This commit fixes a subtle bug that may occur when
a package is a "possible_provider" of a virtual but
no "provides_virtual" can be deduced. In that case
the cardinality constraint on "provides_virtual"
may arbitrarily assign a package the role of provider
even if the constraints for it to be one are not fulfilled.
The fix reworks the logic around three concepts:
- "possible_provider": a package may provide a virtual if some constraints are met
- "provides_virtual": a package meet the constraints to provide a virtual
- "provider": a package selected to provide a virtual
Spack packages can now fetch versions from CVS repositories. Note
this fetch mechanism is unsafe unless using :extssh:. Most public
CVS repositories use an insecure protocol implemented as part of CVS.
Here we are adding an install_times.json into the spack install metadata folder.
We record a total, global time, along with the times for each phase. The type
of phase or install start / end is included (e.g., build or fail)
Signed-off-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: vsoch <vsoch@users.noreply.github.com>
The original implementation of `flag_handler` searched the
`self.compiler.cc` string for `clang` or `gcc` in order to add a flag
for those compilers. This approach fails when using a spack-installed
compiler that was itself built with gcc or clang, as those strings will
appear in the fully-qualified compiler executable paths. This commit
switches to searching for `%gcc` or `%clang` in `self.spec`.
Co-authored-by: Paul Henning <phenning@lanl.gov>
the 4.1.1 release has fixes for problems that kept 4.1.0 from
being the default open mpi version to build using spack.
related to #24396
Signed-off-by: Howard Pritchard <hppritcha@gmail.com>
* remove blueos check on cuda variant, fix typo
* restore necessary compiler guard
* remove axom+cuda from testing because it only partially works outside ppc systems
This PR does the following:
- adds version corresponding to commit at 08/03/2020
- adds missing get_DE_events.py script
- adds dependencies needed by get_DE_events.py
- removes REDItoolDenovo.py.patch and python2to3.patch in favor of
running 2to3 and reindent pre-build
- add batch_sort.patch to handle differences in string/char handling
betweeen python2 and python3
- adds a variant for the Nature Protocol
- adds dependencies for the nature_protocol variant
- added myself as maintainer
This PR adds a new version of reditools from git.
This PR fixes a couple of issues with the opencv package, mostly in
relation to cuda. This is only focused on cuda, not any of the other
variants.
- Added versions to the contrib_vers list. Added for all that can be
retrieved from github. The one for the latest version was missing.
- Added a cmake patch for v3.2.0.
- Deprecated versions 3.1.0 and 3.2.0 as neither of those could be
built, with or without cuda.
- Adjusted constraints on applying initial cmake patch.
- Added cudnn dependency when +cuda.
- Set constraints for cudnn and cuda for older versions of opencv.
* New package: py-pyusb
Change-Id: I606127858b961b5841c60befc5a8353df0f9f38c
* fixup dependencies
Change-Id: I0c9b0ccee693d2c4e847717950d4ce64cb319794
* fixup 2
Change-Id: Ibaccbdafd865e363564f491054e4e4ceb778727b
* Update var/spack/repos/builtin/packages/py-pyusb/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
A patch no longer applies cleanly as its fixed in v4.0.6 - fix it here
==> Installing openmpi-4.0.6-in47f6rxspbnyibkdx6x4ekg6piujobd
==> No binary for openmpi-4.0.6-in47f6rxspbnyibkdx6x4ekg6piujobd found: installing from source
==> Fetching https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.6.tar.bz2
Reversed (or previously applied) patch detected! Assume -R? [n]
Apply anyway? [n]
2 out of 2 hunks ignored -- saving rejects to file opal/include/opal/sys/gcc_builtin/atomic.h.rej
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
The Z3 solver provides a Z3Config.cmake file when built using the CMake build
system. This submission changes the package build system to inherit the
CMakePackage type. In addition to changing the build system, this submission:
- Adds the GMP variant
- Removes v4.4.0 and v4.4.1 as CMake was implemented starting with v4.5.0
This adds a package for `irep`, a tool for reading `lua` input decks from
Fortran, C, and C++.
`irep` can be built with either `lua` or `luajit`. To address this, we also add
a virtual package for lua called `lua-lang`. `luajit` isn't, by default, a drop-in
replacement for `lua`, but we add a `+lualinks` variant to it that adds symlinks
that make it behave like `lua@5.1`. With this variant enabled, it provides the
`lua-lang` virtual. `lua` always provides `lua-lang`.
- [x] add `irep` package
- [x] add `+lualinks` variant to `lua-luajit`
- [x] create `lua-lang` virtual, provided by `lua` and `luajit+lualinks`
Co-authored-by: Kayla Richarda Butler <butler59@quartz1148.llnl.gov>
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
* libdrm: fix one configure error and require libpciaccess
Failure with `LIBS`: the linker can't find `-lrt` so configure fails on
darwin-bigsur %apple-clang@12.0.5
```
>> 22 configure: error: in `/private/var/folders/gy/mrg1ffts2h945qj9k29s1l1dvvmbqb/T/s3j/spack-s
tage/spack-stage-libdrm-2.4.100-ofhk6m25n2pi427ihnxmvjkfmgyzlrqc/spack-src':
>> 23 configure: error: C compiler cannot create executables
24 See `config.log' for more details
See build log for details:
/var/folders/gy/mrg1ffts2h945qj9k29s1l1dvvmbqb/T/s3j/spack-stage/spack-stage-libdrm-2.4.100-ofhk6m25n2pi427ihnxmvjkfmgyzlrqc/spack-build-out.txt
```
* libpciaccess: Mark conflict with darwin
```
make[2]: *** [common_init.lo] Error 1
make[2]: *** Waiting for unfinished jobs....
common_interface.c:75:10: fatal error: 'sys/endian.h' file not found
^~~~~~~~~~~~~~
```
and
```
common_init.c:73:3: error: "Unsupported OS"
```
and others
* update url, add all new versions and fix installation
* add wxparaver package and set the old paraver package as deprecated
* remove update of deprecated package
* remove old version from new wxparaver
* Update url
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
xfsprogs currently does not install with error message:
FATAL ERROR: could not find a valid ini.h header.
Adding this package libinih, and including it as
a dependency for xfsprogs seems to fix the issue. It could be
that we only need to add it for newer versions (if it worked before)
and maybe a maintainer can comment on that.
Signed-off-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: vsoch <vsoch@users.noreply.github.com>
Pagination on Github prevent spack from easily parse all available
versions. Also, due to recent migration to GitHub, tarballs for
versions up to 3.12.13 have be regenerated, changing the hash.
The current URL will apparently be supported, so we keep it, and give
the alternative one as a comment.
This should fix#24278
$INSTALLDIR/lib/python3.7/site-packages/IPython/core/events.py contains an
import from backcall even in @7.3.0, so dependency on py-backcall needs
to start earlier.
Restrict poppler version for texlive to poppler@:0.84
Should fix#19946
See also https://github.com/NixOS/nixpkgs/issues/79170
Looks like poppler@0.84 upgraded their header files to use the C++ cstdio
instead of the C stdio.h. Since TeX is using C, not C++. this causes problems.
* zfp: several package improvements
- add variants for build targets, language bindings, backends
- ensure selected variants are compatible with zfp version
- point to GitHub (not LLNL) tar balls
- add dependencies
- update link to homepage
- add maintainers
* zfp: address suggestions by Spack team
- use conflicts() instead of raising exceptions
- use define() and define_from_variant() where applicable
* Apply suggestions from code review
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* Fix ZFP OpenMP build.
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* [py-keyboard] created template
* [py-keyboard]
- updated homepage
- added dependency for OSX
- added description
- removed fixmes
* [py-keyboard] Until py-pyobjc can be created, specifying conflict with platform=darwin
* [py-keyboard] is verb
* Update of Flecsi Spackage
Update of flecsi spackage to reconcile differences between flecsi@1:1.9
and flecsi@2: for future support purposes
* Removing Unnecessary Conditional
Removing unused conditional. Initially the plan was to switch based on
version in `cmake_args` but this was not necessary as build system
variable names remained mostly the same and conflicts prevent the rest.
For the most part, if a variant is there it does not need to check
against what version of the code is being built.
* Updated CI To Reconcile Flecsi Changes
Updated CI to target flecsi@1.4.2 which best matches the previous
release version and reconciled change in variant name
The common.inc script in TBB uses the environ var 'OS' to determine
the platform it's on. On Linux, this is normally empty and TBB falls
back to uname. But some systems set this to 'CentOS Linux 8' which is
descriptive, but not exactly what common.inc is looking for.
Instead, take the value from python and explicitly set OS to what TBB
expects to avoid this problem.
Since the two packages share a common history, the installation
procedure has been factored into a common base class.
Signed-off-by: vsoch <vsoch@users.noreply.github.com>
* Tcl: fix TCLLIBPATH
* Fix TCL|TK|TIX_LIBRARY paths
* Fix TCL_LIBRARY, no tcl8.6 subdir
* Don't rely on os.listdirs sorting
For tcl and tk, we also install the source directory, so there are
two init.tcl and tk.tcl locations. We want the one in lib/lib64,
which should come before the one in share.
* Add more patches
* Fix dylib on macOS
* Tk: add smoke tests
* Tix: add smoke test
Minimizing compiler mismatches in the DAG and preferring newer
versions of packages are now higher priority than trying to use as
many default values as possible in multi-valued variants.
According to the docs, r is needed for plotting, but plotting is
untested. In addition, the specific version requirement of java for gatk
could lead to multiple installations of r being triggered in an
environment. That might cause people to have to be deliberate about
java in a deployment. All in all, it seems that r is better as a
variant for gatk.
* Set job_id for SGE in darshan-runtime package
* Use a multi value variant for scheduler
Only one scheduler can be selected so make the variant multi valued and
set multi=False.
* hdf-eos5: Fix issue when linking against hdf5+szip (#23411)
Should fix issue #23411 when linking against hdf5+szip
Also fix bug if hdf5 does not depend on zlib
Reluctantly added payerle as a maintainer
Added version 1.1.13
Fixed versions for dependencies based on README.md for package
In particular:
* versions 1.1.x require python@3, at least 3.4 and for 1.1.13 at least 3.6
* py-osqp had been pinned to version 0.4.1, but README.md either shows
no version restriction, of 0.4.1 and higher
* @1.1.13 requires at least 1.1.6 of py-scs
* I am assuming since 1.1.x is python@3 only, py-six no longer required
(it was not explicitly showing up in README.md for these versions)
* add versions 2.2.0.2 and 2.2.1.1
* Add maintainer
Added Ishaan as additional maintainer as he is also maintainer of the Python bindings
* add new major precice version as dependency
* New Package:py-haphpipe@1.0.3
* removed llvm restrict. & changed freebayes
* Style fix
* Removed pip, wheel, added url for deps list
* used proper gsutil naming
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* url src for deps, samtools fix
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* petsc: add hip variant
* libceed: add 0.8, disable occa by default, and let autodetect AVX
Disabling OCCA because backend updates did not make this release and
there are some known bugs so most users won't have reason to use OCCA.
https://github.com/CEED/libCEED/pull/688
* WIP: ceed: 4.0 release
* MFEM package updates (#19748)
* MFEM package updates
* mfem: flake8
* [mfem] Various fixes and tweaks.
[arpack-ng] Add a patch to fix building with IBM XL Fortran.
[libceed] Fix building with IBM XL C/C++.
[pumi] Add C++11 flag for version 2.2.3.
* [mfem] Fix the shared CUDA build.
Reported by: @MPhysXDev
* [mfem] Fix a TODO item
* [mfem] Tweak the AmgX dependencies
* [suite-sparse] Fix the version of the mpfr dependency
* MFEM: add initial HIP support using the ROCmPackage.
* MFEM: add 'slepc' variant.
* MFEM: update the patch for v4.2 for SLEPc.
* mfem: apply 'mfem-4.2-slepc.patch' just to v4.2.
* ceed: apply 'spack style'
* [mfem] Add a patch for mfem v4.2 to work with petsc v3.15.0.
[laghos] Add laghos version 3.1 based on the latest commit in
the repository; this version works with mfem v4.2.
[ceed] For ceed v4.0 use laghos v3.1.
* [libceed] Explicitly set 'CC_VENDOR=icc' when using 'intel'
compiler.
* [mfem] Allow pumi >= 2.2.3 with mfem >= 4.2.0.
[ceed] Use pumi v2.2.5 with ceed v4.0.0.
* [ceed] Explicitly use occa v1.1.0 with ceed v4.0.0.
Use mfem@4.2.0+rocm with ceed@4.0.0+mfem+hip.
* [ceed] Add NekRS v21 as a dependency for ceed v4.0.0.
* [ceed] Fix NekRS version: 21 --> 21.0
* [ceed] Propagate +cuda variant to petsc for ceed v4.0.
* [mfem] Propagate '+rocm' variant to some other packages.
* [ceed] Use +rocm variant of nekrs instead of +hip.
* [ceed] Do not enable magma with ceed@4.0.0+hip.
* [libceed] Fix hip build with libceed@0.8.
* [laghos] For v3.1, use the release .tar.gz file instead of commit.
* Remove cuda & hip variants as they are inherited
* [ceed] Remove comments and FIXMEs about 'magma+hip'.
* [ceed] [libceed] Remove TODOs about occa + hip.
* libceed: use ROCmPackage and +rocm
* petsc: use ROCmPackage for HIP
* libceed, petsc: use CudaPackage
* ceed: forward cuda_arch and amdgpu_target
* [mfem] Use Spack's CudaPackage as a base class; as a result,
'cuda_arch' values should not include the 'sm_' prefix.
Also, propagate 'cuda_arch' and 'amdgpu_target' variants
to enabled dependencies.
* petsc: variant is +rocm, package name is hip
Co-authored-by: Jed Brown <jed@jedbrown.org>
Co-authored-by: Thilina Rathnayake <thilinarmtb@gmail.com>
1. add version 2021.05.15.
2. add patch to build old revs with gcc 11.x, version 2021.15.05
already has patch integrated, fixes#23667.
3. add variant +debug to build unoptimized, debug version.
4. add variant +viewer to include hpcviewer and add viewer path to
hpctoolkit module.
5. add dependency on memkind to workaround a glibc problem found on
some Cray platforms.
* py-lxml: add 4.6.3
Also add missing libxml2 and libxslt versions dependencies [1]
[1] https://github.com/lxml/lxml/blob/lxml-4.6.3/INSTALL.txt
* Update var/spack/repos/builtin/packages/py-lxml/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-lxml: remove cython dependency again
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* qt: skip multimedia when ~opengl
On 5.9 on macOS the multimedia option causes build errors; on other
platforms and versions it should probably be assumed inoperative anyway.
* qt: Omit flags when disabling multimedia
```
ERROR: Unknown command line option '-no-pulseaudio'.
```
* Work around another qt@5.9 error
* qt: Fix build error on darwin
* New Package:py-ucsf-pyem
* Dep additions, eun env deletion
* extraction step change
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* New Package: py-retry-decorator
* pypi link correction
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* embree: allow for compiling with gcc 7.3
strip out unsupported -mprefer-vector-width=256
* embree: fix build on AMD CPUs
The ISAs that embree is compiled for have to match the CPU
features enabled by the compiler, as embree derives theISA
that it compiles for from the latter.
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* New Package: py-google-apitools
* proper python constraints
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* New package:py-coveralls
* dep fixes
* added python constraint
* pyyaml version constraint
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
This also fixes the build with %gcc@11:. According to upstream, the
proper solution is to disable -Werror=array-bounds since the stable
branch will not receive a patch for newer compilers.
* Update py-pint and fix runtime dependency on setuptools
Without the runtime dependency on setuptools, importing pint yields:
0.11:
ModuleNotFoundError: No module named 'pkg_resources'
0.17:
ModuleNotFoundError: No module named 'packaging'
* Fix
* Address comments
Currently if one package does `depends_on('pkg default_library=shared')`
and another does `depends_on('pkg default_library=both')`, you'd get a
concretization error.
With this PR one package can do `depends_on('pkg default_library=shared')`
and another depends_on('default_library=static'), and it would concretize to
`pkg default_library=shared,static`
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
