_X86_64_32S against `PL_opargs' can not be used when making a shared object; recompile with -fPIC
/blah/blah/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/perl-5.24.1-y43dp3p5w66v7qh5xkwgufxohyuodyew/lib/5.24.1/x86_64-linux/CORE/libperl.a: could not read symbols: Bad value
```
It should also address the Intel compiler issue discussed in #3081
while respecting Perl's configuration machinery.
* Rename shared variant and default to True
* Use correct variant to add configure arg
* Restore bits that set ccflags for intel compilers
After some experimentation we've established that setting
the flag to build a shared perl library is tightly tied to
the use of -fPIC.
This commit restores the code that sets ccflags for
intel compilers.
* Flake8 cleanup
See the discussion about installing jar files in #4386.
Also installs a wrapper script that has explicit references to the
prerequisite java exe and to the jar file in it's final resting place.
* Add packages for clustalw and clustalo (and argtable)
Add packages for the classic multiple alignment package, `clustalw`
and its younger sibling, `clustalo`.
`clustalo` needed the `argtable` package (command line arg parsing).
Lightly tested on CentOS 7.
* Remove FIXME (sigh...)
* Add mpi support to R
* Add multiple precision math routines to R
* Updated the URL to match the version
* Remove duplicate packages
* Add packages for r-ergm and it's dependents
* Fixed depends-on types
* Correct flake8 errors
* Correct Build type
* r-factoextra and dependents
* Revert "r-factoextra and dependents"
This reverts commit afbf477fd6.
* Add only r-factoextra files
* Add a package for Trimmomatic
See the discussion about installing jar files in #4386.
Also installs a wrapper script that has explicit references to the prerequisite java exe and to the jar file in it's final resting place.
* Fix bad format statement
Apparently something like this "blah{}".format(...) works (it's missing
something inside the curly braces) but fails the travis test.
The two given versions of mariadb are not fetchable under the given
URL, probably because older versions are purged and only kept in
an archive.
Add two working, latest revisions of each release line.
Somehow the path to `CMakeLists.txt` via the class property
`root_cmakelists_dir` was relative but is now actually relative
to `spack-build/`.
Close 4324 by providing a path relative to the source repo
of the stage via a method instead of a member variable
* Add package for vcftools@0.1.14
The package munges the various perl scripts so that their sbang lines
point to the depended upon perl (perhaps with Spack sbanger in the
dance) instead of relying on `/usr/bin/env perl`.
As it stands it installs its Perl libraries into `prefix/lib` and then
depends on `setup_environment` to prepend that dir onto PERL5LIB.
See my [vcftools issue
80](https://github.com/vcftools/vcftools/issues/80) for a discussion
about fixing its non-functional attempt at isolating itself from
PERL5LIB shenanigans.
* perl dependency should be build/run
* Ensure Config.pm has correct setting for cc
Run a filter after install so that Config.pm records the compiler that
Spack built the package with. If this isn't done, $Config{cc} will be
set to Spack's cc wrapper script.
* Also patch compilers Config_heavy.pl
This patch sets ld=gcc, which appears to work. I'm not sure if
there's a good way to get at the ld that Spack uses.
* Clean up quoting
* Fix pattern for Config.pm
Does not start at beginning of line...
What the user wants, the user etc....
Add info for STAR@2.4.2a. It's URL looks different, so added a URL for
it. This broke the URL for the current version, so added a URL for it
also (known bug).
*Minimally* tested on CentOS 7.
* python: ensure that distutils sets valid compiler options for RPATH on cray
* python: add cray-rpath patches for python@2.3:3.0.1 and python@3.1:
* python: in patch(..., when="@a:b platform=c"), limit b must be specified
* python: assume that python@4 will break the cray patches
* Fix mummerplot when ^perl@5.20:
Calling defined() on a hash has been deprecated for ages. It became
an error in perl@5.20. If we're building with a perl where it's
illegal, we should fix it.
* Simplify call to filter_file
Treat the first arg to filter_file as a string rather than
a regex, so that we don't have to figure out the escapes.
* Patch mummerplot for *any* perl version.
* Fix bwa url's
Work around varying github URLs.
See #4365 for details.
* Restore main url entry
@adamjstewart pointed out that the package still needs a main url
so that `spack versions` works.
- Add a `spack gpg` subcommand in anticipation of signed binaries.
- GPG keys are stored in var/spack/gpg, and the spack gpg command manages them.
- Docs are included on the command.
* Add info for jdk@7u80 (not downloadable)
Add version info for jdk@7u80. Oracle does't seem to be
distributing it any longer so there's no reasonable URL to
provide, but for those of us who already have the tarball
this is useful.
* Flake8 cleanup
* Add mpi support to R
* Add multiple precision math routines to R
* Updated the URL to match the version
* Remove duplicate packages
* Add packages for r-ergm and it's dependents
* Fixed depends-on types
* Correct flake8 errors
* Correct Build type
* r-adegenet and dependent packages
* Touch up string expansion.
I'm chasing this:
```
$ (module purge; spack install perl %gcc/5.4.0)
==> Error: No installed spec matches the hash: '%s'
```
There's something deeper going on, but the error message isn't helpful.
After this change it tells me this:
```
$ (module purge; spack install perl %gcc/5.4.0)
==> Error: No installed spec matches the hash: '5.4.0'
```
Which is weird because `5.4.0` is not a hash... Whatever is going on here, the error message needs to be fixed.
* Flake8 whitespace
* fix parser
* Removed xfails
* cleaned up debug print statements
* make use of these changes in gcc
* Added comment explaining unreachable line, line left for added protection
* cairo: ensure that X support is disabled for variant "~X"
* cairo: explicitly enable X support for +X variant
* cairo: prefer "variant in spec" over spec.satisfies(variant)
* Trailing whitespace cleanup
* Handcraft an install process for mummer (grumble)
Mummer punts on an installation step, they just build in and run from
the same directory.
Mummer also has various hardcoded paths built into it that allow it to
find other executables that it needs as well as its Perl library.
This updates the package to deal with this approach.
It patches the Makefile and scripts/Makefile so that the correct info
is fed to sed when it munges the perl scripts.
The install step is now finer grained and puts things where mummer
relatively wants to find them.
* Add perl dependency
* perl should be build/run dependency
* Fix whitespace
* Delete stray u at top of file
Two changes:
- It seems that Illumina version numbers are dotted and that the
dashed version in the 2.18... filename is an anomaly (based on the
names for 2.17.1.14 and 2.19.0). `url_for_version` does the right
thing for 2.18. It will need to be fixed when support for 2.19 is
added. 2.17 is no longer generally available so it gets a pass.
- Add version and hash for 2.17.1.14.
2.17.1.14 is no longer distributed. If you have a copy of the
source tarball, you can drop it into a local mirror w/ the name
mirror/bcl2fastq2/bcl2fastq2-2.17.1.14.zip and go from there.
* Add mpi support to R
* Add multiple precision math routines to R
* Add packages for r-ergm and it's dependents
* Fixed depends-on types
* Correct flake8 errors
* flex: create variant +lex that creates symlinks for lex and libl.{a,so}
* flex: enable variant +lex by default
* flex: use dso_suffix for portability; replace repetitive code with a loop
* added openmpi support to meme
* openmpi is a link dependency which leverages r_path
* openmpi support now the default - meme does not have configure argument for mpi - if it's found then it's used
* added serial option and set mpi to not be default
* modified meme
* Add the gnupg package and missing dependencies. Update versions of existing dependencies.
* this ended up in the wrong repo
* put versions back, remove uneeded function
* OK ;)
* autopep8
* typo on npth line
* whitespace
* Add a new package for Open Babel
* Add post-installation tests, stolen from the fine folks at Homebrew
* Add patch to fix Python 3.6 support
* Add a more complete patch to get Python 3.6 support working
* Add patch to convert tabs to spaces in test script
testpdbformat.py contains mixed tabs and spaces
causing the unit tests to fail. With this patch,
all tests pass with flying colors.
* Add v1.1.26 and make crypto a variant
I need 1.1.26 for bcl2fastq2.
I also need to build it without crypto support.
* Initial support for bcl2fastq2
* Clean up commentary, messages, names
No substantial changes intended, just cleanup.
* fix flake8 and extra import
* The masked grammarian strikes again...
* Be normal (messages don't end in periods)
* When +crypto, add --with-crypto
Add `--with-crypto` to configure args when user hasn't explicitly set
`~crypto`.
* self.spec.satisfies is unsatisfying, in is in instead
See #4135, self.spec.satisfies has issues. @adamjstewart suggests
simply using in.
* Sphinx no longer supports Python 2.6
* Update vendored sphinxcontrib.programoutput from 0.9.0 to 0.10.0
* Documentation cannot be built in parallel
* Let Travis install programoutput for us
* Remove vendored sphinxcontrib-programoutput
Recent updates to the sphinx package prevent the vendored version
from being found in sys.path. We don't vendor sphinx, so it doesn't
make sense to vendor sphinxcontrib-programoutput either.
* added albacore package as well as dependency py-ont-fast5-api
* added py-cutadapt and dependency py-xopen
* made more changes to albacore and cutadapt as well as dependencies
* made changes again per @adamjstewart
* fixed by python n00b errors i think
* fixed?
* tw=79
* made changes to py-ont-fast5-api ont-albacore
* removed bad characters
* albacore requires setuptools as build and run dependency
* added vmd
* added back albacore
* removed vmd package
* added meme software
* libz is only needed as link depedency for meme
* added libxml2 libxslt libgcrypt as link dependencies
* added albacore package as well as dependency py-ont-fast5-api
* added py-cutadapt and dependency py-xopen
* made more changes to albacore and cutadapt as well as dependencies
* made changes again per @adamjstewart
* fixed by python n00b errors i think
* fixed?
* tw=79
* made changes to py-ont-fast5-api ont-albacore
* removed bad characters
* py-cdat-lite: a python package for managing and analysing climate science data
* py-cdat-lite: depends on py-numpy
* py-cdat-lite: flake8 compliance
* py-cdat-lite: provide a generic URL where multiple versions are listed
* py-cdat-lite: restrict python versions; python required at run-time
* py-cdat-lite: use URL under pypi.io for consistency with other packages
* py-cdat-lite: add run-time dependency on py-numpy
* Initial attempt at flann packaging.
Python2 somehow works. Python3 does not. Still debugging their
obscure setup.py configuration.
* Flann good enough. Python3 broken but close.
Flake8 checks in place. Unsure about CMAKE_BUILD_TYPE and default
spack behavior.
* spack uses RelWithDebInfo as default build type.
* builds py2/3, but direct site-packages install
* prefix working, empty python install dir
* flann package +python installs correctly
* str format {0} instead of {}
* potential doctest fix
* consistency of build env with PythonPackage
* fix python again, test deptype todo, build type
* potentially enable matlab, untested
PR #3367 inadvertently changed the semantics of _find_recursive and
_find_non_recursive so that the returned list are not ordered as the
input search list. This commit restores the original semantic, and adds
tests to verify it.
* Edits to get setup-env.csh working better.
Autosets the sys_type a la setup-env.sh
* More stealing from bash setup script for module roots
* Add error message if SPACK_ROOT isn't set
* Remove _sp_lmod_root per Adam J Stewart
* highfive: New package; this is a C++ wrapper for the HDF5 library
The C++ wrapper that is shipped with the HDF5 library has several shortcomings. The highfive library seems to avoid these.
* highfive: Make MPI variant default to true
* enable cuda support for suite-sparse
* do not use spec.satisfies
* cuda restructure, give clearer comment of why
* str format compatibility
* flake8 checks
* adding 0.5.1 and variant for uint8 bit stream word type
* Revisions as per davydden
* fixing style (flake8) issues
* - switched to derive from MakefilePackage
- fixed typo in variant check
- Confirmed installs correctly with bswtuint8 variant
* added build method; changed zfp_incdir to incdir
* * Adding uber fastmath package to support 'spack install fastmath'
* Adding dims variant boxlib to control compile-time spatial dimension count
* Explicitly disabling many parts of moab to get lib to build. Don't need tools yet.
* Add logic to spack/setup-env to not refer to $SYS_TYPE if its not defined.
* adding mesquite package
* * Added Chombo (still working on Fortran name mangling)
* Made mesquite depend on mpi
* Fixed use of boxlib's dims numerical variant
* adding PUMI
* flake8 compliance
* adding phasta
* fixing flake8 issues
* undue $SYS_TYPE protection change
* fixing install step for fastmath uber package; resolve issues requested by adamjstewart in PR
* revisions as per adamjstewart
* re-enabling trilinos and phasta dependencies
* all changes requested modulu values= and assert statement
* fixing cmake_args usage in pumi; fixing lib installs for chombo
* first pass at numerical variant
* fixing dims variant as per @adamjstewart
* fixing func/var name collision
* fixing means of disabling -Werror
* fix name collision for cmake_args var/func
* fixing chombo homepage/url; make FASTMath use chombo#3.2; remove extraneous comment about boxlib dim
* remove dummy fastmath package; switch to @BarrySmith soln for install of dummy bundle
* fix flake8 import os issue
* remove extraneous comment
* adding url for fastmath scidac site
* final fixes as per @adamjstewart
* adding 1 dims option for boxlib
* switching make(all) to gmake(all)
Added DFLAGS to the `make.inc` file being written.
These macros are also added to the language specific variables
like CFLAGS, CXXFLAGS and FCFLAGS. Changed `spec.satisfies('foo')`
with `'foo' in spec` in `intel-mkl`, see #4135. Added a basic
build interface to `intel-mpi`.
* Add GCC 7
* Allow users to build subset of GCC compilers with multi-value variant.
* Add comment explaining what 'all' actually means
* More specific golang support
* Only require Zip when building Java
* Comment out provide directives that don't currently work
* Add Ada support
* Use conflicts directive
* Fix joining of languages
* Need special flag to build jit
* Explicitly declare GNAT download extension
* Import tty, update lib64 to lib
* BRIG and Go are not supported on macOS
* Simplify formatting and imports
* JIT patch required for newer versions as well
It seems that parse_anonymous_spec may fail if more than one part
(variant, version range, etc.) is given to the function. Added tests to
code against to fix the problem in #4144.
- Full help is now only generated lazily, when needed.
- Executing specific commands doesn't require loading all of them.
- All commands are only loaded if we need them for help.
- There is now short and long help:
- short help (spack help) shows only basic spack options
- long help (spack help -a) shows all spack options
- Both divide help on commands into high-level sections
- Commands now specify attributes from which help is auto-generated:
- description: used in help to describe the command.
- section: help section
- level: short or long
- Clean up command descriptions
- Add a `spack docs` command to open full documentation
in the browser.
- move `spack doc` command to `spack pydoc` for clarity
- Add a `spack --spec` command to show documentation on
the spec syntax.
* Updating bamtools to include a dependency for zlib.
In a standard compile, bamtools will fail if zlib headers are not installed on the target machine. In order to maintain compatibility with all systems -- and since zlib is included already as a dependency for cmake -- this patch adds zlib as a link dependency for the bamtools package.
* Modified cmake rpath include.
Bamtools has a non-standard library location, so we need to append $prefix/lib/bamtools to the rpath. Not sure there's a better way to do this...
* Fixing syntax error in package.py
Fixed a non-terminated parenthesis on line 46.
* Updated bamtools to be a CMakePackage
Removed extraneous code, and altered the package to extend cmake_args
including the non-standard library location.
* UpRemoving cmake dependency and removing blank line from end of file
* Updates to cmake_args.
Removed the duplicate definition of std_cmake_args in favor of simply overriding the CMAKE_INSTALL_RPATH variable that is provided. This should allow the package to be linked correctly to itself.
python+tk will not build because it depends (indirectly) on python~tk
via libxcb. There are efforts to allow multiple instances of a package
to concretize together but they are ongoing so in the meantime this
comments out the dependencies and adds TODOs
* SV variants are evaluated correctly in `when=` statements fixes#4113
The problem here was tricky:
```python
spec.satisfies(other)
```
changes already the MV variants in others into SV variants (where
necessary) if spec is concrete. If it is not concrete it does
nothing because we may be acting at a pure syntactical level.
When evaluating a `when=` keyword spec is for sure not concrete
as it is in the middle of the concretization process. In this case we
have to trigger manually the substitution in other to not end up
comparing a MV variant "foo=bar" to a SV variant "foo=bar" and having
False in return. Which is wrong.
* sv variants: improved error message for typos in "when=" statements
* bash completion: fixed `_spack_create-db-tarball': not a valid identifier
* bash completion: dashes are translated to underscores
This also fixes the name of the subfunction to be called, as apparently
it was not updated after moving the command `create-db-tarball`.
- Add -P <STAT> argument so that caller can specify a sort column for
cProfile. Can specify multiple columns with commas. e.g.:
spack -P cumtime,module
- Add --lines option to Spack spec to control number of profile lines
displayed
- Sort by time by default (because it works in all Python versions)
- Show sort column options in command help.
- Do a short profile run in the unit tests.
Modifications:
- added support for multi-valued variants
- refactored code related to variants into variant.py
- added new generic features to AutotoolsPackage that leverage multi-valued variants
- modified openmpi to use new features
- added unit tests for the new semantics
This allows people on systems that don't have all the fetchers to still
run Spack tests. Mark tests that require git, subversion, or mercurial to
be skipped if they're not installed.
* Filter all system paths introduced by dependencies from PATH
* Make sure path filtering works *even* for trailing slashes
* Revert some of the changes to `filter_system_paths`
* Yes, `bin64` is a real thing (sigh)
* add tests: /usr, /usr/, /usr/local/../bin, etc.
* Convert from rST to Google-style docstrings
The required hash of a submodule might point to the
non-HEAD commit of the current main branch and hence
would lead to a "no such remote ref" at checkout in
a shallow submodule.
## Motivation
Python installations are both important and unfortunately inconsistent. Depending on the Python version, OS, and the strength of the Earth's magnetic field when it was installed, the name of the Python executable, directory containing its libraries, library names, and the directory containing its headers can vary drastically.
I originally got into this mess with #3274, where I discovered that Boost could not be built with Python 3 because the executable is called `python3` and we were telling it to use `python`. I got deeper into this mess when I started hacking on #3140, where I discovered just how difficult it is to find the location and name of the Python libraries and headers.
Currently, half of the packages that depend on Python and need to know this information jump through hoops to determine the correct information. The other half are hard-coded to use `python`, `spec['python'].prefix.lib`, and `spec['python'].prefix.include`. Obviously, none of these packages would work for Python 3, and there's no reason to duplicate the effort. The Python package itself should contain all of the information necessary to use it properly. This is in line with the recent work by @alalazo and @davydden with respect to `spec['blas'].libs` and friends.
## Prefix
For most packages in Spack, we assume that the installation directory is `spec['python'].prefix`. This generally works for anything installed with Spack, but gets complicated when we include external packages. Python is a commonly used external package (it needs to be installed just to run Spack). If it was installed with Homebrew, `which python` would return `/usr/local/bin/python`, and most users would erroneously assume that `/usr/local` is the installation directory. If you peruse through #2173, you'll immediately see why this is not the case. Homebrew actually installs Python in `/usr/local/Cellar/python/2.7.12_2` and symlinks the executable to `/usr/local/bin/python`. `PYTHONHOME` (and presumably most things that need to know where Python is installed) needs to be set to the actual installation directory, not `/usr/local`.
Normally I would say, "sounds like user error, make sure to use the real installation directory in your `packages.yaml`". But I think we can make a special case for Python. That's what we decided in #2173 anyway. If we change our minds, I would be more than happy to simplify things.
To solve this problem, I created a `spec['python'].home` attribute that works the same way as `spec['python'].prefix` but queries Python to figure out where it was actually installed. @tgamblin Is there any way to overwrite `spec['python'].prefix`? I think it's currently immutable.
## Command
In general, Python 2 comes with both `python` and `python2` commands, while Python 3 only comes with a `python3` command. But this is up to the OS developers. For example, `/usr/bin/python` on Gentoo is actually Python 3. Worse yet, if someone is using an externally installed Python, all 3 commands may exist in the same directory! Here's what I'm thinking:
If the spec is for Python 3, try searching for the `python3` command.
If the spec is for Python 2, try searching for the `python2` command.
If neither are found, try searching for the `python` command.
## Libraries
Spack installs Python libraries in `spec['python'].prefix.lib`. Except on openSUSE 13, where it installs to `spec['python'].prefix.lib64` (see #2295 and #2253). On my CentOS 6 machine, the Python libraries are installed in `/usr/lib64`. Both need to work.
The libraries themselves change name depending on OS and Python version. For Python 2.7 on macOS, I'm seeing:
```
lib/libpython2.7.dylib
```
For Python 3.6 on CentOS 6, I'm seeing:
```
lib/libpython3.so
lib/libpython3.6m.so.1.0
lib/libpython3.6m.so -> lib/libpython3.6m.so.1.0
```
Notice the `m` after the version number. Yeah, that's a thing.
## Headers
In Python 2.7, I'm seeing:
```
include/python2.7/pyconfig.h
```
In Python 3.6, I'm seeing:
```
include/python3.6m/pyconfig.h
```
It looks like all Python 3 installations have this `m`. Tested with Python 3.2 and 3.6 on macOS and CentOS 6
Spack has really nice support for libraries (`find_libraries` and `LibraryList`), but nothing for headers. Fixed.
* Make dia build w/ Spack's X bits (and misc)
X related
- need to depend on the +X variant of gtkplus
- need to depend on freetype
misc
- fix path to tarball
* Make freetype a "build" dependency
* Freetype is not just a build dep
* ncurses package will build ncurses and ncursesw
* Added libs property to ncurses, added fix for hstr
* flake8 is a harsh mistress
* make libs() more robust
* atop depends on ncurses
* fish depends on ncurses
* libtermkey and nano depend on ncurses
* Adjust url spacing
* Added a patch to the openblas package to change the openmp flag for
icc to qopenmp.
* Fixed a linking problem where when using Intel compilers, it was still
pulling in -lgfortran
* depend on readline, remove hardcoded -ltermcap
Bowtie should use Spack's readline and not explicitly depend on the
system termcap (which, on CentOS, leads to linking against the
system's tinfo library).
* Add depends_on('zlib')
* Add conflict with gcc@6:
Build seems to have trouble with 6's migration to -std=gnu++14.
When a compiler was not found a stacktrace was displayed to user because
there were three arguments to be substituted in a string with only two
substitutions to be done.
Fixes#4026#1167 updated Database.reindex to keep old installation records to
support external packages. However, when a user manually removes a
prefix and reindexes this kept the records so the packages were
still installed according to "spack find" etc. This adds a check
for non-external packages to ensure they are properly installed
according to the directory layout.
* Dia requires libxml2.
* Clean up dependencies for Dia (and add X11 deps).
+ Remove dependencies on cairo and libpng. The will be satisfied via gtkplus.
+ Add dependencies on X11 libraries: libsm, libuuid, libxinerama, libxrender.
+ From a dependency diagram, it doesn't appear that we need libxml2 since this
dependency should be come in through cairo (via gtkplus). However, Dia will
not build without it.
* Separate build integration tests; simplify test scripts
- Move build tests out of the regular Travis unit tests, add more smoke
test packages to build.
- Run all test scripts with bash -e, which fails on error.
- Factor coverage out into a Travis environment variable, so it's more
obvious from .travis.yml which tests contribute to coverage and which
don't.
- Factor dependency checking and much of the front-matter in tests
scripts into a setup.sh script, which is sourced by all the test
scripts. Extra cruft in each tests script now reduced to 2 lines at
the beginning.
* Hackery to get gtkplus to build
PR #3077 broke gtkplus by introducing gobject-introspection.
This big hack makes things work. It has problems.
1. Rather than deal with the nasty sbang fooey in the
g-ir-tool-template.in derived scripts, it just adds a python
dependency to each package that runs one of the scripts. This lets
the `/usr/bin/env python` sbang do the right thing.
2. It stuffs a several directories on to the XDG_DATA_DIRS environment
variable, which is used for (among other things) locating the .gir
files.
3. It avoids building the gtkplus demos because I can't make the bit
that calls `gdk-pixbuf-csource` work. It doesn't think that it can
load `.png` files and all of the google hits I found suggest a bad
`loader.cache` file. The file's fine and I can strace the command
and watch it read it in... Many, many hours wasted here.
In spite of the demo failing, the tests pass and an emacs built
with this lib seems to work.
* Fix sbang so everyone needn't depend_on python
Rather than have every package that
`depends_on('gobject-introspection')` also need to
`depend_on('python')`, this commit fixes the
scripts (e.g. `g-ir-scanner`).
The interesting bit is in the gobject-introspection package. There is
a beefy comment there that is included below.
The commit also removes the now un-necessary dependencies from various
packages.
I have two reservations about this commit:
1. How portable is the "insertion" sed command? I'm particularly
worried that some sed's might need the line to insert to be on a
different line, which I can't imagine how to cram into the
Makefile.in.
The solution I see to this is rather than extending the existing
sed command in the Makefile I could shim in another line in the
rule and e.g. call a bit of Perl (or Python, I suppose) which would
end up being much neater.
2. As written it always uses Spack's `.../bin/sbang`, which might or
might not be a good idea.
If I use "the solution" from number 1 above, then I can check the
line length before I munge it. Otherwise???
---
This package creates several scripts from |
toosl/g-ir-tool-template.in. In their original form these |
scripts end up with a sbang line like |
|
`#!/usr/bin/env /path/to/spack/python`. |
|
These scripts are generated and then used as part of the build |
(other packages also use the scripts after they've been |
installed). |
|
The path to the spack python can become too long. Because these |
tools are used as part of the build, the normal hook that fixes |
this problem can't help us. |
This package fixes the problem in two steps: |
- it rewrites the g-ir-tool-template so that its sbang line |
refers directly to spack's python (filter_file step below); and |
- it patches the Makefile.in so that the generated Makefile has an |
extra sed expression in its TOOL_SUBSTITUTION that results in |
an `#!/bin/bash /path/to/spack/bin/sbang` unconditionally being |
inserted into the scripts as they're generated. |
* Cairo needs python when it's +X
Cairo needs to depend_on python when it's +X. I think it's an
indirect requirement that's coming in via libxcb).
* Flake8 cleanup
* Make cairo's dep on python be type=build
This seems to be the right thing and seems to produce a result
that works (I can build gtk+ and then emacs+X on top of it).
* ghostscript: add version 9.21 and handle new URL format
* ghostscript: add url of latest version to fix `spack versions`
* ghostscript: use github for all versions our package provides (>= 9.18)
- add Version.__format__ to support new-style formatting.
- Python3 doesn't handle this well -- it delegates to
object.__format__(), which raises an error for fancy format strings.
- not sure why it doesn't call str(self).__format__ instead, but that's
hwo things are.
* perl: provide +gdbm variant for use when system dbm is missing or buggy
* perl: remove gdbm variant; always depends on gdbm
* perl: pass gdbm paths as Configure arguments
The blast+ configure script supports building
--with-{python,perl}=path and --without-{python,perl}.
This commit makes the use of those two languages configurable via
variants and adds dependencies and explicit --with-... or
--without-... flags to configure.
Python was a non-optional dependency, now it is a variant that
defaults to `True`.
Perl was not previously an explicit dependency but the configure
script was likely to discover one on your system (`/usr/bin/perl`).
It is now a variant that defaults to `True`.
I am unable to accurately determine what these flags to the configure
script enable. My users are frustrated by the dependency on Python in
particular because it constrains the other modules that they can have
loaded for new discernible benefit.
* xSDK: a bundle/meta package that simple installs a series of packages with suitable specs
This is based on struggles with previous attempts at such a bundler
Funded-by: IDEAS
Project: IDEAS/xSDK
Time: 12 hours
* PETSc needs c++11 when built with Trilinos
* Added alquimia package
* remove direct setting of cpp in petsc/package.py since it doesn't work on some systems.
Funded-by: IDEAS
Project: IDEAS/xSDK
Time: .3 hours
Reported-by: Mark A. Berrill <berrillma@ornl.gov>
* provide the MPI compilers to PETSc configure with --with-cc etc instead of --with-mpi-dir
Funded-by: IDEAS
Project: IDEAS/xSDK
* Spack bug fix issue #3144
String could contain /n which resulting in spack generating warning message to stderr on each
use of compiler which configure interpreted as failing compiler
Thanks-to: Mark A. Berrill <berrillma@ornl.gov>
* Fixed alquimia package
Alquimia expects PETSC_DIR and PETSC_ARCH to be defined, and
refuses to install if they are not. Spack does not define PETSC_
ARCH, so Alquimia will not install. This patch does two things
to fix the alquimia build:
1. A patch has been added to remove the dependency on PETSC_ARCH.
2. Alquimia currently depends on old versions of PETSc and pflotran.
@ghammond86 updated the alquimia interfaces to use more recent
versions, but his patch is still sitting in an alquimia pull
request. As a result, the spack installer now uses his fork
of alquimia. This is a temporary fix until his pull request is
accepted.
* Need to pass to Alquimia the MPI compilers, not the raw compilers
Otherwise the PETSc tests do not produce executables that can run because they are not
linked against MPI libraries
Funded-by: IDEAS
Project: IDEAS/xSDK
Time: .5 hours
* Add alquimia to xSDK build
Funded-by: IDEAS
Project: IDEAS/xSDK
* Fix flake8 errors for xsdk packages
* Add xsdk support for xsdk version xsdk-0.2.0
Note that currently it is just dummy code, but will eventually use
a xsdk-0.2.0 tag for each package it installs.
Funded-by: IDEAS
Project: IDEAS/xSDK
Time: .7 hours
* Do not build Mumps by default for PETSc since it is not portable, for example to Cray
Allow alquimia to accept PETSc even if the PETSc test executable cannot run since this is a problem on Cray.
Reported-by: Alicia Marie Klinvex <amklinv@sandia.gov>
* Add xsdk-0.2.0-rc1 tag for xsdk-0.2.0 installs
* Switch alquimia download site back to standard location
since they have incorporated Glenn Hammond's fixes
Also it no longer needs the patch to the Alquimia cmake
Funded-by: IDEAS
Project: IDEAS/xSDK
Reported-by: Sergi Molins Rafa <smolins@lbl.gov>
* update hypre to use the latest release candidate for xsdk 0.2.0
Funded-by: IDEAS
Project: IDEAS/xSDK
Reported-by: Ulrike Meier Yang <yang11@llnl.gov>
* Re-added patch to alquimia
The patch was out of date and has been updated accordingly.
* Added Tpetra-free option to Trilinos
The Tpetra stack takes forever to build and is not used by any of the
IDEAS teams, so there should be an option to disable it. I have added
this option and updated the xSDK accordingly. I also disabled
xSDKTrilinos in the xSDK, since none of the apps teams currently use it,
and it's largely Tpetra-based.
* Removed alquimia patch from develop version
The patch has been incorporated into alquimia and is no longer
necessary for the develop version. The tagged version has not
been updated accordingly and still needs the patch for now.
(When the tagged version gets updated, the patch does need to be
removed from spack altogether, or it will break the build.)
* Removed patch from alquimia
It has been incorporated into alquimia, both the develop and
rc2 tagged versions. The 0.2.0 version of alquimia has been updated
to tag rc2 rather than rc1.
* update xsdk-0.2.0 to depend on PETSc xsdk-0.2.0-rc2 which fixes for Apple xcode 8.3
Commit-type: bug-fix
Funded-by: IDEAS
Project: IDEAS/xSDK
* import sys got lost in merge with develop
* Update xsdk packages to use xsdk-0.2.0 tag
Commit-type: feature
Funded-by: IDEAS
Project: ECP
* Fixes for Flake8
note, had to ignore some long lines due to a single string
* simple improvements to XDK packages as suggested by Spack pull request reviewers
Commit-type: style-fix
Funded-by: IDEAS
Project: xSDK
* Removed unneeded : after develop as requested by Denis Davydov in pull request review
Commit-type: style-fix
Funded-by: IDEAS
Project: xSDK
Thanks-to: Denis Davydov
* Removed change that may not be needed due to updates in PETSc spack file such as using mpicc etc directly
Commit-type: bug-fix
Funded-by: IDEAS
Project: xSDK
Thanks-to: Adam J. Stewart
* Do not turn on xSDKTrilinos for xSDK builds since it requires tpetra
Commit-type: bug-fix
Funded-by: IDEAS
Project: xSDK
* comment why MUMPS is disabled by default for PETSc so that others won't try to enable it when modifying petsc package next time
Commit-type: documentation
Funded-by: IDEAS
Project: xSDK
Thanks-to: Denis Davydov
* Properly ignore flake8 F811 redefinition errors
* Add unit tests for flake8 command
* Allow spack flake8 to work on systems with older git
* Skip flake8 unit tests for Python 2.6 and 3.3
* Added a package for the MDAnalysis toolkit.
* Added the hash for the 1.0 release of caffe and put in a conflict
statemet indicating that protobuf requires a c++11 compiler.
* Changed minimum version number.
* Tweaked the minimum version number.
* Fixed flake8 error.
* grib-api: add version 1.21.0
* libemos: add version 4.4.7 and allow choice of eccodes or grib-api
* magics: add version 2.32.0
* libemos: add description for eccodes variant
* eccodes: new package for encoding and decoding meteorological data
* eccodes: remove line breaks from package docstring
* eccodes: simplify names of variants
* eccodes: give a description for each variant
* eccodes: use succinct code for cmake_args
* eccodes: found extra dependency for python variant
* eccodes: add URL for a list of available releases
* treats correctly a change from `explicit=False` to `explicit=True` in an external package DB entry.
* added unit tests
* fixed issues raised by @tgamblin . In particular the PR is no more hash-changing for packages that are not external.
* added a test to check correctness of a spec/yaml round-trip for things that involve an external
* Don't find external module path at each step of concretization
* it's not necessary.. The paths are retrieved at the end of concretizaion
* Don't find replacements for external packages.
* Test root of the DAG if external
* No reason not to test if the root of the DAG is external when external
packages are now first class citizens!
* Create `external` property for Spec (for external_path and external_module)
* Allow users to specify external package paths relative to spack
* Canonicalize external package paths so that users may specify their
locations relative to spack's directory.
* Update tests to use new external_path and external properly.
* skip license hooks on external
- py-setuptools is required by py-yt for importing yt in jupyter notebooks.
- add two dependencies needed for python 2.7
- add the py-subprocess32 package
- Spack doesn't need eggs -- it manages its own directories
- Simplify install layout and reduce sys.path searches by installing all
packages flat (eggs are deprecated for wheels, and this is also what
wheels do).
- We now supply the --single-version-externally-managed argument to
`setup.py install` for setuptools packages and setuptools.
- modify packages to only use setuptools args if setuptools is an
immediate dependency
- Remove setuptools from packages that do not need it.
- Some packages use setuptools *only* when certain args (likeb
'develop' or 'bdist') are supplied to setup.py, and they specifically
do not use setuptools for installation.
- Spack never calls setup.py this way, so just removing the setuptools
dependency works for these packages.
* fetch git submodules recursively
This is useful if the submodules have submodules themselves. On
the other hand doing a recursive update doesn't hurt if there
is only one level.
* fetch submodules with depth=1 as well (fix#2190)
* use git submodule with depth only for git>=1.8.4
- Spack install would previously fail if it could not load a package for
the thing being uninstalled.
- This reworks uninstall to handle cases where the package is no longer
known, e.g.:
a) the package has been renamed or is no longer in Spack
b) the repository the package came from is no longer registered in
repos.yaml
- gcc on macOS says it's version 4.2.1, but it's really clang, and it's
actually the *same* clang as the system clang.
- It also doesn't respond with a full path when called with
--print-file-name=libstdc++.dylib, which is expected from gcc in abi.py.
Instead, it gives a relative path and _gcc_compiler_compare doesn't
understand what to do with it. This results in errors like:
```
lib/spack/spack/abi.py, line 71, in _gcc_get_libstdcxx_version
libpath = os.readlink(output.strip())
OSError: [Errno 2] No such file or directory: 'libstdc++.dylib'
```
- This commit does two things:
1. Ignore any gcc that's actually clang in abi.py. We can probably do
better than this, but it's not clear there is a need to, since we
should handle the compiler as clang, not gcc.
2. Don't auto-detect any "gcc" that is actually clang anymore. Ignore
it and expect people to use clang (which is the default macOS
compiler anyway).
Users can still add fake gccs to their compilers.yaml if they want, but
it's discouraged.
* Checksum code wasn't opening binary files as binary.
- Fixes Python 3 issue where files are opened as unicode text by default,
and decoding fails for binary blobs.
* Simplify fetch test parametrization.
* - add tests for URL fetching and checksumming.
- fix coverage on interface functions in FetchStrategy superclass
- add some extra crypto tests.
* Fix for llvm 4.0.0 on centos
This addresses https://github.com/LLNL/spack/issues/3791
* Only enable this option if on linux
* Change condition to satisfy standard
* Package install remove prior unfinished installs
Depending on how spack is terminated in the middle of building a
package it may leave a partially installed package in the install
prefix. Originally Spack treated the package as being installed if
the prefix was present, in which case the user would have to
manually remove the installation prefix before restarting an
install. This commit adds a more thorough check to ensure that a
package is actually installed. If the installation prefix is present
but Spack determines that the install did not complete, it removes
the installation prefix and starts a new install; if the user has
enabled --keep-prefix, then Spack reverts to its old behavior.
* Added test for partial install handling
* Added test for restoring DB
* Style fixes
* Restoring 2.6 compatibility
* Relocated repair logic to separate function
* If --keep-prefix is set, package installs will continue an install from an existing prefix if one is present
* check metadata consistency when continuing partial install
* Added --force option to make spack reinstall a package (and all dependencies) from scratch
* Updated bash completion; removed '-f' shorthand for '--force' for install command
* dont use multiple write modes for completion file
* Add tests to mercurial package
* Add support for --insecure with mercurial fetching
* Install man pages and tab-completion scripts
* Add tests and latest version for all deps
* Flake8 fix
* Use certifi module to find CA certificate
* Flake8 fix
* Unset PYTHONPATH when running hg
* svn_fetch should use to svn-test, not hg-test
* Drop Python 3 support in Mercurial
Python 3 support is a work in progress and isn't currently
recommended:
https://www.mercurial-scm.org/wiki/SupportedPythonVersions
* Test both secure and insecure hg fetching
* Test both secure and insecure git and svn fetching
* Initial add of flac
* Initial add of id3lib
* Initial add of the opus codec
* Initial add of sox audio processing tools
* Cleanup spec files to be inline with current standard
* Fix pep8 compliance
* Remove un-needed configuration
* ncl: add depends_on statements for bison, flex and libiconv
* ncl: depends on flex for building and linking
* ncl: links with -ll, so requires flex with variant '+lex'
* ncl: depends on szip; external hdf5 may not provide it
* Disable parallel builds
The install step creates a bunch of links to the vim binary, e.g.
`view`. When run with -j greater than 1 there are silent failures.
Running w/out parallelism seems to fix it.
* Only constrain the install phase to be -j 1
Thanks @adamjstewart!
* Add package for nginx@1.12.0
Includes support for:
- zlib
- pcre (and pcre-jit)
- openssl (https support)
Built and basics tested on CentOS 7. I haven't tested the `https`
support [yet].
* Include final bit of doc string sentence.
I trimmed the docstring that I lifed from https://nginx.org/en a bit
too aggressively and left a '...' to remind me to fix it.
Apparently I need more obvious reminders.
Thanks @davydden!
* Install the shell completion scripts
Install the `git-completion.{bash,tcsh,zsh}` and `git-prompt.sh` into
`$(spack location -i git)/share/` (aka `prefix.share/`).
* Use copy_tree to copy all the files
The dest dir already exists, so install_tree()'s not an option.
* Added a package for the MDAnalysis toolkit.
* Added the dependency on setuptools.
* Added the rest of the dependencies to the py-mdanalysis package. Also
added the griddataformats and seaborn packages to satisfy requirements.
* Removed seaborn package since it has been recently added.
* Fixed flake8 error
* Removed inadvertent commits.
* Cleaned up reviewers feedback.
Update the package recipe w.r.t. AutotoolsPackage changes,
now builds "out of source".
Update the package with version info for 1.3.0.
> Mosh 1.3.0 released, with John Hood as release lead. The release includes broader platform compatibility, robustness improvements, better testing, and fixes for excess CPU consumption in some cases. We have switched to semver.org-style versioning and will increment the minor version number whenever we add new functionality. (In our previous practice, this release would probably have been called “1.2.7.”)
Tested on CentOS 7.
* adding 0.5.1 and variant for uint8 bit stream word type
* Revisions as per davydden
* fixing style (flake8) issues
* - switched to derive from MakefilePackage
- fixed typo in variant check
- Confirmed installs correctly with bswtuint8 variant
* added build method; changed zfp_incdir to incdir
* Add the rockstar package
* Add rockstar to yt.
* Correct signature of prep_yt.
* Correct rockstar package installation process
Needed to change the way the necessary prefixes are found as well as
how the completed package is copied.
There should probably be a way to do the copying in a more 'spack' way.
* Add license
* Add description.
* Set no hdf5 variant as default.
* Use copy_tree for copying files
* Use MakefilePackage
* Address concerns from @adamjstewart
* Fix flake8 errors.
Adds a package for mallocMC, a memory allocator for many core
architectures.
This project provides a framework for fast memory managers on
many core accelerators. Currently, it supports NVIDIA GPUs of
compute capability sm_20 or higher through the ScatterAlloc
algorithm. mallocMC is header-only.
Downstream Dependencies
PIConGPU and other projects of HZDR's
*Computational Radiation Physics* group
References
- Markus Steinberger, Michael Kenzel, Bernhard Kainz and Dieter Schmalstieg.
*ScatterAlloc: Massively parallel dynamic memory allocation for the GPU*,
Innovative Parallel Computing (InPar), 2012,
https://doi.org/10.1109/InPar.2012.6339604
- Carlchristian Eckert.
*Enhancements of the massively parallel memory allocator ScatterAlloc and its adaption to the general interface mallocMC*,
Junior Thesis (grosser Beleg), 2014,
http://dx.doi.org/10.5281/zenodo.34461
This adds a maintained version of the (since 2012)
stalled original project.
https://github.com/ComputationalRadiationPhysics/cuda_memtest
Nvidia's NVML (via the GPU deployment kit) could also be
added, providing serial number output of failing GPUs
for multi-GPU nodes.
`set_executable` now checks if a user/group.other had read permission
on a file and if it does then it sets the corresponding executable
bit.
See #1483.
* Fixes patch paths for earlier boost versions
The directory structure of boost changed at version 1.56.0, so the patch
being used for python support did not work on earlier versions. This
adds another patch that matches earlier versions.
* Removes commented out code
* Fixes needed to build htop
* Build libncursesw.so, not libncurses.so
* Remove htop hack now that it is picking up newer ncurses
* Tell packages to link to new ncursesw libraries
- clean up fetch urls
- inherit from AutotoolsPackage instead of Package
- explicit fPIC flags look suspicious, but leave them in there.
- in scalasca, use the cube version that is implicit from
the scorep dependency instead of specifying it twice.
* The beginnings of a package for shiny-server
Just stashing a WIP.
This doesn't work.
This goes for a while and/but blows up with some OpenSSL related issue.
* Make it work!
Yay!
* shiny-server needs R with X support
My environment gets this for "free" from my packages.yaml, but it
should be explicity.
* Address feedback
- python version
- gcc dependency
- Flake8 comment rules
* Richer caveats and warnings.
* Convert to CMakePackage and fix python version typo
* Fix typo: noqab -> noqa
* Ensure proper build location, clean up comments
Fixes#2587
The concretizer falls back on using the root architecture (followed
by the default system architecture) to fill in unspecified arch
properties for a spec. It failed to check cases where the root could
be None.
* Update tinyxml
* url seems to have changed
* spack replaces "_2_6_2" with "_2.6.2" unless the url is explicitly
given
* copyfile is no longuer available by default
* URL version-parsing should work as of #2972
* Remove fake URLs from Spack
* Ignore long lines for URLs that start with ftp:
* Preliminary changes to version regexes
* New redesign of version regexes
* Allow letters in version-only
* Fix detection of versions that end in Final
* Rearrange a few regexes and add examples
* Add tests for common download repositories
* Add test cases for common tarball naming schemes
* Finalize version regexes
* spack url test -> spack url summary
* Clean up comments
* Rearrange suffix checks
* Use query strings for name detection
* Remove no longer necessary url_for_version functions
* Strip off extraneous information after package name
* Add one more test
* Dot in square brackets does not need to be escaped
* Move renaming outside of parse_name_offset
* Fix versions for a couple more packages
* Fix flake8 and doc tests
* Correctly parse Python, Lua, and Bio++ package names
* Use effective URLs for mfem
* Add checksummed version to mitos
* Remove url_for_version from STAR-CCM+ package
* Revert changes to version numbers with underscores and dashes
* Fix name detection for tbb
* Correctly parse Ruby gems
* Reverted mfem back to shortened URLs.
* Updated instructions for better security
* Remove preferred=True from newest version
* Add tests for new `spack url list` flags
* Add tests for strip_name_suffixes
* Add unit tests for version separators
* Fix bugs related to parseable name but in parseable version
* Remove dead code, update docstring
* Ignore 'binary' at end of version string
* Remove platform from version
* Flip libedit version numbers
* Re-support weird NCO alpha/beta versions
* Rebase and remove one new fake URL
* Add / to beginning of regex to avoid picking up similarly named packages
* Ignore weird tar versions
* Fix bug in url parse --spider when no versions found
* Less strict version matching for spack versions
* Don't rename Python packages
* Be a little more selective, version must begin with a digit
* Re-add fake URLs
* Fix up several other packages
* Ignore more file endings
* Add parsing support for Miniconda
* Update tab completion
* XFAILS are now PASSES for 2 web tests
- _spider in web.py was actually failing to spider deeper than a certain
point.
- Fixed multiprocessing pools to not use daemons and to allow recursive
spawning.
- Added detailed tests for spidering and for finding archive versions.
- left some xfail URL finding exercises for the reader.
- Fix noqa annotations for some @when decorators
* add packages for EasyBuild and dependencies
* fix remarks w.r.t. docstrings & download urls, make dependency specs stricter w.r.t. required versions
* fix easybuild-* dep specs, should be open-ended
* correct dep specs for easybuild and easybuild-easyconfigs using @3.1.2[:]
- Clean up spec_syntax tests: don't dependend on DB order.
- spec_syntax hash parsing tests were strongly dependent on the order the
DB was traversed.
- Tests now specifically grab the specs they want from the mock DB.
- Tests are more readable as a result.
- Add Python3 versions to Travis tests.
1. Fix#2807: Can't depend on virtual and non-virtual package
- This is tested by test_my_dep_depends_on_provider_of_my_virtual_dep in
the concretize.py test.
- This was actually working in the test suite, but it depended on the
order the dependencies were resolved in. Resolving non-virtual then
virtual worked, but virtual, then non-virtual did not.
- Problem was that an unnecessary copy was made of a spec that already
had some dependencies set up, and the copy lost half of some of the
dependency relationships. This caused the "can'd depend on X twice
error".
- Fix by eliminating unnecessary copy and ensuring that dep parameter of
_merge_dependency is always safe to own -- i.e. it's a defensive copy
from somewhere else.
2. Fix bug and simplify concretization of deptypes.
- deptypes weren't being accumulated; they were being set on each
DependencySpec. This could cause concretization to get into an infinite
loop.
- Fixed by accumulating deptypes in DependencySpec.update_deptypes()
- Also simplified deptype normalization logic: deptypes are now merged in
constrain() like everything else -- there is no need to merge them
specially or to look at dpeendents in _merge_dependency().
- Add some docstrings to deptype tests.
- Get rid of pkgsort() usage for preferred variants.
- Concretization is now entirely based on key-based sorting.
- Remove PreferredPackages class and various spec cmp() methods.
- Replace with PackagePrefs class that implements a key function for
sorting according to packages.yaml.
- Clear package pref caches on config test.
- Explicit compare methods instead of total_ordering in Version.
- Our total_ordering backport wasn't making Python 3 happy for some
reason.
- Python 3's functools.total_ordering and spelling the operators out
fixes the problem.
- Fix unicode issues with spec hashes, json, & YAML
- Try to use str everywhere and avoid unicode objects in python 2.
- Remove ascii encoding assumption from spack_yaml
- proc.communicate() returns bytes; convert to str before adding.
- Fix various byte string/unicode issues for Python 2/3 support
- Need to decode subprocess output as utf-8 in from_sourcing_files.
- Fix comments in strify()
- convert print, StringIO, except as, octals, izip
- convert print statement to print function
- convert StringIO to six.StringIO
- remove usage of csv reader in Spec, in favor of simple regex
- csv reader only does byte strings
- convert 0755 octal literals to 0o755
- convert `except Foo, e` to `except Foo as e`
- fix a few places `str` is used.
- may need to switch everything to str later.
- convert iteritems usages to use six.iteritems
- fix urllib and HTMLParser
- port metaclasses to use six.with_metaclass
- More octal literal conversions for Python 2/3
- Fix a new octal literal.
- Convert `basestring` to `six.string_types`
- Convert xrange -> range
- Fix various issues with encoding, iteritems, and Python3 semantics.
- Convert contextlib.nested to explicitly nexted context managers.
- Convert use of filter() to list comprehensions.
- Replace reduce() with list comprehensions.
- Clean up composite: replace inspect.ismethod() with callable()
- Python 3 doesn't have "method" objects; inspect.ismethod returns False.
- Need to use callable in Composite to make it work.
- Update colify to use future division.
- Fix zip() usages that need to be lists.
- Python3: Use line-buffered logging instead of unbuffered.
- Python3 raises an error with unbuffered I/O
- See https://bugs.python.org/issue17404
- Update YAML version to support Python 3
- Python 3 support for ordereddict backport
- Exclude Python3 YAML from version tests.
- Vendor six into Spack.
- Make Python version-check tests work with Python 3
- Add ability to add version check exceptions with '# nopyqver' line
comments.
* Run python setup.py test if --run-tests
* Attempt to import the Python module after installation
* Add testing support to numpy and scipy
* Remove duplicated comments
* Update to new run-tests callback methodology
* Remove unrelated changes for another PR
* perl: make extendable and add Module::Build package
* perl: allow 'spack create' to identify perl packages from their contents
* perl-module-build: fix indenting of package docstring
* perl: split install() method for extensions into phases
* perl: auto-detect build method (Makefile.PL vs Build.PL) and define a 'check' method
* PerlPackage: use import statements similar to those in AutotoolsPackage
* PerlModule: fix detection of Build.PL
* PerlPackageTemplate: remove extraneous lines to avoid flake8 warnings
* PerlPackageTemplate: split into separate templates for Makefile.PL and Build.PL
* PerlPackage: add cross-references to docstrings
* AutotoolsPackage: fix ambiguous cross-references to avoid errors in doc tests
* PerlbuildPackageTemplate: depend on perl-module-build if Build.PL exists
* ENH: add package for building OpenFOAM (1612) from www.openfoam.com
- provide 'openfoam' as virtual package.
- package as openfoam-com to reflect the distribution point.
This initial spack packaging for OpenFOAM supports a number of possible
variants and should handle 64-bit labels properly now that the scotch
package has been updated accordingly.
* ENH: update package for foam-extend (extend-project.de)
- provide 'openfoam' as virtual package.
- much of the build is now aligned with how the openfoam-com package
looks, with the aim of future refactoring.
- avoid installing intermediate targets.
- contains its own environment sourcing script for the build, for more
flexibility and robustness (doesn't touch the python build environ)
* ENH: added package for building from openfoam.org
- provide 'openfoam' as a virtual package.
- this is largely a direct copy of the openfoam-com package.
It has been supplied as a courtesy for users and to ensure maximum
consistency in quality and naming between the foam-extend,
openfoam-com and openfoam-org packages.
* CONFIG: add openfoam into bash completion providers list
* ENH: have openfoam-com use spack as USERMPI
- also simplify the generation of mplib/compiler rules
* ENH: have openfoam-org use spack as SYSTEMMPI
- this setup requires more environment settings than USERMPI
(openfoam-com), but is currently the only means of integration
for openfoam-org
- simplify generation of mplib/compiler rules
* ENH: simplify generation of mplib/compiler rules (foam-extend)
- rename mpi rules from SPACK,SPACKMPI to USER,USERMPI for consistency
with openfoam-com and to generalize for any build system.
* STYLE: record spack tree as a log file (openfoam)
- can be useful for future diagnostics and general record keeping
* libint: updated version, ported to AutotoolsPackage
* elpa: updated version, ported to AutotoolsPackage
* wannier90: updated version, ported to MakefilePackage
* pexsi: updated version, ported to MakefilePackage
* cp2k: updated version, removed wannier 90 from dependencies if cp2k@4.1
* plumed: updated version
Modifications:
* modules has been turned into a single variant, as different versions
have different modules available
* added dictionaries for patches
* netlib-scalapack: ported to CMakePackage
* Add Blast+ package.
Adds support for NCBI's blast+@2.6.0. I'll be adding a few historical versions in the near future.
It's a fairly direct transliteration of the [Homebrew Science recipe][hbs].
I skipped the mysql support.
There is a problem with HDF5 support. Blast's configure script test program defines a macro 'HOST' to a string value and one of the HDF5 bits has an variable named 'HOST'. Fun things happen. I've disabled support for now.
I've run very very basic tests. I'll get this out to my users and ensure that it works and fine tune the options and etc....
[hbs]: https://github.com/Homebrew/homebrew-science/blob/master/blast.rb
* Flake8 fixes
* Update w.t.r. mamelara's PR and cleanup
Add paths to things in the --with-* config args
Add add'l config flags from #3394.
Update patch to no-op and add comment.
Add add'l dependencies after studying `configure --help`.
* Flake8 cleanup
* Add support for blast+@2.2.30
Need to work around a configure bug. See https://github.com/Homebrew/homebrew-science/issues/2337#issuecomment-170011511.
* Re-wrap comment, line length not a problem.
I'd broken a comment across to line in a fit of flake8
induced fear. Adam pointed out that it's ok.
* Remove explicit prefix config
Remove explicit prefix config, the autotools package does it for us.
* Added packages for Structural Simulation Toolkit and Dumpi trace
* sst-dumpi deps
Remove extraneous dependency from sst-dumpi
* Removed redundant function and fake-url from sst-dumpi package
* Fixed URL, Added git branches, requested changes
sst-dumpi version listed as 6.1, made an upstream change to 6.1.0
sst-macro and sst-dumpi can be installed as v6.1.0 and master branch
* Added bootstrap. Tweaked URLs and description
- Spack find would fail with "unknown namespace" for some queries when a
package from an unknown namespace was installed.
- Solve by being conservative: assume unknown packages are NOT providers
of virtual dependencies.
- deactivate -a wouldn't work if the installation's package was no longer
available.
- Fix installed_extensions_for so that it doesn't need to look at the
package.py file.
- drop old TCL support from paraview build.
- add +plugins variant to have include directories installed. This is
enabled by default since the additional diskspace for includes is
really minimal and since this also allows re-use of the VTK libraries
from ParaView without necessarily requiring a separate VTK
installation.
- +opengl2 is now the default. As per all newer VTK and paraview versions.
BUG: broken install for paraview-5.0.1 with includes and without python
- incorrect conditional for ui_pqExportStateWizard.h when python is
disabled and includes are to be installed.
gcc compiler detection patch.
These have both been fixed in paraview 5.3.0
ENH: refactor as a CMakePackage.
- Note that "spack install paraview" works as expected, but
"spack build paraview" fails in weird unrelated ways.
* Fix nettle dependency
GnuTLS requires a nettle from the 2.7 series, won't work
with 3.x (so sayeth configure when it crashes...).
* Fix configure symlinking GNUmakefile to itself
I'm confused about how this ever worked, but....
As configure runs, it does something like this:
```
config.status: linking /home/hartzelg/tmp/spack/var/spack/stage/gnutls-3.3.9-uq2u4ecucncv2l3akran765aystyvkys/gnutls-3.3.9/GNUmakefile to GNUmakefile
```
and since that is the cwd the build crashes with:
```
==> 'make' '-j28'
make: GNUmakefile: Too many levels of symbolic links
make: stat: GNUmakefile: Too many levels of symbolic links
make: *** No rule to make target `GNUmakefile'. Stop.
```
Since the comment in the configure script points out that the
GNUmakefile is "only for the maintainer" I've just commented out the
bit that leads to the symlinking.
Builds for me on CentOS 7. (I do have a recent-ish set of auto-*
things in my patch via linuxbrew)
* Wordsmith
* Fix symbolic link problem properly
Autotools magic. See #3565 for the details.
* Flake8 cleanup
* Add some headroom on the version number constraint
We really want < 3.0 but there's not a good way to express it.
We'd like to avoid having to update the file if they release 2.7.2.
This seems like a good compromise.
* Add url_for_version and depends_on('libiconv')
Fetching is broken. See https://github.com/LLNL/spack/issues/3554.
libgd, when used in gnuplot at least, needs a dependency
on libiconv.
* Undo change from debugging pokery
* pnfft: new package
* Convert some packages with overridden install from AutotoolsPackage to Package
* pnfft: fix URL
* Switch FFTW-derived packages back to AutotoolsPackage
* Disable unneeded build phases in FFTW and derived packages
* Separate build phases for FFTW and derived packages
* Fix broken merge
* fftw: pfft_patches for 3.3.6
* fftw: address @adamjstewart’s review comments
* Clean up the gcc package
* Add preliminary testing support
* Older versions of GCC do not depend on MPC
* DejaGnu 1.4.4 cannot be built in parallel
* Fix GCC test dir
* Add two more deps required to run the testsuite
there were various updated packages, both for the 2.x, 2.0.x,
and 1.10.x release branches of Open MPI.
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
(cherry picked from commit 3b671935783fc3af76dc642a54461c2f02ab8ebf)
This fixes the problem described in #3374, which describes `spack find` ignore explicit/implicit.
I believe that this was broken in #2626.
This restores the behavior of implicit/explicit for me.
I believe that it does not screw anything else up, but ....
* Replacing failing git clone by valid url
* Moving to previous version package (0.163)
* Removing automake and autoconf dependencies and adding url_list to pick up newer versions
* Corrected typo
* Reorder versions and removed libtool
* Order listed compiler sections
"spack compiler list" output compiler sections in an arbitrary order.
With this commit compiler sections are ordered primarily by compiler
name and then by operating system and target.
* Compiler search lists config files with compilers
If a compiler entry is already defined in a configuration file that
the user does not know about, they may be confused when that compiler
is not added by "spack compiler find". This commit adds a message at
the end of "spack compiler find" to inform the user of the locations
of all config files where compilers are defined.
* Add missing dependencies to gawk
* Fix make check
* Add mawk packages and awk virtual dependency
* Use mawk instead of gawk to build ncurses
* Rearrange order of patches and dependencies
* hpx5: Convert to AutotoolsPackage, several updates
- convert to AutotoolsPackage
- add several variants
- add several dependencies
- add new version 4.0.0
- don’t set compiler flags explicitly
* hpx5: Don’t import os
* hpx5: Clean up configure arguments
* hpx5: Correct libffi configure declaration
Also add new variant “+instrumentation”.
* hpx5: Correct CUDA, MPI, OpenCL configuration
* hpx5: Use built-in libffi
Spack’s libffi installs its headers in a strange place, and hpx5 can’t pick them up.
* libpciaccess: Convert to AutotoolsPackage, remove Darwin work-around
Other packages that depend on libpciaccess can do so via a conditional dependency (via a variant); we don’t need a dummy package for Darwin any more.
* Disable libpciaccess dependency on non-Darwin platforms
* hwloc: Remove direct dependency on libpciaccess
* Added support for building Theano with GPU support. Added a package
for the libgpuarry libary needed for Theano.
* Added dependency on py-pexpect package which ipython requires.
Fixes#1476
Concretization uses compilers defined in config files and if those
are not available defaults to searching typical paths where the
detected operating system would have a compiler. If there is an OS
update, the detected OS can change; in this case all compilers
defined in the config files would no longer match (because they would
be associated with the previous OS version). The error message in
this case was too vague. This commit adds logic for detecting when it
is likely that the OS has been updated (in particular when that
affects compiler concretization) and improves the information provided
to the user in the error message.
* Dont propagate flags between different compilers
Fixes#2786
Previously when a spec had no parents with an equivalent compiler,
Spack would default to adding the compiler flags associated with the
root of the DAG. This eliminates that default.
* added test for compiler flag propagation
* simplify compiler flag propagation logic
Fixes#3428
Users can run 'spack compiler find' to automatically initialize their
compilers.yaml configuration file. It also turns out that Spack will
implicitly initialize the compilers configuration file as part of
detecting compilers if none are found (so if a user were to attempt to
concretize a spec without running 'spack compiler find' it would not
fail). However, in this case Spack was overlooking its own implicit
initialization of the config files and would report that no new
compilers were found. This commit removes implicit initialization when
the user calls 'spack compiler find'.
This did not surface until #2999 because the 'spack compiler' command
defaulted to using a scope 'user/platform' that was not accounted for
in get_compiler_config (where the implicit initialization logic
predates the addition of this new scope); #2999 removed the scope
specification when checking through config files, leading to the
implicit initialization.
* hwloc: Add missing dependencies
- add several missing dependencies
- add variants for various features
- add new version 1.11.6
* hwloc: Add descriptions to variants
* New package pocl
* pocl: Update dependencies, add self-test
* pocl: Don't require LLVM shared libraries
LLVM build fails with shared libraries.
* Add patch
* Update
* Update
* Make build and install work; install test still fails
* Split pocl into pocl proper and pocl-test
* Add debug output
* pocl: Update to 0.14-rc
* pocl: Correct flake8 error
* pocl: Heed code review recommendations
* pocl: Add newline at end of file
* pocl: Correct flake8 error
I don’t want to use an even longer line by putting the whole variant declaration onto a single line, nor do I think that having an overlong line and adding `# noqa` at the end is more readable than splitting a string over three lines.
* pocl: Correct dependency type for libtool
Previously, this would fail with a NoSuchMethodError:
class Package(object):
# this is the default implementation
def some_method(self):
...
class Foo(Package):
@when('platform=cray')
def some_method(self):
...
@when('platform=linux')
def some_method(self):
...
This fixes the implementation of `@when` so that the superclass method
will be invoked when no subclass method matches.
Adds tests to ensure this works, as well.
* Add paths to PKG_CONFIG_PATH to find cray .pc file
Adds two paths: /usr/lib64/pkgconfig and /usr/local/lib64/pkgconfig.
cray pkg-config looks at two different paths which are not included
in PKG_CONFIG_PATH environment variable. This PR addresses #3167.
* Flake8 fixes
* flake8 fix again
* default scope for config command is made consistent with cmd/__init__ default
* dont specify a scope when looking for compilers with a matching spec (since compiler concretization is scope-independent)
* config edit should default to platform-specific file only for compilers
* when duplicate compiler specs are detected, the exception raised now points the user to the files where the duplicates appear
* updated error message to emphasize that a spec is duplicated (since multiple specs can reference the same compiler)
* 'spack compilers' is now also broken down into sections by os and target
* Added tests for new compiler methods
* cosmomc: New package CosmoMC
* cosmomc: Improve version numbering scheme
* planck-likelihood: New package
* cosmomc: Pacify flake8
* cosmomc: Code cleanup as requested in the review
* cosmomc: Various updates suggested during review
* cosmomc: Limit compiler versions (as documented in the build instructions)
* cosmomc: Correct flake8 error
* cosmomc: Use `libs` instead of `lapack_libs`
* planck-likelihood: Make makefile output more verbose and readable
* planck-likelilhood: Correct order of libraries when calling linker
* cosmomc: Clean up check for suitable compiler
* planck-likelihood: Use modern mechanism to set environment variables
Modifications:
- `dump_packages` copies build dependencies into `$prefix/.spack`, as well as the link/run dependencies that we already copied there.
- fake installs copy dependency packages into `$prefix/.spack` as well
* Cleanup list of offered versions (only the latest update release of each minor version is kept: 1.4.4, 1.5.2, 1.6.6, 1.7.1); introduced master revision (via Git). Slightly more selective installation of the documentation; copy README.md and LICENSE files to documentation folder. Removed outdated build options (make_args); generally stay with LIBXSMM's defaults (general purpose build). Introduced one build variant ("debug").
* Incorporated comments of PR #3371 (https://github.com/LLNL/spack/pull/3371).
* Fixed flake8 complaints.
* Made the full list of versions available starting with version 1.4 (there are earlier releases, however those have been released before the Spack specification became available; original spec. also started with 1.4).
* Made DBG and TRACE actually two separate arguments.
The tests fail on some systems (e.g. Comet at SDSC) that impose limits on the number of processes or threads one can run simultaneously on the head node. Thus the tests should not be run by default.
* ADIOS: change the invocation of python script that generates test files
The python script ADIOS*/utils/gpp/gpp.py is invoked directly in the
ADIOS*/tests/genarray/Makefile and the name of the python interpreter
can be quite long if it is one built under spack, i.e. longer than the
80 characters allowed by the #! line in bash. The name of the shbang
line is truncated at 80 characters and bash cannot find the python
interpreter specified.
This fix changes how the script is executed, by invoking it under
python. This way, the shbang line is ignored.
* adios: fixed flake8 errors from previous commit.
* adio: Switch to AutotoolsPackage class from Package class
Switched in order to add support for the ppc64le platform.
* Adding highwayhash package from Google
* Added the highwayhash package for Tensorflow
* Fixed the numerous flake8 issues
* fixed requested changes
* added conditionals for some installs
* forgot an import
* create install directories before you install anything in them
* Add new package for PaGMO/PyGMO
* Rename py-pygmo to pagmo
* Fix concretization bug
* Correct Python detection, use correct flags
* Install PyGMO to the pagmo prefix, not the Python prefix
This commits address build issues reported in issue #3268.
In particular, makes cleaner the dependency on parallel-netcdf
when +ncmpi variant is requested and adds CFLAGS=-D H5_USE_16_API
to handle the fact that Ior uses old 1.6 style APIs when +hdf5 is
requested.
These changes make Ior build fine and create modules for HDF5 versions
1.8.x and 1.10.0.
Even though build is successfull the modules haven't been tested in a
run.
* Make libgcc_s relocatable
* spack specifies full path to lib64
* don't need trailing /
* setting rpath is different on macos
* add -headerpad_max_install_names linker options
* formatting fixes
* Add Adam's recommendation
* add various variants to vim
* default to --enable-fail-if-missing
* vim package: -{python,ruby,lua,perl} sets build option to `no`
* vim's interpreter build options are `--enable-XXXXinterp={yes,no,dynamic}`
* dynamic seems to work only on windows builds
* `=no` is the default => use it in spack if the variant is disabled
- Added a new interface for Specs to pass build information
- Calls forwarded from Spec to Package are now explicit
- Added descriptor within Spec to manage forwarding
- Added state in Spec to maintain query information
- Modified a few packages (the one involved in spack install pexsi) to showcase changes
- This uses an object wrapper to `spec` to implement the `libs` sub-calls.
- wrapper is returned from `__getitem__` only if spec is concrete
- allows packagers to access build information easily
It seems the tests in `packages.py` were running just because we had a specific order of execution. This should fix the problem, and make the test_suite more resilient to running order.
Declare that (i) Trilinos can be only built against 32bit Hypre
(ii) SLEPc can not be built with Arpack when 64bit indices are used
(iii) reflect those constraints in deal.II's depends_on
While there, add extra release flags for best performance.
* Updating SAMRAI package file with new urls and new versions. Also using Spack's MPI compilers.
* Using default optimization for Samrai and setting type to build for m4 dependency.
* Adding debug variant to Samrai.
* Converting Samrai to AutotoolsPackage.
* Add git-review
* Fix flake8 errors
* use PythonPackage for git-review
* added dependencies for git-review
* fix flake8
* moved url's to pypi.io based urls
* fixed flake8... again
* mostly url fixes, not tested, will do tomorrow
* flake8 fix
* changed URL for py-pysocks
* Fixed URL for pysocks
* fixed url
The new repository for the development version points to the most
up-to-date official source for Adol-C. The previous SVN repository was
only occasionally sync'd with this repository.
* Fix build issue #3190 on bg-q :
- disable parallel build as it produces weired linker errors
in cross compiling environment
- update ldflags for bg-q as per Makefile provided Makefile.inc.ppca2_ibm_bgq
* Added note about -lpthread vs -pthread
* Corrected extrae package homepage and url
* Corrected paraver package homepage and url
* To fix 'undefined reference to libintl_dgettext' appearing in extrae package when using binutils+libiberty
* Adding support to previous paraver version and reverting binutils changes to open another PR
* Add installer for petsc4py and slepc4py
* @adamjstewart requested changes on this pull request; make these type=('build', 'run')
* @citibeth suggestion Remove unneeded indirect dependencies
Zoltan expects mpi libraries with option --with-mpi-libs.
If this option is not provided then it uses '-lmpi' which
may not be correct. To avoid this, we have to explicitly
pass empty string.
This adds notes to the source explaining the change.
* Add log4cxx package
* add missing patch files to log4cxx
* remove unnecessary dependencies
* this fails at 'make check'
* this is the AutotoolsPackage version
* fixed install bug
* Update the krell institute products to use the latest features of spack for building on cluster platforms.
* Address travis error messages and resubmit the pull request.
* Update the contents of openspeedshop package.py so it passes the flake8 tests.
* Fix flake8 error-whitespack issue in mrnet package.py file.
* Add updates based on spack reviewer feedback.
* More fixes based on comments from reviewers. Switch using extend to using append, remove additional setting of PATH and LD_LIBRARY_PATH that should not be required due to RPATH.
* More review related changes. Update MPIOption.append lines and take out xercesc references.
* Create a base options function for common openspeedshop base cmake options to reduce redundencies.
* Add libxml2+python depends on to get around issues with the libxml2 package file.
* Using boost over 1.60.0 causes compile errors. This is a known boost bug. Also, dyninst-9.2.0 is set to be the vesrion of dyninst to use with OSS, as of now. The newer version fails to build.
* Fix bad syntax in specifying the boost version range.
* Update the version numbers for the krell institute components and tools: cbtf and openspeedshop.
* Do not build glib for qt3, it is not needed and causes build problems at this time anyway.
* A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set.
* Update the fix for qt3 build by setting LD_LIBRARY_PATH instead of checking for whether it is set or not per Adams comment that spack clears LD_LIBRARY_PATH.
* A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set.
* Trim comments to fit more concisely.
* Fix tabs versus spaces and swap if and else clause check from a negative to a positive check.
Update package file for netlib-lapack to work with IBM XL compiler
The flag -qzerosize is redundant, as the IBM XL compiler should set this flag
by default. However, at this time the default flag appears to be ignore.
Hence, I am setting it in the package file as well, as it has no negative
effect if set twice.
graphviz:
* Download from Fedora projet, as main graphviz site not working.
* Disable java because Spack does not yet support Java, and the system might not have it installed.
* Added all language binding variants; disabled enough in the default configuration to avoid dependencies.
* Removed alternate download location (turned into comments).
* Turn off all language bindings by default.
* Raise an exception on bindings that have not been verified to work.
* Added text indicating what works and doesn't work when user runs `spack info`.
* New package.py for ExM C-Utils: An initial package dependency for Swift/T
* New package.py for ADLB/X: A 2nd package dependency for Swift/T
* New package.py for Turbine
* New package.py for STC
Spack wants URL info even for external packages. Without it, I get
the following error:
NoURLError: Package SpectrumMpi has no version with a URL.
File "/home_local/serbanspack/spack/lib/spack/spack/repository.py", line 580, in get
self._instances[key] = package_class(copy)
File "/home_local/serbanspack/spack/lib/spack/spack/package.py", line 562, in __init__
f = fs.for_package_version(self, self.version)
File "/home_local/serbanspack/spack/lib/spack/spack/fetch_strategy.py", line 878, in for_package_version
url = pkg.url_for_version(version)
File "/home_local/serbanspack/spack/lib/spack/spack/package.py", line 682, in url_for_version
raise NoURLError(cls)
* Creating a spack package for LLNL's LBANN (Livermore Big
Artificial Neural Network) training toolkit.
* Recipe for building LBANN toolkit. Contains limited feature set and
is optimized for building with GNU gcc and OpenBLAS.
* Removed unnecessary dependencies based on reviewers feedback.
* Added support for the int64 data type in the Elemental library. This
is required for supporting indices for large matrices.
* Added a variant to force a sequential weight matrix initialization.
This is slow, but provides an initialization that is independent of
model parallelism.
* Added a guard to prevent building Elemental with the Intel compiler
for versions that have known bugs.
* New package.py for ExM C-Utils: An initial package dependency for Swift/T
* New package turbine
* Fix package.py as requested by @adamjstewart
* New package.py for ADLB/X: A 2nd package dependency for Swift/T
* Add latest version of GNU Parallel (#3106)
* Address formatting guidelines from @adamjstewart
* WIP on new Turbine package.py
* Formatting fixes
* Complete Turbine package.py
[The fix](https://github.com/golang/go/issues/17986) for the small buglet addressed by `misc-cgo-testcshared.patch` has been merged into the tree a while back. I was surprised to see that it wasn't in 1.7.5 and did a bit of digging. It is *has not* been merged into the 1.7 branch but it *has* been merged into 1.8 (and therefor the patch will no longer be necessary).
Figured I'd document my digging for the next person to come along.
* spectrum-mpi: Add new package file for external package
IBM Spectrum MPI is a commercial implementation of MPI based on
OpenMPI. It is usually install in /opt/ibm/spectrum_mpi.
Users need to add the Spectrum MPI package in their packages.yaml
file as follows:
packages:
spectrum-mpi:
version: ['10.1.0.2']
paths:
spectrum-mpi@10.1.0.2: /opt/ibm/spectrum_mpi/
buildable: False
all:
providers:
mpi: [spectrum-mpi@10.1.0.2]
* spectrum-mpi: Added license files and removed the versions
No need for versions as the package is external.
* spectrum-mpi: Remove extraneous defines
Keep only the defines that other MPI implementation define in their
package file:
self.spec.mpicc
self.spec.mpicxx
self.spec.mpif77
self.spec.mpifc
- Fix format printing to match command line for hashes and full name formats
- Update spack graph to use new format
- Changed format string signifier for hashes from `$#` to `$/`
Update the go package to v1.7.5.
- This release no longer needs the time-test patch (it's been merged upstream).
- This release still seems to need the cgo-testcshared patch.
- Also add a comment about environment set up that I need to build it successfully on a very large server.
Tested on CentOS 7.
Modules generated by the module creation machinery currently print out
a notice that warnts the user that things are being autoloaded. In
some situations those warnings are problematic. See #2754 for
discussion.
This is a first cut at optionally disabling the warning messages:
- adds a helper tothe EnvModule base class that encapsulates the
config file variable;
- adds a method to the base class that provides a default (empty)
code fragment for generating a warning message;
- passes the warning fragment into the bit that formats the autoload
string;
- adds specialized autload_warner() methods in the tcl and lmod
subclasses;; and finally
- touches up the autoload_format strings in the specialized classes.
The repository used by the texlive installer defaults to a redirector
that sends one off to various URLs depending on <fill in the blank>.
This is problematic because all of the mirrors do not update in
synchrony and bad tarballs often hang around for a while.
This leads to problems that are particularly hard to diagnose because
you're likely to end up using a different repo the next time around.
This commit constraints the package to a particular, mainstream,
repository. It's not fast, but it's consistent and usually correct.
It also updates the installer digest, because no day is complete
without updating it at least (sigh) once.
Add the ability to the modules generation process to blacklist
packages that were installed implicitly. One can still whitelist
modules that were installed implicitly.
This changes adds a `blacklist_implicts` boolean as a peer to the
`whitelist` and `blacklist` arrays, e.g.:
```
modules:
enable::
- lmod
lmod:
whitelist:
- 'lua'
- 'py-setuptools'
blacklist:
- '%gcc@4.8.3'
blacklist_implicits: True
```
It adds a small helper in `spec.py` and then touches up the package
filtering code in `modules.py`.
* Different versions of cmake need diff vers of openssl. See Issue https://github.com/LLNL/spack/issues/2990 for background.
Versions of cmake through 3.6.9 seem to need OpenSSL up to 1.0.99. Later
versions can use the current release (thanks to @citibeth for
[digging up details](https://cmake.org/pipermail/cmake/2016-November/064631.html)).
@davydden suggested this change.
Without it I *am not* able to build `cmake@3.6.1` on CentOS 7 and I *am*
able to build `cmake@3.7.2`.
Tested with `cmake@3.7.2` and `cmake@3.6.1` on CentOS 7.
With this change I am able to build both `cmake@3.6.1` and `cmake@3.7.2`
on CentOS 7.
There was a new release of Ant (1.9.8) which led to the v1.9.7
tarball disappearing.
This changes the URL to Ant's archive dir, which seems to contain
*everything* including the two current releases (1.9.8 and 1.10.0)
It adds a digest for 1.9.8.
It adds and comments out a digest for 1.10.0 (which requires Java 8),
as I have not tested it.
We just released 2.0.2 yesterday, so add in that release for
spack. Don't need the PMI patch for this release.
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
cran.r-project.org runs on a single old-school server in Austria
and could potentially be overloaded if "everyone" used it.
cloud.r-project.org is a cloud-based repository that "automatic redirection to servers worldwide [...]", cf. https://cran.r-project.org/mirrors.html.
I assume, that cloud.* can be scale up as needed. Out of the official CRAN mirror, this should be the safest one to pick if a static CRAN mirror is needed.
* Replace `spack urls` and `spack url-parse` with `spack url`
* Allow spack url list to only list incorrect parsings
* Add spack url test reporting
* Add unit tests for new URL commands
* Add several new R packages
* Add a few more R packages
* Update more versions
* Convert Package to RPackage
* Add a few more packages
* Add missing dependencies
* AutotoolsPackage: added configure_directory to permit build out of source. The configure script executable is now invoked with an absolute path. Modified a few packages accordingly.
* build_systems: functions returning directories are now properties
* build_systems: fixed issues with tcl and tk
* AutotoolsPackage: reworked recipe for autoreconf
* Spec.satisfies accesses Spec.concrete as property
Fixes#2760
When copying a spec, _concrete is always set to False for each
dependency. "Spec.satisfies" was accessing the member "_concrete"
directly instead of using the property "concrete". This means that
if you copy a spec, the dependencies will be considered equal, but
did not necessarily satisfy one another. Spec.satisfies is a
prerequisite for a package to be considered an extension; as a
consequence, an extension with run-time dependencies that were also
extensions did not activate those extensions. This updates
Spec.satisfies to avoid checking the cached member "_concrete"
directly.
* Added test to check for activation of dependency extension
* Added test to check for transitive satisfiability between a spec and its copy
* Update libquo's homepage, url, and description.
Recently LANL moved to lanl (from losalamos).
* Fix formatting.
Conform to style guidelines.
* More style updates.
Doesn't appear to be necessary, but for good measure.
* oce: fix fetching
apparently the fetcher is confused when there is a mixture of 3-digits
versions and 2-digits versions, i.e. 0.18 and 0.17.2
* flake8
* Updating udunits.
Udunits 2.2.21 is no longer on the unidata ftp site.
The latest is 2.2.23, adding that and it's md5sum.
* Updating udunits2 download URL.
The Unidata ftp site does not keep previous versions of udunits.
However all the tagged versions are in their github.com repository.
Updating the URL to use github.
* Updating udunits2 with a autoreconf def.
The udunits packages on github do not contain a configure script.
One has to run autoreconf to generate it, so adding that to
package file.
Also updated to the latest version and all md5 checksums.
- Allows hashes to be specified after other parts of the spec
- Does not allow other parts of the spec to be specified after the hash
- The hash must either end input or be followed by another separate spec
- The next spec cannot be an anonymous spec (it must start with a package name or a hash)
See #2769 (after it was merged) for further discussion of this interface addition. That discussion resulted in these requirements:
```
python # 1 spec
/abc123 # 1 spec
python /abc123 # 1 spec
/456789 # 1 spec
python /abc123 /456789 # 2 specs
python /456789 /abc123 # 2 specs
/abc123 /456789 # 2 specs
/456789 /abc123 # 2 specs
/456789 /abc123 python # 3 specs
```
assuming `abc123` and `456789` are both hashes of different python specs.
* Add support for IBM threaded compilers, xl*_r
Added new compiler class, xl_r; added default flags to the compilers.yaml file.
* Add cppflags to the set of default flags to be added to the compilers stanza in compiler.yaml.
These flags are optional. Only defined flags will be listed in the compilers.yaml file.
* Fix scripting warnings revealed by flake8.
Updated __init__.py and xl_r.py to conform with flake8 rules.
* Add justification to the definition of the XL default compiler flags.
* PackageMeta: `run_before` is an alias of `precondition`, `run_after` an alias of `sanity_check`
* PackageMeta: removed `precondition` and `sanity_check`
* PackageMeta: decorators are now free-standing
* package: modified/added docstrings. Fixed the semantics of `on_package_attributes`.
* package: added unit test assertion as side effects of install
* build_systems: factored build-time test running into base class
* r: updated decorators in package.py
* docs: updated decorator names
* Add dependency on perl
The build process uses perl and also needs `Test::More`.
Some distros, e.g. CentOS, break the core Perl distribution
into separate packages, so it's possible to "have perl" but
not have all the bits one needs to build OpenSSL.
We'll just install one of ours, which comes with all of its
factory parts included.
* Remove uninformative comment
> # Also requires make
doesn't really add any value...
* documentation: reworked packaging guide to add build-system phases
* documentation: improvements to AutotoolsPackage autodocs
* build_systems: updated autodocs
* run-tests: added a few information on how to run tests fixes#2606 fixes#2605
* documentation: fixed items brought up by @davydden
* typos in docs
* consistent use of 'build system' (i.e. removed 'build-system' from docs)
* added a note on possible default implementations for build-time tests
* documentation: fixed items brought up by @citibeth
* added note to explain the difference between build system and language used in a package
* capitalized bullet items
* added link to API docs
* documentation: fixed multiple cross-references after rebase
* documentation: fixed minor issues raised by @tgamblin
* documentation: added entry in table for the `PythonPackage` class
* docs: fixed issues brought up by @citybeth in the second review
* Fix configure's zlib version check
R wants a version of zlib that is 1.2.5 or newer.
The version checking code just does a lexicographic comparison
of the first 5 characters of the string, so it seesthat the latest
zlib version, 1.2.10, as 1.2.1 and fails.
This patch changes the comparison to use zlibs' hex ZLIB_VERNUM
so that it does not suffer from this problem.
A version of this patch is wending it's way through the R comunity
community and will/should be included in a future release.
I tested the patch with the current R, 3.3.1.
* Tighten zlib dependency version (>= 1.2.5)
* Convert patch to level=1 format.
* libmonitor does not exist at
http://libmonitor.googlecode.com/svn/trunk/
Change location to HPCToolkit version at github. Specify the hash corresponding
to the 20130218 version.
* When xcb is version 1.11, patch the configure file so it doesn't trip on
pthread-stubs and xau.
* Add os.getcwd()/lib to LD_LIBRARY_PATH, instead of nuking
existing LD_LIBRARY_PATH.
* cfitsio: Allow building as shared libraries
- Allow building as shared libraries
- Also add optional bzip2 variant
- Also update to newest version
This requires the recent correction to “fix_darwin_install_name”.
* cfitsio: Simplify code, default to +shared
Previously, fix_darwin_install_name would only handle dependencies that have no path set, and it ignore dependencies that have the build directory as path baked in. Catch this, and replace it by the install directory.
* Adding 'self.' to the spec call for configure_args
* Updating this to set spec to self.spec
* More updates to the configure_args spec calls
* Another spec issue
* Another spec issue.
* And another spec issue
* Switching cmor back to self.spec.
In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation.
## Our Standards
Examples of behavior that contributes to creating a positive environment include:
* Using welcoming and inclusive language
* Being respectful of differing viewpoints and experiences
* Gracefully accepting constructive criticism
* Focusing on what is best for the community
* Showing empathy towards other community members
Examples of unacceptable behavior by participants include:
* The use of sexualized language or imagery and unwelcome sexual attention or advances
* Trolling, insulting/derogatory comments, and personal or political attacks
* Public or private harassment
* Publishing others' private information, such as a physical or electronic address, without explicit permission
* Other conduct which could reasonably be considered inappropriate in a professional setting
## Our Responsibilities
Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
## Scope
This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
## Enforcement
Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team at maintainers@spack.io. The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
## Attribution
This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [http://contributor-covenant.org/version/1/4][version]
to learn how to use spack, write packages, or deploy packages for users
at your site.
See also:
* [Technical paper](http://www.computer.org/csdl/proceedings/sc/2015/3723/00/2807623.pdf) and
[slides](https://tgamblin.github.io/files/Gamblin-Spack-SC15-Talk.pdf) on Spack's design and implementation.
* [Short presentation](https://tgamblin.github.io/files/Gamblin-Spack-Lightning-Talk-BOF-SC15.pdf) from the *Getting Scientific Software Installed* BOF session at Supercomputing 2015.
Get Involved!
------------------------
@@ -53,37 +53,44 @@ packages to bugfixes, or even new core features.
### Mailing list
If you are interested in contributing to spack, the first step is to
join the mailing list. We're using a Google Group for this, and you
can join it here:
If you are interested in contributing to spack, join the mailing list.
We're using Google Groups for this:
* [Spack Google Group](https://groups.google.com/d/forum/spack)
### Slack channel
Spack has a Slack channel where you can chat about all things Spack:
* [Spack on Slack](https://spackpm.slack.com)
[Sign up here](https://spackpm.herokuapp.com) to get an invitation mailed
to you.
### Contributions
Contributing to Spack is relatively easy. Just send us a
If you want to report a build error for some package, or a bug in core please use the following template as a guideline:
-----
Summary
### Expected Result
What you expected
### Actual Result
What happened instead
### Steps to reproduce the issue
```console
$ spack <command1> <spec>
$ spack <command2> <spec>
...
```
### Information on your system
This includes:
1. which platform you are using
2. any relevant configuration detail (custom `packages.yaml` or `modules.yaml`, etc.)
-----
We encourage you to try, as much as possible, to reduce your problem to the minimal example that still reproduces the issue. That would help us a lot in fixing it quickly and effectively!
If you want to ask a question about the tool (how to use it, what it can currently do, etc.), try the `#general` channel on our Slack first. We have a welcoming community and chances are you'll get your reply faster and without opening an issue.
Other than that, thanks for taking the time to contribute to Spack!
The names should look familiar, as they resemble the output from ``spack find``.
You *can* use the modules here directly. For example, you could type either of these commands
to load the ``cmake`` module:
..code-block::console
$ use cmake-3.7.2-gcc-6.3.0-fowuuby
..code-block::console
$ module load cmake-3.7.2-gcc-6.3.0-fowuuby
Neither of these is particularly pretty, easy to remember, or
easy to type. Luckily, Spack has its own interface for using modules and dotkits.
^^^^^^^^^^^^^
Shell support
^^^^^^^^^^^^^
To enable additional Spack commands for loading and unloading module files,
and to add the correct path to ``MODULEPATH``, you need to source the appropriate
setup file in the ``$SPACK_ROOT/share/spack`` directory. This will activate shell
support for the commands that need it. For ``bash``, ``ksh`` or ``zsh`` users:
..code-block::console
@@ -42,73 +81,20 @@ For ``csh`` and ``tcsh`` instead:
..code-block::console
$ set SPACK_ROOT ...
$ source $SPACK_ROOT/share/spack/setup-env.csh
Note that in the latter case it is necessary to explicitly set ``SPACK_ROOT``
before sourcing the setup file (you will get a meaningful error message
if you don't).
..note::
You can put the source line in your ``.bashrc`` or ``.cshrc`` to
have Spack's shell support available on the command line at any login.
When ``bash`` and ``ksh`` users update their environment with ``setup-env.sh``, it will check for spack-installed environment modules and add the ``module`` command to their environment; This only occurs if the module command is not already available. You can install ``environment-modules`` with ``spack bootstrap`` as described in :ref:`InstallEnvironmentModules`.
Finally, if you want to have Spack's shell support available on the command line at
any login you can put this source line in one of the files that are sourced
at startup (like ``.profile``, ``.bashrc`` or ``.cshrc``). Be aware though
that the startup time may be slightly increased because of that.
----------------------------
Using module files via Spack
----------------------------
If you have shell support enabled you should be able to run either
``module avail`` or ``use -l spack`` to see what module/dotkit files have
been installed. Here is sample output of those programs, showing lots
==> pkg-config is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkg-config-0.29.2-ae2hwm7q57byfbxtymts55xppqwk7ecj
...
==> openmpi is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f
==> Installing arpack-ng
==> Using cached archive: /usr/local/var/spack/cache/arpack-ng/arpack-ng-3.5.0.tar.gz
==> Already staged arpack-ng-3.5.0-bloz7cqirpdxj33pg7uj32zs5likz2un in /usr/local/var/spack/stage/arpack-ng-3.5.0-bloz7cqirpdxj33pg7uj32zs5likz2un
==> No patches needed for arpack-ng
==> Building arpack-ng [Package]
==> Executing phase: 'install'
==> Error: RuntimeError: Unable to recursively locate netlib-lapack libraries in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-lapack-3.6.1-jjfe23wgt7nkjnp2adeklhseg3ftpx6z
RuntimeError: RuntimeError: Unable to recursively locate netlib-lapack libraries in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-lapack-3.6.1-jjfe23wgt7nkjnp2adeklhseg3ftpx6z
/usr/local/var/spack/repos/builtin/packages/arpack-ng/package.py:105, in install:
==> Warning: Spack was unable to fetch url list due to a certificate verification problem. You can try running spack -k, which will not check SSL certificates. Use this at your own risk.
==> Created package file: $SPACK_ROOT/var/spack/repos/builtin/packages/mpileaks/package.py
And Spack should spawn a text editor with this file:
@@ -192,29 +200,27 @@ Now when we try to install this package a lot more happens:
..code-block:: console
$ spack install mpileaks
...
==> libdwarf is already installed in SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libdwarf-20160507-er4jrjynul6uba7wiu5tasuj35roxw6m
==> dyninst is already installed in SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/dyninst-9.3.2-t7mau34jv3e76mpspdzhf2p2a6k7qubg
==> callpath is already installed in SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/callpath-1.0.4-ikbbkvfmsfmqzo624nvvrbooovf7egoc
==> Installing mpileaks
==> openmpi is already installed in /usr/workspace/wsa/legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/openmpi-2.0.1-5ee5j34c2y4kb5c3joygrgahidqnwhnz
==> callpath is already installed in /usr/workspace/wsa/legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/callpath-1.0.2-zm4pf3gasgxeibyu2y262suktvaazube
==> adept-utils is already installed in /usr/workspace/wsa/legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/adept-utils-1.0.1-7p7ezxwtajdglj6cmojy2vybjct4j4jz
==> Using cached archive: /usr/workspace/wsa/legendre/spack/var/spack/cache/mpileaks/mpileaks-1.0.tar.gz
==> Already staged mpileaks-1.0-eum4hmnlt6ovalwjnciaygfb3beja4gk in /usr/workspace/wsa/legendre/spack/var/spack/stage/mpileaks-1.0-eum4hmnlt6ovalwjnciaygfb3beja4gk
==> Already patched mpileaks
==> Building mpileaks [AutotoolsPackage]
==> Executing phase : 'autoreconf'
==> Executing phase : 'configure'
==> Error: ProcessError: Command exited with status 1:
24 checking dependency style of SPACK_ROOT/lib/spack/env/gcc/g++... gcc3
25 checking for SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc... SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc
26 Checking whether SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc responds to '-showme:compile'... yes
>> 27 configure: error: unable to locate adept-utils installation
checking dependency style of /usr/workspace/wsa/legendre/spack/lib/spack/env/gcc/g++... gcc3
checking for /usr/workspace/wsa/legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/openmpi-2.0.1-5ee5j34c2y4kb5c3joygrgahidqnwhnz/bin/mpicc... /usr/workspace/wsa/legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/openmpi-2.0.1-5ee5j34c2y4kb5c3joygrgahidqnwhnz/bin/mpicc
Checking whether /usr/workspace/wsa/legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/openmpi-2.0.1-5ee5j34c2y4kb5c3joygrgahidqnwhnz/bin/mpicc responds to '-showme:compile'... yes
configure: error: unable to locate ``adept-utils`` installation
checking dependency style of SPACK_ROOT/lib/spack/env/gcc/g++... gcc3
checking for SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc... SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc
Checking whether SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc responds to '-showme:compile'... yes
configure: error: unable to locate adept-utils installation
This gives us the output from the build, and it's fairly obvious that
mpileaks isn't finding its ``adept-utils`` package. Spack has
This gives us the output from the build, and mpileaks isn't
finding its ``adept-utils`` package. Spack has
automatically added the include and library directories of
``adept-utils`` to the compiler's search path, but some packages like
mpileaks can sometimes be picky and still want things spelled out on
@@ -292,26 +333,26 @@ From here we can manually re-run the build:
checking installation directory variables... yes
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for gcc... /usr/workspace/wsa/legendre/spack/lib/spack/env/gcc/gcc
checking for gcc... SPACK_ROOT/lib/spack/env/gcc/gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking dependency style of /usr/workspace/wsa/legendre/spack/lib/spack/env/gcc/g++... gcc3
checking for /usr/workspace/wsa/legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/openmpi-2.0.1-5ee5j34c2y4kb5c3joygrgahidqnwhnz/bin/mpicc... /usr/workspace/wsa /legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/openmpi-2.0.1-5ee5j34c2y4kb5c3joygrgahidqnwhnz/bin/mpicc
Checking whether /usr/workspace/wsa/legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/openmpi-2.0.1-5ee5j34c2y4kb5c3joygrgahidqnwhnz/bin/mpicc responds to '-showme:compile'... yes
checking dependency style of SPACK_ROOT/lib/spack/env/gcc/g++... gcc3
checking for SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc... SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc
Checking whether SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc responds to '-showme:compile'... yes
configure: error: unable to locate adept-utils installation
We're seeing the same error, but now we're in a shell where we can run
@@ -339,37 +380,35 @@ This is all we need for working mpileaks! If we install now we'll see:
..code-block:: console
$ spack install mpileaks
spack install mpileaks
...
==> Installing mpileaks
==> openmpi is already installed in /usr/workspace/wsa/legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/openmpi-2.0.1-5ee5j34c2y4kb5c3joygrgahidqnwhnz
==> callpath is already installed in /usr/workspace/wsa/legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/callpath-1.0.2-zm4pf3gasgxeibyu2y262suktvaazube
==> adept-utils is already installed in /usr/workspace/wsa/legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/adept-utils-1.0.1-7p7ezxwtajdglj6cmojy2vybjct4j4jz
==> Using cached archive: /usr/workspace/wsa/legendre/spack/var/spack/cache/mpileaks/mpileaks-1.0.tar.gz
==> Already staged mpileaks-1.0-eum4hmnlt6ovalwjnciaygfb3beja4gk in /usr/workspace/wsa/legendre/spack/var/spack/stage/mpileaks-1.0-eum4hmnlt6ovalwjnciaygfb3beja4gk
==> Already patched mpileaks
==> Building mpileaks [AutotoolsPackage]
==> Executing phase : 'autoreconf'
==> Executing phase : 'configure'
==> Executing phase : 'build'
==> Executing phase : 'install'
==> Using cached archive: SPACK_ROOT/var/spack/cache/mpileaks/mpileaks-1.0.tar.gz
We took a few shortcuts for this package that are worth highlighting.
Spack automatically detected that mpileaks was an Autotools-based package
when we ran ``spack create``. If this had been a CMake-based package we
would have been filling in a ``cmake_args`` function instead of
``configure_args``. If Spack hadn't been able to detect the build
system, we'd be filling in a generic install method that would manually
be calling build commands, such as is found in the ``zlib`` package:
There are some special circumstances in package that are worth highlighting.
Normally spack would have automatically detected that mpileaks was an
Autotools-based package when we ran ``spack create`` and made it an``AutoToolsPackage`` class (except we added the ``-t generic`` option to skip this). Instead of
a full install routine we would have just written:
@@ -394,18 +433,15 @@ configure line (output truncated for length):
..code-block:: console
$ spack install --verbose mpileaks stackstart=4
...
==> Installing mpileaks
==> openmpi is already installed in /usr/workspace/wsa/legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/openmpi-2.0.1-5ee5j34c2y4kb5c3joygrgahidqnwhnz
==> callpath is already installed in /usr/workspace/wsa/legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/callpath-1.0.2-zm4pf3gasgxeibyu2y262suktvaazube
==> adept-utils is already installed in /usr/workspace/wsa/legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/adept-utils-1.0.1-7p7ezxwtajdglj6cmojy2vybjct4j4jz
==> Using cached archive: /usr/workspace/wsa/legendre/spack/var/spack/cache/mpileaks/mpileaks-1.0.tar.gz
========================== 1 failed in 0.04 seconds ===========================
Due to ``pytest``'s detailed assertion introspection, only plain ``assert`` statements are used. See `getting-started <http://docs.pytest.org/en/latest/getting-started.html#our-first-test-run>`_ for more examples.
Features
--------
- Detailed info on failing `assert statements <http://docs.pytest.org/en/latest/assert.html>`_ (no need to remember ``self.assert*`` names);
- Rich plugin architecture, with over 150+ `external plugins <http://docs.pytest.org/en/latest/plugins.html#installing-external-plugins-searching>`_ and thriving community;
Documentation
-------------
For full documentation, including installation, tutorials and PDF documents, please see http://docs.pytest.org.
Bugs/Requests
-------------
Please use the `GitHub issue tracker <https://github.com/pytest-dev/pytest/issues>`_ to submit bugs or request features.
Changelog
---------
Consult the `Changelog <http://docs.pytest.org/en/latest/changelog.html>`__ page for fixes and enhancements of each version.
License
-------
Copyright Holger Krekel and others, 2004-2016.
Distributed under the terms of the `MIT`_ license, pytest is free and open source software.
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