* Several tests can be enabled on Windows with no changes to logic
(either the test logic or logic being tested)
* Test for `spack location` requires modification of the test logic,
but with a minor change can be enabled on Windows
using self.compiler.cc_pic_flag here results in these errors:
==> sqlite: Executing phase: 'install'
==> Error: AttributeError: 'AutotoolsBuilder' object has no attribute 'compiler'
change it to self.pkg.compiler.cc_pic_flag instead.
* imoroved-rdock: new test API
* Make test subpart names and or descriptions more accurate
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* e4s ci: enable some disabled specs
* comment out cp2k +cuda due to unsupported cuda_arch
* comment out dealii+cuda due to concretize error
* work through concretize errors
* e4s: comment out failing builds
* e4s stack: disabled non-building specs
* comment out failing specs
* comment out failing specs
* cleanup comments
* rust: rework external find to require both rustc and cargo
* rust: handle unable to parse version
* [@spackbot] updating style on behalf of wdconinc
* rust: not x or not y -> not (x and y)
Co-authored-by: Alec Scott <hi@alecbcs.com>
* rust: pick first rustc found
Co-authored-by: Alec Scott <hi@alecbcs.com>
* rust: list comprehensions
Co-authored-by: Alec Scott <hi@alecbcs.com>
---------
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
Co-authored-by: Alec Scott <hi@alecbcs.com>
* libmesh: add missing v1.7.1 release
* libmesh: avoid pulling in petsc if only +mpi or +metis is given
* libmesh: add shared variant
Co-authored-by: rbberger <rbberger@users.noreply.github.com>
The "use_store" context manager is used to swap the value
of a global variable (spack.store.STORE), while keeping
another global variable consistent (spack.config.CONFIG).
When doing that it tries to evaluate the previous value
of the store, if that was not done already. This is wrong,
since the configuration might be in an "intermediate" state
that was never meant to trigger side effects.
Remove that operation, and add a unit test to
prevent regressions.
Add language dependencies `c`, `cxx`, and `fortran`.
These `depends_on` statements are auto-generated based on file extensions found
in source tarballs/zipfiles.
The `# generated` comment can be removed by package maintainers after
validating correctness.
* detray: new package
This commit adds the detray package, a detector description library for
HEP experiments that is designed to be GPU-friendly.
* Update var/spack/repos/builtin/packages/detray/package.py
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
* Update var/spack/repos/builtin/packages/detray/package.py
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
---------
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
* vasp: add new version 6.4.3 and rework package
* vasp: remove redundant cuda dep
* vasp: bump fftlib variant version restriction
* vasp: honor the still existing scalapack variant
---------
Signed-off-by: Shane Nehring <snehring@iastate.edu>
Since the the MetaPathFinder now owns a lazily constructed RepoPath object, we need to deserialize environments before the package that needs to be restored. Before we were relying on globals to be inconsistent in a way that let the entire process go.
The patch which enables icx/ifx compilers is only added for `wrf@4.4:`. This PR prints a useful message at concretization time instead of failing the installation later on.
Co-authored-by: stephenmsachs <stephenmsachs@users.noreply.github.com>
* slate: changed from old to new format
* make code tighter
* replace assert method
* SkipTest plus other cleanup
---------
Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
* vecmem: add infrastructure for working with SYCL
The vecmem package uses an unorthodox build system where, instead of
expecting a SYCL-capable compiler in the `CXX` environment variable, it
expects one in `SYCLCXX`. It also needs the correct SYCL flags to be
set. This commit adds a custom build environment for the vecmem package
which allows it to be built in this way. I've also added an extra CMake
flag to ensure that the build system doesn't download any unwanted
dependencies.
* Update var/spack/repos/builtin/packages/vecmem/package.py
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
---------
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
- Add explicit conflict on ppc64le for 12.5 and newer.
- Update/fix intel compiler conflict to reflect that intel@2021 is compatible
only since 11.4.1 and not since 11.1.1.
- Add intel compiler conflicts to reflect strict support matrix since
12.2.0.
As discussed in https://github.com/spack/spack/pull/44881#issuecomment-2218411735 a `spack install py-globus-cli` fails to concretize on an Ubuntu 22.04 under Windows WSL2 because of too strict of explicit dependencies.
Let's try to remove them here (since these are "just in case" and in all honesty should be handled by `py-globus-sdk` anyways).
* Now builds with latest fmt release (11.0.1)
* Missing array include in nem_spread
* Fix timestep conssitency check in file-per-rank case if one or more dbs have no timesteps.
If an external happens to be a provider of anything, the solver would
set its weight to 0, meaning that it is most preferred, even if
packages.yaml config disagrees.
That was done so that `spack external find mpich` would be sufficent to
pick it up as mpi provider.
That may have made sense for mpi specifically, but doesn't make sense
for other virtuals. For example `glibc` provides iconv, and is an
external by design, but it's better to use libiconv as a separate
package as a provider.
Therefore, drop this rule, and instead let users add config:
```
mpi:
require: [mpich]
```
or
```
mpi:
buildable: false
```
which is well-documented.
This change makes `spack external find --not-buildable` mark virtuals
provided by detected packages as non-buildable, so that it's sufficient
for users to let spack detect say mpich and have the concretizer pick it
up as mpi provider even when openmpi is "more preferred".
Consistently with ArmPL@24:, the include directory for acfl@24:
has changed to include. The change wants to update to this change
and distinguish the include path for releases previous to 24.04
and the future ones
* rocm-cmake: changed test format from old to new
* Rename cmake variable
* post-conflict resolution: remove remaining version check
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* Added Release 0.0.4 and 0.0.5
* Changed requirement for gotcha
use gotcha 1.0.5 for 0.0.2 and 0.0.3
* Combine gotcha 1.0.7 for master and develop
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
in case of inheritance the static tags prop may be updated multiple
times, and it turns out builder classes magically inherit from
traditional package classes
While trying to build packages with the OneAPI compiler version 2024.1 I
ran into the following error, indicating that the compiler is unable to
find some necessary libraries:
```
/storage/Software/oneapi/2024.1/compiler/2024.1/bin/sycl-post-link: error
while loading shared libraries: libonnxruntime.1.12.22.721.so: cannot open
shared object file: No such file or directory
icpx: error: unable to execute command: No such file or directory
icpx: error: sycl-post-link command failed due to signal (use -v to see
invocation)
```
Indeed, `libonnxruntime.1.12.22.721.so` does come bundled with the
OneAPI compiler, but it is not available in the build environment by
default. In this commit, I update the custom environment created by
OneAPI to include the `lib/` directory in which these libraries reside
in the `LD_LIBRARY_PATH` environment variable.
In my enthusiasm to add dfelibs to Spack, I didn't realise that the
unit tests of dfelibs use Boost and, as such, Boost is required as a
testing dependency.
Originally if you had `x -> y -> z`, and an env with `x` in its speclist that is concretized but not installed, then `spack find -c y` would not show anything. This was intended: `spack find` has up-until-now only ever listed out installed specs (and `-c` was for adding a preamble section about roots).
This changes `spack find` so:
* `-c` makes it search through all concretized specs in the env (in a sense it is anticipated that a concretized environment would serve as a "speculative" DB and users may want to query it like they query the DB outside of envs)
* Adds a `-i/--install-status` option, equivalent to `-I` from `spack spec`
* Shows install status for either `-c` or `-i`
* As a side effect to prior point, `spack find -i` can now distinguish different installation states (upstream/external)
Examples:
```
$ spack find -r
==> In environment findtest
==> 1 root specs
- raja
==> 6 installed packages (not shown)
==> 12 concretized packages to be installed (not shown)
```
```
$ spack find
==> In environment findtest
==> 1 root specs
- raja
-- darwin-ventura-m1 / apple-clang@14.0.3 -----------------------
berkeley-db@18.1.40 bzip2@1.0.8 diffutils@3.10 gmake@4.4.1 gnuconfig@2022-09-17 libiconv@1.17
==> 6 installed packages
==> 12 concretized packages to be installed (show with `spack find -c`)
```
```
$ spack find -c
==> In environment findtest
==> 1 root specs
- raja
-- darwin-ventura-m1 / apple-clang@14.0.3 -----------------------
[+] berkeley-db@18.1.40 [+] bzip2@1.0.8 - cmake@3.29.4 [+] diffutils@3.10 [+] gmake@4.4.1 [+] libiconv@1.17 - nghttp2@1.62.0 - pkgconf@2.2.0 - readline@8.2
- blt@0.6.2 - camp@2024.02.1 - curl@8.7.1 - gdbm@1.23 [+] gnuconfig@2022-09-17 - ncurses@6.5 - perl@5.38.2 - raja@2024.02.2 - zlib-ng@2.1.6
==> 6 installed packages
==> 12 concretized packages to be installed
```
$ spack -E find
...
==> 82 installed packages
```
* Add py-datasets version 2.20.0
* Add dependency requirements for version 2.20 + refactor
* Add missing tqdm and requests versions and to install latest py-datasets
* Add missing python requirements for 2.8.0 and 2.20.0
Fix a bug where Spec.tree with cover=nodes reduces deptypes from all
in-edges, including from nodes not reachable from the root, which almost
always happens for concrete specs
`Spec.__getitem__` queries dependent edges, which almost always point to
nodes outside the sub-dag considered. It should only ever look at edges
being traversed.
When using a newer Clang for Kokkos than supported by a given CUDA version, the
CUDA compiler detection in Legion's CMake still needs to be passed
CMAKE_CUDA_FLAGS to pass the compiler check.
This modifies heuristic to decay to clingo default
over time. The hope is that this helps with specs
that have an optimal solution with a high penalty.
Let target and compiler heuristic decay too, do not
guess compiler
* dfelibs: new package
This commits adds the `dfelibs` package, which is an Acts project fork
of dfelibs.
* dfelibs: docstring typo
---------
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
Add MatrixSwitch package
Add libOMM package
Use libOMM as external in ELSI
Add include paths for all libraries
Fortran modules need one directory up (can't use libs.directories since they are just the include/ directories)
This addresses a few issues in the kentutils package:
- Issue #44372
- Cleaning up formattting and styles
- Removing old versions that are not avaialble anymore
- Removing newer versions that are also not available anymore
- The installer does not install the static libs
that are expected by packages that depend on kentutils
- There are conflicts and less-than-desirable dependencies
that can be addressed via variants
Signed-off-by: Teague Sterling <teaguesterling@gmail.com>
* Bumping up to ROCm 6.1.2
* Bump up rocmlir & amdsmi to 6.1.2
* Removing llvm dependency from amdsmi
* Removed redundant for loops and brought rocm-cmake in for loop
* Removing version check of deprecated versions
This adds spack.util.spack_yaml.anchorify, which takes a non-cyclic
dict/list structure, and replaces identical values with (back)
references to the first instance, so that yaml serialization will use
anchors.
`repr` is used to identify sub-dags, which in principle is quadratic
complexity in depth of the graph, but in practice the depth is O(1) so
this should not matter.
Then this is used in CI to reduce the size of generated YAML files to
30% of their original size.
* lammps: add new versions
* lammps: add directories for plugins
* lammps-example-plugin: new package
Example illustrating how to install a LAMMPS plugin, based on the
example part of the LAMMPS distribution.
If netlib-lapack is built with ~external-blas, it internally links
liblapack.so with libblas.so, meaning that whenever netlib-lapack is
used as a lapack provider, the package must also be a blas provider.
Conversely using netli-lapack as a blas provider does not imply that it
also must provide lapack, but nothing is lost disallowing that...
In practice people don't care about having their build dependencies reinstalled with say cflags=-O3 if that is what is set at the input spec, so restrict propagation to link/run deps only.
Also simplify the encoding in asp.
* Changed test method from old method to new method
* Corrected test name and added docstring
* Split test method into stand alone-tests
* Added SkipTest
* code refactor
* removed repeated code
* Remove exe from test part purpose
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* Improve proj version selection to avoid too new of a proj with older api usage in vtk9
* Proj constraint range around 8.2.1
---------
Co-authored-by: John Parent <john.parent@kitware.com>
Fix the following on Windows:
* `spack load --list` (this printed 0 packages even if packages were
loaded)
* `spack unload <package>` (this said that the package is not loaded
even if it was)
Update unit tests for `spack load` to also run on Windows (specifically
for ".bat"). This involved refactoring a few tests to parameterize
based on whether the unit tests are being run on a Windows system
(and to account for batch syntax).
* Adding additional versions to plink2 and switching to tarballs to allow for better version detection in the future
---------
Signed-off-by: Teague Sterling <teaguesterling@gmail.com>
The pcluster pipeline runs spack external find and autodetects the most ancient of zlib versions on the system: 1.2.7, release date May 3, 2012.
Turns out some packages require parts of the zlib api added within the last decade.
* update e4s stacks
* adios2 +rocm: disable kokkos due to spack issue #44832
* comment out mgard+cuda due to spack issue #44833
* comment out cabana, legion, arborx due to kokkos spack issue #44832
* comment out slepc, petsc due to petsc spack issue #44600
* comment out adios2+rocm due to kokkos rocm spack issue #44832
* comment out kokkos due to spack issue #44832
When we changed how to deal with errors in November,
we didn't realize that for an unconstrained choice
rule it is more important in the heuristic to guess
what is NOT in the answer set, since it will be the
majority of options.
Previously this was following automatically from what
was in the answer set, via `1 { ... } 1` cardinality
constraints.
Here we improve the heuristic and the solve time for specs.
* Patched CMakeLists.txt to find drm include at libdrm - archlinux
* Restricted usage patch to versions 34 onwards
* Update var/spack/repos/builtin/packages/rdma-core/libdrm.patch
---------
Co-authored-by: Mark Abraham <Mark.J.Abraham@gmail.com>
* Spglib: add version 2.4.0
* DLA-Future: fix +test option
* elsi
* elsi improvements
* [@spackbot] updating style on behalf of RMeli
* remove test variants
* fix ntpoly and and use externals as default
---------
Co-authored-by: RMeli <RMeli@users.noreply.github.com>
* py-multiqc: updating to @1.21, adding new dependency py-pyyaml-env
* Correcting dependencies
* Drop matplotlib depends_on() for versions of multiqc not included in package.py
---------
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
* Allow zlib to find external installations.
* Apply suggestions from code review
* Fixed the determine_version function to loop over all of the potential
libraries that could be installed by zlib.
---------
Co-authored-by: John W. Parent <45471568+johnwparent@users.noreply.github.com>
* Update hohqmesh and feq-parse versions
Update feq-parse homepage to new documentation page
Update feq-parse license to be consistent with 2.2.2 release
---------
Co-authored-by: fluidnumerics-joe <fluidnumerics-joe@users.noreply.github.com>
This commit adds new versions of actsvg. I have also taken the liberty
of adding myself a maintainer as I work actively on the ACTS project and
its dependencies, and would like to start keeping the Spack specs more
up to date.
* e4s external rocm ci: bump rocm stack to v6.1.1
* comment out exago+rocm due to issue with raja@0.14.0 see spack issue #44593
* comment out adios2+rocm due to spack issue #44594
* comment out petsc+rocm due to spack issue #44600
* comment out sundials+rocm due to spack issue #44601
* comment out slepc+rocm due to petsc spack issue #44600
* comment out tau+rocm due to spack issue #44659
* comment out ecp-data-vis-sdk due to spack issue #44745
* packages: register rocm-core as external
* re-enable tau due to issue #44659 having been resolved
* use latest ci image: ecpe4s/ubuntu22.04-runner-amd64-gcc-11.4-rocm6.1.1:2024.06.17
* comment out paraview due to spack issue #44745
* comment out ecp-data-vis-sdk +vtkm due to issue https://gitlab.spack.io/spack/spack/-/jobs/11632511
* Update for 2.0.1
* cloudpickle dependency is only 'run'
* Follow new formatting guidelines
* black wants trailing commas
* Simplified version ranges, as recommended by @tldahlgren
* vtk-m: Changed test method names and skipping non-applicable tests from old to new approach
-----
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* add cray detection taken from upcxx
* add CUDA/ROCm support
* add numerous pass-through options to Chapel build,
like gpu_mem_strategy, comm_substrate, etc.; all variants are
translated to analogous CHPL_* environment variables. As a side
effect, this defines a number of environment variables that are
not actually used by Chapel.
* Define LD_LIBRARY_PATH, LIBRARY_PATH, and PKG_CONFIG_PATH to
help programs built with Chapel properly locate needed runtime
dependencies
---------
Co-authored-by: bonachea <dobonachea@lbl.gov>
* Projsync needs curl
This fixes a proj compilation error from paraview
* tiff does not set TIFF_INCLUDE_DIR tested by proj
* TIFF patch exists for proj 9.2
* Add comments with location of proj patch
* Use TIFF patches for different cmake versions
* Use modules starting cmake 3.28 and variables before that
* Fix black style
* Simpler patches, add newer proj
* Remove duplicated flag
* Deprecate PROJ 4.8 and older
* Remove PRIVATE
* Deprecate PROJ 7.0.0
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Not sure why I had this here, as `/bin/sh` will find the first spack in `PATH` just like
`env`.
- [x] remove `/usr/bin/env` and avoid an extra process launch.
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
* omega-h: reformatted from old test method to new test method
* omega-h: added proper output checking
--------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
The ``+cluster` variant requires there be an MPI family known in the
spec. When using externals it is easy to miss-configure this requirement
leading to a runtime exception which is not desirable. This converts the
exception to a package rule.
* xorg libs: new versions
* xorg pkgs: update homepage from cgit to gitlab
* xorgs pkgs: fix homepage since, yeah, I did edit those 122 files by hand...
* libxmu: don't need the .0 patch version here
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* Fixed some issues with installation breaking due to mysql_client
* Remove debugging details
* Adding client_only to deps
* Adding client_only to variant and deps
* Undoingw client_only to variant and deps
* py-pyopengl: new simple package
* py-pyopengl: Fix typo in comment
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-pyopengl: add variants and dependencies
* py-pyopengl: build from source and improve variants
* py-pyopengl: use corrected freeglut libs
* py-pyopengl: update copyright
* py-pyopengl: remove duplicate conflict clause
* py-pyopengl: change dependency to link
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Core change: logic for extracting RPATHs from modules may return
`None`: filter this out of the set of RPATHs that is auto-generated
* Core change: `CachedCMakePackage` no longer adds ldflags to
`CMAKE_STATIC_LINKER_FLAGS`: generally these flags are not appropriate
for static linking (e.g. invocation of `ar`)
* [mfem] Add version 4.7
* [mfem] Add variant for precision (single/double). Enforce consistency
for precision amongst mfem and hypre/petsc/mumps dependencies
* [mfem] Add cxxstd (and related constraints preventing use of
old cxxstd values for newer versions of some dependencies)
* [hypre] In line with prior point, added support for specifying
precision
* [petsc] Add config option to avoid error when building against
`superlu-dist+rocm`
* [hiop] add proper `raja`/`umpire`/`camp` version constraints for
`hiop` versions 0.3.99-0.4.x; require `+raja` for `+rocm`, and
add dependency on `hiprand` for `+rocm`
* [butterflypack, mfem, strumpack, suite-sparse] Require
`CRAYLIBS_{target-family}` env var to be defined
* [suite-sparse] versions `@7.4:` changed install location of headers:
add symlink from old location to new location
* [zlib-ng] Fix error where shared libs were not successfully built for
`%cce@17` (the build did not fail, but the finished `zlib-ng%cce@17`
install did not have shared libs)
* suite-sparse library path can be lib or lib64
* fixing style check error
* Adding the missing import os
* Style check error fix
* Updating patch for 6.1.0 with correct lib path
* Preserve higher weight for CLI git ref versions
Currently the concretizer fails if you reuse a git ref version
that has already been installed but modify the spec at all.
See #38484 for futher diagnosis
The issue here is that since there is no established provenance for
these versions the highest weight they are currently assigned is
that of prior install. Re-use checks then fail because the weight of
the version is identical to the solver.
Ironically, these versions are given the highest weights possible when
specified on the CLI for the first time. They should only appear in a
DAG if they are an exact match or if the user specifies them at the CLI.
Therefore it makes sense to preserve their higher ordering.
Getting this right is critical to moving all branch based versions to a pinned
git-ref in the future.
* [@spackbot] updating style on behalf of psakievich
* Update lib/spack/spack/solver/asp.py
Co-authored-by: Greg Becker <becker33@llnl.gov>
* Add provenance specific to git ref installs
* Sensitvity to name that I could not track down
* Add regression test
* Adjust test
* Add prefer standard unit-test
* Style
* Add required mock
* Format and mark
* Make unit-test case reproduce CLI investigation
* Remove unnecessary mock package
* [@spackbot] updating style on behalf of psakievich
* Use already developed fixture
* Add zlib-ng to mocks again
* Remove accidental adds
* Remove maintainer
* [@spackbot] updating style on behalf of psakievich
* Rename test file
* [@spackbot] updating style on behalf of psakievich
* Remove unused imports
* Update tests
* [@spackbot] updating style on behalf of psakievich
* Style
* Update lib/spack/spack/test/concretize.py
Co-authored-by: Greg Becker <becker33@llnl.gov>
* Update solver rule
* Duplicate installed rules for installed_git_version
* Revert "Duplicate installed rules for installed_git_version"
This reverts commit 17223fc8d1.
---------
Co-authored-by: psakievich <psakievich@users.noreply.github.com>
Co-authored-by: Greg Becker <becker33@llnl.gov>
* libdistributed: renamed test to check_test
* libpressio-rmetric: renamed test method
* libpressio-tools: renamed test method
* Renamed build-time test methods for: libpressio-opt, libpressio-tthresh, opened
---------
Co-authored-by: Jackson Peter Lawrence <lawrence31@borax5.llnl.gov>
* Provide instructions for building a developmental version of lcov.
* style fix
* style fix
* Promote single version git URL to the package level.
* Formatting fix.
* verilator: Some environment varibles are no longer required
* Revert depends_on for flex back to the deafult case
* Use decorator, when, for setup_run_environment insdtead of if inside function
* libtiff: add v4.6.0 and default disable opengl (#44545)
* libtiff: Fix typo in CMake key
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* libtiff: Broader description of OpenGL variant
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* libtiff: reformat using spack style black recommendation
* libtiff: couple opengl flag with autotools
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
There hasn't been a release in almost a decade, and build failures with
GCC 14 were reported. I don't think it makes sense to patch it, since
the project moved over to `util-linux`, and Spack's default provider is
that package. Better to just get rid of it in the next Spack release.
* py-your: new package
Spack package recipe for YOUR, Your Unified Reader. YOUR processes pulsar data in different formats.
Output below from spack install py-your
spack install py-your
[+] /usr (external glibc-2.28-oj2wjfl2ao5inhfz4qehw6hlck2hizvp)
[+] /opt/apps/spack/gcc-runtime-8.5.0-5k6kvi5
[+] /opt/apps/spack/libxcrypt-4.4.35-zigqpjo
[+] /opt/apps/spack/ncurses-6.4-xbvwv2w
[+] /opt/apps/spack/erfa-2.0.0-4qkta2n
[+] /opt/apps/spack/zlib-ng-2.1.6-ccn5qny
[+] /opt/apps/spack/pcre-8.45-33dfhul
[+] /opt/apps/spack/libpciaccess-0.17-2qdxdjo
[+] /opt/apps/spack/libmd-1.0.4-zbdiprt
[+] /opt/apps/spack/qhull-2020.2-klc7ewb
[+] /opt/apps/spack/bzip2-1.0.8-t65bq3t
[+] /opt/apps/spack/xz-5.4.6-axoznvt
[+] /opt/apps/spack/alsa-lib-1.2.3.2-a7icjdy
[+] /opt/apps/spack/zstd-1.5.6-nyk6gt6
[+] /opt/apps/spack/libffi-3.4.6-ibucrfe
[+] /opt/apps/spack/yasm-1.3.0-v4etmmm
[+] /opt/apps/spack/openblas-0.3.26-pfyk2vi
[+] /opt/apps/spack/pkgconf-1.9.5-ckjdqjm
[+] /opt/apps/spack/wcslib-7.3-zvcqq7o
[+] /opt/apps/spack/libiconv-1.17-jskazis
[+] /opt/apps/spack/unzip-6.0-mqftjtp
[+] /opt/apps/spack/libjpeg-turbo-3.0.0-vjvivme
[+] /opt/apps/spack/readline-8.2-2ys6ede
[+] /opt/apps/spack/openssl-3.2.1-4lqdgni
[+] /opt/apps/spack/pigz-2.8-rx263bp
[+] /opt/apps/spack/libpng-1.6.39-kiuku4y
[+] /opt/apps/spack/libbsd-0.12.1-njt5grs
[+] /opt/apps/spack/swig-4.0.2-fortran-z3sbnze
[+] /opt/apps/spack/binutils-2.42-vkjcvfr
[+] /opt/apps/spack/util-linux-uuid-2.38.1-w3kgjq3
[+] /opt/apps/spack/hdf5-1.14.3-sbuiw6q
[+] /opt/apps/spack/libedit-3.1-20230828-676jwbd
[+] /opt/apps/spack/nghttp2-1.57.0-u72gxms
[+] /opt/apps/spack/ffmpeg-6.1.1-2vhrbda
[+] /opt/apps/spack/libxml2-2.10.3-37klvxv
[+] /opt/apps/spack/gdbm-1.23-cylmqwx
[+] /opt/apps/spack/sqlite-3.43.2-axuxulg
[+] /opt/apps/spack/tar-1.34-wjzs4wj
[+] /opt/apps/spack/freetype-2.13.2-in4taxi
[+] /opt/apps/spack/expat-2.6.2-7kfe3hb
[+] /opt/apps/spack/curl-8.6.0-gpzsr3p
[+] /opt/apps/spack/hwloc-2.9.1-fhoz6al
[+] /opt/apps/spack/gettext-0.22.4-zjsp346
[+] /opt/apps/spack/lua-5.3.6-47356ia
[+] /opt/apps/spack/cfitsio-3.49-mmy3dbr
[+] /opt/apps/spack/python-3.10.13-fz7fymx
[+] /opt/apps/spack/elfutils-0.190-uswzaiw
[+] /opt/apps/spack/py-pytz-2023.3-ojdlhrd
[+] /opt/apps/spack/py-cycler-0.11.0-b7mjvv7
[+] /opt/apps/spack/py-pip-23.0-lxkcvby
[+] /opt/apps/spack/python-venv-1.0-2cz5c3s
[+] /opt/apps/spack/py-numpy-1.26.4-t5acjcv
[+] /opt/apps/spack/llvm-14.0.6-3nosumn
[+] /opt/apps/spack/py-packaging-23.1-wkeyuk6
[+] /opt/apps/spack/py-six-1.16.0-iv6iv3q
[+] /opt/apps/spack/py-pybind11-2.12.0-5rvupjv
[+] /opt/apps/spack/py-setuptools-69.2.0-3do76jw
[+] /opt/apps/spack/py-pyparsing-3.1.2-fq6imlt
[+] /opt/apps/spack/py-wheel-0.41.2-brm3k3h
[+] /opt/apps/spack/py-llvmlite-0.41.1-qom3l5h
[+] /opt/apps/spack/py-astropy-4.0.1.post1-xbojixg
[+] /opt/apps/spack/py-python-dateutil-2.8.2-kzdfskc
[+] /opt/apps/spack/py-numexpr-2.8.4-fc5xc5s
[+] /opt/apps/spack/py-h5py-3.11.0-y6drk3j
[+] /opt/apps/spack/py-tifffile-2023.8.30-oof4try
[+] /opt/apps/spack/py-pygments-2.16.1-stgrccl
[+] /opt/apps/spack/py-mdurl-0.1.2-nqk43ry
[+] /opt/apps/spack/py-scipy-1.13.0-vxjgfov
[+] /opt/apps/spack/py-contourpy-1.0.7-jg5lhss
[+] /opt/apps/spack/py-pillow-10.3.0-ijh2cju
[+] /opt/apps/spack/py-kiwisolver-1.4.5-vdh5sq5
[+] /opt/apps/spack/py-fonttools-4.39.4-x5ydbox
[+] /opt/apps/spack/py-bottleneck-1.3.7-ztsm4lg
[+] /opt/apps/spack/py-lazy-loader-0.4-k7hgvka
[+] /opt/apps/spack/py-numba-0.58.1-hzvrjwj
[+] /opt/apps/spack/py-markdown-it-py-3.0.0-l4p4qv5
[+] /opt/apps/spack/py-imageio-2.34.0-z5hu4yc
[+] /opt/apps/spack/py-matplotlib-3.8.4-azq2fzm
[+] /opt/apps/spack/py-pandas-1.5.3-p3gnh6t
[+] /opt/apps/spack/py-rich-13.4.2-okhgwwz
[+] /opt/apps/spack/py-networkx-3.1-b54br7r
[+] /opt/apps/spack/py-scikit-image-0.23.2-cvyzh3t
==> Installing py-your-0.6.7-djfzsn2lutp24ik6wrk6tjx5f7hil76x [83/83]
==> No binary for py-your-0.6.7-djfzsn2lutp24ik6wrk6tjx5f7hil76x found: installing from source
==> Fetching https://github.com/thepetabyteproject/your/archive/refs/tags/0.6.7.tar.gz
==> No patches needed for py-your
==> py-your: Executing phase: 'install'
==> py-your: Successfully installed py-your-0.6.7-djfzsn2lutp24ik6wrk6tjx5f7hil76x
Stage: 1.43s. Install: 0.99s. Post-install: 0.12s. Total: 3.12s
* Removed setup_run_environment
After some testing, both spack load and module load for the package will include the bin directory generated by py-your as well as the path to the version of python the package was built with, without the need for the setup_run_environment function.
I removed that function (Although, like Tamara I thought it would be necessary based on other package setups I used as a basis for this package).
Note: I also updated the required version of py-astropy from py-astropy@4.0: to @py-astropy@6.1.0: In my test builds, the install was picking up version py-astropy@4.0.1.post1 and numpy1.26. However when I tried to run some of the code I was getting errors about py-astropy making numpy calls that are now removed. The newer version of py-astropy corrects these. Ideally this would be handled in the py-astropy package to make sure numpy isn't too new
#40773 introduced python-venv, which improved build isolation and avoids issues with,
e.g., `ubuntu`'s system python modifying `sysconfig` to include a (very unwanted)
`local` directory within the default install layout.
This addresses a few cases where #40773 removed functionality, without harming the
default cases where we use `python-venv`.
Traditionally, *every* view with `python` in it was essentially a virtual environment,
because we would copy the `python` interpreter and `os.py` into every view when linking.
We now rely on `python-venv` to do that, but only when it's used (i.e. new builds) and
only for packages that have an `extends("python")` directive.
This again makes every view with `python` in it a virtual environment, but only
if we're not already using a package like `python-venv`. This uses a different
mechanism from before -- instead of using the `virtualenv` trick of copying `python`
into the prefix, we instead create a `pyvenv.cfg` like `venv` (the more modern way
to do it).
This fixes two things:
1. If you already had an environment before Spack `v0.22` that worked, it would
stop working without a reconcretize and rebuild in `v0.22`, because we no longer
copy the python interpreter on link. Adding `pyvenv.cfg` fixes this in a more
modern way, so old views will keep working.
2. If you have an env that only includes python packages that use `depends_on("python")`
instead of `extends("python")`, those packages will now be importable as before,
though they won't have the same level of build isolation you'd get with `extends`
and `python-venv`.
* views: avoid making client code deal with link functions
Users of views and ViewDescriptors shouldn't have to deal with link functions -- they
should just say what type of linking they want.
- [x] views take a link_type, not a link function
- [x] views work out the link function from the link type
- [x] view descriptors and commands now just tell the view what they want.
* python: simplify logic for avoiding pyvenv.cfg in copy views
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
In #30882, we made Spack ignore `-Werror` calls so that it could more easily build
projects that inject `-Werror` into their builds. We did this by translating them to
`-Wno-error` in the compiler wrapper. However, some compilers (like `nvhpc`) do not
support `-Wno-error`. We need to exclude them from this feature until they do.
- [x] make a property on `PackageBase` for `keep_werror` that knows not to use it for
`nvhpc`.
- [x] update property so that it keeps only the specific `-Werror=...` args for newer nvhpc's,
which support `-Wno-error` but not `-Wno-error=...`
---------
Co-authored-by: William Mou <william.mou1024@gmail.com>
Co-authored-by: Tom Scogland <scogland1@llnl.gov>
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
When Spack concretizes environments, it prints every (newly concretized) root spec
individually with all of its dependencies. For most reasonably sized environments, this
is too much output. This is true for three commands:
* `spack concretize` when concretizing an environment with newly added specs
* `spack install` when installing an environment with newly added specs
* `spack spec` with no arguments in an environment
The output dates back to before we had unified environments or nicer spec traversal
routines, and we can improve it.
This PR makes environment concretization output analogous to what we do for regular
specs. Just like `spack spec` for a single spec, we show all root specs with no
indentation, so you can easily see the specs you explicitly requested. Dependencies are
shown:
1. With indentation according to their depth in a breadth-first traversal starting at
the roots;
2. Only once if they appear on paths from multiple roots
So, the default is now consistent with `spack spec` for one spec--it's `--cover=nodes`.
i.e., if there are 100 specs in your environment, you'll get 100 lines of output.
If you want to see more details, you can do that with `spack spec` using the arguments
you're already familiar with. For example, if you wanted to see dependency types and
*all* dependencies, you could use `spack spec -l --cover=edges`. Or you could add
deptypes and namespaces with, e.g. `spack spec -ltN`.
With no arguments in an environment, `spack spec` concretizes (if necessary) and shows
the concretized environment. If you run `spack concretize` *first*, inspecting the
environment repeatedly with `spack spec` will be fast, as everything is already in the
`spack.lock` file.
- [x] factor most logic of `Spec.tree()` out of `Spec` class into `spack.spec.tree()`,
which can take multiple specs as roots.
- [x] make `Spec.tree()` call `spack.spec.tree()`
- [x] `spack.environment.display_specs()` now uses `spack.spec.tree()`
- [x] Update `spack concretize`
- [x] Update `spack install`
- [x] Update `spack spec` to call `spack.spec.tree()` for environments.
- [x] Continue to output specs individually for `spack spec` when using
`--yaml` or `--json`
* Apply patch from upstream to allow vtk compilation with %gcc 12 and 14.
* Fixes#44331
* fix soec usage
* fix compiler version range
* Finalize version range, switch to .diff file
---------
Co-authored-by: Chrismarsh <Chrismarsh@users.noreply.github.com>
* Now need to explicitly depend on libfabric for Cray EX
* Ensure build uses the selected CUDA and ROCm versions
* Correct spelling on `configure --with-ldflags`
* Patch a defect regarding `configure --with-ldflags`
* Default to Spack's copy of GASNet-EX, which is newer than embedded
e2fsprogs: adding version 1.47.0 and fuse2fs variant
fuse-overlayfs: adding version 1.13
squashfuse: adding version 0.5.1 and 0.5.2
e2fsprogs: fixing audit errors
apptainer: expanding deps to cover more versions, fix binary_path logic.
apptainer: add go version deps, fix e2fsprogs patch sums, rework dep paths
fuse-overlayfs: tightening up the libfuse dep
Signed-off-by: Shane Nehring <snehring@iastate.edu>
* util-macros: ensure url_for_version only used for older versions
* util-macros: use url.substitute_version after xz -> bz2
* util-macros: mv url_for_version down the file
`BuildcacheBootstrapper` uses `Spec.intersects` to match specs needed
for bootstrapping against the binary cache. The specs were not
sufficiently-detailed to prevent matching e.g. cached binaries for
Mac OS on Windows; this commit adds the platform to each requested
bootstrap spec to prevent that.
* initial commit for RoCm-6.1.1 release
* fix style issues
* update the version for rocmlir and rocm-cmake
* restrict the patch for 6.0.0 release
* fix build failure for hipsolver-6.1.1 release
* update the hipblaslt for rocm-6.1.1 release
* add the patch for hipsparselt for 6.1.1 rel
Remove support for `cray` as a separate platform.
Any platform previously detected as `cray` is now detected as `linux`.
Users who still need platform=cray have to stick to Spack 0.22
Fixes a bug in the concretizer where specs depending on a host
incompatible libc would be used. This bug triggers when nothing is
built.
In the case where everything is reused, there is no libc provider from
the perspective of the solver, there is only compatible_libc. This
commit ensures that we require a host compatible libc on any reused
spec, additionally to requiring compat with the chosen libc provider.
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* Patch to add hsa prefix/include path:wq
* Style check error fix
* The patch need to be applied to 2024.01.stable. ROCm 6.0 requires hpctoolkit 2024.01.1 or later
* Fixing style chec error
* Adding a py4j variant that requires Java via spack to avoid situations where a system doesn't have Java and py4j expects it
* Adding new versions of py-pyspark
* Adding a new variant to require java (via py4j) and clean up dependency handling
* Adding myself as a maintainer for py-pyspark and py-py4j
* Fix overlooked version bump in py4j
* Version bump to meet py-spark expectations
* Version bump to add latest compatibile version with pyspark
* Matching py-grpcio bump
* Adding variants and dependents for pyspark
* Adding runtime deps
* Changing default java requirement. I'm not sure this is the right call
* Changing py4j with java dependency handling
* Fix style
* Update package.py fix unnecessary f-strinh
* Make +java the default for both
* Fix nested deps
* Revert styles after default change
* Added new versions and GCC 14 compatbility conflicts
* Added new versions and compatibility conflicts for gcc 14
* Added new versions paired to arrow (for gcc14 compat)
* Update py-protobuf compiler conflict
* Update depends to match
See https://github.com/grpc/grpc/blob/master/src/python/grpcio_status/setup.py
* Updating dependencies and conflicts for py-googleapis-common-protos. Added new version to avoid future issues
* Remove upper bound version on py-protobuf and add default_args
* Adding new versions and updating dependencies back to versions 1.35.0
* Updating oldest numpy deps
* Fixing merge
* bit more cleaniness for var/spack/repos/builtin/packages/py-googleapis-common-protos/package.py
* Adding latest matching version of py-grpcio and py-grpcio-status
* Update package.py
https://github.com/spack/spack/pull/44263#discussion_r1612317943
* Update dependencies
* Adding additional versions for dependent packages. Deprecated two versions: 1.16 is old, built for python ~3.6, and does not build for 3.8. 1.52.0 was removed from pypi
* Revert py-grpcio-tools changes. Will include in separate PR
* Adding patches and constraints to get 1.48 to build as it's a dependency that is called out for some other packages
* Updating to account for yanked packages for dependencies
* Fix style
* Update sha256 for py-grpcio v0.16.0 to reflect change
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* py-astropy: Add version 6.1
Added build info for version 6.1 in py-astropy. Requires a new additional package, astropy-iers-data which has been included as py-astropy-iers-data to match with spack's general naming conventions.
Below is the output of the spack install showing successful build fro version 6.1 and the new py-astropy-iers-data package
[+] /usr (external glibc-2.28-oj2wjfl2ao5inhfz4qehw6hlck2hizvp)
[+] /opt/apps/spack/gcc-runtime-8.5.0-5k6kvi5
[+] /opt/apps/spack/bzip2-1.0.8-t65bq3t
[+] /opt/apps/spack/libmd-1.0.4-zbdiprt
[+] /opt/apps/spack/libiconv-1.17-jskazis
[+] /opt/apps/spack/util-linux-uuid-2.38.1-w3kgjq3
[+] /opt/apps/spack/libxcrypt-4.4.35-zigqpjo
[+] /opt/apps/spack/xz-5.4.6-axoznvt
[+] /opt/apps/spack/zlib-ng-2.1.6-ccn5qny
[+] /opt/apps/spack/libyaml-0.2.5-fxathvq
[+] /opt/apps/spack/ncurses-6.4-xbvwv2w
[+] /opt/apps/spack/zstd-1.5.6-nyk6gt6
[+] /opt/apps/spack/pcre2-10.42-fu62kky
[+] /opt/apps/spack/libunistring-1.2-whrov3e
[+] /opt/apps/spack/nghttp2-1.57.0-u72gxms
[+] /opt/apps/spack/openblas-0.3.26-pfyk2vi
[+] /opt/apps/spack/berkeley-db-18.1.40-jftva2u
[+] /opt/apps/spack/wcslib-7.3-zvcqq7o
[+] /opt/apps/spack/libffi-3.4.6-ibucrfe
[+] /opt/apps/spack/erfa-2.0.0-4qkta2n
[+] /opt/apps/spack/pkgconf-1.9.5-ckjdqjm
[+] /opt/apps/spack/libbsd-0.12.1-njt5grs
[+] /opt/apps/spack/openssl-3.2.1-4lqdgni
[+] /opt/apps/spack/pigz-2.8-rx263bp
[+] /opt/apps/spack/readline-8.2-2ys6ede
[+] /opt/apps/spack/libidn2-2.3.7-vnie4rz
[+] /opt/apps/spack/libedit-3.1-20230828-676jwbd
[+] /opt/apps/spack/libxml2-2.10.3-37klvxv
[+] /opt/apps/spack/expat-2.6.2-7kfe3hb
[+] /opt/apps/spack/curl-8.6.0-gpzsr3p
[+] /opt/apps/spack/tar-1.34-wjzs4wj
[+] /opt/apps/spack/gdbm-1.23-cylmqwx
[+] /opt/apps/spack/sqlite-3.43.2-axuxulg
[+] /opt/apps/spack/cfitsio-3.49-mmy3dbr
[+] /opt/apps/spack/gettext-0.22.4-zjsp346
[+] /opt/apps/spack/perl-5.38.0-gzljgek
[+] /opt/apps/spack/python-3.10.13-fz7fymx
[+] /opt/apps/spack/krb5-1.20.1-tqiapsx
[+] /opt/apps/spack/py-pyyaml-6.0-rju7jls
[+] /opt/apps/spack/py-tomli-2.0.1-eanxpu2
[+] /opt/apps/spack/py-numpy-1.26.4-t5acjcv
[+] /opt/apps/spack/python-venv-1.0-2cz5c3s
[+] /opt/apps/spack/py-pip-23.0-lxkcvby
[+] /opt/apps/spack/openssh-9.7p1-jxrkzso
[+] /opt/apps/spack/py-pyerfa-2.0.0.1-kyfazhs
[+] /opt/apps/spack/py-packaging-23.1-wkeyuk6
[+] /opt/apps/spack/py-typing-extensions-4.8.0-ujwbb6g
[+] /opt/apps/spack/py-setuptools-69.2.0-3do76jw
[+] /opt/apps/spack/py-wheel-0.41.2-brm3k3h
[+] /opt/apps/spack/git-2.45.1-tuc5jnb
[+] /opt/apps/spack/py-cython-3.0.0-zx62ssd
==> Installing py-astropy-iers-data-main-ukchsfzhfcyz6e6fxar6mtykqiavporj [52/55]
==> No binary for py-astropy-iers-data-main-ukchsfzhfcyz6e6fxar6mtykqiavporj found: installing from source
==> No patches needed for py-astropy-iers-data
==> py-astropy-iers-data: Executing phase: 'install'
==> py-astropy-iers-data: Successfully installed py-astropy-iers-data-main-ukchsfzhfcyz6e6fxar6mtykqiavporj
Stage: 1.74s. Install: 0.93s. Post-install: 0.52s. Total: 3.36s
[+] /opt/apps/spack/py-astropy-iers-data-main-ukchsfz
[+] /opt/apps/spack/py-extension-helpers-0.1-a5hmr6j
[+] /opt/apps/spack/py-setuptools-scm-8.0.4-qdhxchg
==> Installing py-astropy-6.1.0-f4pffru3kmyion2kq6muomgrfs5y4gdo [55/55]
==> No binary for py-astropy-6.1.0-f4pffru3kmyion2kq6muomgrfs5y4gdo found: installing from source
==> Fetching https://files.pythonhosted.org/packages/source/a/astropy/astropy-6.1.0.tar.gz
==> Ran patch() for py-astropy
==> py-astropy: Executing phase: 'install'
==> Warning: Module file /opt/modulefiles/spack/Core/py-astropy/6.1.0.lua exists and will not be overwritten
==> py-astropy: Successfully installed py-astropy-6.1.0-f4pffru3kmyion2kq6muomgrfs5y4gdo
Stage: 1.29s. Install: 1m 5.77s. Post-install: 0.60s. Total: 1m 7.94s
* Removed extra-whitespace
A blank line had white space, removed the white space
* Additional formatting changes for black
* Additional package updates
Based on previous recommendations updated py-astropy and py-astropy-iers-data packages. Also added a new version to py-pyerfa package to match the 6.1.0 dependencies better
Of importance in these updates, I did add pypi and version info to py-astropy-iers-data. Originally I had argued that this package updates quite frequently (on a weekly basis) and so it did not make sense to include pypi/versions and we should instead use the non-version git-repo structure based on the master branch. However, when I tried to build the package py-setuptools-scm errored out when trying to build the package:
/opt/apps/spack/py-setuptools-scm-8.0.4-ax2zqro/lib/python3.10/site-packages/setuptools_scm/git.py:163: UserWarning: "/tmp/root/spack-stage/spack-stage-py-astropy-iers-data-main-iw2mdzlukb37mkcbcozjjefjoefw2eyp/spack-src" is shallow and may cause errors
I believe this is due to the download file/stage directory not containing the version and instead including the branch. I changed the package to use versions instead and it worked just fine as shown below. In addition, when I had done some preliminary testing, the package installed fine using the non-version master branch. When I checked, that installation it used py-setuptools-scm@7.1 while in this installation run it used a much more recent 8.0.4 so it is possible that somewhere between scm7.1 and 8.0.04 something changed that caused this error to show up. Since the setuptools-scm package has something to do extracting package versions, I imagine it's some kind of mismatch issue
Output from build:
spack install py-astropy
[+] /usr (external glibc-2.28-oj2wjfl2ao5inhfz4qehw6hlck2hizvp)
[+] /opt/apps/spack/gcc-runtime-8.5.0-5k6kvi5
[+] /opt/apps/spack/wcslib-7.3-zvcqq7o
[+] /opt/apps/spack/xz-5.4.6-axoznvt
[+] /opt/apps/spack/libffi-3.4.6-ibucrfe
[+] /opt/apps/spack/erfa-2.0.0-4qkta2n
[+] /opt/apps/spack/libmd-1.0.4-zbdiprt
[+] /opt/apps/spack/util-linux-uuid-2.38.1-w3kgjq3
[+] /opt/apps/spack/libiconv-1.17-jskazis
[+] /opt/apps/spack/berkeley-db-18.1.40-jftva2u
[+] /opt/apps/spack/zstd-1.5.6-nyk6gt6
[+] /opt/apps/spack/ncurses-6.4-xbvwv2w
[+] /opt/apps/spack/bzip2-1.0.8-t65bq3t
[+] /opt/apps/spack/libunistring-1.2-whrov3e
[+] /opt/apps/spack/pcre2-10.42-fu62kky
[+] /opt/apps/spack/pkgconf-1.9.5-ckjdqjm
[+] /opt/apps/spack/zlib-ng-2.1.6-ccn5qny
[+] /opt/apps/spack/openblas-0.3.26-pfyk2vi
[+] /opt/apps/spack/libxcrypt-4.4.35-zigqpjo
[+] /opt/apps/spack/libyaml-0.2.5-fxathvq
[+] /opt/apps/spack/libbsd-0.12.1-njt5grs
[+] /opt/apps/spack/readline-8.2-2ys6ede
[+] /opt/apps/spack/libidn2-2.3.7-vnie4rz
[+] /opt/apps/spack/nghttp2-1.57.0-u72gxms
[+] /opt/apps/spack/libedit-3.1-20230828-676jwbd
[+] /opt/apps/spack/libxml2-2.10.3-37klvxv
[+] /opt/apps/spack/openssl-3.2.1-4lqdgni
[+] /opt/apps/spack/pigz-2.8-rx263bp
[+] /opt/apps/spack/expat-2.6.2-7kfe3hb
[+] /opt/apps/spack/sqlite-3.43.2-axuxulg
[+] /opt/apps/spack/gdbm-1.23-cylmqwx
[+] /opt/apps/spack/curl-8.6.0-gpzsr3p
[+] /opt/apps/spack/tar-1.34-wjzs4wj
[+] /opt/apps/spack/perl-5.38.0-gzljgek
[+] /opt/apps/spack/cfitsio-3.49-mmy3dbr
[+] /opt/apps/spack/gettext-0.22.4-zjsp346
[+] /opt/apps/spack/krb5-1.20.1-tqiapsx
[+] /opt/apps/spack/python-3.10.13-fz7fymx
[+] /opt/apps/spack/openssh-9.7p1-jxrkzso
[+] /opt/apps/spack/py-tomli-2.0.1-eanxpu2
[+] /opt/apps/spack/py-setuptools-69.2.0-3do76jw
[+] /opt/apps/spack/py-numpy-1.26.4-t5acjcv
[+] /opt/apps/spack/python-venv-1.0-2cz5c3s
[+] /opt/apps/spack/py-packaging-23.1-wkeyuk6
[+] /opt/apps/spack/py-pip-23.0-lxkcvby
[+] /opt/apps/spack/git-2.45.1-zu6qkoc
[+] /opt/apps/spack/py-markupsafe-2.1.3-isgtki6
[+] /opt/apps/spack/py-wheel-0.41.2-brm3k3h
==> Installing py-extension-helpers-0.1-a5hmr6jtrvpcq3ibwkwhvwlydthjif5a [49/57]
==> No binary for py-extension-helpers-0.1-a5hmr6jtrvpcq3ibwkwhvwlydthjif5a found: installing from source
==> Fetching ac8a6fe91c.tar.gz
==> No patches needed for py-extension-helpers
==> py-extension-helpers: Executing phase: 'install'
==> py-extension-helpers: Successfully installed py-extension-helpers-0.1-a5hmr6jtrvpcq3ibwkwhvwlydthjif5a
Stage: 0.37s. Install: 0.88s. Post-install: 0.52s. Total: 1.89s
[+] /opt/apps/spack/py-extension-helpers-0.1-a5hmr6j
==> Installing py-cython-3.0.0-zx62ssdy4p6ddwuqbixel2vcsihjcs6m [50/57]
==> No binary for py-cython-3.0.0-zx62ssdy4p6ddwuqbixel2vcsihjcs6m found: installing from source
==> Fetching 350b18f967.tar.gz
==> No patches needed for py-cython
==> py-cython: Executing phase: 'install'
==> py-cython: Successfully installed py-cython-3.0.0-zx62ssdy4p6ddwuqbixel2vcsihjcs6m
Stage: 1.07s. Install: 2m 49.80s. Post-install: 0.40s. Total: 2m 51.37s
[+] /opt/apps/spack/py-cython-3.0.0-zx62ssd
[+] /opt/apps/spack/py-jinja2-3.1.2-wacpq7j
[+] /opt/apps/spack/py-typing-extensions-4.8.0-ujwbb6g
[+] /opt/apps/spack/py-pyyaml-6.0-rju7jls
[+] /opt/apps/spack/py-setuptools-scm-8.0.4-ax2zqro
==> Installing py-astropy-iers-data-0.2024.5.20.0.29.40-wckxjf6icqn3aqhyjidfir3byyjq5aq6 [55/57]
==> No binary for py-astropy-iers-data-0.2024.5.20.0.29.40-wckxjf6icqn3aqhyjidfir3byyjq5aq6 found: installing from source
==> Using cached archive: /opt/spack/var/spack/cache/_source-cache/archive/7f/7fff3d3404ae8560533ac0e685db7acc02c4d8984faa4ac3d607096879fba2d1.tar.gz
==> No patches needed for py-astropy-iers-data
==> py-astropy-iers-data: Executing phase: 'install'
==> py-astropy-iers-data: Successfully installed py-astropy-iers-data-0.2024.5.20.0.29.40-wckxjf6icqn3aqhyjidfir3byyjq5aq6
Stage: 0.07s. Install: 1.21s. Post-install: 0.39s. Total: 1.88s
[+] /opt/apps/spack/py-astropy-iers-data-0.2024.5.20.0.29.40-wckxjf6
==> Installing py-pyerfa-2.0.1.1-pkokp6usk7m2bjxcba3nwgqgrjufumcp [56/57]
==> No binary for py-pyerfa-2.0.1.1-pkokp6usk7m2bjxcba3nwgqgrjufumcp found: installing from source
==> Fetching https://files.pythonhosted.org/packages/source/p/pyerfa/pyerfa-2.0.1.1.tar.gz
==> No patches needed for py-pyerfa
==> py-pyerfa: Executing phase: 'install'
==> py-pyerfa: Successfully installed py-pyerfa-2.0.1.1-pkokp6usk7m2bjxcba3nwgqgrjufumcp
Stage: 0.93s. Install: 17.72s. Post-install: 0.33s. Total: 19.15s
[+] /opt/apps/spack/py-pyerfa-2.0.1.1-pkokp6u
==> Installing py-astropy-6.1.0-5brbkjnjzfg3lc6h34qku24ep5pwsxzs [57/57]
==> No binary for py-astropy-6.1.0-5brbkjnjzfg3lc6h34qku24ep5pwsxzs found: installing from source
==> Fetching https://files.pythonhosted.org/packages/source/a/astropy/astropy-6.1.0.tar.gz
==> Ran patch() for py-astropy
==> py-astropy: Executing phase: 'install'
==> py-astropy: Successfully installed py-astropy-6.1.0-5brbkjnjzfg3lc6h34qku24ep5pwsxzs
Stage: 1.16s. Install: 1m 3.34s. Post-install: 1.05s. Total: 1m 5.77s
[+] /opt/apps/spack/py-astropy-6.1.0-5brbkjn
* Updated to match with black formatting
Change the installer to take `([pkg], args)` in the constructor instead
of `[(pkg, args)]`. The reason is that certain arguments are global
settings, and the new API ensures that those arguments cannot be
different across different "build requests".
The `explicit` install arg is now a list of hashes, and the installer is
no longer responsible for determining what package is installed
explicitly. This way environment installs can simply pass the list of
environment roots, without them necessarily being explicit build
requests. For example an env with two roots [a, b], where b depends on
a, would not always cause spack install to mark b as explicit.
Notice that `overwrite` already took a list of hashes, this makes
`explicit` consistent.
`package.do_install(explicit=True)` continues to take a boolean.
* legion: add pip dependency for build
pip is needed for the build when the Legion Python binding is enabled
* legion: add variants for gc logging and system OpenMP use
This also removes the `cmake_cxx_flags` variable from `cmake_args()`
because that variable had no effect.
* [@spackbot] updating style on behalf of mpokorny
* legion: use spec.satisfies() in cmake_args()
e.g, replace use of '"+foo" in spec' with 'spec.satisfies("+foo")'
* legion: avoid configuring with multiple "-DLegion_REDOP_COMPLEX=ON" arguments
In the previous version, when both '+redop_complex' and '+bindings'
was set, two instances of "-DLegion_REDOP_COMPLEX=ON" arguments were
generated for cmake configuration.
* legion: fix value of "Legion_OUTPUT_LEVEL" for configuration
the previous version had no effect on setting the configuration value
---------
Co-authored-by: mpokorny <mpokorny@users.noreply.github.com>
The windows wrappers for basic functions like `os.symlink`,
`os.readlink` and `os.path.islink` in the `llnl.util.symlink` module
have bugs, and trigger more file system operations on non-windows than
they should.
This commit just binds `llnl.util.symlink.symlink = os.symlink` etc so
built-in functions are used on non-windows
`spack clean <spec>` will now resolve specs based on the active environment if one is active.
If an env is active but no matching spec is found, this will fall back on fully concretizing.
Before this PR, if Spack could see a possibility to reuse a spec that
doesn't match a strong preference, it would do so. After the PR, a
strong preference would take precedence.
`glibc` and `musl` provide a basic implementation of `iconv` (`iconv`,
`iconv_open`, `iconv_close`), but in practice the installation may be
missing the character encoding methods to make them usable. On Fedora
for example, users need to
```yum install glibc-gconv-extra```
to get the character encodings that `gettext` requires during configure,
namely EUC-JP. Users may not have permissions to install the missing
parts of glibc.
Since Spack can install `libiconv`, it is simpler to use that by
default.
* Spglib: add version 2.4.0
* dla-future-fortran: new package version 0.1.0
* [@spackbot] updating style on behalf of RMeli
* apply suggestion and add maintainer
---------
Co-authored-by: RMeli <RMeli@users.noreply.github.com>
* [emacs] When installing on Mac OS, build and install the native
Emacs.app along with the standard executables.
* [emacs] Make the GUI build on Mac optional by adding "gui" variant
* Apply reviewer suggestion
Co-authored-by: Alec Scott <hi@alecbcs.com>
* Add emacs version 29.3
---------
Co-authored-by: Alec Scott <hi@alecbcs.com>
avoid calling `spec.target` when None.
When an external compiler package has an `os` set but no `target` set, Spack
currently falls into a codepath that calls `spec.target` (which itself calls
`spec.architecture.target.Microarchitecture`) when `spec.architecture.target`
is None, throwing an error.
e.g.
```
packages:
gcc:
externals:
- spec: gcc@12.3.1 os=rhel7
prefix: /usr
```
---------
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
* glew: rework dependency on gl
This simplifies the package and ensures a single gl implementation is
pulled in. Before we were adding direct dependencies, and those are
not unified through the virtual.
* mesa-demos: rework dependency on gl
This simplifies the package and ensures a single gl implementation is
pulled in. Before we were adding direct dependencies, and those are
not unified through the virtual.
* mesa-glu: rework dependency on gl
This simplifies the package and ensures a single gl implementation is
pulled in. Before we were adding direct dependencies, and those are
not unified through the virtual.
* paraview: fix dependency on glew
* mesa: group dependency on when("+glx")
* Add missing dependency on libxml2
* paraview: remove the "osmesa" and "egl" variant
Instead, enforce consistency using the "gl" virtual that allows
only one provider.
* visit: remove osmesa variant
* Disable paraview in the aws-isc stacks
* data-vis-sdk: rework constrains to enforce front-ends
* e4s-power: remove redundant paraview
* Pipelines: update osmesa variants
* trilinos-catalyst-ioss-adapter: make gl a run dependency
Starting from 24.04, armpl-gcc will only have three packages files: dev, rpm, and macOS.
Only one version for gcc is provided, so the changes in the code reflect that the tar provided
for gcc is only one rather than many.
* Remove mesa18 and libosmesa
mesa18 was introduced in #19528 as a way to maintain the old
autotools build of mesa separate from the new meson build.
We could add a second build system to mesa, but since mesa18 has
been deprecated for a long time, we'll just remove it.
libosmesa was used to multiplex the gl provider between mesa18
and mesa, and is thus unecessary. Remove it to reduce complexity
in the graphical stack.
* Remove references to mesa18 and libosmesa
* vtk: rework dependency on gl and osmesa
* memsurfer: rework dependency on vtk
* visit: minimal fix to avoid having both osmesa and glx
* Use hdf5::hdf5 on Windows from Paraview CMake
This patch is already applied on VTK 9 or greater.
* Add comments stating that vtk and paraview patches are the same and should be modified in concert.
This fixes a bug occurring when two root specs need to select
old versions, and these versions have the same penalty in the
optimization. This sometimes caused an older version to be
preferred to a more recent one.
The issue was the omission of `PackageNode` in the optimization
tuple.
* rayleigh: new package
* Update var/spack/repos/builtin/packages/rayleigh/package.py
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
* split edit into three methods
* add comments to clarify use of configure
* rayleigh: copyright year
---------
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
Use correct path separator in get_all_package_diffs for all platforms.
Ensures correct package change computation on Windows when pruning unchanged specs in Gitlab CI
* Update, fix serenity & serenity-libint
Version 1.6.1 of `serenity` is added, some dependencies are made more
explicit, some options are improved or fixed.
The url of `serenity-libint` is fixed. The old url is not reachable
anymore.
* Use upstream patch, modify cmake patch
* Update var/spack/repos/builtin/packages/serenity/package.py
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* heimdall: Astronomy software package. Requires dedisp and psrdada (included as part of this commit)
* Updated packages to align with Spack's style
Minor updates based on wdconinc's comments regarding Spack's style guide
* [@spackbot] updating style on behalf of aweaver1fandm
* Minor edits to fix copyright year and dedisp install
Fixed copyright year to be 2024 instead of 2023
Removed the overridden version of install and created a preinstall function to create the missing lib and inc directories, therefore allowing the default install to run
Here is output from the spack install of heimdall showing successful build with cuda. If necessary I do a spack clean and freshly install it
./spack install heimdall +cuda cuda_arch=86
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/libiconv-1.17-enpmbhsi3kztebwmpclpub2afhlbr3gy
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/xz-5.4.1-pte76kujkezxb3laqse3o4sctlbygsaw
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/zlib-1.2.13-utlfo5ltxz5v5bckirn5v3amtbxjdvwh
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/bzip2-1.0.8-x6navz7ucgfnb5xq7aelqmgd4zxsz5bs
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/libmd-1.0.4-ncomhrodpdul4dm64o6b7426fhmc2u64
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/ncurses-6.4-c77h34rooycbzapxjvc27sg5td5jiwyb
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/zstd-1.5.5-eporpybumydxveg5rwtfzysrsu4eqzcv
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/libffi-3.4.4-vskntokaojclfqxjfzkbyirkeogddbpx
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/libxcrypt-4.4.33-gtpn32p6mxztul3c3dxzqj7gvcyh555j
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/util-linux-uuid-2.38.1-g322a5peqjaad6gl5q64cdu4qo7kvw6o
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/libxml2-2.10.3-pza3kz2mtbncbbeim6rejfqkgftnf4rz
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/openssl-1.1.1t-adbquvgg4qpc3vq6jynf44qzq3gfwrv5
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/pigz-2.7-e7mxj4ya2u4a6zb4hu64g7docujmkxeb
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/libbsd-0.11.7-wh4xleivbe7wndiqt5nsehzlfrccnjcg
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/readline-8.2-hhb647bwmbcj7iwpmtetbylninfm5rxf
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/cuda-11.7.1-osue2sx5rv7dgzhsmaemydpwhyribxng
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/tar-1.34-35f5gki2ycxmy5zd7zs5tsvp3xoszxum
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/expat-2.5.0-4gizyhhqklciuyrbyinq2tdggt73gds4
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/gdbm-1.23-w3uzihtubj2iwv6es55fis6nt2q5zwlr
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/sqlite-3.40.1-m4ntzvuupsnbtkdfbz7oqpbjdlaffp2a
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/dedisp-1.0-pq6r3jnyxq6jzoygz3fp2e6jc2ojpvap
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/gettext-0.21.1-hglzdeadmgkzjb76bmemt6dnulfkrpha
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/python-3.10.10-khu36qq4p2te7jf475ewr2h7egidekfl
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/psrdada-master-by4w6mrpcfnoihlhos2jcfo2roiyagaz
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/heimdall-1.0-ohtdnltuhhejysshcert25h6nmuvluqp
* [@spackbot] updating style on behalf of aweaver1fandm
Restrict the hpcrun-fmt.txt patch to :2022. It's fixed in the code
after that, and in recent develop, some code paths have moved causing
this patch to fail.
This fixes an issue where ghcr, gitlab and possibly other container registries paginate tags by default, which violates the OCI spec v1.0, but is common practice (the spec was broken itself). After this commit, you can create build cache indices of > 100 specs on ghcr.
Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
* pythia8: prefer 8.310
* [@spackbot] updating style on behalf of wdconinc
* pythia8: filter_file to remove sed n
* Revert "[@spackbot] updating style on behalf of wdconinc"
This reverts commit e2a3decaffbd3f464d1bd992025e1812df49f088.
* Revert "pythia8: prefer 8.310"
This reverts commit 568cb056b87129085e245d9dbef1732ee1c6c0aa.
* [@spackbot] updating style on behalf of wdconinc
* pythia8: comment for fix
* pythia8: fix style
* pythia8: filter_file with raw string because of escaped pipe
---------
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
The release tarballs are not available anymore which means autoconf, automake and libtool are always needed.
The NVHPC specific patches don't make sense anymore being that the patched files are not distributed in the new tar files.
Add support for Gitlab CI on Windows
This PR adds the config changes required to configure and execute
Gitlab pipelines running Windows builds on Windows runners using
the existing Gitlab CI infrastructure (and newly added Windows
infrastructure).
* Adds support for generating child pipelines dispatched to Windows runners
* Refactors the relevant pre-scripts, scripts, and post scripts to be compatible with Windows
* Adds Windows config section describing Windows jobs
* Adds VTK as Windows build stack (to be expanded later)
* Modifies proj to build on Windows
* Refactors Windows rpath symlinking to avoid system libs and externals
---------
Co-authored-by: Ryan Krattiger <ryan.krattiger@kitware.com>
Co-authored-by: Mike VanDenburgh <michael.vandenburgh@kitware.com>
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com>
Symlinks on Windows can use longpath prefixes (\\?\); these are fine
in the context of win32 API interactions but break numerous facets of
Spack behavior that rely on string parsing/matching (archiving,
binary distributions, tarball extraction, view regen, etc).
Spack's internal readlink method (llnl.util.symlink.readlink)
gracefully handles this by removing the prefix and otherwise behaving
exactly as os.readlink does, so we should prefer that in all cases.
* py-matplotlib: qualify when to do a post install
Older versions of py-matplotlib don't seem to have some of the
files that the post install step is trying to install.
Looks like the files first appeared in 3.6.0 and later.
Signed-off-by: Howard Pritchard <hppritcha@gmail.com>
* Change install paths for older matplotlib
---------
Signed-off-by: Howard Pritchard <hppritcha@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add maintainer and fix linting
* allow for fewer deps in archive
* use meson for archive packages
* Fix version spec and f-string
* fix blas dependency links
* Add new release to spack
* Fix checksums for latest release
* Update version of iperf3 from 3.6 to 3.16
Spack currently only explicitly has version 3.6 of the iPerf3 package
(out of ESnet / LBNL). This makes the default the latest version of 3.16,
and adds some other versions (found in some Linux distros, for possible
compatibility purposes).
* iperf3: update to 3.17; update 3.6 hash for new url
* protobuf: update hash for patch needed when="@3.4:3.21"
* Revert "protobuf: update hash for patch needed when="@3.4:3.21""
This reverts commit 4d168d0b27.
* initial commit to enable tensorflow-2.14 for spack built ROCm
* fix style errors
* modify hipcc patch
* updates for rocm 6.1
* updates for tf-rocm-enhanced 2.16
* fix styling
* fix styling
* add patch for 2.16
* add patch for 2.16
* Update var/spack/repos/builtin/packages/py-tensorflow/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* update rocm enhanced version names
* changes for rocm-enhanced version name change
* fix styling
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Fix gromacs installation with SVE. Issue 44062
* [@spackbot] updating style on behalf of paolotricerri
* Remove `neoverse_n2` target
We have removed the neoverse_n2 target as its detection is more involved
compared to neoverse_v*.
Set MPI_C_COMPILER etc. env vars when building with fujitsu-mpi, which
override CMake logic. Without using these variables to explicitly
request the Fujitsu MPI wrappers, the builtin CMake logic is unwilling
to use these wrappers unless the Fujitsu compiler is used, but they
should be used for %clang as well.
This avoids patching CMake module files like in #16864, primarily to
avoid the possibility of altering behavior for specs that do not use
%fj or ^fujitsu-mpi.
* Add openfoam to aws-pcluster-neoverse_v1 stack
* Add more apps to aws-pcluster-x86_64_v4 stack
* Remove WRF while hdf5 cannot build in buildcache at the moment
* Update comment
* Add more apps for aws-pcluster-neoverse_v1 stack
* Remove apps that currently do not build
* Disable those packages that won't build
* Modify syntax such that correct cflags are used
* Changing syntax again to what works with other packages
* Fix overriding packages.yaml entry for gettext
* Use new `prefer` and `require:when` clauses to clarify intent
* Use newer spack version to install intel compiler
This removes the need for patches and makes sure the `prefer` directives in
`package.yaml` are understood.
* `prefer` not strong enough, need to set compilers
* Revert "Use newer spack version to install intel compiler"
This reverts commit ecb25a192c.
Cannot update the spack version to install intel compiler as this changes the
compiler hash but not the version. This leads to incompatible compiler paths. If
we update this spack version in the future make sure the compiler version also updates.
Tested-by: Stephen Sachs <stesachs@amazon.com>
* Remove `prefer` clause as it is not strong enough for our needs
This way we can safely go back to installing the intel compiler with an older
spack version.
* Prefer gcc or oneapi to build gettext
* Pin gettext version compatible with system glibc-headers
* relax gettext version requirement to enable later versions
* oneapi cannot build older gettext version
* octave: use pcre2 for @8:
* Add 'pcre2' variant to octave to control pcre vs. pcre2
* Update var/spack/repos/builtin/packages/octave/package.py
Co-authored-by: Alec Scott <hi@alecbcs.com>
---------
Co-authored-by: Alex Richert <alexander.richert@noaa.gov>
Co-authored-by: Alec Scott <hi@alecbcs.com>
Apparently urllib can throw a range of different exceptions:
1. HTTPError
2. URLError with e.reason set to the actual exception
3. TimeoutError from getresponse, which is not wrapped
* New package: qpdf
* Update var/spack/repos/builtin/packages/qpdf/package.py
Co-authored-by: Alec Scott <hi@alecbcs.com>
* Fix format of cmake_args
---------
Co-authored-by: Alec Scott <hi@alecbcs.com>
* archive: relative links only
Ensure all links written into tarfiles generated from Spack prefixes do not contain symlinks pointing outside the prefix
* binary_distribution: limit extraction to prefix
Ensure files extracted from spackballs are not links pointing outside of the prefix
* Ensure rpaths are properly set on Windows
* hard error on extraction of absolute links
* refactor for non link-modifying approach
* Restore tarball extraction to original impl
* use custom readlink
* cleanup symlink module
* make lstrip
* flux-sched: set the version if the ver file is missing
problem: flux-sched needs a version, it normally gets this from a
release tarball or from git tags, but if using a source archive or a git
clone without tags the version is missing
solution: set the version through cmake based on the version spack sees
when the version file is missing
* Update var/spack/repos/builtin/packages/flux-sched/package.py
Co-authored-by: Alec Scott <hi@alecbcs.com>
---------
Co-authored-by: Alec Scott <hi@alecbcs.com>
Problem: the libsodium download endpoints are not reliable,
they fail multiple times a day for several of our automated
pipelines.
Solution: use the GitHub releases and branches.
Signed-off-by: vsoch <vsoch@users.noreply.github.com>
GCC C++ headers like cstdlib use `#include_next <stdlib.h>` to wrap libc
headers. We're using `-isystem` for libc, which puts those headers too
early in the search path. `-idirafter` fixes this so `include_next`
works.
* add darshan-3.4.5 packages, update URLs
* py-setuptools version switches for py-darshan
* more py-darshan test dependencies
* try a conditional importlib_resources dependency
Add the ability to include any number of (potentially nested) concrete environments, e.g.:
```yaml
spack:
specs: []
concretizer:
unify: true
include_concrete:
- /path/to/environment1
- /path/to/environment2
```
or, from the CLI:
```console
$ spack env create myenv
$ spack -e myenv add python
$ spack -e myenv concretize
$ spack env create --include-concrete myenv included_env
```
The contents of included concrete environments' spack.lock files are
included in the environment's lock file at creation time. Any changes
to included concrete environments are only reflected after the environment
is re-concretized from the re-concretized included environments.
- [x] Concretize included envs
- [x] Save concrete specs in memory by hash
- [x] Add included envs to combined env's lock file
- [x] Add test
- [x] Update documentation
Co-authored-by: Kayla Butler <<butler59@llnl.gov>
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.co
m>
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
Currently SPACK_COLOR=always is not respected in the build process on
macOS, because the global `_force_color` is re-evaluated in global scope
during module setup, where it is always `None`.
So, move global init bits from main.py to the module itself.
Some specs which were excluded from reuse,
are currently added back to the solve when
we traverse dependencies of other reusable
specs.
This fixes the issue by keeping track of what
we can explicitly reuse.
This commit adds a layer of indirection to improve build isolation with
and without external Python, as well as usability of environment views.
It adds `python-venv` as a dependency to all packages that `extends("python")`,
which has the following advantages:
1. Build isolation: only `PYTHONPATH` is considered in builds, not
user / system packages
2. Stable install layout: fixes the problem on Debian, RHEL and Fedora where
external / system python produces `bin/local` subdirs in Spack install prefixes.
3. Environment views are Python virtual environments (and if you add
`py-pip` things like `pip list` work)
Views work whether they're symlink, hardlink or copy type.
This commit additionally makes `spec["python"].command` return
`spec["python-venv"].command`. The rationale is that packages in repos we do
not own do not pass the underlying python to the build system, which could still
result in incorrectly computed install layouts.
Other attributes like `libs`, `headers` should be on `python` anyways and need no change.
Currently bootstrapping from source fails because clingo requires gnupg
requires clingo.
This commit stops eager bootstrapping. We don't need `patchelf` nor `gnupg`
generally. They're bootstrapped when needed.
This creates shared infrastructure for compiler packages to implement the
detailed search capabilities from the `spack compiler find` command for the
`spack external find` command.
After this commit, `spack compiler find` can be replaced with
`spack external find --tag compiler`, with the exception of mixed toolchains.
A named env cannot contain `.` and `/`.
So when a user runs `spack env create ./here` do not error but treat it
as `spack env create -d ./here`.
Also fix help string of `spack env create`, which seems to have been
copied from `activate` incorrectly.
Since reuse is the default now, `--reuse-deps` can be confusing, as it
technically does not imply roots are fresh.
So add `--fresh-roots`, which is also easier to discover when running
`spack concretize --fre<tab>`
* WIP NWChem with ARMCI-MPI and TCE optional
* rename armci-mpi to armcimpi
* add version for git
* add ARMCI-MPI support to NWChem package
EXTERNAL_ARMCI_PATH needs to be set to the ARMCI-MPI package install prefix.
I could not get it from spec["armcimpi"] but it worked to use the dependent build environment method to export a generic environmental variable to use instead.
* i suppose i can maintain NWChem as well
* check rejects option that dozens of packages use
i do not have time to fight with this nonsense
Run . share/spack/setup-env.sh
==> Error: armcimpi version 'master' has extra arguments: 'branch'
Valid arguments for a url fetcher are:
'url', 'sha256', 'md5', 'sha1', 'sha224', 'sha384', 'sha512', and 'checksum'
Error: Process completed with exit code 1.
* style
* ARMCI-MPI needs depends_on; the rest seems fixed
* fix ARMCI selection per review feedback from @zzzoom
https://github.com/spack/spack/pull/43883#discussion_r1585014147
* address reviewer feedback from @yizeyi18
https://github.com/spack/spack/pull/43883#discussion_r1587228084
elaborate on what +extratce does, in terms of the NWChem build environment variables,
some of which are documented on https://nwchemgit.github.io/TCE.html.
* style
* Update var/spack/repos/builtin/packages/nwchem/package.py
---------
Signed-off-by: Jeff Hammond <jeff.science@gmail.com>
Co-authored-by: Carlos Bederián <4043375+zzzoom@users.noreply.github.com>
* [TAU package] Update with +rocprofv2. Updated some tests.
pdated with +rocprofv2 flag. Only works with rocm-core >= 6.0.0
Can be tested with (Omnia):
spack install tau@master +rocm+rocprofv2 %gcc@11
Needs the last commit in our local repository, can be done by modifying the "git = " line, or waiting until the public one is updated.
In the case that tests cause issues when building TAU, there is the flag:
disable_tests = False
The rocm test is disabled by default, as the PR regarding tests loading dependencies is not solved (PR#43682).
* [@spackbot] updating style on behalf of jordialcaraz
---------
Co-authored-by: jordialcaraz <jordialcaraz@users.noreply.github.com>
* py-tensorflow: fix aarch64 build
* [@spackbot] updating style on behalf of aweits
* patch format
* change patch strategy, actually get the logic correct in
the patch
* only patch 2.16.1 onwards for aarch64
* __CUDACC__ not __NVCC__
* !(defined(__NVCC__) && defined(__CUDACC__))
---------
Co-authored-by: aweits <aweits@users.noreply.github.com>
We recently switched to using the new ReadTheDocs with "addons". That includes its own
analytics, which is nice, but we also want to continue using our GA4 analytics.
Adding GA4 is no longer supported by RTD, so we have to add it manually.
- [x] re-add the gtag to all pages, manually
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
PR #43701 is broken, preventing scorep from being installed. As explained in #43700 the issue is internal to scorep and can not be fixed in the package, at least by the method being attempted here.
Adds a pre-concretization check for the Windows SDK and WGL (Windows
GL) packages as non-buildable externals.
This is a redo of https://github.com/spack/spack/pull/43459, but makes
sure to modify the configuration scope outside of the bootstrap scope:
whichever is highest-precedence in the user's environment at the time
the concretization runs, which should either be an env scope or the
~ scope.
Adds pytest fixture mocking the check for WGL and WSDK as if they were
present.
This PR gives users finer control over which specs are reused during concretization.
The value of the `concretizer:reuse` config option now can take an object with the following properties:
- `roots`: true if reusing roots, false if reusing just dependencies
- `exclude`: list of constraints used to select reusable specs
- `include`: list of constraints used to select reusable specs
- `from`: allows to select the sources of reused specs
### Examples
#### Reuse only specs compiled with GCC
```yaml
concretizer:
reuse:
roots: true
include:
- "%gcc"
```
#### `openmpi` must be used from externals, and it must be the only external used
```yaml
concretizer:
reuse:
roots: true
from:
- type: local
exclude:
- "openmpi"
- type: buildcache
exclude:
- "openmpi"
- type: external
include:
- "openmpi"
```
With v2.10+, ADIOS added a campaign manager. This is auto-enabled
if SQLite3 is found.
Add explicit control for it now and disables it by default, to avoid
picking up system dependencies or bloating by default the ADIOS2
dependencies. Also, not yet fully mature to be used by default:
https://github.com/ornladios/ADIOS2/issues/4148
* pypi build of py-simpy
* [py-simpy] toml explicitly called out
* py-simpy: New version
* py-setuptools-scm: Added new version
* py-setuptools-scm: add url_for_version
Because versions @:7 have an underscore (setuptools_scm) in the URL, and
newer versions have a dash (setuptools-scm).
* py-setuptools-scm: fix flake8 line too long
* py-simpy: Fix hash
---------
Co-authored-by: Sid Pendelberry <sid@rit.edu>
Co-authored-by: Jen Herting <jen@herting.cc>
* PackageStillNeededError: add pkg that needs spec to exception msg
* PackageStillNeededError: f-string with short fmt and hash
* PackageStillNeededError: split long string
The old concretizer creates a cyclic graph when expanding virtuals for
`iconv`, which is a bug. This hack drops glibc and musl as possible
providers for `iconv` in the old concretizer to work around it.
* Added package to build Ollama
* Update package.py
Add license and documentation
* [@spackbot] updating style on behalf of teaguesterling
* We can now use OVERRIDE_GIT_DESCRIBE to set the version in DuckDB
* Update duckdb/package.py
- use f-string
- fix version specs to address inconsistencies
* Update package.py
Fix spec definitions further
* [@spackbot] updating style on behalf of teaguesterling
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
The "DOTNET_CLI_TELEMETRY_OPTOUT" environment variable should be defined when using the product, not when installing it (the installation phase is just extract the files anyway).
Also use `~` instead of `-` to check for the variant and fix the second argument for `env.set` which should also be a string.
Add debug log for external detection tests. The debug log
is used to print which test is being executed.
Skip version audit on Windows where appropriate
* Update package.py to osg 1.119 and igtf 1.128
* Remove unnecessary white space
* Add missing comma
* change url to use git and use commit hash from repository instead of ssh256sum of tar.gz
* [@spackbot] updating style on behalf of rahmans1
---------
Co-authored-by: rahmans1 <rahmans1@users.noreply.github.com>
* * Add initial tests-sos package
* Remove failing call of missing setup_compiler_environment from sos
package
* Add several variants for sos package
* [@spackbot] updating style on behalf of jack-morrison
We run `extend spack_flags_list SPACK_LDFLAGS` for `$mode in ld|ccld`.
That's problematic, cause `ccld` needs `-Wl,--flag` whereas `ld` needs
`--flag` directly. Only `-L` and `-l` are common to compiler & linker.
In all build systems `LDFLAGS` is for the compiler not the linker, cause
any linker flag `-x` can be passed as a compiler flag `-Wl,-x`, and there
are many compiler flags that affect the linker invocation, like `-fopenmp`,
`-fuse-ld=`, `-fsanitize=` etc.
So don't pass `LDFLAGS` to the linker directly.
This way users can set `ldflags: -Wl,--allow-shlib-undefined` in compilers.yaml
to work around an issue where the linker tries to resolve the `libcuda.so.1`
stub lib which cannot be located by design in `cuda`.
* Updates for rocm
Updated for rocm@6
Added conflict between rocprofiler and roctracer.
Request either +rocprofiler or +roctracer when +rocm. In this case, it automatically builds for one, instead of displaying the message.
Request +rocm when using either +rocprofiler or +roctracer. In this case, it automatically builds with +rocm, instead of displaying the message.
Disabled the tests. Will update them with the new test method.
* [@spackbot] updating style on behalf of jordialcaraz
---------
Co-authored-by: jordialcaraz <jordialcaraz@users.noreply.github.com>
Some packages can't be redistributed in source or binary form. We need an explicit way to say that in a package.
This adds a `redistribute()` directive so that package authors can write, e.g.:
```python
redistribute(source=False, binary=False)
```
You can also do this conditionally with `when=`, as with other directives, e.g.:
```python
# 12.0 and higher are proprietary
redistribute(source=False, binary=False, when="@12.0:")
# can't redistribute when we depend on some proprietary dependency
redistribute(source=False, binary=False, when="^proprietary-dependency")
```
To prevent Spack from adding either their sources or binaries to public mirrors and build caches. You can still unconditionally add things *if* you run either:
* `spack mirror create --private`
* `spack buildcache push --private`
But the default behavior for build caches is not to include non-redistributable packages in either mirrors or build caches. We have previously done this manually for our public buildcache, but with this we can start maintaining redistributability directly in packages.
Caveats: currently the default for `redistribute()` is `True` for both `source` and `binary`, and you can only set either of them to `False` via this directive.
- [x] add `redistribute()` directive
- [x] add `redistribute_source` and `redistribute_binary` class methods to `PackageBase`
- [x] add `--private` option to `spack mirror`
- [x] add `--private` option to `spack buildcache push`
- [x] test exclusion of packages from source mirror (both as a root and as a dependency)
- [x] test exclusion of packages from binary mirror (both as a root and as a dependency)
If there's no compiler we currently don't have any external libc for the solver.
This commit adds a fallback on libc from the current Python process, which works if it is dynamically linked.
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
When looking at where we spend our time in solver setup, I noticed a fair bit of time is spent
in `Spec.format()`, and `Spec.format()` is a pretty old, slow, convoluted method.
This PR does a number of things:
- [x] Consolidate most of what was being done manually with a character loop and several
regexes into a single regex.
- [x] Precompile regexes where we keep them
- [x] Remove the `transform=` argument to `Spec.format()` which was only used in one
place in the code (modules) to uppercase env var names, but added a lot of complexity
- [x] Avoid escaping and colorizing specs unless necessary
- [x] Refactor a lot of the colorization logic to avoid unnecessary object construction
- [x] Add type hints and remove some spots in the code where we were using nonexistent
arguments to `format()`.
- [x] Add trivial cases to `__str__` in `VariantMap` and `VersionList` to avoid sorting
- [x] Avoid calling `isinstance()` in the main loop of `Spec.format()`
- [x] Don't bother constructing a `string` representation for the result of `_prev_version`
as it is only used for comparisons.
In my timings (on all the specs formatted in a solve of `hdf5`), this is over 2.67x faster than the
original `format()`, and it seems to reduce setup time by around a second (for `hdf5`).
The reverse provider lookup may have stale entries for deleted packages, which used to cause errors. It's hard to invalidate those cache entries, so this commit simply drops entries w/o invalidating the cache.
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
This commit differentiate linux from other platforms by
using libc compatibility as a criterion for deciding
which buildcaches / binaries can be reused. Other
platforms still use OS compatibility.
On linux a libc is injected by all compilers as an implicit
external, and the compatibility criterion is that a libc is
compatible with all other libcs with the same name and a
version that is lesser or equal.
Some concretization unit tests use libc when run on linux.
Some logic to detect what libc the c / cxx compilers use by default,
based on `-dynamic-linker`.
The function `compiler.default_libc()` returns a `Spec` of the form
`glibc@x.y` or `musl@x.y` with the `external_path` property set.
The idea is this can be injected as a dependency.
If we can't run the dynamic linker directly, fall back to `ldd` relative
to the prefix computed from `ld.so.`
In the future we may transform the database from a single JSON object to
a stream of JSON objects.
This paves the way for constant time writes and constant time rereads
when only O(1) changes are made. Currently both are linear time.
This commit gives just enough forward compat for Spack to produce a
friendly error when we would move to a stream of json objects, and a db
would look like this:
```json
{"database": {"version": "<something newer>"}}
```
* compiler wrapper: prioritize spack managed paths in search order
This commit partitions search paths of -L, -I (and -rpath) into three
groups, from highest priority to lowest:
1. Spack managed directories: these include absolute paths such as
stores and the stage dir, as well as all relative paths since they
are relative to a Spack owned dir
2. Non-system dirs: these are for externals that live in non-system
locations
3. System dirs: your typical `/usr/lib` etc.
It's very easy for Spack to known the prefixes it owns, it's much more
difficult to tell system dirs from non-system dirs. Before this commit
Spack tried to distinguish only system and non-system dirs, and failed
for very trivial cases like `/usr/lib/x/..` which comes up often, since
build systems sometimes copy search paths from `gcc -print-search-dirs`.
Potentially this implementation is even faster than the current state of
things, since a loop over paths is replaced with an eval'ed `case ...`.
* Trigger a pipeline
* Revert "Trigger a pipeline"
This reverts commit 5d7fa863de.
* remove redudant return statement
* Add conflicts for some blas implementations that don't build on
Windows (or with %msvc)
* Need to enclose CC/CXX variables in quotes in case those paths
have spaces, otherwise Meson runs into errors
* On Windows, Python dependencies now add <prefix>/Scripts to the
PATH (this is established as a standard in PEP 370)
* Later versions of oneAPI have moved, so update detection to find it
in both old and new location
* Remove reliance on ONEAPI_ROOT env variable when determining Fortran
compiler version for %msvc
* When finding a Fortran compiler for MSVC, there was logic enforcing
a maximum MSVC version for a given oneAPI Fortran version. This
mapping was out of date and excluding valid combinations, so has
been removed (the logic now just picks the latest available
oneAPI Fortran compiler for any given MSVC version).
On Windows, bootstrapping logic now searches for and adds the win-sdk
and wgl packages to the user's top scope as externals if they are not
present.
These packages are generally required to install most packages with
Spack on Windows, and are only available as externals, so it is
assumed that doing this automatically would be useful and avoid
a mandatory manual step for each new Spack instance.
Note this is the first case of bootstrapping logic modifying
configuration other than the bootstrap configuration.
* gxsview: compiles againts system qt and vtk on rhel8
* Update gxsview/package.py for blanks around operator
* Update gxsview/package.py import blank line
* Update gxsview/package.py for style
* Update gxsview/package.py checking vtk version
Score-P does not accept "--with-foo=yes", but only "--with-foo" or "--with-foo=some-valid-specific-choice-or-path". This keeps Spack from generating config flags that will cause Score-P to barf.
This adds some improvements to `spack find` output when in environments based
around some thoughts about what users want to know when they're in an env.
If you're working in an enviroment, you mostly care about:
* What are the roots
* Which ones are installed / not installed
* What's been added that still needs to be concretized
So, this PR adds a couple tweaks to display that information more clearly:
- [x] We now display install status next to every root. You can easily see
which are installed and which aren't.
- [x] When you run `spack find -l` in an env, the roots now show their concrete
hash (if they've been concretized). They previously would show `-------`
(b/c the root spec itself is abstract), but showing the concretized root's
hash is a lot more useful.
- [x] Newly added/unconcretized specs still show `-------`, which now makes more
sense, b/c they are not concretized.
- [x] There is a new option, `-r` / `--only-roots` to *only* show env roots if
you don't want to look at all the installed specs.
- [x] Roots in the installed spec list are now highlighted as bold. This is
actually an old feature from the first env implementation , but various
refactors had disabled it inadvertently.
Reduce incidence of spurious errors by:
* Ensuring we're passing the buffer by reference
* Get the correct short string size from Windows API instead of computing ourselves
* Ensure sufficient space for null terminator character
Add test for `windows_sfn`
Currently if you request pkg +example where example is a conditional
variant, and you have a pkg in the database for which the condition
did not hold (so no +example nor ~example), the solver would reuse it
regardless, not imposing +example.
The change rules out exactly one thing: variant_set without variant_value,
which in practice could only happen when not node_has_variant (i.e. when
under the current package.py rules the variant's when condition did not
trigger).
Add a "default" option that passes no option to configure. Existing
options changed in the MPICH 4.2.0 release, so update the package to
reflect those changes.
Currently, some of the tests in `spec_format` and `spec_semantics` fetch
the actual zlib repository when run, because they call `str()` on specs
like `zlib@foo/bar`, which at least currently requires a remote git clone
to resolve.
This doesn't change the behavior of git versions, but it uses our mock git
repo infrastructure and clones the `git-test` package instead of the *real*
URL from the mock `zlib` package.
This should speed up tests. We could probably refactor more so that the git
tests *all* use such a fixture, but the `checks` field that unfortunately
tightly couples the mock git repository and the `git_fetch` tests complicates
this. We could also consider *not* making `str()` resolve git versions, but
I did not dig into that here.
- [x] add a mock_git_test_package fixture that sets up a mock git repo *and*
monkeypatches the `git-test` package (like our git test packages do)
- [x] use fixture in `test_spec_format_path`
- [x] use fixture in `test_spec_format_path_posix`
- [x] use fixture in `test_spec_format_path_windows`
- [x] use fixture in `test_parse_single_spec`
Commit 330a9a7c9a aimed at preventing
generation of .cfg files when a given compiler does not exist
in the particular release. However the check does not
contain the full paths so it always fails resulting in empty
.cfg files. This commit fixes it.
* add new axom releases, sync changes between repos
* add new version of axom and add fallback depends for umpire/raja
* remove now redundant flags, add flags to cuda flags to flags output by cachedcmakepackage
Co-authored-by: white238 <white238@users.noreply.github.com>
* w3nco %oneapi cflags: append -Wno-error=implicit-function-declaration
* update flag for %apple-clang, %clang
* [@spackbot] updating style on behalf of eugeneswalker
Upon close inspection of clingo answer sets, in some cases we have "equivalent" (i.e. same hash for the concrete spec) duplicates that differ only because of virtual nodes that are added to the answer set, without any edge using them.
This commit adds a property `autopush` to mirrors. When true, every source build is immediately followed by a push to the build cache. This is useful in ephemeral environments such as CI / containers.
To enable autopush on existing build caches, use `spack mirror set --autopush <name>`. The same flag can be used in `spack mirror add`.
* Simplify config command and add BLAS/LAPACK location
* Use BLAS_ROOT and LAPACK_ROOT and disable use of system
package registry
* Adds location of BLAS_LIBRARIES and LAPACK_LIBRARIES to CMake
* Adds CMake variables to prevent picking up system installations
of BLAS/LAPACK. Fixes previous PR #43328 that was picking up
incorrect installations
* Adds versions 7.2.1
* libzip: add up to v1.10.1
- update homepage and change download url to GitHub
- change build system to CMake for releases starting with 1.4
* [@spackbot] updating style on behalf of aumuell
* libzip: fix urls
* [@spackbot] updating style on behalf of aumuell
* libzip: do not add versions from libzip.org
these are old, and urllib refuses to fetch them
* libzip: deprecate versions from libzip.org
urllib refuses to fetch them, only curl would work
---------
Co-authored-by: aumuell <aumuell@users.noreply.github.com>
* acts: new version 33.1.0
* actsvg: new version 0.4.41
* geomodel: new package
* [@spackbot] updating style on behalf of wdconinc
* acts: plugin_cmake_variant(geomodel)
* geomodel: with when(+visualization)
---------
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
* Include recent change for Ubuntu
Select option -disable-no-pie-on-ubuntu for some Ubuntu systems
823971df01
* Added conflict for new variant
* Updated conflict version
* Added mention of Ubuntu to variant description
* Kokkos Kernels: adding missing TPLs and pre-conditions
Adding variants and dependencies for rocBLAS and rocSPARSE.
Also adding a "when=" close to the TPL variants that prevents
enabling the TPLs in versions of the library when it was not
yet available.
* Kokkos Kernels: remove comment for better format
* Kokkos Kernels: adding cusolver and rocsolver for at version 4.3.00
* Kokkos Ecosystem: updating packages for release 4.3.00
* Kokkos: adding arch for SG2042
* Removing sg2042 from spack_micro_arch_map
Removing it here and will work to add it in the proper generic spack location, likely: `spack/lib/spack/external/archspec/json/cpu/microarchitectures.json` ?
Allow reuse of specs that were built with compilers not in the current configuration. This means that specs from build caches don't need to have a matching compiler locally to be reused. Similarly when updating a distro. If a node needs to be built, only available compilers will be considered as candidates.
* add c++11 header to gold for compiler not defaulting to c++11
* glibc: add 2.39
* llvm: add 18.1.3
* fix#42314, remove cxx11 flag for llvm; should be controlled by cmake.
* modify patch
* llvm version
* add gmake version request
* yoda: new versions 1.9.9, 1.9.10, and 2.0.0
* [@spackbot] updating style on behalf of wdconinc
---------
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
As in the original makefile "FFLAGS_PROMOTION = -fdefault-real-8
-fdefault-double-8" is only used when `precision=double`. This is the default
for the Spack package, so no change if `precision` is left unset.
* Generally use os.replace on Windows and Linux
* Windows behavior for os.replace differs when the destination exists
and is a symlink to a directory: on Linux the dst is replaced and
on Windows this fails - this PR makes Windows behave like Linux
(by deleting the dst before doing the rename unless src and dst
are the same)
* Nalu: updating Trilinos recipe a bit
Basic changes to build/install nalu properly using Spack.
Some more changes would be nice for instance adding an
option to build against Trilinos master or develop. Adding
a dependency on googletest to avoid the annoying build
failures in the unit-tests.
* Nalu: adding release 1.6.0
Nalu v1.6.0 can build cleanly against Trilinos 14.0.0 with the
proposed changes. The only other combo is master / master but
than one is "floating" as these branch evolve over time. When a
new Nalu comes out we might want to add another fixed version to
keep this recipes up to date!
the autotools build system does something funky which causes a link line
where gccs default link dirs are explicitly added and end up before the
-L from spack's libunwind, so that ultimately it links against system
libunwind.
the cmake build system does better.
* upgrade new versions
* style fix
* update jaxlib deps (not cuda and bazel yet)
* update jaxlib cuda versions
* update jaxlib cuda versions
* update jaxlib cuda versions
* chore: style fix
* Update package.py
* Update package.py
* fix: typo
* docs: add source for cuda version
* py-jaxlib 0.4.14 also doesn't build on ppc64le
* Add 0.4.26
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* ParaView: Update version 5.12.0
Add 5.12.0 release
Update default to 5.12.0
* Add patch for building ParaView 5.12 with kits
* Drop VTKm from neoverse
* For avx build, the start address of values_ buffer in KernelParameters
is not a correct as it is computed based on 16-byte alignment.
* Style check error fix
* updating package.py for py-celery, py-kombu, py-amq
* added more py-kombu package versions
* fix copyrights and stype on py-kombu/package.py
* removed extra spaces
* added py-billiard 4.2.0 and added back the license('BSD-3-Clause')
* removed extra spaces in py-celery/package.py
* fixed py-amqp 2.4.0 sha; fixed py-celery's dependency of py-click (when version restrictions)
* more clean up on specifying version bounds
* Relax compiler and target mismatches
The mismatch occurs on an edge. Previously it was assigned
the parent priority, now it is assigned the child priority.
This should make reuse from buildcaches or store more likely,
since most mismatches will be counted with "reused" priority.
* Optimize version badness for runtimes at very low priority
We don't want to e.g. switch other attributes because we
cannot reuse an old installed runtime.
* Optimize runtime attributes at very low priority
This is such that the version of the runtime would
not influence whether we should reuse a spec.
Compiler mismatches are considered for runtimes,
to avoid situations where compiling foo%gcc@9
brings in gcc-runtime%gcc@13 if gcc@13 is among
the available compilers
* Exclude specs without runtimes from reuse
This should ensure that we do not reuse specs that
could be broken, as they expect the compiler to be
installed in a specific place.
The installer runs `get_dependent_ids`, which follows edges outside the
subdag that's being installed, so it returns a superset of the actual
dependents.
That's generally fine, except that it calls `s.package` on every
dependent, which triggers a package class to be instantiated, which is a
lot of work.
Instead, compute the package id from the spec, since that's all that's
used anyways and does not trigger *lots* of slow and redundant
instantiations of package objects.
If ONEAPI_ROOT is not set as an environment variable, the current approach will raise an error.
Instead we can compute the OneAPI_ROOT from the compiler paths like we do with vcvarsall.
The installation mechanism used on Linux to install py-pip (using pip
from the downloaded wheel to install the wheel) does not work on Windows.
This updates the installation of py-pip on Windows to download and
use a zipapp of a specific pip version in order to install the wheel
pip version that is requested.
`dpcpp` is deprecated by intel and has been superseded by `oneapi` compilers for a very long time.
---------
Co-authored-by: becker33 <becker33@users.noreply.github.com>
* SEACAS: Update package.py to handle new SEACAS project name
The base project name for the SEACAS project has changed from
"SEACASProj" to "SEACAS" as of @2022-10-14, so the package
needed to be updated to use the new project name when needed.
The refactor also changes several:
"-DSome_CMAKE_Option:BOOL=ON"
to
define("Some_CMAKE_Option", True)
* SEACAS, EXODUSII: New version; deprecate older versions; better variant descriptions
* [@spackbot] updating style on behalf of gsjaardema
* Fix long lines reported by flake8
---------
Co-authored-by: gsjaardema <gsjaardema@users.noreply.github.com>
* Add release 2.8.0
* Changing C compiler to hipcc
* Final release version
* Adding new cmake definition for rocm support
* Enabling rocm version support
* Update sha256
* Updating website URL
* Removing unnecessary C compiler spec
* Adding rocm-core dependency
* fixing rocm-core version
* fixing rocm-core version
* fixing style
* bugfix
* Add systemd
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* gobject-introspection: Correct glib versions
- The meson.build requirement that the glib version
is >= the gobject-introspective version is not in place
until v1.76.1.
- Prior to that, the requirement was glib >= 2.58.0.
- Bug introduced in acbf0d99c4, PR #42222.
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* util-linux: add v2.39.3
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* py-natsort: add new versions
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* geopm-service: default systemd support to true
- Make the dependency sticky to force a failure
if systemd compilation fails, or force
the user to disable the option.
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* geopm-service: Add initial multi-architecture support
- Restrict arch conflicts to 3.0.1
- Disable cpuid at configure time on non-x86_64 platforms.
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* geopm-service: update docstrings
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* Add py-geopmdpy
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* Add geopm-runtime recipe
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
---------
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
This PR allows the user to specify a path to a custom cert file (or directory) in
Spack's config:
```yaml
# This is where custom certs for proxy/firewall are stored.
# It can be a path or environment variable. To match ssl env configuration
# the default is the environment variable SSL_CERT_FILE
ssl_certs: $SSL_CERT_FILE
```
`config:ssl_certs` can be a path to a file or a directory, or it can be and environment
variable that resolves to one of those. When it posts to something valid, Spack will
update the ssl context to include custom certs, and fetching via `urllib` and `curl`
will trust the provided certs.
This should resolve many issues with fetching behind corporate firewalls.
---------
Co-authored-by: psakievich <psakievich@users.noreply.github.com>
Co-authored-by: Alec Scott <alec@bcs.sh>
After #41373, where we stopped considering the source directory to be the stage for develop builds,
we resumed *deleting* the stage even after a successful build.
We don't want this for develop builds because developers need to iterate; we should keep the artifacts
unless they explicitly run `spack clean`.
Now:
- [x] Build artifacts for develop packages are not removed after a successful install
- [x] They are also not removed before an install starts, i.e. develop packages always
reuse prior artifacts, if available.
- [x] They can be deleted in any other context, e.g. by running `spack clean --stage`
Prior FleCSI releases relied on commits on the control-replication branch (cr)
of Legion. That branch has now been merged into master and is part of the
24.03.0 Legion release.
* (py-)onnx: new version 1.14.{0,1}, 1.15.0
Notes on `onnx`:
- The C++ standard was changed to 14 in 1.15, so no more filter_file is needed. (The C++ standard has since changed to 17 in master.)
Notes on `py-onnx`:
- `py-pybind11` was an unlisted requirement in CMakeLists.txt since 1.3 or so (before earliest spack package).
* py-onnx: depends_on pybind11 with type link, not run
* py-onnx: depends_on py-setuptools@64:
Users requested an option to filter between local/upstream results in `spack find` output.
```
# default behavior, same as without --install-tree argument
$ spack find --install-tree all
# show only local results
$ spack find --install-tree local
# show results from all upstreams
$ spack find --install-tree upstream
# show results from a particular upstream or the local install_tree
$ spack find --install-tree /path/to/install/tree/root
```
---------
Co-authored-by: becker33 <becker33@users.noreply.github.com>
* sundials: add new version
* note previous default
* update when clause for removed options
---------
Co-authored-by: David J. Gardner <gardner48@llnl.gov>
* SEACAS: Update package.py to handle new SEACAS project name
The base project name for the SEACAS project has changed from
"SEACASProj" to "SEACAS" as of @2022-10-14, so the package
needed to be updated to use the new project name when needed.
The refactor also changes several:
"-DSome_CMAKE_Option:BOOL=ON"
to
define("Some_CMAKE_Option", True)
* exodusii -- refactor and bring up-to-date
* Add missed patch file
* [@spackbot] updating style on behalf of gsjaardema
* Apply seacas windows patch here also.
* Update url so old checksums valid; redo new checksums
---------
Co-authored-by: gsjaardema <gsjaardema@users.noreply.github.com>
* Initial commit to bump rocprofiler-dev to 6.0 and add aqlprofile recipe
* bump to 6.0.2 and extracting binaries from deb pkg
* fixes for hpctoolkit build errors
* add yum and zyp aqlprofile packages
* fix style issues
* Allow compilers to function across compatible OS's
* Add documentation in the default yaml
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Co-authored-by: Gregory Becker <becker33@llnl.gov>
* py-libsonata: new package starting at 0.1.25
* align spack version with the git branch
* Fix min required versions / use spack packages instead of submodules
* Create devcontainer.json
* Ensure codespace can be setup for current branch
* fix: find compilers in site scope
* fix: use cloud_pipelines ubuntu20.04 image
* fix: spack config --scope site add
* fix: use develop, not develop-root mirror
This adds a dependency on pkg-config which in turn builds pkg-config
on pipelines using %onapi/%cce: update the pkg-config build to disable
specific warnings-as-errors from these compilers.
Co-authored-by: Reid Priedhorsky <1682574+reidpr@users.noreply.github.com>
* Add macos-14 as a runner (Apple M1)
* Mark a test xfail
We need to check later if this test needs modifications
on Apple Silicon chips.
---------
Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
Co-authored-by: alalazo <alalazo@users.noreply.github.com>
* buildcache sync: manifest-glob with arbitrary destination
The current implementation of the --manifest-glob is a bit restrictive
requiring the destination to be known by the generation stage of CI.
This allows specifying an arbitrary destination mirror URL.
* Add unit test for buildcache sync with manifest
* Fix test and arguments for manifest-glob with override destination
* Add testing path for unused mirror argument
* Remove a few compilers from static test data
These compilers were used only in a bunch of tests, so
they are added only there.
* Remove clang@3.3 from unit test configuration
* Parametrize compilers.yaml
* Remove specially named gcc from static data
The compilers are used in two tests
* Remove apple-clang and macOS compilers from static data
The compiler was used only in multimethod tests
* Remove clang@3.5 (compiler seems to be unused)
* Remove gcc@4.4.0 (compiler seems to be unused)
* Exclude x86_64 tests on other architectures
* Mark two tests as for clingo only
* Update version syntax in compilers.yaml
* Parametrize tcl tests on architectures
* Parametrize lmod tests on architectures
* Substitute gcc@4.5.0 with gcc@4.8.0 so it can be used on aarch64
* Fix a few issues with aarch64 and unit-tests
It's now possible to add config on the command line with `spack -c <CONFIG_VARS> ...`, but the new `command_line` scope isn't reflected in the help output for `--scope`:
```bash
> spack help config
...
--scope {defaults,system,site,user}[/PLATFORM] or env:ENVIRONMENT
configuration scope to read/modify
...
```
This PR adds:
- A new runtime for `%oneapi` compilers, called `intel-oneapi-runtime`
- Information to both `gcc-runtime` and `intel-oneapi-runtime`, to ensure
that we don't mix compilers using different soname for either `libgfortran`
or `libifcore`
To do so, the following internal mechanisms have been implemented:
- Possibility to inject virtual dependencies from the `runtime_constraints`
callback on packages
Information has been added to `gcc-runtime` to provide the correct soname
under different conditions on its `%gcc`.
Rules injected into the solver looks like:
```prolog
% Add a dependency on 'gfortran@5' for nodes compiled with gcc@=13.2.0 and using the 'fortran' language
attr("dependency_holds", node(ID, Package), "gfortran", "link") :-
attr("node", node(ID, Package)),
attr("node_compiler", node(ID, Package), "gcc"),
attr("node_compiler_version", node(ID, Package), "gcc", "13.2.0"),
not external(node(ID, Package)),
not runtime(Package),
attr("language", node(ID, Package), "fortran").
attr("virtual_node", node(RuntimeID, "gfortran")) :-
attr("depends_on", node(ID, Package), ProviderNode, "link"),
provider(ProviderNode, node(RuntimeID, "gfortran")),
attr("node", node(ID, Package)),
attr("node_compiler", node(ID, Package), "gcc"),
attr("node_compiler_version", node(ID, Package), "gcc", "13.2.0"),
not external(node(ID, Package)),
not runtime(Package),
attr("language", node(ID, Package), "fortran").
attr("node_version_satisfies", node(RuntimeID, "gfortran"), "5") :-
attr("depends_on", node(ID, Package), ProviderNode, "link"),
provider(ProviderNode, node(RuntimeID, "gfortran")),
attr("node", node(ID, Package)),
attr("node_compiler", node(ID, Package), "gcc"),
attr("node_compiler_version", node(ID, Package), "gcc", "13.2.0"),
not external(node(ID, Package)),
not runtime(Package),
attr("language", node(ID, Package), "fortran").
```
The default url couldn't be the one with v0.0.0-aws since spack was
replacing v0.0.0-aws with v<version_number> for example, deleting the
-aws suffix. I used the url_for_version method to specify this suffix.
This adds support for prereleases. Alpha, beta and release candidate
suffixes are ordered in the intuitive way:
```
1.2.0-alpha < 1.2.0-alpha.1 < 1.2.0-beta.2 < 1.2.0-rc.3 < 1.2.0 < 1.2.0-xyz
```
Alpha, beta and rc prereleases are defined as follows: split the version
string into components like before (on delimiters and string boundaries).
If there's a string component `alpha`, `beta` or `rc` followed by an optional
numeric component at the end, then the version is prerelease.
So `1.2.0-alpha.1 == 1.2.0alpha1 == 1.2.0.alpha1` are all the same, as usual.
The strings `alpha`, `beta` and `rc` are chosen because they match semver,
they are sufficiently long to be unambiguous, and and all contain at least
one non-hex character so distinguish them from shasum/digest type suffixes.
The comparison key is now stored as `(release_tuple, prerelease_tuple)`, so in
the above example:
```
((1,2,0),(ALPHA,)) < ((1,2,0),(ALPHA,1)) < ((1,2,0),(BETA,2)) < ((1,2,0),(RC,3)) < ((1,2,0),(FINAL,)) < ((1,2,0,"xyz"), (FINAL,))
```
The version ranges `@1.2.0:` and `@:1.1` do *not* include prereleases of
`1.2.0`.
So for packaging, if the `1.2.0alpha` and `1.2.0` versions have the same constraints on
dependencies, it's best to write
```python
depends_on("x@1:", when="@1.2.0alpha:")
```
However, `@1.2:` does include `1.2.0alpha`. This is because Spack considers
`1.2 < 1.2.0` as distinct versions, with `1.2 < 1.2.0alpha < 1.2.0` as a consequence.
Alternatively, the above `depends_on` statement can thus be written
```python
depends_on("x@1:", when="@1.2:")
```
which can be useful too. A short-hand to include prereleases, but you
can still be explicit to exclude the prerelease by specifying the patch version
number.
### Concretization
Concretization uses a different version order than `<`. Prereleases are ordered
between final releases and develop versions. That way, users should not
have to set `preferred=True` on every final release if they add just one
prerelease to a package. The concretizer is unlikely to pick a prerelease when
final releases are possible.
### Limitations
1. You can't express a range that includes all alpha release but excludes all beta
releases. Only alternative is good old repeated nines: `@:1.2.0alpha99`.
2. The Python ecosystem defaults to `a`, `b`, `rc` strings, so translation of Python versions to
Spack versions requires expansion to `alpha`, `beta`, `rc`. It's mildly annoying, because
this means we may need to compute URLs differently (not done in this commit).
### Hash
Care is taken not to break hashes of versions that do not have a prerelease
suffix.
Generate CI scripts as powershell on Windows. This is intended to
output exactly the same bash scripts as before on Linux.
Co-authored-by: Ryan Krattiger <ryan.krattiger@kitware.com>
As the cmake build is triggered by scikit build, the usual spack option
for enabling tests had no effect and the heavy test suite ran all the time.
Used https://github.com/scikit-build/cmake-python-distributions/issues/172#issuecomment-890322263
to implement how to pass options to the actual `cmake` build.
I also excluded some tests that failed for me on alma9 (gcc 11.4.1),
so the rest of the test suite can be run.
Enable OpenBLAS's built-in CPU capability detection and kernel selection.
This allows run-time selection of the "best" kernels for the running CPU, rather
than what is specified at build time. For example, it allows OpenBLAS to use
AVX512 kernels when running on ZEN4, and built targeting the "ZEN" architecture.
Co-authored-by: Branden Moore <branden.moore@amd.com>
* Changes to re-enable aws-pcluster pipelines
- Use compilers from pre-installed spack store such that compiler path relocation works when downloading from buildcache.
- Install gcc from hash so there is no risk of building gcc from source in pipleine.
- `packages.yam` files are now part of the pipelines.
- No more eternal `postinstall.sh`. The necessary steps are in `setup=pcluster.sh` and will be version controlled within this repo.
- Re-enable pipelines.
* Add and
* Debugging output & mv skylake -> skylake_avx512
* Explicilty check for packages
* Handle case with no intel compiler
* compatibility when using setup-pcluster.sh on a pre-installed cluster.
* Disable palace as parser cannot read require clause at the moment
* ifort cannot build superlu in buildcache
`ifort` is unable to handle such long file names as used when cmake compiles
test programs inside build cache.
* Fix spack commit for intel compiler installation
* Need to fetch other commits before using them
* fix style
* Add TODO
* Update packages.yaml to not use 'compiler:', 'target:' or 'provider:'
Synchronize with changes in https://github.com/spack/spack-configs/blob/main/AWS/parallelcluster/
* Use Intel compiler from later version (orig commit no longer found)
* Use envsubst to deal with quoted newlines
This is cleaner than the `eval` command used.
* Need to fetch tags for checkout on version number
* Intel compiler needs to be from version that has compatible DB
* Install intel compiler with commit that has DB ver 7
* Decouple the intel compiler installation from current commit
- Use a completely different spack installation such that this current pipeline
commit remains untouched.
- Make the script suceed even if the compiler installation fails (e.g. because
the Database version has been updated)
- Make the install targets fall back to gcc in case the compiler did not install
correctly.
* Use generic target for x86_64_vX
There is no way to provision a skylake/icelake/zen runner. They are all in the
same pools under x86_64_v3 and x86_64_v4.
* Find the intel compiler in the current spack installation
* Remove SPACK_TARGET_ARCH
* Fix virtual package index & use package.yaml for intel compiler
* Use only one stack & pipeline per generic architecture
* Fix yaml format
* Cleanup typos
* Include fix for ifx.cfg to get the right gcc toolchain when linking
* [removeme] Adding timeout to debug hang in make (palace)
* Revert "[removeme] Adding timeout to debug hang in make (palace)"
This reverts commit fee8a01580489a4ea364368459e9353b46d0d7e2.
* palace x86_64_v4 gets stuck when compiling try newer oneapi
* Update comment
* Use the latest container image
* Update gcc_hashes to match new container
* Use only one tag providing tags per extends call
Also removed an unnecessary tag.
* Move generic setup script out of individual stack
* Cleanup from last commit
* Enable checking signature for packages available on the container
* Remove commented packages / Add comment for palace
* Enable openmpi@5 which needs pmix>3
* don't look for intel compiler on aarch64
* py-python-lsp-server: add v1.10.0
* Apply suggestions from code review
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Remove py-wheel from package
* Apply suggestions from code review
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Running a `spack-python` script like this:
```python
import spack
import multiprocessing
def echo(args):
print(args)
if __name__ == "__main__":
pool = multiprocessing.Pool(2)
pool.map(echo, range(10))
```
will fail in `develop` with an error like this:
```console
_pickle.PicklingError: Can't pickle <function echo at 0x104865820>: attribute lookup echo on __main__ failed
```
Python expects to be able to look up the method `echo` in `sys.path["__main__"]` in
subprocesses spawned by `multiprocessing`, but because we use `InteractiveConsole` to
run `spack python`, the executed file isn't considered to be the `__main__` module, and
lookups in subprocesses fail. We tried to fake this by setting `__name__` to `__main__`
in the `spack python` command, but that doesn't fix the fact that no `__main__` module
exists.
Another annoyance with `InteractiveConsole` is that `__file__` is not defined in the
main script scope, so you can't use it in your scripts.
We can use the [runpy.run_path()](https://docs.python.org/3/library/runpy.html#runpy.run_path) function,
which has been around since Python 3.2, to fix this.
- [x] Use `runpy` module to launch non-interactive `spack python` invocations
- [x] Only use `InteractiveConsole` for interactive `spack python`
Often in containers, the files we use to detect whether a cray system supports new features are not available.
Given that the cray containers only support the newer versions, and that these versions have been
around for a while at this point and few sites don't support them, this PR changes the logic for
detecting cray systems so that:
1. Don't even consider whether something is the `cray` platform if `opt/cray` is not in `MODULEPATH`
2. Only use the `cray` platform if we can read files in /opt/cray/pe and positively detect an older version
3. Otherwise, assume we're *not* on a cray (includes newer Cray PE's, which we treat as Linux)
Compilation with the old flags fails on PowerPC (power8le) due to syntax
errors in the output from the preprocessor. Compilation with the
extended set of flags works both on PowerPC and x86_64.
The correct set of flags was suggested from the berkeleygw developers:
https://groups.google.com/a/berkeleygw.org/g/help/c/ewi3RZgOyeE/m/jSIoe45PAgAJ
Uses spack-provided compiler prefix to call cpp when compiling berkeleygw with gcc.
Adds variants to turn off tests
Add variants for some missing TPL options
Add the variables required to build in ~shared
* Add pamgen to Trilinos as a variant to support SEACAS
This adds the ability to turn off and on pamgen as needed
through the variant interface for the Trilinos package.py.
Add changes for seacas package.py to build the appropriate
Trilinos variants.
Add zlib-api as depends_on instead of zlib directly for SEACAS
package.py
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* Add variant typescript for py-jupyter-server@:1, which then requires npm/node. Patch the build system for ~typescript so that it doesn't find any npm/node installations and attempts to build the typescript extension even though it shouldn't
* Fix formatting in var/spack/repos/builtin/packages/py-jupyter-server/package.py
* Constrain typescript variant to py-jupyter-server versions 1.10.2:1
* with when not needed if variant doesn't exist for other versions
This should fix issue #43192
Basically, had issue where a make variable was set to the output
of a shell function which included cd commands, and then the value
of that variable used as a makefile target.
The cd commands in the shell function caused assorted informational
messages (e.g. "Entering directory ...") which got included in the
return of the shell function, corrupting the value of the variable.
The presence of colons in the corrupted value caused make to issue
"multiple target" erros.
This fix adds --no-print-directory flags to the calls to the
make function in the package's build method, which resolves the
issue above.
It is admittedly a crude fix, and will remove *all* informational
messages re directory changes, thereby potentially making it more
difficult to diagnose/debug future issues building this package.
However, I do not see a way for to turn off these messages in a
more surgical manner.
* mgard: don't restrict protobuf version more than necessary
successfully built:
mgard@2022-11-18 ^protobuf@3.{4,21,25}
mgard@2023-01-10 ^protobuf@3.{4,25}
mgard@2023-03-31 ^protobuf@3.{4,25}
compile failures:
mgard@2022-11-18 ^protobuf@3.3
mgard@2023-01-10 ^protobuf@3.3
mgard@2023-03-31 ^protobuf@3.3
* mgard: add conflicts to address CI errors
* mgard: conflict between cuda and abseil@20240116.1
compiling mgard+cuda with gcc@12.3.0 and nvcc from cuda@12.3.0 against
protobuf pulling in abseil-cpp@20240116.1 results in the errors reported
here: https://github.com/abseil/abseil-cpp/issues/1629
* py-shacl: new version, update dependencies
Also updates the dependencies py-prettytable and py-rdflib.
* review comments
* Update var/spack/repos/builtin/packages/py-pyshacl/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-poetry-core: add required 1.8.1
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
`jinja2` can be a costly import, and right now it happens at startup every time we run
Spack. This slows down `spack --print-shell-vars` a bit, which is needed by `setup-env.*sh`.
Patch allowing Clingo to build with VS22 has landed both in Spack
and Clingo upstream, update Spack's bootstrap constraints to handle
this.
Additionally, properly scope the patch application in the clingo
package to handle upstream patch.
Currently (outside of this PR) when you `spack develop` a path, this path is treated as the staging
directory (this means that for example all build artifacts are placed in the develop path).
This PR creates a separate staging directory for all `spack develop`ed builds. It looks like
```
# the stage root
/the-stage-root-for-all-spack-builds/
spack-stage-<hash>
# Spack packages inheriting CMakePackage put their build artifacts here
spack-build-<hash>/
```
Unlike non-develop builds, there is no `spack-src` directory, `source_path` is the provided `dev_path`.
Instead, separately, in the `dev_path`, we have:
```
/dev/path/for/foo/
build-{arch}-<hash> -> /the-stage-root-for-all-spack-builds/spack-stage-<hash>/
```
The main benefit of this is that build artifacts for out-of-source builds that are relative to
`Stage.path` are easily identified (and you can delete them with `spack clean`).
Other behavior added here:
- [x] A symlink is made from the `dev_path` to the stage directory. This symlink name incorporates
spec details, so that multiple Spack environments that develop the same path will not conflict
with one another
- [x] `spack cd` and `spack location` have added a `-c` shorthand for `--source-dir`
Spack builds can still change the develop path (in particular to keep track of applied patches),
and for in-source builds, this doesn't change much (although logs would not be written into
the develop path). Packages inheriting from `CMakePackage` should get this benefit
automatically though.
Add current versions of the 17 and 18 releases
Stop making it nearly impossible to compose this correctly with code built with gcc
Build for compatibility by default like we do in every other llvm package
The `patch()` directive can now be invoked with `reverse=True` to apply a patch in reverse.
This is useful for reverting commits that caused errors in projects, even if only the forward
patch is available, e.g. via a GitHub commit patch URL.
`patch(..., reverse=True)` runs `patch -R` behind the scenes. This is a POSIX option so we
can expect it to be available on the `patch` command.
---------
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
set the FC variable to the MPI Fortran compiler and also set the F90 variable
to the same compiler for versions 9.8 and up. FC needs to be set because the
configure script still uses FC.
* unmaintained packages: add new versions
* Fix parallel and numactl
* Revert numactl changes
* rollback lua-sol2 version
* Update alluxio version format
* py-psyclone and py-fparser new releases added
* py-fparser: add missing releases for py-psyclone
* py-psyclone: actioned @adamjstewart comments
* py-psyclone: removed py-pytest-pylint
* py-pytest-pylint: added package @ latest version
* py-pytest-pylint: reformatted
* Update var/spack/repos/builtin/packages/py-psyclone/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-pytest-pylint: added build deps and runtime dep versions
* py-pytest-pylint: removed version from setuptools
* py-psyclone: add py-pytest-pylint test dep and alphabetize deps
* Update var/spack/repos/builtin/packages/py-pytest-pylint/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-psyclone: deps ordered
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
fixes#43097
Before this PR the behavior of mixins used together with
builders was to mask completely the callbacks defined from
the class coming later in the MRO.
Here we fix the behavior by accumulating all callbacks,
and de-duplicating them later.
* package/qgis: add new version
* improve Qsci.pro
* improve
* fix undefined symbol qsciprinter error
* add import test
* fix bug
* add version 3.36
* [@spackbot] updating style on behalf of Sinan81
* fix long line
* only run import test when +python
* first attempt at stand-alone test
* add TODO
---------
Co-authored-by: sbulut <sbulut@3vgeomatics.com>
Co-authored-by: Sinan81 <Sinan81@users.noreply.github.com>
Co-authored-by: Sinan81 <Sinan@world>
* proj: correct CMake arg for shared build with proj older than 7.0.0
* Actually use new CMake arg
* Update var/spack/repos/builtin/packages/proj/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
This adds Spack packages for these Perl distributons:
- Bio::DB::EUtilities and its dependencies:
- Bio::ASN1::EntrezGene
- Bio::Cluster
- Bio::Variation
* Properly specify Curl builder interface for static vs shared curl
with NMake system to ensure all built curls export expected
symbols.
* Symlinks curl library build artifact to more idiomatic name for
FindCurl.cmake implementations and other NMake consumers.
* Deprecating py-pylint@2.3 as it cannot build with python@3.8:
* Style fix
* Removed versions because can't build with python@3.7
---------
Co-authored-by: Gava, Francesco <francesco.gava@mclaren.com>
* py_cheap_repr: add initial package.py
* Update var/spack/repos/builtin/packages/py-cheap-repr/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-cheap-repr: use pypi link instead
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Added new versions @1.5.1 and @1.4.1 (sfcgal moved from github to gitlab)
Placed restrictions on what versions of cgal are supported for different
cfcgal versions. These restrictions are based on what was found in the
version history at https://gitlab.com/sfcgal/SFCGAL/-/blob/v1.5.1/NEWS?ref_type=tags
as well as the CMakeLists.txt for different versions.
@1.4 and @1.5 seem to require a specific version of cgal based on CMakeLists.txt
Earlier versions (@1.3.8:1.3.10) claim to support cgal@4.3: (but Spack recipe
claims did not work until @4.7, so sticking with that as minimum). CMakeList.txt
suggests they support cgal@5 as well, but version history suggests otherwise.
* Expanding the duckdb package to fix the version number (required for external extensions to work) being pulled from git and have variants for the built-in extensions at build-time. This also changes the build system from CMakePackage to Makefile package (as advised from upstream).
* - Reorganized and cleaned up variants
- Updated the patch to work for 0.10.0+
- Removed (or made non-default) some unecessary variants
- Added ninja as the default generator
- Set up some shared library dependencies;
* enable tensorflow-2.11 support for ROCm
* add latest sha for mesa and limit the patches to older version.similar
changes in #37910 to enable gitlab-ci pass
* address review commemts
Remove dependency on `importlib_metadata` and `pkg_resources`, which can be problematic if the version in PYTHONPATH is incompatible with the interpreter Spack is running under.
* Kokkos Kernels: adding missing TPLs and pre-conditions
Adding variants and dependencies for rocBLAS and rocSPARSE.
Also adding a "when=" close to the TPL variants that prevents
enabling the TPLs in versions of the library when it was not
yet available.
* Kokkos Kernels: remove comment for better format
* Kokkos Kernels: fix issue with unpacking wrong number of args
After changing the tpls dictionary we need to update the unpacking
logic to catch the right number of outputs out of it!
* Kokkos Kernels: updating doc string for tpls var and using f-string
Improving comment a bit and switching to f-string for more readability.
When setup to do more testing will try to use f-string in the CMake
options generation part of the package.
* Style change
* sst-core now effectively depends on ncurses
* use --with-curses
* sst-core: update comment about ncurses
* should have curses for build, link, and run
Closes#43052.
Maybe moving the argument to the `find` subcommand is a good idea, but I
just wanted to get the docs fix out.
Co-authored-by: Patrice Peterson <patrice.peterson@itz.uni-halle.de>
This PR adds the ability to load spack extensions through `importlib.metadata` entry
points, in addition to the regular configuration variable.
It requires Python 3.8 or greater to be properly supported.
#42878 adds a post install filter of the netCDFConfig.cmake file
that replaces a valid CMake target on Windows with an invalid one.
Don't do this replacement on Windows.
* Updates for migraphx 6.0.0 & 6.0.2
* Style check error and audit check error fix
* Adding patch for half-include-directory
* The parameter GPU_TARGETS is used from 5.7 in migraphx
* Adding rocmlir dependency in migraphx and 6.0 updates in rocmlir
* Applying upcoming changes to make CK JIT optional and enable
compilation on Windows in order to build without ck dependency
* mpfr: missing dependency for version 4.0.1
mpfr 4.0.1 (like 4.0.2) needs autoconf-archive where it takes the
AX_PHREAD macro from
* autoconf-archive is also required for mpfr@4.0.0
New changes have been made to nvptx-tools that address dropping support
for sm_30 in later CUDA versions (12.0+).
Also refactor gcc to make nvptx-tools a dependency instead of a resource.
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
Adds CHI::Driver::Memcached.
Modified perl-chi to make the tests work. Testing modules in perl-chi
were not loaded when testing CHI::Driver::Memcached, so added the "run"
type to these.
* ASP-based solver: improve reusing nodes with gcc-runtime
This PR skips emitting dependency constraints on "gcc-runtime",
for concrete specs that are considered for reuse.
Instead, an appropriate version of gcc-runtime is recomputed
considering also the concrete nodes from reused specs.
This ensures that root nodes in a DAG have always a runtime
that is at a version greater or equal than their dependencies.
* Add unit-test for view with multiple runtimes
* Select latest version of runtimes in views
* Construct result keeping track of latest
* Keep ordering stable, just in case
1) support for version @3.0
Unfortunately, download seems to require registration now
so using manual_download mechanism for @3:
2) copying from hdf-eos5 patch from @vanderwb to enable
use of Spack compiler wrappers instead of h4cc
3) Patching an issue in hdf-eos2 configure script. The
script will test for jpeg, libz libraries, succeed and
append HAVE_LIBJPEG=1, etc to confdefs.h, and then abort
because HAVE_LIBJPEG not set in running environment.
4) Add some LDFLAGS to build environment. Otherwise
seems to fail to build test script due to rpc dependence
in HDF4.
Adds Net::Server::SS::PreFork and its dependencies.
Installed OK with build-time tests. Added dependencies:
- Server::Starter
- Net::Server
- HTTP::Server::Simple
Adds Catalyst::Action::RenderView and its dependencies.
Installed OK with build-time tests. Added dependencies:
- Catalyst::Action::RenderView
- Catalyst::Action::RenderView
- Catalyst::Action::RenderView
* package/imagemagick add new version, improve
* confimed that build fails when libsm is missing on linux
---------
Co-authored-by: Sinan81 <Sinan@world>
* perl-chi and deps: new packages
Adds CHI and its dependencies.
Installed OK with build-time tests. Added dependencies:
- CHI
- CHI
- CHI
- CHI
- CHI
- CHI
- CHI
- CHI
- CHI
- CHI
- CHI
- CHI
* Add license
* legion: Add 23.09.0 and 23.12.0, remove control_replication.
The branch control_replication has been merged to master and should no
longer be used.
* flecsi: Switch to Legion master branch.
Legion control_replication has been merged to master.
* Fix Legion 23.09.0 and 23.12.0 build for ROCm 6.
* Add ncvis and opengl option for wxwidgets
* Style fixes for ncvis
* Replace in with satisfies for opengl constraint
Co-authored-by: Alec Scott <alec@bcs.sh>
---------
Co-authored-by: Alec Scott <alec@bcs.sh>
* when built with cmake, libogg does not build with a shared libary by default. This resolves that
* spack style fixes
* Clean up imports
* enforce +pic when +shared
* Execute `args.help` after setting main options so that extension commands will show with `spack -h`
---------
Co-authored-by: psakievich <psakiev@sandia.gov>
* Update package.py
1. add one compiler type named 'musl'
2. add a variant name 'multilib'
3. add a variant name 'cmodel'
* Added one compiler type named 'musl'.
Added a variant named 'multilib'.
Added a variant named 'cmodel'.
Added several versions.
* aarch64 is not supported.
The deps were added in #40945 to make it work on macOS 11, because the
old configure scripts only detect macOS 10. Apparently people reported the
autoreconf script caused issues, later fixed in #41057. However, also
with that fix, things are incorrect, cause people now report:
```
libtool: You should recreate aclocal.m4 with macros from libtool 2.4.7
libtool: and run autoconf again.
```
HOWEVER, all this is unnecessary, because the underlying issue was
already fixed long ago, it's just that it regressed at some point, but
it's back in place since #41205.
This adds Readonly::XS. Since this module can not be used by itself, the
Spack package comes with a test override. This anticipates that the perl
builder will one day have a generic standalone module usage test.
This should fix issue #40780
We explicitly cast self.spec["python"].command to str in the filter_file
call in _fix_dtrace_shebang to avoid the error
==> Error: TypeError: expected str, bytes or os.PathLike object, not Executable
Not sure why the error is appearing (is it only for specific python versions, etc?),
but the fix should be quite safe.
* e4s: new packages: glvis, laghos
* gl: require: osmesa
* be explicit: glvis ^llvm so that llvm-amdgpu not chosen
* glvis fails on oneapi stack due to issue 42839
Spack merges ranges and concrete versions if they have non-empty
intersection. That is not enough for adjacent version ranges.
This commit ensures that disjoint ranges in version lists are simplified
if their union is not disjoint:
```python
"@1.0:2.0,2.1,2.2:3,4:6" # simplifies to "@1.0:6"
```
Libraries for openexr are named libOpenEXR*.so, etc., so the default libs
handler in spec does not find them.
Add a custom libs property to address this.
Partial fix for #42273
Co-authored-by: payerle <payerle@users.noreply.github.com>
for various reasons had to advance dependency of 5.0.2 to at least
pmix 4.2.4. 5.0.1 and 5.0.0 can also build with 4.2.4 pmix or newer.
related to #42651
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
Refactoring `SpackSolverSetup` is a bit easier with type annotations, so I started
adding some. This adds annotations for the (many) instance variables on
`SpackSolverSetup` as well as a few other places.
This also refactors `condition()` to reduce redundancy and to allow
`_get_condition_id()` to be called independently of the larger condition
function.
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* py-ipyvuetify: new package
* Limit py-jupyter-packing version to 0.7.x
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Fix py-jupyterlab version and type
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Fix py-ipyvue version range to exclude 2
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* rm py-wheel, already considered for PythonPackage
* fix: pynpm only required for build, reorder dependencies as in the pyproject.toml
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* snakemake: add Snakemake 8 with dependencies
* snakemake: add missing description
* Whitespace
* Whitespace
* Whitespace
* Whitespace
* py-conda-inject: add constraint for Python
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-snakemake-executor-plugin-azure-batch: add constraint for Python
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-snakemake-executor-plugin-cluster-generic: add constraint for Python
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-snakemake: add upper bound for Python
* py-snakemake-executor-plugin-drmaa: specify dependency type
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-snakemake-executor-plugin-googlebatch: correct dependency version
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-snakemake-executor-plugin-tes: correct dependency version
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-snakemake-storage-plugin-s3: reorder
* snakemake: remove newly added variants
* snakemake: remove newly added variants
* snakemake: remove newly added variant
* snakemake: update version
* snakemake: update version
* snakemake: whitespace
* py-snakemake-storage-plugin-s3: update version
* snakemake: use newer version
* snakemake: whitespace
* snakemake: update interfaces
* py-snakemake-storage-plugin-gcs: link issue
* snakemake: update versions
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* package/libspatialite: add conflict, new version
* depends on new version of freexl
* fix bug
* remove manual download stuff
* improve style
* first depracate
* [@spackbot] updating style on behalf of Sinan81
* get rid of conflict, reorder deps
* remove manual download
---------
Co-authored-by: sbulut <sbulut@3vgeomatics.com>
Co-authored-by: Sinan81 <Sinan81@users.noreply.github.com>
* Allow awscli-v2 to be installed without examples/ dir
* [@spackbot] updating style on behalf of AlexanderRichert-NOAA
* Update var/spack/repos/builtin/packages/awscli-v2/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
The CMake-based build is anticipated to work in all cases where the
Autotools-based build did, and to address all prior issues with less
maintenance of the package. In detail:
* Fixes#42735 (CMake's find_package helps with linking to proper
netcdf-c)
* Replaces older Autotools-based build
* All preexisting variants are handled
* Record hdf5 as an explicit dependency (was missing before)
* Add +tests option
Co-authored-by: Chrismarsh <Chrismarsh@users.noreply.github.com>
* proj: apply stdint.h patch in version 8
* Update var/spack/repos/builtin/packages/proj/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Some builds on Windows break when encountering paths with spaces. This
reencodes some paths in Windows 8.3 filename format (when on Windows):
this serves as an equivalent identifier for the file, but in a form that
does not have spaces.
8.3 filenames are also truncated in length, which could be helpful, but
that is not the primary intended purpose of using this format.
Overall
* nmake/msbuild packages do this generally for the install prefix
* curl/perl require additional modifications (as written now, each package
may require calls to `windows_sfn` to work when the Spack
root/install/staging prefixes contain spaces)
Some items for follow-up:
* Spack itself does not create paths with spaces "on top" of whatever
the user configures or where it is placed (e.g. the Spack root, the
staging directory, etc.), so it might be possible to edit some of these
paths once and avoid a proliferation of individual `windows_sfn`
calls in individual packages.
* This approach may result in the insertion of 8.3-style paths into
build artifacts (on Windows), handling this may require additional
bookkeeping (e.g. when relocating).
* Move spec_list into its own file, instead of __init__.py
* Remove spack.schema.spack
This module was introduced in #33960 It's almost an exact duplicate of
spack.schema.env, and is not used anywhere.
* Fix typo
* adds the spack recipe for py-jwcrypto
* split long line to fix E501
* Specify versions for py-cryptography and py-typing-extensions
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* adds the spack recipe for reacton python package
* Fix versions for ipywidgets and typing-extensions
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-find-libpython: new package
* Update var/spack/repos/builtin/packages/py-find-libpython/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* add spack recipe for ipyvue
* Specify version for ipywidgets
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update package.py
fix bug.
* Update var/spack/repos/builtin/packages/pdal/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-ansible: add v2.16.3
* Apply suggestions from code review
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add specific python version requirements from setup.cfg
* Add additional ranges for py-setuptools
* Update var/spack/repos/builtin/packages/py-ansible/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Compiling version 2.2.4 fails (on a Debian system with only a minimum set of packages installed) with an error because `INT_MAX` is undeclared:
```
263 gd_gd2.c: In function '_gd2GetHeader':
>> 264 gd_gd2.c:212:54: error: 'INT_MAX' undeclared (first use in this function)
265 212 | if (*ncx <= 0 || *ncy <= 0 || *ncx > INT_MAX / *ncy) {
266 | ^~~~~~~
267 gd_gd2.c:87:1: note: 'INT_MAX' is defined in header '<limits.h>'; did you forget to '#include <limits.h>'?
```
* pythia6: deal with dead pythiasix.hepforge.org
* pythia6: rm main81.f from CMakeLists.txt
* [@spackbot] updating style on behalf of wdconinc
---------
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
Any package `X` used as `depends_on("x", type="build")` will have
`X.setup_run_environment(env)` called, because it has to be able to
"run" in the build environment.
So there is no point in calling `setup_run_environment` from
`setup_dependent_build_environment`.
Also it's redundant to call `setup_run_environment` in
`setup_dependent_run_environment`, cause (a) the latter is called _for
every parent edge_ instead of once per node, and (b) it's only called
after `setup_run_environment` is called anyways. Better to call
`setup_run_environment` once and only once.
fftw object was originally created with spec["fftw:openmp"], but
referencing spec["fftw"] overwrites the 'last_query' in the spec object,
so later use of fftw.libs was not returing FFTW OpenMP libs.
Also allow the post-install fixup to support amdfftw as well as fftw.
Co-authored-by: Branden Moore <branden.moore@amd.com>
Co-authored-by: Phil Tooley <phil.tooley@amd.com>
Co-authored-by: Greg Becker <becker33@llnl.gov>
* new builtin package: py-biobb-model
* Update var/spack/repos/builtin/packages/py-biobb-model/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* add package py-jacobi
* fix: add description
* fix: add description
* fix: add description
* [@spackbot] updating style on behalf of jonas-eschle
* Update package.py
* Update package.py
* Update var/spack/repos/builtin/packages/py-jacobi/package.py
I don't think that numpy is used in "build"? But not important
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: jonas-eschle <jonas-eschle@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-google-cloud-storage: add new versions
* py-google-api-core: add new versions
* py-proto-plus: add new package
* py-google-api-core: add grpc variant
* py-google-api-core: add grpc variant
* py-google-api-core: add missing prefix
* py-google-cloud-batch: add new package
* py-google-cloud-logging: add new package
* py-google-cloud-appengine-logging: add new package
* py-google-cloud-audit-log: add new package
* py-grpc-google-iam-v1: add new package
* py-proto-plus: remove obvious dependency
* Whitespace
* Whitespace
* py-google-cloud-audit-log: correct conflict
* py-proto-plus: correct dependency type
* Whitespace
* py-google-auth: add new version
* py-google-resumable-media: add new version
* py-google-cloud-storage: constrain version of dependency
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-grpcio-status: use newer version
* py-google-resumable-media: add upper bound of dependency
* Add types of dependencies.
* py-grpcio: add new version
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-smote-variants: Added package py-smote-variants
Also added py-minisom and py-metric-learn as dependencies
* py-metric-learn: Added build dependency on setuptools
* py-smote-variants: Added a dependency on py-pytest-runner
As well as a comment about why statistics isn't included
* [@spackbot] updating style on behalf of alex391
---------
Co-authored-by: Alex C Leute <aclrc@rit.edu>
* py-charm4py: needs Cython<3.0
* Update var/spack/repos/builtin/packages/py-charm4py/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Kokkos Ecosystem: update for release 4.2.01
Will rebase this on top of develop once Kokkos Core PR merges.
* Kokkos Ecosystem: update license statement to reflect current license
* helics: Add version 3.5.0
* helics: define CMAKE_CXX_STANDARD=20 when GCC>=13 is used to compile
---------
Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
Co-authored-by: Ryan Mast <mast9@llnl.gov>
* Add support for clang in oneapi packages with OpenMP
* Add fallback search for libomp in OneApi package with OpenMP threading
* Add requires for the compiler when using threads=openmp in intel-oneapi-mkl
* Cosmetic changes to messages in oneapi.py
* Update error message in oneapi.py
Co-authored-by: Robert Cohn <rscohn2@gmail.com>
* Update another error message in oneapi.py
Co-authored-by: Robert Cohn <rscohn2@gmail.com>
* Inline helper error function in oneapi.py
* Update one more error message in oneapi.py
* Wrap long line in oneapi.py
---------
Co-authored-by: Robert Cohn <rscohn2@gmail.com>
* allow packages to request no submodules be updated when self.submodules is a
callable function
* Extend the test added in Allow more fine-grained control over what submodules are
updated: part 2 #27293 to include this case
* Update the type signature for the submodules arg of version() in directives.py
---------
Co-authored-by: tjfulle <tjfulle@users.noreply.github.com>
* cmake: Enable CMAKE_EXPORT_COMPILE_COMMANDS
Enabling this option causes CMake to generate a compile_commands.json file
containing a compilation database that can be used to drive third-party tools.
CMAKE_EXPORT_COMPILE_COMMANDS only exists for CMake >= 3.5
Exporting compilation databases is only supported for Makefile and Ninja
generators, so check these conditions as well.
CMAKE_EXPORT_COMPILE_COMMANDS is only enabled in supported configurations
* khmer: new package @2.1.1
* rationalising patch
* adding dep, modifying patch
* Update var/spack/repos/builtin/packages/khmer/package.py
Indeed!
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update package.py
---------
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* possvm: new package @1.2
* black!
* appeasing flake8
* Updating commit ID
* Adding graphing dep
* Update var/spack/repos/builtin/packages/py-markov-clustering/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update package.py
---------
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-pysftp: add new package
* py-pysftp: correct version
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Adds the spack recipe for building the pynpm python package
* fix license header
* Update var/spack/repos/builtin/packages/py-pynpm/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-fastremap: new package @1.14.1
* py-pyqtgraph: new package @0.13.3
* py-roifile: new package @2024.1.10
* py-superqt: new package @0.6.1
* cellpose: new package @2.2.3
* Appeasing black ...
* Dropping the cuda variant
* Update var/spack/repos/builtin/packages/py-fastremap/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Adding python version dependency
* Update var/spack/repos/builtin/packages/py-pyqtgraph/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-pyqtgraph/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-roifile/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-superqt/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Adding missing dep & conflict
* Appeasing black
* Adding missing py- prefix for dep
* Switching over to py-pyqt6
* Switching over to py-pyqt6
---------
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* new builtin package: py-biobb-structure-checking
* Update var/spack/repos/builtin/packages/py-biobb-structure-checking/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* dependencies are also build dependencies
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* new builtin package: py-biobb-io
* Update var/spack/repos/builtin/packages/py-biobb-io/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* new builtin package: py-biobb-gromacs
* Update var/spack/repos/builtin/packages/py-biobb-gromacs/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* added setuptools dependency
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Bump up the version for rocm-6.0.2 release
* extend the patches that were created for apps for rocm-6.0.0 and rocm-6.0.2 releases
(but apply hipfft patch for only 6.0.0)
* gitlab: remove requests for unreferenced packages
The packages removed in this commit are not built by any of
our current GitLab CI stacks.
* gitlab: update memory requests for "huge" packages
* gitlab: reduce memory requests for overprovisioned packages
* gitlab: more memory for py-torch (again)
* gitlab: update memory but keep CPU the same
This fixes bugs, performance issues, and removes no longer necessary code.
Short version:
1. Creating views from Python extensions would error if the Spack `opt` dir itself was in some symlinked directory. Use of `realpath` would expand those, and keying into `merge_map` would fail.
2. Creating views from Python extensions (and Python itself, potentially) could fail if the `bin/` dir contains symlinks pointing outside the package prefix -- Spack keyed into `merge_map[target_of_symlink]` incorrectly.
3. In the `python` package the `remove_files_from_view` function was broken after a breaking API change two years ago (#24355). However, the entire function body was redundant anyways, so solved it by removing it.
4. Notions of "global view" (i.e. python extensions being linked into Python's own prefix instead of into a view) are completely outdated, and removed. It used to be supported but was removed years ago.
5. Views for Python extension would _always_ copy non-symlinks in `./bin/*`, which is a big mistake, since all we care about is rewriting shebangs of scripts; we don't want to copy binaries. Now we first check if the file is executable, and then read two bytes to check if it has a shebang, and only if so, copy the entire file and patch up shebangs.
The bug fixes for (1) and (2) basically consist of getting rid of `realpath` entirely, and instead simply keep track of file identifiers of files that are copied/modified in the view. Only after patching up regular files do we iterate over symlinks and check if they target one of those. If so, retarget it to the modified file in the view.
--with-ch4-max-vcis=default is no longer accepted by MPICH configure
since the 4.1 release. Just omit the option from the +vci variant, since
configure will select the default value in its absence.
Problem: Older versions of the flux-core package require czmq and
jsonschema, but these dependencies have been dropped in recent
versions.
Add `when=` arguments to drop these requirements for the appropriate
versions of flux-core.
* fix wrong versioning
use doc version and not the one extrapolated from the path (i.e. 0.2.0.1)
* nvpl-lapack requires nvpl-blas
propagate matching variants to nvpl-blas dependency
Co-authored-by: albestro <albestro@users.noreply.github.com>
* rct: update packages (RE, RG, RP, RS, RU) with new versions
* rct: updated style
* rct: 1.46 release
* rct: RP 1.46.1 (hotfix applied)
* rct: deprecated old versions
* Update var/spack/repos/builtin/packages/py-radical-entk/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-radical-pilot/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-radical-saga/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* rct: brought back dependencies for deprecated versions
* rct: RP hotfix release 1.46.2
* rct: new stack release 1.47.0
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-ucsf-pyem: updating to commit e92cd4d
* py-pyfftw: updating to @0.13:1
* py-ucsf-pyem: correcting install of scripts
* Upper limits
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Upper limits
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* updates from github review
---------
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* add new package libsixel
* reorder to group variants and dependencies together
* Switch to using source from fork
The original developer of libsixel, Hayaki Saito (@saitoha), disappeared
in early 2020 and has not updated the repository or been seen since.
However, a fork of the project has been created at libsixel/libsixel,
and that fork has been getting much more regular updates. In this commit
I switch the package to using the better-maintained, now apparently
canonical fork of the project.
That project switched the build system from autotools to Meson, so much
of the build arguments code needed to be rewritten. The newest official
release also contained an error in meson.build which would break on
newer versions of Meson. That error only applied to the libjpeg and
libpng variants, though, so I switched the default to use libgd which
has broader format support anyway.
* blacken
* broke description into multiple lines
* allow libjpeg, etc to be loaded automatically
* apply patch to all compilers as per spack/issues/42007
* [@spackbot] updating style on behalf of Chrismarsh
* Resolve flake8 style issue from spackbot
* fix flake8 trailing whitespace
---------
Co-authored-by: Chrismarsh <Chrismarsh@users.noreply.github.com>
These 7 hooks were not used.
- Six of them related to install phases were unused after `spack`
`monitor` was removed, and the code seems to have bit rotten as there
were reports they were not (always?) triggered when they should.
- The post environment one was made redundant after spack install for
environment started following the common code path for generating
module files in #42147.
It should not be a breaking change to remove, since users cannot define
hooks in extensions, they would have to fork Spack.
If we ever _were_ to make those hooks extendable outside of core Spack,
it would also be better to start with fewer rather than more, cause
everything you expose gets relied upon...
Removing those also allows us to rethink what hooks we really need, and
in particular it seems like we need a hook that runs post install also when
the spec is inserted into the database.
The lack of a rule to avoid enforcing requirements on multi-valued variants, when the condition activating the environment was not met, resulted in multiple optimal solutions. The fix is to prevent imposing a requirement if the when= rule activating it is not met.
The section was highly outdated as it referred to old defaults, and
failed to mention `hide_implicits: true`.
This commit restructures it, moves some deeply nested sections a level
up, and promotes `hide_implicits: true` + `autoload: direct` before
talking about `exclude`.
It is useful to enable/disable stacks in order to handle turning
specific stacks on/off based on runner availability, stack stability,
testing requirements, etc.
The disabled stack list takes precedence over the enable stack list. The
assumption is that stacks that are disabled are so due to some
functionality missing or broken for that stack.
The enable stack list implicitly disables all stacks not listed in the
enable list.
* Registry queries can fail due to simultaneous access from other
processes. Wrap some of these accesses and retry when this may
be the cause (the generated exceptions don't allow pinpointing
this as the reason, but we add logic to identify cases which
are definitely unrecoverable, and retry if it is not one of
these).
* Add make recursion optioal for most registry search functions;
disable recursive search in case where it was originally always
recursive.
* py-pythran: apply patch to fix compilation with GCC 13
* Update var/spack/repos/builtin/packages/py-pythran/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* fix ipyrad numpy depedencies
ipyrad versions through 0.9.90 use np.int, which is deprecated in numpy 1.20.
* fix whitespace
* Correct numpy dependency restrictions
Fix two separate problems:
1. We want to always visit parents before children while creating views
(when it comes to ignoring conflicts, the first instance generated in
the view is chosen, and we want the parent instance to have precedence).
Our preorder traversal does not guarantee that, but our topological-
order traversal does.
2. For copy style views with packages x depending on y, where
<x-prefix>/foo is a symlink to <y-prefix>/foo, we want to guarantee
that:
* A conflict is not registered
* <y-prefix>/foo is chosen (otherwise, the "foo" symlink would become
self-referential if relocated relative to the view root)
Note that
* This is an exception to [1] (in this case the dependency instance
overrides the dependent)
* Prior to this change, if "foo" was ignored as a conflict, it was
possible to create this self-referential symlink
Add tests for each of these cases
* Sqlite requires the user to provide a command line arg (DYNAMIC_SHELL)
to export shared symbols to import lib from .def
* Add other options recommended by Sqlite docs:
https://github.com/sqlite/sqlite/blob/master/doc/compile-for-windows.md
* Some of these options mean we can restore variants that were
disabled for Windows (fts, functions, rtree).
* Updated with generic test functions
* Added level_zero test
As the compiler is not installed by TAU, it should be loaded first and run with --dirty. Will check if there is a way to make it work without --dirty.
* Update var/spack/repos/builtin/packages/tau/package.py
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
---------
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
The main script body is over-written for power. Putting thet timing
aggregation in the after script allows it to be called on all of the
current pipelines.
* Update package.py
Add support for OpenSubdiv 3.5.x
* Fixed Dependencies
I was getting errors about cmake not being able to find `xf86vm`, and adding a dependency on `libxxf86vm` fixes it.
Sometimes the logs are too long and the copy & paste command is not
shown. In that case I'd like to just copy the failing GitLab job URL in
my browser to `spack reproduce-build <url>`.
Currently, the `SpackSolverSetup` and the `PyclingoDriver` are more coupled than necessary:
1. The driver object needs a setup object to be injected during a solve,
2. And the setup object will get a reference back to the driver
This design is necessary because we use the low-level `clingo.backend` interface to setup our problem. This interface though is meant to bypass the grounder and add symbols directly in the grounded table, which is a feature we don't currently use.
The PR simplifies the encoding by having the setup object returning the problem-specific facts / rules as a list of strings, and the driver ingesting them using the [clingo.Control.add](https://potassco.org/clingo/python-api/5.6/clingo/control.html#clingo.control.Control.add) method. This removes any use of the low level interface.
Using this encoding makes it easy to hash the output of the setup phase, since it is returned as a string.
* py-nbconvert: avoid install-time downloads
* install css files as resources for py-nbconvert
* Update var/spack/repos/builtin/packages/py-nbconvert/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update package.py
* py-nbconvert: update dependencies for 7.14.1
* [@spackbot] updating style on behalf of AlexanderRichert-NOAA
* Update var/spack/repos/builtin/packages/py-nbconvert/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update resources & remove style.min.css file
* Update package.py
* [@spackbot] updating style on behalf of AlexanderRichert-NOAA
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
This "breaks" the deprecated schema by allowing unknown attributes
to the attributes section of the job types. The breaking change here is
that deprecated stacks will no longer ignore attributes that are unknown
but rather assume the new CI schema behavior of injecting them into the
generated CI configuration. This change is required to secure
authentication in Spack CI.
Improve naming, so it's clear file "extensions" are not taken in the
`PurePath(path).suffix` sense as the original function name suggests,
but rather that the files are opened and their magic bytes are
classified.
Add type hints.
Fix a bug where `stream.read(num_bytes)` was run on the compressed
stream instead of the uncompressed stream, which can potentially break
detection of tar.bz2 files.
Ensure that when peeking into streams for magic bytes, they are reset to
their original position upon return.
Use new API in `spack logs`.
Relocation of `PT_INTERP` in ELF files already happens to work from long to short path, thanks to generic binary relocation (i.e. find and replace). This PR improves it:
1. Adds logic to grow `PT_INTERP` strings through patchelf (which is only useful if the interpreter and rpath paths are the _only_ paths in the binary that need to be relocated)
2. Makes shrinking `PT_INTERP` cleaner. Before this PR when you would use Spack-built glibc as link dep, and relocate
executables using its dynamic linker, you'd end up with
```
$ file exe
exe: ELF 64-bit LSD pie executable, ..., interpreter /////////////////////////////////////////////////path/to/glibc/lib/ld-linux.so
```
With this PR you get something sensible:
```
$ file exe
exe: ELF 64-bit LSD pie executable, ..., interpreter /path/to/glibc/lib/ld-linux.so
```
When Spack cannot modify the interpreter or rpath strings in-place, it errors out without modifying the file, and leaves both tasks to patchelf instead.
Also add type hints to `elf.py`.
Certain versions of ifx (the majority of those available) have an issue
where they are not compatible with TMP directories with dot chars
This precludes their use with CMake.
Remap TMP to point to the stage directory rather than whatever the TMP
default is
* Add fenics development version and ufl-legacy
* Make sure python and setuptools are added to ufl-legacy and add version 2022.3.0 as well
* Run black and add maintainer to fenics package
* Fix typo
* Use Fiat version 2019.1.0
* Run black
* Add back master branch of fiat
* Remove master from the list of dolfin versions and add one extra line of each deps instead
* Run black
* Do not specify python version in ufl-legacy
* Remove python dependency from ufl-legacy
* Remove python dependency from ffc
* Add special case for master in ffc
* Run black
* Remove master from loop in ffc
* Run black again
* geopm: Mark all as deprecated
- This recipe will be removed in a future release.
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* Add py-sphinx-emoji
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* Add py-dasbus
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* py-pygobject: Add v3.46.0
- Previous versions error during build phase.
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* py-sphinx-tabs: Add new versions
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* Add geopm-service
- Previous geopm package is now 2 packages:
geopm-service and geopm-runtime.
- The GEOPM service is designed as a systemd/dbus
service providing a userspace interface to
privileged hardware telemetry and configurations.
- Installing via spack will enable some userspace
testing, but generally most users will want to
install the GEOPM service via the system package
manager as root to get full functionality.
- This recipe will enable the creation of the fully
userspace geopm-runtime recipe which will replace
the old geopm recipe.
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
---------
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* py-textual: New package py-textual
* py-textual: Depend on py-mdit-py-plugins
* py-textual: Added dependency on python@3.8:3
* py-textual: Added a comment about why there is a dependency on
py-mdit-py-plugins
* py-textual: Ran black
---------
Co-authored-by: Alex C Leute <aclrc@rit.edu>
* add pytest-aiohttp
* black
* py-setuptools -> py-setuptools-scm
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
VTK struggles to consume some Spack-derived packages on Windows:
Patch VTK to allow a smoother integration
Also add install for examples as they are not part of the install
interface.
gl2ps tries to build static and shared libs simultaneously with
the same target name on the generator side. This causes a name
clash issue for Ninja on Windows (where the extension is .lib
in both cases).
Add a variant on Windows to force building only one of shared
or static, and patch the CMake build to enable use of this
variant.
* gitlab: remove commented-out duplicate entries
* gitlab: reclassify some packages from "huge" to "large"
Our observed max memory usage for these packages is as follows:
hipblas: 7.7G
qt: 6.6G
visit: 9.7G
All of these should fit within a "large" request (currently 12G).
* gitlab: remove pango from list of huge packages
This package is not currently built by any of our CI stacks.
* gitlab: update requests for high memory packages
Refine resource requests for memory-intensive packages based on
max memory usage data.
- Adds perl-sql-translator and its missing deps:
- Adds perl-import-into
- Adds perl-package-variant
- Adds perl-strictures
Built with build-time tests and comes with a simple run-time test.
Add the empty deptype `spack.deptypes.NONE`.
Test the case `traverse_nodes(deptype=spack.deptypes.NONE)` to not
traverse dependencies, only de-duplicate.
Use the construct in environment views that otherwise would branch on
whether deps are enabled or not.
* ensure umpire~cuda~rocm when ~cuda~rocm
* MDAnalysis: add v2.7.0
* Apply suggestions from code review
* license
* review changes
* add gsd and py-cmake versions
* Update package.py
* py-cmake
* Update package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* fix and reorder
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* add py-vl-convert-python
* code format
* Update package.py
add homepage
* Update var/spack/repos/builtin/packages/py-vl-convert-python/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* remove old versions, add todo
* Update var/spack/repos/builtin/packages/py-vl-convert-python/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* remove blank line
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* New package: py-metrics
* [py-metrics] cleaned up extra comment
* Updated copyright and ran black
* py-pathspec: Added version 0.5.5
---------
Co-authored-by: vehrc <vehrc@rit.edu>
Co-authored-by: Jen Herting <jen@herting.cc>
Co-authored-by: Alex C Leute <aclrc@rit.edu>
* py-frozendict: patch up for Python 3.11
See also Marco-Sulla/python-frozendict#68, rely on a pure Python
implementation when 3.11+ is used.
* mention related Github issue
* new builtin package: biobb-common
* removed whitespace for the style test
* replaced ' by " for the style test
* changed import line for the style test
* Update var/spack/repos/builtin/packages/biobb-common/package.py
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* Update var/spack/repos/builtin/packages/biobb-common/package.py
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* Update var/spack/repos/builtin/packages/biobb-common/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* removed test
* using pypi instead of git
I hope this is declared the right way.
I tried to test it locally but I am having problems with a dependency (openblas) thus I can not even try if this works.
* upgraded version
* Added py prefix
* removed biopython version restriction
* directory with new py-prefixed name
* Delete old non-prefixed package
* Update var/spack/repos/builtin/packages/py-biobb-common/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* update tarball urls, add new versions and update maintainers
* remove unnecessary variant like cross-compile
* use self.define and self.define_from_variant
* improve regex / bug that matches with -DMPICH_SKIP_MPICXX=1
Co-authored-by: Matthias Wolf <matthias.wolf@epfl.ch>
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Previously, for abstract specs like:
```
foo ^[virtuals=a] bar ^[virtuals=b] bar
```
the second requirement was silently discarded on concretization. Now they're merged, and the abstract spec is equivalent to:
```
foo ^[virtuals=a,b] bar
```
* Added countdown repo
* Added fixed version of COUNTDOWN
* Style fixes
* Changed mantainer syntax
* Variants listed in alphabetical order by name
* Added conflicts and some reordering
* Fixed conflicts syntax
* Style fixes
* [@spackbot] updating style on behalf of danielecesarini
---------
Co-authored-by: danielecesarini <danielecesarini@users.noreply.github.com>
CMake may write and read from `~/.cmake` through `export(...)` and read `find_package(...)` respectively. We don't want this as it may influence the build in a non-deterministic way, so disable it for all versions of `cmake`.
* Trilinos: Add AMD to SuiteSparse TPL list
When Trilinos is built with SuiteSparse support, it should enable AMD as
one of the TPLs. It was previously enabling only UMFPACK. The Xyce
package uses AMD (but not UMFPACK).
* Xyce: Add 7.8 release and various improvements
In addition to adding the latest Xyce release (7.8), all the earlier
releases were deprecated, with the exception of 7.7.
The Trilinos specification was updated to remove unneeded packages,
explicitly enable all needed packages, and specify additional
do-not-build packages.
The serial build is now the default, with MPI still being an option.
I also epanded the explanation for one of the patches; and, finally, I
took the opportunity to update the Xyce description to better match the
current Xyce README description.
Fixes a bug where Spack did not generate module files of non-roots during
spack install with an active environment.
The reason being that Environment.new_installs only contained roots.
This PR:
Drops special casing of automatic module generation in post-install hooks
When `use_view`, compute environment variable modifications like always, and
applies a view projection to them afterwards, like we do for spack env activate.
This ensures we don't have to delay module generation until after the view is
created.
Fixes another bug in use_view where prefixes of dependencies would not be
projected -- previously Spack would only temporarily set the current spec's prefix.
Removes the one and only use of the post_env_write hook (but doesn't drop it to
make this backportable w/o changes)
Previously `std_args` was called on non-roots in a build context, which is redundant, and also leads to issues when `std_args` expects build deps of the `pkg` to be installed.
HPCToolkit `develop` now can optionally be built via Meson. This PR adds the `build_system=(autotools|meson)` variant and splits the build-system-dependent pieces into `AutotoolsBuilder` and `MesonBuilder`. The default is to build with `autotools`.
As of writing, the Meson is simply a wrapper around the original Autotools build, hence the build requires a native file listing install prefixes of all dependencies (which are internally mapped to `--with-{pkg}={prefix}` arguments for `./configure`). This is an unconventional but temporary state of affairs until the build system is fully ported to Meson and conventional dependency acquisition techniques like `pkg-config` and `cmake` are practically available.
* Environments: fix environment config
* Don't change the lockfile manifest path
* Update activate's comments to tie the manifest to the configuration
* Add spec_list override method
* Remove type checking from 'activate' since already have built-in check
* Refactor global methods tied to the manifest to be in its class
* Restore Environment's 'env_subdir_path' and pass its config_stage_dir to EnvironmentManifestFile
* Restore global env_subdir_path for use by Environment and EnvironmentManifestFile
The CUDA target should be specified at build time, otherwise
by default `autodock-gpu` will be built for compute capabilities
52, 60, 61, 70, which may cause errors on unsopported cards.
Currently requirements allow to express "strong preferences" and "conflicts" from
configuration using a convoluted syntax:
```yaml
packages:
zlib-ng:
require:
# conflict on %clang
- one_of: ["%clang", "@:"]
# Strong preference for +shared
- any_of: ["+shared", "@:"]
```
This PR adds syntactic sugar so that the same can be written as:
```yaml
packages:
zlib-ng:
conflict:
- "%clang"
prefer:
- "+shared"
```
Preferences written in this way are "stronger" that the ones documented at:
- https://spack.readthedocs.io/en/latest/packages_yaml.html#package-preferences
`spack install` early exit behavior was sometimes convenient, except
that it had and has bugs:
1. prior bug: we didn't mark env roots of already installed specs as
explicit in the db
2. current bug: `spack install --overwrite` is ignored
So this PR simplifies by letting the installer do its thing even if
everything is supposedly installed.
* Bump up the version for ROCm-6.0.0
* Adding patch files
* Style check failure fix
* Style check fixes
* Style check error fixes
* Patch to remove hipblas client file installation in 6.0
* Patch need to be applied on all 5.7 relases
* 6.0 update for math libs and other packages, new github url etc
* Correct package-audit failures
* Correcting shasum for rocfft patch and limiting patch in rocblas
* Reverting updates in rocprofiler-dev due to ci-gitlab failure
* Fixes for ci-gitlab failure due to disabling hip backward compatibilit
* Adding patch file to Change HIP_PLATFORM from HCC to AMD and NVCC to NVIDIA
* Use the gcnArchName inplace of gcnArch as gcnArch is deprecated from rocm-6.0.0
* Patches to fix magma and blaspp build error with rocm 6.0.0
* Patch for mfem and arborx for rocm 6.0
* Style check error fix
* Correcting style check errors
* Uodating dependent version
* Update for petsc to build with rocm 6.0
Need reverting-operator-mixup-fix-for-slate.patch for rocm 6.0
* Reverting the change in url for 2.7.4-rocm-enhanced
* hip-tensor 6.0.0 update
This commit ensures that CMake packages that also have Python as a build/link dep get a couple defines for the Python path so that CMake's builtin `FindPython3`, `FindPython`, `FindPythonInterp` modules can locate Python correctly.
The main problem with those CMake modules is that they first search for Python versions known at the time of release, meaning that old CMake maybe find older system Python 3.8 even though Python 3.11 comes first in `CMAKE_PREFIX_PATH` and `PATH`.
Package maintainers can opt out of this by overriding the `find_python_hints = False` attribute in the package class.
* Add nglview package
* Use slightly older version
* py-nglview: Correct py-versioneer version
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-nglview: Correct version of py-jupyter-packaging dependency
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add py-versioneer-518 package
* py-versioneer-518: Correct version
* py-nglview: Numpy is needed during build for the tests
* py-nglview: dependency needed for tests
* py-nglview: Correct dependency types
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* e4s ci: use latest intel/hpckit 2024 based image
* use latest container image: ecpe4s/ubuntu22.04-runner-amd64-oneapi-2024.0.0:2023.12.01
* comment out failing specs
* update to use patched container
* remove generalized package preference for intel-oneapi-mkl@2023
* change packages commented out
* VecGeom: new version 1.2.7 and fix URLs
* vecgeom: remove deprecated ancient RC version with incorrect hash
* geant4: remove support for @10.3+vecgeom
The piece of code that is removed in this PR predates environment views.
Spack would symlink build logs in `<env>/.spack-env/logs/*`, but this is
redundant because:
1. Views already add `<prefix>/.spack` (and there's logic there to avoid
clashes)
2. The code was broken anyways: it would only symlink the logs of
environment roots, not their deps, even if they were just built.
If users disable views, I'm pretty sure they're not waiting for
`.spack-env/logs` either. So, imo we can delete this code, and it was
probably overlooked in the past.
For a requirement like
```
packages:
foo:
require:
- "+debug"
```
(not `one_of:`, `any_of:`, or `spec:`)
`spack config change` would ignore the string. This was particularly evident if toggling a variant for a previously unmentioned package:
```
$ spack config change packages:foo:require:+debug
$ spack config change packages:foo:require:~debug
```
This fixes that and adds a test for it.
```
$ curl 'https://thepeg.hepforge.org/downloads/?f=ThePEG-2.3.0.tar.bz2' | sha256sum
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 1904k 0 1904k 0 0 1075k 0 --:--:-- 0:00:01 --:--:-- 1074k
ac35979ae89c29608ca92c156a49ff68aace7a5a12a0c92f0a01a833d2d34572 -
```
* Reduce the size on disk for logs
This PR does two things:
1. Store a compressed `spack-build-out.txt.gz`
2. Get rid of phase logs, as they are duplicates of
`spack-build-out.txt`
The logs are not compressed in the stage dir, so on build failure the
workflow for users is no different.
It's just that on install the logs are rarely used, and if needed, users
can easily `gzip -d` or `zgrep` them.
In the case of GCC installs, the compressed logs are <5% of the original
size, which is typically dozens of MBs.
* get rid of "backwards compat" of file names in stage dirs
Sbangs don't exist on Native Windows, and the hook is causing errors
due to the file comparison + behavior of os.rename on Windows. Skip
the hook on Windows.
New patch 7.5.3p5, new bugfix 7.7.2, new minor 7.8.0.
Only possible impact on spack is the potential addition of a variant to select the memory manager in 7.8.0, see [diff](https://github.com/Open-Cascade-SAS/OCCT/compare/V7_7_2...V7_8_0). Not adding a variant at this time.
Like `spack change` for specs in environments, this can e.g. replace `examplespec+debug` with `examplespec~debug` in a `require:` section.
Example behavior for a config like:
```
packages:
foo:
require:
- spec: +debug
```
* `spack config change packages:foo:require:~debug` replaces `+debug` with `~debug`
* `spack config change packages:foo:require:@1.1` adds a requirement to the list
* `spack config change packages:bar:require:~debug` adds a requirement
As observed in #40944, when using `spack config add <path>`, the `path` might
contain keys that are enclosed in quotes.
This was broken in https://github.com/spack/spack/pull/39831, which assumed that
only the value (if present, the final element of the path) would use quotes.
This preserves the primary intended behavior of #39931 (allowing ":" in values when
using `spack config add`) while also allowing quotes on keys.
This has complicated the function `process_config_path`, but:
* It is not used outside of `config.py`
* The docstring has been updated to account for this
* Created an object to formalize the DSL, added a test for that, and
refactored parsing to make use of regular expressions as well.
* Updated the parsing and also updated the `config_path_dsl` test with an explicit check.
At a higher level, split the parsing to check if something is either a key or not:
* in the first case, it is covered by a regex
* in the second, it may be a YAML value, but in that case it would have to be the last
entry of x:y:z, so in that case I attempt to use the YAML handling logic to parse it as such
- Use MakefilePackage and simplified package.py
- Deprecate old versions - they did not build for me with OCaml 4.13.1
that is currently in Spack. Also, the changes from the previous
versions seem to be quite significant.
Spack packages may not have a public download option, and can implement
`download_instr` to inform users how to obtain the artifacts needed to
build. `spack checksum` however did not account for this and would print
out a confusing error message when invoked on such packages ("Could not
find any remote versions").
This PR updates the error message to output the manual download instructions
if `spack checksum` is invoked on a package with `manual_download = True`.
Currently when you repeatedly create a bootstrap mirror that includes
`clingo-bootstrap@spack` you get different tarballs every time.
This is a general problem with mirroring checkouts from version control
as tarballs. I think it's best to create tarballs ourselves, since that way we
have more control over its contents.
This PR ensures normalized tarballs like we do for build caches:
- normalize file permissions (in fact that was already inspired by git, so
should be good)
- normalized file creation/modification time (timestamp 0)
- uid / guid = 0, no usernames
- normalized gzip header
- dir entries are ordered by `(is_dir, name)` where strings are not locale aware ;)
- POSIX says st_mode of symlinks is unspecified, so work around it and
force mode to `0o755`
R embeds an absolute path to the `which` executable in the sources for
`Sys.which`. This gets ultimately stored as serialized byte code in some
custom database format, which uses compression for entries.
As a result, Spack cannot relocate `<prefix which>/bin/which` when
installing from a build cache.
The patch works around this by making R create a symlink to `which` in
its own prefix, have the R sources call that, so that relocation works
again.
See https://github.com/r-devel/r-svn/pull/151
Explicitly requested namespaces are annotated during
the setup phase, and used to retrieve the correct package
class.
An attribute for the namespace has been added for each node.
Currently, a single namespace per package is allowed
during concretization.
* add new versions of py-altair
* fix year
* Update var/spack/repos/builtin/packages/py-altair/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-altair/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* reorder dependencies
* remove rc
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add py-nanoplot and py-nanostat
* Add myself as spack package maintainer
* Remove python version requirement
* Remove python dependency
* Apply suggestions from code review
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update package.py: remove python dependency
* Set dependency types
* Update py-nanomath package.py
* Update py-nanoplot package.py
* Update py-nanostat package.py
* Add missing py-python-deprecated dependency
* Make kaleido a source package
* Fix py-nanoget deps
* Kaleido lint
* Nanoget lint
* Nanomath lint
* Nanoplot lint
* Nanostat lint
* Another kaleido lint I missed
* py-nanoplot missed lint
* py-nanostat missed lint
* py-kaleido even more missed lint
* The linter really can't make up its mind
* The linter REALLY can't make up its mind
* Add py-python-deprecated package
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* perl-class-accessor-lvalue: New package
Adds Class::Accessor::Lvalue
* perl-date-utils and deps: New packages
This adds:
- perl-date-utils and its dependencies:
- perl-date-exception
- perl-term-ansicolor-markup
The current `mkdir {{ paths.environment }}` will generate an error if:
* `{{ paths.environment }}` already exists, or
* `{{ paths.environment }}` is nested in non-existing dirs.
Adding `-p` to the command will make this robust to both possibilities.
Set noclobber bash option when writing manifest.
* Add GASNet-EX release 2023.9.0
Add level_zero variant
Deprecate old versions that are no longer supported
Add version enforcement to accelerator variants
* Add UPC++ release 2023.9.0
Deprecate old versions that are no longer supported
Add version enforcement to accelerator variants
* perl-rose-datetime: New package plus updates
- perl-rose-datetime: New package
- perl-datetime: New version, updated dependencies to enable build
time tests and added a runtime test
* Remove copyright line
* New year
* bigdft: convert the use of format strings to fstrings everywhere
* Fix formatting
* reformat with black
* Update compiler flags in bigdft-core
* Revert "Update compiler flags in bigdft-core"
This reverts commit f7524ed784.
* Bump the build cache layout version from 1 to 2
* Version to lists parent directories of the prefix in the tarball too, which is required from some container runtimes
* Move in vs. satisfies to a note and mention special cases of in
* Address feedback: oveoverlap -> intersect
* Re-word the satisfies versus in note.
---------
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
This fixes an issue where pkg.stage throws because a patch cannot be found,
but the patch is redundant because the spec is reused from a build cache and
will be installed from existing binaries.
Part 4 of reworking all package metadata to key by `when` conditions.
Changes conflict dictionary structure from this:
{ provided_spec: {when_spec, ...} }
to this:
{ when_spec: {provided_spec, ...} }
`make_when_spec()` was being used in the solver, but it has semantics that are specific
to parsing when specs from `package.py`. In particular, it returns `None` when the
`when` spec is `False`, and directives are responsible for ignoring that case and not
adding requirements, deps, etc. when there's an actual `False` passed in from
`package.py`.
In `asp.py`, we know that there won't ever be a raw boolean when spec or constraint, so
we know we can parse them without any of the special boolean handling. However, we
should report where in the file the error happened on error, so this adds some parsing
logic to extract the `mark` from YAML and alert the user where the bad parse is.
- [x] refactor `config.py` so that basic `spack_yaml` mark info is in its own method
- [x] refactor `asp.py` so that it uses the smarter YAML parsing routine
- [x] refactor `asp.py` so that YAML input validation for requirements is done up front
Part 3 of reworking all package metadata to key by `when` conditions.
Changes conflict dictionary structure from this:
{ (requirement_spec, ...): [(when_spec, policy, msg)] }
to this:
{ when_spec: [((requirement_spec, ...), policy, msg), ...] }
Part 2 of reworking all package metadata to key by `when` conditions.
Changes conflict dictionary structure from this:
{ conflict_spec: [(when_spec, msg), ...] }
to this:
{ when_spec: [(conflict_spec, msg), ...] }
Also attempts to consistently name the variables used to iterate over conflict
dictionaries.
Part 1 of making all package metadata indexed by `when` condition. This
will allow us to handle all the dictionaries on `PackageBase` consistently.
Convert the current dependency dictionary structure from this:
{ name: { when_spec: [Dependency ...] } }
to this:
{ when_spec: { name: [Dependency ...] } }
On an M1 mac, this actually shaves 5% off the time it takes to load all
packages, I think because we're able to trade off lookups by spec key
for more lookups by name.
* Boost: add version 1.84.0
* Conflict with 98/03
* Set C++11 as default
Starting with 1.84.0, the minimum required is c++11. It has been a very
long time since 98/03 has been required. It's time to bump the minimum.
* Add OpenMPI 5.0.0/5.0.1 release
* Fix a problem with dlopen syms with 5.0.0
* Crank up lex buffer to 1MB so that Open MPI's compiler wrapper can parse the enormously long lines present in, for example, mpicc-wrapper-data.txt when the spack install is utilizing Spack's path padding feature.
* Disable romio by default for 5.0.0 and beyond owing to problems compiling the romio package when using the Intel OneAPI compiler.
* Patch for addiing cuda lib location in case of non-standard location of libcuda.so
* build accel components as DSOs. It appears from looking at some of the spack CI that it implicitly assumes that Open MPI is built with components as DSOs. The default behavior for Open MPI was changed between the 4.1.x release stream and the 5.0.x release stream changed and this premise is now incorrect.
Turns out that starting with Open MPI 5.0.0 building static
does not work when using a now very important variant, namely cuda.
In older versions of Open MPI the libcuda.so was dlopened at
run time when needed, but now libcuda is linked in to the cuda
components of openmpi directly. This works when using Open MPI's
dynamically loadable component option, but doesn't work now for
a lot of the Spack CI pipelines because they don't include libcuda.so
in LD_LIBRARY_PATH of packages that dont think they are using
cuda themselves.
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
Co-authored-by: Jack Morrison <jack.morrison@cornelisnetworks.com>
Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
Needed for #40326, which can changes the iteration order over package dependencies during concretization.
While clingo doesn't have this problem, the original concretizer (which we still use for bootstrapping) can be sensitive to iteration order when evaluating dependency constraints in `when` conditions. This can cause it to ignore conditional dependencies unless the dependencies in the condition are listed first in the package.
The issue was in the way the original concretizer would disconnect specs *every* time `normalize()` ran. When specs were disconnected, `^dependency` constraints wouldn't see the dependency in the dependency condition loop.
We now only only disconnect *all* dependencies at the start of `concretize()` and `normalize()`, and we disconnect any leftover dependents from replaced externals at the *end* of `normalize()`. This trims stale connections while keeping the ones that are needed to trigger dependency conditions.
- [x] refactor `flat_dependencies()` to not disconnect the spec by default.
- [x] `flat_dependencies()` is never called with `copy=True` -- remove the `copy` kwarg.
- [x] disconnect only once at the beginning of `normalize()` or `concretize()`.
- [x] add a test that perturbs dependency iteration order to ensure this doesn't regress.
- [x] disconnect unused dependents at end of `normalize()`
* setup-env: Fix back and forth between two instances
* setup-env.csh: Fix SPACK_ROOT when switch to a different instance
i.e. Always look for the current SPACK_ROOT
* setup-env: Update comments
This adds options to `spack list` that allow you to list only packages from specific
repositories/namespaces, e.g.:
```console
spack list -r builtin
```
only lists packages from the `builtin` repo, while:
```console
spack list -r myrepo -r myrepo2
```
would list packages from `myrepo` and `myrepo2`, but not from `builtin`. Note that you
can use the same argument multiple times.
You can use either `-r` / `--repo` or `-N` / `--namespace`. `-N` is there to match the
corresponding option on `spack find`.
- [x] add `-r` / `--repo` / `-N` / `--namespace` argument
- [x] add test
* Add rust-analyzer as variant to rust build
* Expose cargo module only when +cargo
* rust: add v1.74.0 and v1.75.0 and remove variants in favor of +dev
* [@spackbot] updating style on behalf of alecbcs
* Fix variant typo
---------
Co-authored-by: alecbcs <alecbcs@users.noreply.github.com>
This method is vestigial; the only arg we ever used was `ignore=`, and that was
eliminated in #29317 and #35588.
The `kwargs` field of the extensions dictionary is actually completely unused now. Add a
note for future removal.
Literal compiler config in `test_requires_directive` specifically lists `target:
x86_64`, but it doesn't need to, and the unnecessary target makes the test fail on
non-`x86_64` machines.
- [x] Remove target from config yaml in `test_requires_directive`
* py-torch: set env OpenBLAS_HOME
Because [`FindOpenBLAS.cmake`](https://github.com/pytorch/pytorch/blob/main/cmake/Modules/FindOpenBLAS.cmake) uses a hardcoded list of search paths for includes and libraries, we have to pass the `OpenBLAS_HOME` environment variable.
* py-torch: patch for ${OpenBLAS_HOME}/include/openblas
The context of this patch is unchanged since v0.4.0.
* py-torch: move patch before def patch
* py-torch: also set Atlas_ROOT_DIR and BLIS_HOME
* py-torch: fix openblas patch range to @:2.1
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Xorg pkgs: updated version to current latest
This updates the versions of multiple Xorg packages to their current
latest version. Verified the requirements and version dependencies, and
updated where needed. Modified one homepage (xkbcomp) in the interest of
conformity with the other packages.
Summary of dependency changes:
- libsm:
- depends_on("libice@1.1.0:", when="@1.2.4:")
- libx11:
- depends_on("libxcb@1.11.1:", when="@1.6.4:")
- libxcomposite:
- depends_on("xproto@7.0.22:", when="@0.4.6")
- libxfixes:
- depends_on("fixesproto@5.0:", when="@5")
- depends_on("fixesproto@6.0:", when="@6")
- libxi:
- depends_on("inputproto@2.2.99.1:", when="@1.7:")
- depends_on("inputproto@2.3.99.1:", when="@1.8:")
* xcb-proto, libxcb: new version 1.15
* xorg libs: additional new versions
New minor version upgrades:
- libXcursor (no changed needed)
- libXres
- depends_on("resourceproto@1.0:", when="@1.0")
- depends_on("resourceproto@1.2:", when="@1.2")
* libxpm: ... depends_on ncompress only when 3.5.15
* Xorg libs: add maintainer
* xtrans: new version 1.5.0
* xcb-proto: new version 1.16.0
* libxt: new version 1.3.0
* libxrandr: new version 1.5.4
* libxpm: new versions 3.5.16, 3.5.17
* libxi: new version 1.8.1
* libxft: new version 2.3.8
* libxfixes: new version 6.0.1
* libxcb: new version 1.16
* libx11: new version 1.8.5, 1.8.6, 1.8.7
* libxfixes: comment out problematic fixesproto versions
* libxi: comment out problematic inputproto versions
* libxfixes, libxi: add reference to issue that blocks updates
* patch on variant fftw3; fix for #41577
* a line of doubtful blas/fftw +openmp. Are they needed with nwchem+openmp?
* Update var/spack/repos/builtin/packages/nwchem/package.py
Co-authored-by: Rocco Meli <r.meli@bluemail.ch>
---------
Co-authored-by: Rocco Meli <r.meli@bluemail.ch>
* gaudi: add a patch for catch2
* Fix indentation
* Add a diff at the end of the path
* gaudi: canonicalize patch url
* gaudi: canonicalize patch url for gitlab diff
---------
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
PAPI CI checks a `spack install` of `papi@master`, and the open range here breaks their
CI with the fix because the patch is no longer needed (see #26784, #27625 for why it's
difficult to avoid this).
The patch issue is going to be fixed in PAPI upstream with whatever release is after
`7.1.0`, so we can restrict the patch to `7.1.0` and avoid this issue.
* shell: fix zsh color formatting for PS1 in environments
The `colorize` function in `llnl.util.tty.color` only applies proper formatting for Bash
ANSI and for console output, but this is not what zsh expects for environment variables.
In particular, when using `zsh`, `spack env activate -p` produces a `PS1` prompt that
looks like this:
```
\[\033[0;92m\][ENVIRONMENT]\[\033[0m\]
```
For zsh the formatting should be:
```
\e[0;92m[ENVIRONMENT]\e0;m
```
- [x] Add a `zsh` option to `colorize()` to enable zsh color formatting
- [x] Add conditional to choose the right `PS1` for `zsh`, `bash`, and `sh`
- [x] Don't use color escapes for `sh`, as they don't print properly
* convert lots of += lines to triple quotes
No online release notes or repository, but the new tarball has the following in `NEWS`:
* ThePEG-2.3.0 release: 2023-12-11
** gcc-12/c++17/c++20 compatibility added
** hepmc3 compatibility added
** rivet interface improved
** inforstructure for dark interaction added
PAPI 7.1.0 unconditionally adds `FFLAGS = -ffree-form` in the sysdetect tests,
regardless of the compiler.
This was added in https://github.com/icl-utk-edu/papi/pull/108 to make a build with
`armflang` work, but it breaks CCE (and our `develop` pipeline).
- [x] Add a patch that fixes both problems
- [x] Patch PAPI when at 7.1.0 or higher
Add a "checked_by" field to the `license()` directive so that we can track who verified
the license for a project. also check the license of 18 or so projects and mark them
checked.
This patch adds license information for about 5,300 packages from automated sources.
The license information was obtained from Alpine Linux and PyPI and processed
using tooling available in https://github.com/boomanaiden154/spack-license-utils.
The license field was added in after all other directives in an automated fashion.
Note that while this license information is probably fairly accurate, it is not
guaranteed to be accurate. In addition some of the license strings from Alpine Linux
might not be valid SPDX license strings. Invalid SPDX identifiers can be picked up
and fixed once we have validation/parsing infrastructure in place for the solver,
and issues can be fixed as they come up.
This adds a few options to `spack gc`.
One to give you a little more control over dependencies:
* `-b` / `--keep-build-dependencies`: By default, `spack gc` considers build dependencies to be "no longer needed" once their dependents are installed. With this option, we'll keep build dependencies of needed installations as well.
And two more to make working with environments easier:
* `-E` / `--except-any-environment`: Garbage collect anything NOT needed by an environment. `spack gc -E` and `spack gc -bE` are now easy ways to get rid of everytihng not used by some environment.
* `-e` / `--except-environment` `ENV`: Instead of considering all environments, garbage collect everything not needed by a *specific* environment. Note that you can use this with `-E` to add directory environments to the list of considered envs, e.g.:
spack gc -E -e /path/to/direnv1 -e /path/to/direnv2 #...
- [x] rework `unused_specs()` method on DB to add options for roots and deptypes
- [x] add `all_hashes()` method on DB
- [x] rework `spack gc` command to add 3 more options
- [x] tests
* Add all versions back to 0.20, add more depends_on (flex, bison, libffi and ccache), add the ability to enable or disable both abc and ccache, abc is enabled by default, ccache is disabled by default
* Fixed style with black
* Removed unused f-string setups
* Fixed style with black (again)
* Add enum34, numdifftools, and updated pyomo packages
* Syntax error
* Apply black style
* Trying to get around Python spec issue
* All SHAs were somehow wrong
* Change enum version
* Change optional dependencies to be on run, not build
* Add Pyomo 6.7.0
* Update SHA and version mismatch
* Remove py-enum34
* Add three new packages to address comments
* Fix linting errors; move casadi to py-casadi
* Update license; add in dependency
* Update setuptools version
* Update class name to python class
* Remove other boielerplate stuff
* Update homepage addresses; update py-casadi
* Add PAPI 7.0.1
* Add comment about skipping PAPI 7.0.0
* Add patch to avoid adding Intel ifort/ifx flag on Cray ftn
* Modify patch to include Cray-specific flags
* Adjust recipe to always apply patch for 7.0.1
* Expand Cray compiler checks in patch
* Forgot to update recipe
* Adjust recipe so it looks for hipcc in the correct path
* Revert "Adjust recipe so it looks for hipcc in the correct path"
This reverts commit 0db3df4fe2.
* Patch HIP_PATH to work with Spack-built HIP
* Patch LDFLAGS with llvm-amdgpu path
* Forgot the depends_on line
* libomptarget only builds with clang
* Try a self-consistent build of llvm-amdgpu
* Try making llvm-amdgpu depend on llvm for llvmoffloadarch library
* Update prereq to use rocm-openmp-extras instead
* Refactor llvm-amdgpu to use a version dict
* Fix typo
* Hack to exclude older versions without matching rocm-openmp-extras
* Add PAPI 7.1.0
* Revert changes to llvm-amdgpu
* Fix PAPI 7.1.0 checksum
For now, this only includes packages that I personally maintain.
Notable removals:
* Anaconda 2
* Catalyst
* Ancient numpy/scipy
* Ancient PyTorch
* Ancient Bazel/TF
To work properly, Spack requires a few directories from its repository to be added to
`sys.path`. Previously these were buried in `spack_installable.main.main()`, but it's
sometimes useful to get the paths separately, e.g., if you want to set up your own
functioning spack environment.
With this change, adding the paths is much simpler:
```python
import spack_installable
sys.path[:0] = get_spack_sys_paths(spack_prefix)
```
- [x] Add `get_spack_sys_paths()` method with extra paths in order.
- [x] Refactor `spack_installable.main.main()` to use it.
With an improper/incomplete/broken installation of Clingo, it can be
importable but not have any of the expected attributes
Improve error reporting in this case
* Restore PackageBase class, and modify only ASP
This prevents a noticeable slowdown in concretization
due to the number of directives involved.
* Fix issue with 'clang' being preferred to 'gcc',
due to runtime version weights
* Constraints on runtimes are declared by compilers
The declaration of available runtime versions, and of
their compatibility constraints are in the associated
compiler class.
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
The gcc-runtime package adds a separate node for gcc's dynamic runtime
libraries.
This should help with:
1. binary caches where rpaths for compiler support libs cannot be
relocated because the compiler is missing on the target system
2. creating "minimal" container images
The package is versioned like `gcc` (in principle it could be
unversioned, but Spack doesn't always guarantee not mixing compilers)
If you are calling Spack from the python API, you might have written something like this
before #41529:
```
find = SpackCommand("find")
find('--format={name}', 'saxpy@1.0.0', '+rocm', 'amdgpu_target="gfx90a"')
```
But with the breaking change in #41529, you should write:
```
find = SpackCommand("find")
find('--format={name}', 'gromacs', '+rocm', 'amdgpu_target=gfx90a')
```
Note that we don't need quotes in Python strings, and that this is what would come in
via argv if you typed a quoted variant on the CLI.
The error messages for strings like this are not great -- you get something like this:
```
==> No package matches the query: gromacs+rocm amdgpu_target="gfx90a"
```
Which doesn't indicate that the issue might be your quoting. This is because we were
simply outputting the argv we got, instead of using spec.format() to output the error
message. This PR fixes such errors to use `spec.format()` and to look like this:
```
==> No package matches the query: gromacs+rocm amdgpu_target='"gfx90a"'
```
So users should have an easier time understanding that Spack considers the variant value
to contain quotes here.
- [x] update ConstraintAction to store parsed Specs
- [x] refactor commands to display formatted parsed Specs instead of raw input
Users expect that changes to the externals sections in packages.yaml config apply immediately, but reuse concretization caused this not to be the case. With this commit, the concretizer is only allowed to reuse externals previously imported from config if identical config exists.
This PR adds a flag `--tag/-t` to `buildcache push`, which you can use like
```
$ spack mirror add my-oci-registry oci://example.com/hello/world
$ spack -e my_env buildcache push --base-image ubuntu:22.04 --tag my_custom_tag my-oci-registry
```
and lets users ship a full, installed environment as a minimal container image where each image layer is one Spack package, on top of a base image of choice. The image can then be used as
```
$ docker run -it --rm example.com/hello/world:my_custom_tag
```
Apart from environments, users can also pick arbitrary installed spec from their database, for instance:
```
$ spack buildcache push --base-image ubuntu:22.04 --tag some_specs my-oci-registry gcc@12 cmake
$ docker run -it --rm example.com/hello/world:some_specs
```
It has many advantages over `spack containerize`:
1. No external tools required (`docker`, `buildah`, ...)
2. Creates images from locally installed Spack packages (No need to rebuild inside `docker build`, where troubleshooting build failures is notoriously hard)
3. No need for multistage builds (Spack just tarballs existing installations of runtime deps)
4. Reduced storage size / composability: when pushing multiple environments with common specs, container image layers are shared.
5. Automatic build cache: later `spack install` of the env elsewhere speeds up since the containerized environment is a build cache
These packages were written before the "requires" directive,
and so they are conflicting with all compilers but Fujitsu
to express they _require_ `%fj`
* Ensure a spack libproj is used instead of a system libproj when libproj < 8.
spack/spack/issues/41299
* Fix style as per ci-bot
* Fix style as per ci-bot
* Ensure 3.5:3.8.
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* add trim function to `Spec` and `--ignore` option to 'spack diff'
Allows user to compare two specs while ignoring the sub-DAG of a particular dependency, e.g.
spack diff --ignore=mpi --ignore=zlib trilinos/abcdef trilinos/fedcba
to focus on differences closer to the root of the software stack
Sometimes env variables computed in `setup_run_environment` depend on tests
w.r.t. files in `spec.prefix`, but Spack temporarily projects `spec.prefix` to
the view.
This is problematic for two reasons:
1. Some packages iterate over `<prefix>/bin`: they expect only the current
package's executables, but find all linked in the view, leading to false
positives.
2. Some packages test for `os.path.islink(...)`, which is always true in a view
`gcc` is an example that does both.
This PR lets Spack compute the environment modifications using the original
prefix, and projects to the view afterwards
Currently, a virtual spec is composed of just a name and a version. When a virtual spec contains other components, such as variants, Spack won't emit warnings or errors but will silently drop them - which is unexpected by users.
This adds three new versions in the 31.* series. Release notes of 31.0.0 at https://github.com/acts-project/acts/releases/tag/v31.0.0. No changes to the CMakeLists.txt files that need addressing in the package recipe.
The only new feature I'm a bit concerned about is https://github.com/acts-project/acts/pull/2626, which replaces testing for C++20 concepts support by the feature-testing macro `__cpp_concepts`, which is also a C++20 feature. So technically we now should require `cxxstd=20` even though Acts itself still allows (and defaults to) 17. Judging by https://en.cppreference.com/w/cpp/compiler_support/20, the support for feature-testing macros was added very early by most compilers.
This PR changes the default behavior of `spack config get` and `spack config blame`
to print a flattened version of the entire spack configuration, including any active
environment, if the commands are invoked with no section arguments.
The new behavior is used in Gitlab CI to help debug CI configuration, but it can also
be useful when asking for more information in issues, or when simply debugging Spack.
Convert the 'develop' section of an environment to a dedicated configuration section.
This means for example that instead of having to define `develop` specs in the
`spack.yaml`, the environment can `include:` another `develop.yaml` configuration
which specifies which specs should be developed in the environment.
This change is not expected to be disruptive given that existing environment `spack.yaml`
files will conform to the new schema.
(Update 11/28/2023) I have implemented the `develop`/`undevelop` commands in terms
of more-generic modification functions added to the `config` module: `change_or_add`
and `update_all`. It is assumed that the semantics added here (described in 11/18 update)
would be desirable to extend to other config update actions (e.g. adding compilers,
changing package requirements, adding mirrors).
(Update 11/18/2023) I have updated this such that `spack develop`, and
`spack undevelop` to potentially modify all writable scopes, like
https://github.com/spack/spack/pull/41147. https://github.com/spack/spack/pull/35307
will be useful for modifying included scopes, but generally speaking specifying a
`--scope` will not be required for `spack develop`: `spack develop` will add new
develop specs to whatever scope already has develop specs defined, or to the
highest-priority writable scope (which should be the env scope).
TODOs:
- [x] If you `spack undevelop` a package which is mentioned at multiple layers of
configuration, then currently this would only modify one of them. That's not
technically a new issue (has always existed for configuration modification), but
may be confusing to users when presented via an interface other than `spack config set`
- [x] Need to add (or confirm) the ability to modify individual config files by providing
a path (rather than using a scope identifier as a key to retrieve associated config).
- [x] `spack develop` adds new develop specs to the scope that defines them
(potentially skipping higher priority scopes to e.g. augment included scope files)
---------
Co-authored-by: scheibelp <scheibelp@users.noreply.github.com>
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
* py-plum-dispatch: add new package
* Update var/spack/repos/builtin/packages/py-plum-dispatch/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-htgettoken: use os.environ, avoid AttributeError
This avoids the following error:
```
Warning: could not load runtime environment due to AttributeError: 'EnvironmentModifications' object has no attribute 'get'
```
* py-htgettoken: allow for undefined variables
* py-htgettoken: use dict get()
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* mpifileutils: add DAOS variant
* mpifileutils: Add daos dep when +daos
Add dependency on DAOS when +daos
Pass DAOS prefix to ensure correct DAOS is found by during configuration
* Change in to satisfies for boolean variants
---------
Co-authored-by: Ryan Krattiger <ryan.krattiger@kitware.com>
* perl-datetime-format-strptime: New package
Adds package:
- perl-datetime-format-strptime
And adds these because they are test dependencies:
- perl-test-file-sharedir
- perl-test2-plugin-nowarnings
- perl-test2-suite
And modifies these to enable build time tests:
- perl-b-hooks-endofscope
- perl-class-singleton
- perl-datetime-locale
- perl-datetime-timezone
- perl-file-sharedir
- perl-namespace-autoclean
- perl-namespace-clean
- perl-params-validationcompiler
- perl-specio
* Add myself as maintainer
* add new cpp compiler version
* empty ftn for 2023.2.3
* OLD ftn in 2023.2.3 version
* tolerate missing fortran compiler
---------
Co-authored-by: Robert Cohn <robert.s.cohn@intel.com>
* geant4: new version 11.2.0
* geant4: depends_on geant4-data@11.2:
* geant4-data: new version 11.2.0
* g4abla: new version 3.3
* g4emlow: new version 8.4
* g4incl: new version 1.1
* geant4: depends_on vecgeom@1.2.6:
* geant4: depends_on qt@5.9: when @11.2: +qt
* vecgeom: new version 1.2.6
This PR does several things:
- [x] Allow any character to appear in the quoted values of variants and flags.
- [x] Allow easier passing of quoted flags on the command line, e.g. `cflags="-O2 -g"`.
- [x] Handle quoting better in spec output, using single quotes around double
quotes and vice versa.
- [x] Disallow spaces around `=` and `==` when parsing variants and flags.
## Motivation
This PR is motivated by the issues above and by ORNL's
[tips for launching at scale on Frontier](https://docs.olcf.ornl.gov/systems/frontier_user_guide.html#tips-for-launching-at-scale).
ORNL recommends using `sbcast --send-libs` to broadcast executables and their
libraries to compute nodes when running large jobs (e.g., 80k ranks). For an
executable named `exe`, `sbcast --send-libs` stores the needed libraries in a
directory alongside the executable called `exe_libs`. ORNL recommends pointing
`LD_LIBRARY_PATH` at that directory so that `exe` will find the local libraries and
not overwhelm the filesystem.
There are other ways to mitigate this problem:
* You could build with `RUNPATH` using `spack config add config:shared_linking:type:runpath`,
which would make `LD_LIBRARY_PATH` take precedence over Spack's `RUNPATHs`.
I don't recommend this one because `RUNPATH` can cause many other things to go wrong.
* You could use `spack config add config:shared_linking:bind:true`, added in #31948, which
will greatly reduce the filesystem load for large jobs by pointing `DT_NEEDED` entries in
ELF *directly* at the needed `.so` files instead of relying on `RPATH` search via soname.
I have not experimented with this at 80,000 ranks, but it should help quite a bit.
* You could use [Spindle](https://github.com/hpc/Spindle) (as LLNL does on its machines)
which should transparently fix this without any changes to your executable and without
any need to use `sbcast` or other tools.
But we want to support the `sbcast` use case as well.
## `sbcast` and Spack
Spack's `RPATHs` break the `sbcast` fix because they're considered with higher precedence
than `LD_LIBRARY_PATH`. So Spack applications will still end up hitting the shared filesystem
when searching for libraries. We can avoid this by injecting some `ldflags` in to the build, e.g.,
if were were going to launch, say, `LAMMPS` at scale, we could add another `RPATH`
specifically for use with `sbcast`:
spack install lammps ldflags='-Wl,-rpath=$ORIGIN/lmp_libs'
This will put the `lmp_libs` directory alongside `LAMMPS`'s `lmp` executable first in the
`RPATH`, so it will be searched before any directories on the shared filesystem.
## Issues with quoting
Before this PR, the command above would've errored out for two reasons:
1. `$` wasn't an allowed character in our spec parser.
2. You would've had to double quote the flags to get them to pass through correctly:
spack install lammps ldflags='"-Wl,-rpath=$ORIGIN/lmp_libs"'
This is ugly and I don't think many users will easily figure it out. The behavior was added in
#29282, and it improved parsing of specs passed as a single string, e.g.:
spack install 'lammps ldflags="-Wl,-rpath=$ORIGIN/lmp_libs"'
but a lot of users are naturally going to try to quote arguments *directly* on the command
line, without quoting their entire spec. #29282 used a heuristic to detect unquoted flags
and warn the user, but the warning could be confusing. In particular, if you wrote
`cflags="-O2 -g"` on the command line, it would break the flags up, warn, and tell you
that you could fix the issue by writing `cflags="-O2 -g"` even though you just wrote
that. It's telling you to *quote* that value, but the user has to know to double quote.
## New heuristic for quoted arguments from the CLI
There are only two places where we allow arbitrary quoted strings in specs: flags and
variant values, so this PR adds a simpler heuristic to the CLI parser: if an argument in
`sys.argv` starts with `name=...`, then we assume the whole argument is quoted.
This means you can write:
spack install bzip2 cflags="-O2 -g"
directly on the command line, without multiple levels of quoting. This also works:
spack install 'bzip2 cflags="-O2 -g"'
The only place where this heuristic runs into ambiguity is if you attempt to pass
anonymous specs that start with `name=...` as one large string. e.g., this will be
interpreted as one large flag value:
spack find 'cflags="-O2 -g" ~bar +baz'
This sets `cflags` to `"-O2 -g" ~bar +baz`, which is likely not what you wanted. You
can fix this easily by either removing the quotes:
spack find cflags="-O2 -g" ~bar +baz
Or by adding a space at the start, which has the same effect:
spack find ' cflags="-O2 -g" ~bar +baz'
You may wonder why we don't just look for quotes inside of flag arguments, and the
reason is that you *might* want them there. If you are passing arguments like:
spack install zlib cppflags="-D DEBUG_MSG1='quick fox' -D DEBUG_MSG2='lazy dog'"
You *need* the quotes there. So we've opted for one potentially confusing, but easily
fixed outcome vs. limiting what you can put in your quoted strings.
## Quotes in formatted spec output
In addition to being more lenient about characters accepted in quoted strings, this PR fixes
up spec formatting a bit. We now format quoted strings in specs with single quotes, unless
the string has a single quote in it, in which case we JSON-escape the string (i.e., we add
`\` before `"` and `\`).
zlib cflags='-D FOO="bar"'
zlib cflags="-D FOO='bar'"
zlib cflags="-D FOO='bar' BAR=\"baz\""
* adding necessary headers, to fix https://github.com/spack/spack/issues/41398
* deleting something imported by accident
* [@spackbot] updating style on behalf of yizeyi18
* undo commit 7688fed according to suggestion from @msimberg
* patching camp@:2022.10.1 for compatibility with gcc-13
* adding the patch
* fixing paths in the patch
* [@spackbot] updating style on behalf of yizeyi18
* Update camp patch using LLNL/camp@05e1c35
Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>
* changing patch name
---------
Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>
`setup_dependent_package` is not a build phase, it should just set
globals for a package.
It's called during setup of runtime environment of packages, and there
have been reports of it actually failing due to a read only file system
(not sure under what exact conditions that is possible).
This license annotation is currently invalid as it specifies a URL
rather than an SPDX expression. Remove it for now until we have a
consensus on how to represent this case.
* New package Model Coupling Toolkit (MCT)
* Remove ~mpi variant from mct, build is not working correctly
* Remove boilerplate stuff from var/spack/repos/builtin/packages/mct/package.py
MySQL was performing a core API call to `Spec.flat_dependencies`
when setting up the build environment. This function is an
implementation detail of the old concretizer, where multiple nodes
from the same package are not allowed.
This PR uses a more idiomatic way to check if "python" is
in the DAG.
For reference, see #11356 to check why the call was introduced.
* [protobuf] New versions, explicit cxxstd variant
* New versions 3.15.8, 3.25.0, 3.25.1.
* New explicit variant `cxxstd` with support for older Protobuf
versions.
* Support testing.
* Use Protobuf's `protobuf_BUILD_SHARED_LIBS` instead of
`BUILD_SHARED_LIBS`.
* Support building with LLVM/Clang's `libc++`.
* Address audit issue
* Variant default does not honor `when` clause
* Use `self.spec.satisfies()` instead of `with when()`
* Fix silliness; improve consistency
* Today was apparently a go-back-to-bed day
* initial commit for rocm-5.7.0 and 5.7.1 releases
* bump up ther version for 5.7.0 and 5.7.1 releases
* update recipes to support 5.7.0 and 5.7.1 releases
* bump up the version for ROCm 5.7.0 and ROCm-5.7.1 releases
* bump up the version for composable-kernel amd miopen-hip
* fix style errors
* fix style errors in hip etc
* renaming composable-kernel recipe
* changes for composable_kernel
* Revert "renaming composable-kernel recipe"
This reverts commit 0cf6c6debf.
* Revert "changes for composable_kernel"
This reverts commit 05272a10a7.
* bump up the version for hiprand
* using the checksum for hiprand-5.7.1
* bump up the version for 5.7.0 and 5.7.1 releases
* fix style errors
* fix merge conflicts with the develop.
* temp workaround for the error seen with rocm-5.7.0 when trying
to generate the dependency file for runtime/legion/legion_redop.cu
* fix build issue(work around) with legion
* add patch for migraphx package to turn off ck
* update to hip recipe
* fix hip-path detection inside llvm clang driver
* update llvm-amdgpu and rocm-validation-suite recipes
* fix style errors
* bump up the version for amdsmi for rocm-5.7.0 release
* add support for gfx941,gfx942 for rocm-5.7.0 release onwards
* revert changes to rocm.py file
* added gfx941 and gfx942 to rocm.py and add the gfx942 to kokkos and new checksum
the new version seem to support gfx942
* bump up the version for rccl for 5.7.1
* update the patch for rocm-openmp-extras for 5.7.0
* update mivisionx recipe for 5.7.0 release
* add new dependencies for rocfft tests
* port the fix for avx build, the start address of values_ buffer in KernelParameters is not
correct as it is computed based on 16-byte alignment
* set HIP_PATH=ROCM_PATH for 5.7.0 onwards
* address review comments
* revert adding xnack- and xnack+ to gfx940,gfx941,gfx942 as the prechecks were failing
* Add `signed` property to mirror config
* make unsigned a tri-state: true/false overrides mirror config, none takes mirror config
* test commands
* Document this
* add a test
The new feq-parse version includes fixes for ifort and ifx compilers
Additionally, evaluation of parser objects with multidimension arrays is
now supported.
* samtools/htslib add latest version
* Given I work at the same institute as the authors I think it fair I am willing to review changes, if it's complex I can ask them over tea.
---------
Co-authored-by: James Beal <jb23@sanger.ac.uk>
* New variants:
- `tmvz-cpu`
- `tmvz-gpu`
- `tmvz-pymva`
- `tmvz-sofie`
* Improve X-related dependencies.
* Improve TMVA-related dependencies with more specificity.
* Patch possible missing standard header include in Eve7.
* Patch Protobuf handling to support new Protobuf-provided CMake config
files required to handle transitive `abseil-cpp` dependence.
* Add missing terminal newline to `webgui` patch to remove patch
warning.
* Handle deprecated/removed build options.
* geant4/geant4-data: add builtin_clhep variant and v10.0.4.
* geant4: revert addition of builtin_clhep variant.
* geant4: fix vecgeom variant only being available for v10.3 and above.
Fix filer_compiler_wrapper for cases where the compiler returned in None, this happens on some installed gcc systems that do not have fortran built into them as standard, e.g. gcc@11.4.0 on ubuntu 22.04
Before (hard to read, doesn't fit on small terminals):
:
```console
-I, --install-status show install status of packages
packages can be: installed [+], missing and needed by an installed package [-], installed in an upstream instance [^], or not installed (no annotation)
```
After (fits in 80 columns):
```console
-I, --install-status show install status of packages
[+] installed [^] installed in an upstream
- not installed [-] missing dep of installed package
```
* Fix cdash reporter time stamps (#38818).
The cdash reporter is created before packages are installed so save the
starttime then instead of the endtime.
* Use endtime instead of starttime for the endtime of update
---------
Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
Participation in the venerable Spack google group has dwindled, though we still have
540+ subscribers there. I've made the mailing list announcement-only, and I've given
a few maintainers posting privileges.
This PR adds some notes to the README indicating that the mailing list is only for
announcements.
* Ensure that additional environment variables are set when a module
file is generated.
* Fixed the detection of the opal_prefix / MPI_ROOT field to use ompi_info.
---------
Co-authored-by: Greg Becker <becker33@llnl.gov>
* depend_on python
There is an ill-named variant "python" that enables the pytrilinos1
variant. This made it through our testing but broke on our actual
CI test machines.
* adjust "python" variant based on Trilinos version
For Trilinos <= 14, enable PyTrilinos(1). For later versions
of Trilinos, enable PyTrilinos2.
We still support directly enabling PyTrilinos2 via the "pytrilinos2"
variant.
* remove pytrilinos2 variant
* correct depends_on constraints
- we don't have a fallback if make is not installed
- we assume file system locking works
- we don't verify that make is gnu make (bootstrapping fails on FreeBSD as a result)
- there are some weird race conditions in writing spack.yaml on concurrent spack install
- the view is updated after every package install instead of post environment install.
Forbid nested dependencies in depends_on declarations, by running an audit in CI.
Fix the packages not passing the new audit:
- amd-aocl
- exago
- palace
- shapemapper
- xsdk-examples
ginkgo: add a commit sha to v1.5.0.glu_experimental
* New variants:
- `tmvz-cpu`
- `tmvz-gpu`
- `tmvz-pymva`
- `tmvz-sofie`
* Improve X-related dependencies.
* Improve TMVA-related dependencies with more specificity.
* Patch possible missing standard header include in Eve7.
* Patch Protobuf handling to support new Protobuf-provided CMake config
files required to handle transitive `abseil-cpp` dependence.
* Add missing terminal newline to `webgui` patch to remove patch
warning.
* Handle deprecated/removed build options.
* Handle unwanted system paths in various `PATH`-like environment
variables.
The condition on swig can be interpreted as "true if true,
false if false" and gives clingo the option to add swig
or not.
If not other optimization criteria break the tie, then
the concretization is non-deterministic.
* added external libxc/elpa choice
* fixed formatting issues and 1 unused variant found by reviewer
* try to fix a string formatting issue
* try to fix some other string formatting issues
* fixed 1 flake8 style issue
* use explicit fftw-api@3
* Add `url_list` to facilitate finding new versions.
* `cxxstd` is not meaningful when `@:2.99.99` as it was a header-only
package before v3.
* Support C++20/23, remove C++14 support.
* Add @greenc-FNAL to maintainers.
* Add CMake arguments to support testing, build of extras and examples.
* Only build tests for proj package if required
Even if tests are not explictly required to be built, proj build them
anyway and tries to download Google Test.
* proj: fix name of test activation flag
* proj: Always set test activation flag
* proj: Patch test activation logic for versions 5.x
* py-python-pptx: new package
* py-python-pptx: use pil instead of pillow, remove version constraint on python
---------
Co-authored-by: LydDeb <lyderic.debusschere@eolen.com>
* py-tldextract: new package
* py-tldextract: add version 5.1.1
* py-tldextract: fix version constraint on py-setuptools-scm
---------
Co-authored-by: LydDeb <lyderic.debusschere@eolen.com>
* Add a new version of ruff
* Add a comment about where the dependency can be found
---------
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
* Update py-werkzeug version dependency for py-graphene-tornado@2.6.1
* Add note on diverging version requirements for py-werkzeug in py-graphene-tornado
* legion: correct cuda dependency for cr version
* Update var/spack/repos/builtin/packages/legion/package.py
---------
Co-authored-by: Davis Herring <herring@lanl.gov>
* py-gidgethub: add new package
* Add main branch version and scope flit/flit-core dependency
* Update var/spack/repos/builtin/packages/py-gidgethub/package.py
Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>
* Add optional dependencies as variants of package
* Add git url for main version
* Fix variant and dependency ordering
---------
Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>
* gidgetlab: add new package
* Convert both cachetools and aiohttp to optional deps with variants
* Fix forgotten variant conditional on cachetools dependency
* Add git url and main version for dev workflows
* Fix variant and dependency ordering
* Remove cachetools variant and merge dependency with aiohttp variant
* grep WM_PROJECT_VERSION from etc/bashrc
This fixes the problem when building from a manually checked out repo
which might have a different version wrt the one defined in the spack
package (e.g. anything later than 5.0 is known as 5.x by the build
system)
* patch applies to just 5.0, in newer versions it is already addressed
In `5.20171030` there's a commit
c66fba323c
very similar (almost identical) to what the patch `50-etc.patch` does.
So the patch should not be applied to other than `5.0` otherwise it errors.
References:
- https://github.com/OpenFOAM/OpenFOAM-5.x/commits/20171030/etc/bashrc
- 197d9d3bf2/etc/bashrc (L45-L47)
This was missed while backporting the new `spack info` command from #40326.
Variants should be sorted by name when invoking `spack info --variants-by-name`.
Intel made an incompatible change in XED in 2023.08.21 that breaks
hpctoolkit (at run time). Hpctoolkit develop can adapt (soon will),
but older versions must use xed :2023.07.09.
* Updating the LBANN, Hydrogen, and DiHydrogen recipes for both new
variants and to make sure that RPATHs are properly setup.
Co-authored-by: bvanessen <bvanessen@users.noreply.github.com>
Deprecating intel package, which contains intel classic compilers. This package has not been updated in 3 years. Please use intel-oneapi-compilers instead.
* gipaw.x installed by cmake if version >= 5c4a4ce.
gipaw.x will only be installed with cmake if the qe-gipaw version
is >= 5c4a4ce. Currently, QE source uses the older f5823521 one.
Here a patch to the submodule_commit_hash_records to use a newer
qe-gipaw version.
* Update package.py
* Delete var/spack/repos/builtin/packages/quantum-espresso/gipaw-eccee44.patch
* Update package.py
* Restoring gipaw-eccee44 patch
* Update package.py
* Add fox variant in quantum-espresso
* Fix an issue introduced in #36484. Patches are 7.1 only.
* Change plugin handling.
* formatting.
* Typo correction
* Refine conflict
---------
Co-authored-by: S. Alexis Paz <alexis.paz@gmail.com>
* Add EGL support to ParaView and Glew
add a package for egl that provides GL but also adds
EGL libs and headers for projects that need them
Fix a header problem with the opengl package
Format files using black
* better description for egl variant description
Co-authored-by: Vicente Bolea <vicente.bolea@gmail.com>
* better check/setup of non egl variant dependencies
Co-authored-by: Vicente Bolea <vicente.bolea@gmail.com>
* Add biddisco as maintainer
* Fix unused var style warning
* Add egl conflicts for other gl providers
---------
Co-authored-by: Vicente Bolea <vicente.bolea@gmail.com>
* py-pyglet: version bump
* py-pyglet: use zip instead of whl, update dependencies
* py-pyglet: 2.0.9 and 2.0.10 zips should be downloaded from github
* py-pyglet: style
* py-pyglet: use virtual packages in dependencies
Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>
* py-pyglet: doesn't depend on py-future any more
* py-pyglet: remove glx dependency
* py-pyglet: back to the pypi zipfiles with patch instead
---------
Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>
* Add initial version of verible to spack
* Update to use explict url path for each release, as the release tagh includes extra data, also added the bottom most point of gcc, gcc9
* py-pycma: new package
* rename py-pycma in py-cma; py-cma: use pypi instead of github sources
---------
Co-authored-by: LydDeb <lyderic.debusschere@eolen.com>
* lammps: add new stable version 20230802.1
* lammps: add missing potential download for +mesont
* lammps: fix python package install
* Update var/spack/repos/builtin/packages/lammps/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* lammps: py-numpy and py-mpi4py should be build and run deps
* lammps: add new 20231121 release
- MPIIO package has been removed -> disable mpiio variant
- LAMMPS_EXCEPTIONS is now always on -> disable exceptions variant
- CMake 3.16+ is now required
- Kokkos 4.1.0 is now supported
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add missing runtime dependency on py-colorama to py-ansimarkup
* Add py-metomi-isodatetime@3.1.0
* New package py-graphql-relay
* Update py-cylc-flowi, add version 8.2.3
* Fix merge conflict
* Revert mistake in var/spack/repos/builtin/packages/py-cylc-flow/package.py
* Update py-metomi-isodatetime dependencies for py-cylc-flow
* Add 'climbfuji' to list of maintainers for py-cylc-flow
* py-beartype: new package with version 0.15.0
* Update var/spack/repos/builtin/packages/py-beartype/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-beartype: depend on python 3.8 or higher
* py-beartype: add new version 0.16.2
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-mpi4py: fix build with Apple Clang
* [@spackbot] updating style on behalf of adamjstewart
---------
Co-authored-by: adamjstewart <adamjstewart@users.noreply.github.com>
* mochi-thallium: added a few newer versions
* mochi-thallium: added constraint on the version of margo required
* removed thallium 0.12 which needs updating
* mochi-thallium: fixed hash for version 0.12.0
* removed thallium 0.12 which needs updating (again)
When using `spack external find acfl`, we get the full version string
with 4 components in `packages.yaml`. This PR truncates the version
nubmer when finding the `armpl` component to be able to run without
intervention.
* developer tools stack try 2
This version is actually in use locally and has largely stabilized, at
least on x86. Some packages are still a challenge on ppc64le, but maybe
worth keeping this working as a set.
* add packages, try to get container with newer gcc
* remove reuse: true
* try to get cmake to build on medium, 25 minutes is too long
* add lsd package and add to dev tools stack
* clean up fzf dependency and sorting
* Update share/spack/gitlab/cloud_pipelines/stacks/developer_tools/spack.yaml
* cuda: add 12.3.0 (#40827)
* Switch to dashes
* yet more underscores
---------
Co-authored-by: Paul R. C. Kent <kentpr@ornl.gov>
This looks to me like the best compromise regarding externals in a
build cache. I wouldn't want `spack install` on my machine to install
specs that were marked external on another. At the same time there are
centers that control the target systems on which spack is used, and
would want to use external in buildcaches.
As a solution, reuse concretization will now consider those externals
used in buildcaches that match a locally configured external in
packages.yaml.
So for example person A installs and pushes specs with this config:
```yaml
packages:
ncurses:
externals:
- spec: ncurses@6.0.12345 +feature
prefix: /usr
```
and person B concretizes and installs using that buildcache with the
following config:
```yaml
packages:
ncurses:
externals:
- spec: ncurses@6
prefix: /usr
```
the spec will be reused (or rather, will be considered for reuse...)
* gipaw.x installed by cmake if version >= 5c4a4ce.
gipaw.x will only be installed with cmake if the qe-gipaw version
is >= 5c4a4ce. Currently, QE source uses the older f5823521 one.
Here a patch to the submodule_commit_hash_records to use a newer
qe-gipaw version.
* initial commit to update hipblas rocalution, rocsolver, rocsparse to new syntax
* add rocblas test changes and fixes for hipblas and rocsolver tests
* fix styling
* remove updates for rocblas
* solver: use a unique counter for condition, triggers and effects
* Do not reset counters when re-running setup
What we need is just a unique ID, it doesn't need
to start from zero every time.
* Update SST packages to 13.1.0
* Allow mismatch between sst-core dependency and current macro version
* SST does not work with Python 3.12 yet
* Sanity check install binaries for sst-core
* Elements compiles with OTF2 but not OTF
* Version bounds in specs are inclusive
* Remove not-strictly-necessary file check
* oneapi 2024.0.0 release
* oneapi v2 directory support and some cleanups
* sycl abi change requires 2024 compilers for packages that use sycl
---------
Co-authored-by: Robert Cohn <robert.s.cohn@intel.com>
* update spack recipe
* [@spackbot] updating style on behalf of toxa81
* change from @develop to @7.5.0
* return dependency on boost_filesystem
* return dependency on boost_filesystem
* remove boost filesystem as agreed by @RMeli and @simonpintarelli
---------
Co-authored-by: toxa81 <toxa81@users.noreply.github.com>
* Update to latest version
* Add dependency
* revert
* address PR comments
* Correct dependencies for 0.7 to 0.8 transition
* Fix cmake line.
* Update nanobind dep
---------
Co-authored-by: Matt Archer <ma595@cam.ac.uk>
Co-authored-by: Jack S. Hale <mail@jackhale.co.uk>
Co-authored-by: Garth N. Wells <gnw20@cam.ac.uk>
* add 0.12.0
* remove whitespace
* update deps
* Update var/spack/repos/builtin/packages/py-neo/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* add dep for python 3.8+
* add dep for python 3.8+ with 0.12.0
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
PR #40929 reverted the argument parsing to make `spack --verbose
install` work again. It looks like `--verbose` is the only instance
where this kind of argument inheritance is used since all other commands
override arguments with the same name instead. For instance, `spack
--bootstrap clean` does not invoke `spack clean --bootstrap`.
Therefore, fix multi-line aliases again by parsing the resolved
arguments and instead explicitly pass down `args.verbose` to commands.
This commit discards type mismatches or failures to validate a package preference during concretization. The values discarded are logged as debug level messages. It also adds a config audit to help users spot misconfigurations in packages.yaml preferences.
This roughly restores the order of operation from Spack 0.20,
where where `AutotoolsPackage.setup_build_environment` would
override the env variable set in `setup_platform_environment` on
macOS.
When improving the error message, we started #showing in the
answer set a lot more symbols - but we forgot to suppress the
debug messages warning about UNKNOWN SYMBOLs
* onnxruntime: fix the call to as_string() operator
* Update var/spack/repos/builtin/packages/py-onnxruntime/package.py
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
* Update var/spack/repos/builtin/packages/py-onnxruntime/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-onnxruntime/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-onnxruntime: rm now-unused stringpiece_1_10.patch
---------
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* packages/hub: add new version, update to module
Hub now uses a go module to build, needs different env vars, and we're
on a very, very old version before that. Deprecate the old ones so we
can clean out that old build once we pass a spack version.
* cleanup suggested by @adamjstewart
* Update to latest version
* Fix linebreak
* Make suggested changes
* bumped to 0.6.1
* Update var/spack/repos/builtin/packages/py-scikit-build-core/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Chris Richardson <cnr12@cam.ac.uk>
Co-authored-by: Matt Archer <ma595@cam.ac.uk>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
In practice, one can only compiler for the Intel Data Center Max GPU
via a SYCL build and the oneAPI compiler. This is unlikely to change,
so we can be explicit about that.
* elbencho add new version and git master branch
* Update var/spack/repos/builtin/packages/elbencho/package.py
Co-authored-by: Alec Scott <alec@bcs.sh>
* formatting fix requested by @alecbcs
* remove whitespace added in blank line by github auto resolve
---------
Co-authored-by: Ethan W <mail@ethanwilliams.xyz>
Co-authored-by: Alec Scott <alec@bcs.sh>
* gromacs: Add new variants and clarify existing ones
Add new variants that reflect existing capabilities and defaults in
the upstream build system. Add other existing constraints that were
not yet specified.
* conform to style
* Fix missing hyphens
* Correct cmake variable names
* add elephant version v0.12.0 and 0.13.0
* update copyright
* reformat according to black format errors
* restore maintainers directive
* Update var/spack/repos/builtin/packages/py-elephant/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* add dependency python 3.8+
* sorted dependencies
* sort dependencies from newest to oldest
* add deps for @master
* removed dependency for master, since it is included in 0.12.0:
* removed dependency for python 3.7+ , since 3.7+ is the lowest supported version anyway
* removed specific deps for master, since master is always newer than all stable releases
* updated numpy dependency for Elephant 0.12.0:
* Update var/spack/repos/builtin/packages/py-elephant/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-elephant/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* removed upper bounds for py-quantities, omitting v0.14.0
* add elephant v0.14.0
* update required quantities version
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-cleo: add versions 2.0.0 2.0.1; add maintainers
* py-cleo: add forgotten dependence
* py-cleo: update from review: remove preferred version, remove a dependence, fix py-rapidfuzz version
* py-cleo: deprecated version 1.0.0a5; add version 1.0.0; update dependences
* py-cleo: add version 2.1.0; update version range of dependences
* py-crashtest: add version 0.4.1, dependence of py-cleo
* py-cleo: update dependence
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-cleo: update dependence py-clikit
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-cleo: update dependence py-rapidfuzz
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-rapidfuzz: add version 2.2.0 dependence of py-cleo@2
* py-cleo: fix version range of py-crashtest
* py-rapidfuzz: fix dependences; add py-rapidfuzz-capi and py-jarowinkler
---------
Co-authored-by: LydDeb <lyderic.debusschere@eolen.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Using Python 3.12 in a freshly cloned Spack repository results in
warnings such as this:
```
==> Warning: invalid escape sequence '\$'
==> Warning: invalid escape sequence '\('
==> Warning: invalid escape sequence '\.'
==> Warning: invalid escape sequence '\.'
```
These will turn into errors in 3.13, so fix them. All of them actually
do not need to be regexes, so convert them into normal strings.
* add version 0.14.1
* formatting
* style checks
* fix style errors
* remove old versions
* fix typo
* style
* update maintainers directive
* sort dependencies from newest to oldest
* Update var/spack/repos/builtin/packages/py-quantities/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-quantities/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* sort dependencies from newest to oldest
* removed upper bounds for python version
* Update var/spack/repos/builtin/packages/py-quantities/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* remove dependency on Python 3.7 +, since 3.7 is the lowest supported version anyway
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Added recent versions to ecflow/package.py, as well as added a cxxstd variant that is
needed to set BOOST_NO_CXX98_FUNCTION_BASE appropriately when building with C++17 standard.
* Fixed pep8 style error in the ecflow package.py script.
* Remov
* Removed cxxstd variant since the ecflow cmake configuration was already specifying
to use the c++17 standard for newer versions. The use of the BOOST_NO_CXX98_FUNCTION_BASE
define is now triggered by the ecflow version.
* Permit packages that depend on Intel oneAPI packages to access sdk
* Implement and use IntelOneapiLibraryPackageWithSdk
* Restore libs property to IntelOneapiLibraryPackage
* Conform to style
* Provide new class to infrastructure
* Treat sdk/include as the main include
* root: new version 6.30.00
There is a new release of ROOT, v6.30.00, with release notes at https://root.cern/doc/v630/release-notes.html.
In addition to some deprecations of build options, this updates the C++ standard to 17 or higher (well, 20), and increases the vc minimum version.
* vc: new version 1.4.4
* [@spackbot] updating style on behalf of wdconinc
---------
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
message: "If you are referencing Spack in a publication, please cite the paper below."
title: "The Spack Package Manager: Bringing Order to HPC Software Chaos"
abstract: >-
Large HPC centers spend considerable time supporting software for thousands of users, but the complexity of HPC software is quickly outpacing the capabilities of existing software management tools.
Scientific applications require specific versions of compilers, MPI, and other dependency libraries, so using a single, standard software stack is infeasible.
However, managing many configurations is difficult because the configuration space is combinatorial in size.
We introduce Spack, a tool used at Lawrence Livermore National Laboratory to manage this complexity.
Spack provides a novel, re- cursive specification syntax to invoke parametric builds of packages and dependencies.
It allows any number of builds to coexist on the same system, and it ensures that installed packages can find their dependencies, regardless of the environment.
We show through real-world use cases that Spack supports diverse and demanding applications, bringing order to HPC software chaos.
Large HPC centers spend considerable time supporting software for thousands of users, but the
complexity of HPC software is quickly outpacing the capabilities of existing software management
tools. Scientific applications require specific versions of compilers, MPI, and other dependency
libraries, so using a single, standard software stack is infeasible. However, managing many
configurations is difficult because the configuration space is combinatorial in size. We
introduce Spack, a tool used at Lawrence Livermore National Laboratory to manage this complexity.
Spack provides a novel, re- cursive specification syntax to invoke parametric builds of packages
and dependencies. It allows any number of builds to coexist on the same system, and it ensures
that installed packages can find their dependencies, regardless of the environment. We show
through real-world use cases that Spack supports diverse and demanding applications, bringing
order to HPC software chaos.
preferred-citation:
title: "The Spack Package Manager: Bringing Order to HPC Software Chaos"
type: conference-paper
@@ -71,7 +75,7 @@ preferred-citation:
type: doi
value: 10.1145/2807591.2807623
- description: "The DOE Document Release Number of the work"
$ spack mirror set --signed <name> # enable signing and verification for an existing mirror
$ spack mirror set --unsigned <name> # disable signing and verification for an existing mirror
Or you can directly edit the ``mirrors.yaml`` configuration file:
..code-block::yaml
mirrors:
<name>:
url:<url>
signed:false# disable signing and verification
See also :ref:`mirrors`.
----------
Relocation
@@ -182,6 +218,41 @@ section of the configuration:
padded_length:128
.._binary_caches_oci:
---------------------------------
Automatic push to a build cache
---------------------------------
Sometimes it is convenient to push packages to a build cache as soon as they are installed. Spack can do this by setting autopush flag when adding a mirror:
..code-block::console
$ spack mirror add --autopush <name> <url or path>
Or the autopush flag can be set for an existing mirror:
..code-block::console
$ spack mirror set --autopush <name> # enable automatic push for an existing mirror
$ spack mirror set --no-autopush <name> # disable automatic push for an existing mirror
Then after installing a package it is automatically pushed to all mirrors with ``autopush: true``. The command
..code-block::console
$ spack install <package>
will have the same effect as
..code-block::console
$ spack install <package>
$ spack buildcache push <cache> <package> # for all caches with autopush: true
..note::
Packages are automatically pushed to a build cache only if they are built from source.
-----------------------------------------
OCI / Docker V2 registries as build cache
@@ -250,87 +321,13 @@ To significantly speed up Spack in GitHub Actions, binaries can be cached in
GitHub Packages. This service is an OCI registry that can be linked to a GitHub
repository.
A typical workflow is to include a ``spack.yaml`` environment in your repository
that specifies the packages to install, the target architecture, and the build
.. Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)
@@ -73,9 +73,12 @@ are six configuration scopes. From lowest to highest:
Spack instance per project) or for site-wide settings on a multi-user
machine (e.g., for a common Spack instance).
#.**plugin**: Read from a Python project's entry points. Settings here affect
all instances of Spack running with the same Python installation. This scope takes higher precedence than site, system, and default scopes.
#.**user**: Stored in the home directory: ``~/.spack/``. These settings
affect all instances of Spack and take higher precedence than site,
system, or defaults scopes.
system, plugin, or defaults scopes.
#.**custom**: Stored in a custom directory specified by ``--config-scope``.
If multiple scopes are listed on the command line, they are ordered
@@ -196,6 +199,45 @@ with MPICH. You can create different configuration scopes for use with
mpi: [mpich]
.._plugin-scopes:
^^^^^^^^^^^^^
Plugin scopes
^^^^^^^^^^^^^
..note::
Python version >= 3.8 is required to enable plugin configuration.
Spack can be made aware of configuration scopes that are installed as part of a python package. To do so, register a function that returns the scope's path to the ``"spack.config"`` entry point. Consider the Python package ``my_package`` that includes Spack configurations:
..code-block::console
my-package/
├── src
│ ├── my_package
│ │ ├── __init__.py
│ │ └── spack/
│ │ │ └── config.yaml
└── pyproject.toml
adding the following to ``my_package``'s ``pyproject.toml`` will make ``my_package``'s ``spack/`` configurations visible to Spack when ``my_package`` is installed:
..code-block::toml
[project.entry_points."spack.config"]
my_package="my_package:get_config_path"
The function ``my_package.get_extension_path`` in ``my_package/__init__.py`` might look like
(5 durations < 0.005s hidden. Use -vv to show these durations.)
=========================================== 5 passed in 5.06s ============================================
---------------------------------------
Registering Extensions via Entry Points
---------------------------------------
..note::
Python version >= 3.8 is required to register extensions via entry points.
Spack can be made aware of extensions that are installed as part of a python package. To do so, register a function that returns the extension path, or paths, to the ``"spack.extensions"`` entry point. Consider the Python package ``my_package`` that includes a Spack extension:
..code-block::console
my-package/
├── src
│ ├── my_package
│ │ └── __init__.py
│ └── spack-scripting/ # the spack extensions
└── pyproject.toml
adding the following to ``my_package``'s ``pyproject.toml`` will make the ``spack-scripting`` extension visible to Spack when ``my_package`` is installed:
..code-block::toml
[project.entry_points."spack.extenions"]
my_package="my_package:get_extension_path"
The function ``my_package.get_extension_path`` in ``my_package/__init__.py`` might look like
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