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351 Commits

Author SHA1 Message Date
Carson Woods
4188080899 Add new Podman package versions and fix patch (#38234)
* Add new podman versions and correct the versions which patch is applied to
* Replace the existing maintainer with alecbcs at maintainers request
2023-06-10 20:40:58 +02:00
Fabien Bruneval
ef6ea2c93f correct SHA for ABINIT 9.8.3 and add ABINIT 9.8.4 (#38283) 2023-06-09 12:24:28 -07:00
Greg Becker
3c672905d0 install status arg: update to default true and add inverse (#38252)
* install status arg: update to default true and add inverse

* update bash completion

* fix tests broken by output change
2023-06-09 10:38:05 -07:00
Jen Herting
ee106c747f [py-typer] new package (#38270)
* [py-typer] new package

* [py-typer] added version 0.7.0
2023-06-09 12:10:09 -05:00
Jen Herting
295726e6b8 [py-catalogue] added version 2.0.8 (#38266) 2023-06-09 12:01:04 -05:00
afzpatel
2654d64a3c comgr: enable testing (#35605) 2023-06-09 18:04:19 +02:00
Stephen Sachs
d91ec8500f [gromacs] Fix intel (classic) libstdc++ path (#37822)
* [gromacs] Fix intel (classic) libstdc++ path

Gromacs's `cmake` run will look for `--gcc-toolchain` (e.g. LLVM, icpx) or
`--gcc-name` (e.g. icpc) in `CMAKE_CXX_FLAGS`. Only if it does not find a good
g++ candidate there it will look for `GMX_GPLUSPLUS_PATH`:
cb6b311c39/cmake/FindLibStdCpp.cmake (L97)

Spack installed intel compilers already define a g++ for std libs. But in
`icp{c,x}.cfg` instead of the compile line. If we use the pre-defined g++ we not
only have less chance of mixing g++ versions, but also don't need to explicitly
add `gcc` as dependency to `gromacs`.

* Fix format

* Use a variant

As there is no way to check if a file exists at depends_on stage

* Fix format

* New name and fail if variant is used with other compiler

* Line too long.
2023-06-09 09:17:49 -04:00
Jonathon Anderson
c354cc51d0 containerize: use an ENTRYPOINT script (#37769) 2023-06-09 09:25:13 +02:00
Massimiliano Culpo
d5747a61e7 Hotfix to avoid building compilers from sources in pcluster pipelines (#38256)
The pcluster image has am internal buildcache without an index.

Also, we need to force reuse to avoid rebuilding GCC, since the default is 
to only reuse dependencies - and that is subject to changes in the GCC 
recipe.
2023-06-09 07:56:28 +02:00
Chris White
e88c747abc BLT package: add version 0.5.3 (#38247) 2023-06-09 00:36:00 -04:00
Martin Pokorny
cfe9e5bca4 glab: add new versions (#38236)
* glab: add new versions

* Update var/spack/repos/builtin/packages/glab/package.py

Co-authored-by: Alec Scott <alec@bcs.sh>

---------

Co-authored-by: Alec Scott <alec@bcs.sh>
2023-06-08 20:36:16 -07:00
Manuela Kuhn
48f7655a62 py-mako: add 1.2.4 (#38194) 2023-06-08 19:10:02 -04:00
Manuela Kuhn
a1111a9858 py-lxml: add 4.9.2 (#38191) 2023-06-08 19:09:41 -04:00
Manuela Kuhn
b8b9a798bf py-looseversion: add 1.2.0 (#38190) 2023-06-08 19:03:05 -04:00
Manuela Kuhn
7a1e94c775 py-msgpack: add 1.0.5 (#38230) 2023-06-08 18:02:42 -04:00
Manuela Kuhn
8c4b2173d2 py-mistune: add 2.0.5 (#38214) 2023-06-08 17:43:51 -04:00
George Young
4c4cd7b3ea py-llvmlite: add 0.40.0, update llvm dependency information (#38171)
* py-llvmlite: add 0.40.0, update llvm dependency information

* Update var/spack/repos/builtin/packages/py-llvmlite/package.py

Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>

* Update var/spack/repos/builtin/packages/py-llvmlite/package.py

Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>

* Update var/spack/repos/builtin/packages/py-llvmlite/package.py

Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>

* Update var/spack/repos/builtin/packages/py-llvmlite/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-06-08 16:10:48 -05:00
George Young
e92554414b gatk: add 4.4, update to java@17 (#38211)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-08 16:01:56 -04:00
George Young
d165e2c94b bowtie2: add 2.5.1 (#38201)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-08 16:01:34 -04:00
George Young
a97bd31afe trimgalore: add 0.6.10, adding variants (#38206)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-08 15:55:03 -04:00
George Young
d7719b26f9 seqtk: add 1.4 (#38193)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-08 15:48:54 -04:00
Manuela Kuhn
855c0fd9e0 py-markupsafe: add 2.1.3 (#38198) 2023-06-08 15:37:26 -04:00
Daniele Cesarini
4156397027 New packages: eprosima-fastdds and dependencies (#38079) 2023-06-08 12:27:06 -07:00
Juan Miguel Carceller
b4bbe5e305 ocaml: don't use the spack compiler (#38251)
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-06-08 12:17:29 -07:00
Adam J. Stewart
f5b595071e py-lightning: add v2.0.3 (#38260) 2023-06-08 15:14:28 -04:00
George Young
b6f2184cce bedtools2: patching to build with gcc@13 (#38254)
* bedtools2: patching to build with gcc@13

* bedtools2: patching to build with gcc@13

* Update var/spack/repos/builtin/packages/bedtools2/package.py

Yep, sure. Makes sense.

Co-authored-by: Alec Scott <alec@bcs.sh>

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Alec Scott <alec@bcs.sh>
2023-06-08 14:59:01 -04:00
Axel Huebl
9288067380 Mold: 1.11.0 (#38235)
* Mold: 1.11.0

Add the latest release of the `mold` linker.

* SHA for 1.7.1: zip to tar
2023-06-08 11:34:57 -07:00
Massimiliano Culpo
ddfc43be96 Forbid using env: as a top level environment attribute (#38199)
* Remove "env" from environment schema

* Remove spack.env.schema.keys

* Remove spack.environment.config_dict
2023-06-08 14:34:17 -04:00
Adam J. Stewart
63cad5d338 py-lightly: add v1.4.7 (#38259) 2023-06-08 14:04:16 -04:00
Ivan Maidanski
436ecdfb19 bdw-gc: add v8.2.4 (#37969)
* bdw-gc: add v8.2.4
* bdw-gc: Fix download URL for old package versions

---------

Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
2023-06-08 14:03:57 -04:00
John W. Parent
06817600e4 CMake/Windows bugfix: Make CMAKE_INSTALL_PREFIX a posix path (#36842)
CMake gives off a warning when passed Windows style paths as
install prefixes as the resultant path often causes invalid
escape sequences.
2023-06-08 10:05:38 -07:00
Wouter Deconinck
4ae1a73d54 (r-rcpp)ensmallen: new package (#38249)
* ensmallen: new package
  ensmallen is a high-quality C++ library for non-linear numerical optimization.
* r-rcppensmallen: new package

---------

Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
2023-06-08 09:53:02 -07:00
Massimiliano Culpo
f29aab0d03 Fix compiler removal from command line (#38057)
* Improve lib/spack/spack/test/cmd/compiler.py

* Use "tmp_path" in the "mock_executable" fixture

* Return a pathlib.Path from mock_executable

* Fix mock_executable fixture on Windows

"mock_gcc" was very similar to mock_executable, so use the latter to reduce code duplication

* Remove wrong compiler cache, fix compiler removal

fixes #37996

_CACHE_CONFIG_FILES was both unneeded and wrong, if called
subsequently with different scopes.

Here we remove that cache, and we fix an issue with compiler
removal triggered by having the same compiler spec in multiple
scopes.
2023-06-08 09:38:20 -07:00
eugeneswalker
cea1b3123e e4s oneapi ci: use official intel oneapi-derived runner image (#38176)
* e4s oneapi ci: use official intel oneapi-derived runner image

* update oneapi image

* tau builds ok, but only with libdrm - comment out for now, follow up with pr later
2023-06-08 09:17:22 -07:00
Alec Scott
b22ccf279d junit4: add v4.13.2 (#38122) 2023-06-08 11:54:09 -04:00
Wouter Deconinck
81e15ce36e (r-rcpp)armadillo: new version 12.4.0 (#38246)
* armadillo: new version 12.4.0
   No build system changes necessary, https://gitlab.com/conradsnicta/armadillo-code/-/compare/12.2.x...12.4.x
* r-rcpparmadillo: new version 0.12.4.0.0
2023-06-08 11:49:17 -04:00
George Young
8907e52933 bismark: add 0.24.1, add HISAT2 dependency (#38210)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-08 11:49:00 -04:00
Carlos Bederián
80cefedac5 quantum-espresso: add 7.2 (#38223) 2023-06-08 11:23:54 -04:00
Seth R. Johnson
b85a66f77a trilinos: drop preferred version (#38086) 2023-06-08 11:18:44 -04:00
Alec Scott
a0ba3d890a cni-plugins: add v1.3.0 (#38064) 2023-06-08 10:27:20 +02:00
Manuela Kuhn
315873cbd3 py-keyring: add 23.13.1 (#38183)
* py-keyring: add 23.13.1

* [@spackbot] updating style on behalf of manuelakuhn
2023-06-07 23:00:05 -05:00
Thomas Bouvier
e05095af90 py-nvidia-dali: update versions up to v1.26.0 (#38022)
* `py-nvidia-dali`: update versions up to v1.26.0

* Add proper `cuda` dependency version
2023-06-07 22:52:52 -05:00
Thomas Bouvier
e0d6a73f96 py-horovod: add versions v0.27.0 and v0.28.0 (#38016)
* `py-horovod`: add versions v0.27.0 and v0.28.0

* fix: typo

* Add upper version bound for `py-pyarrow`
2023-06-07 22:51:19 -05:00
Manuela Kuhn
6ebfb41ad9 py-json5: add 0.9.14 (#38178) 2023-06-07 22:16:28 -05:00
Manuela Kuhn
d0aa01c807 py-jaraco-classes: add 3.2.3 (#38167) 2023-06-07 21:48:58 -05:00
Manuela Kuhn
1265c7df47 py-jupyter-client: add 8.2.0 (#38180) 2023-06-07 21:48:12 -05:00
Alec Scott
91e3f14959 hbase: add v2.5.3 (#38073) 2023-06-07 18:11:21 -07:00
Alec Scott
5f03eb650d chemfiles: add v0.10.4 (#38063) 2023-06-07 18:05:37 -07:00
Martin Pokorny
e0e6133444 casacore: add v3.5.0 (#37806) 2023-06-07 23:12:08 +02:00
Nate deVelder
ee68baf254 OpenFAST: add v3.3.0, v3.4.0 and v3.4.1 (#37407) 2023-06-07 23:10:39 +02:00
Christopher Kotfila
785c1a2070 Add documentation about package signing model (#30939)
Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com>
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-06-07 23:05:44 +02:00
Dan Lipsa
79656655ba Guard for define in netcdf 4.9.0 and later. (#37853)
* Guard for define in netcdf 4.9.0 and later.

This code is already available in ParaView 5.11.0 so no patching
needed there.

* Add latest needed version (even if not in spack).

---------

Co-authored-by: Dan Lipsa <dan.lipsa@khq.kitware.com>
2023-06-07 14:20:27 -05:00
Sajid Ali
74921788a8 llvm: add new versions and set default for libomptarget according to os (#38092)
* llvm: add new versions and set default for libomptarget according to os

	modified:   var/spack/repos/builtin/packages/llvm/package.py

* Incorporate reviewer suggestions

Co-authored-by: Sergey Kosukhin <skosukhin@gmail.com>

---------

Co-authored-by: Sergey Kosukhin <skosukhin@gmail.com>
2023-06-07 10:55:46 -05:00
Carlos Bederián
b313b28e64 nwchem: remove -mtune=native flags (#37892)
Co-authored-by: Edoardo Aprà <edoardo.apra@gmail.com>
2023-06-07 09:02:35 +02:00
eugeneswalker
5f1bc15e80 E4S Cray CI Stack (#37837)
* e4s cray ci stack

* e4s ci: add cray

* add zen4 tag

* WIP: new defintions just for cray

* updates

* remove ci signing job overrride, not necessary

* echo $PATH and show modules loaded

* add mirror

* add external def for cray-libsci

* comment out quantum-espresso

* use /etc/protected-runner as key path

* cray ci stack: do not remove tags: [spack, public]

* make cray stack composable

* generate job should run on public tagged runner, override default config:install_tree:root

* CI: Use relative path in default script

* CI: Use relative includes paths for shell runners

* Use concrete_env_dir for relpath

* ml-darwin-aarch64-mps: jax has bazel codesign issue

---------

Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com>
Co-authored-by: Ryan Krattiger <ryan.krattiger@kitware.com>
2023-06-06 18:41:32 -07:00
Mikael Simberg
fa9fb60df3 CachedCMakePackage: fix bug where CMAKE_CUDA_ARCHITECTURES=none is set (#38169)
#37592 updated cached cmake packages to set CMAKE_CUDA_ARCHITECTURES.
The condition `if archs != "none"` lead to `CMAKE_CUDA_ARCHITECTURES=none`
when cuda_arch=none (incorrect check on the value of a multi-valued
variant), i.e. CMAKE_CUDA_ARCHITECTURES is always set. This PR udpates
the condition to if archs[0] != "none" to ensure CMAKE_CUDA_ARCHITECTURES
is only set if cuda_arch is not none (which seems to be the pattern used
in other packages).

This does the same for HIP (although in general ROCmPackage disallows
amdgpu_target=none when +rocm).
2023-06-06 14:41:02 -07:00
Mosè Giordano
e759e6c410 julia: Update patch for llvm 14 without binary files (#37959) 2023-06-06 21:53:20 +02:00
Jonathon Anderson
f41446258a containers: don't install epel-release on Fedora (#37766) 2023-06-06 21:50:46 +02:00
Erik Schnetter
268649654d openssl: add versions 1.1.1u, 3.0.9, 3.1.1 (#38023) 2023-06-06 21:49:01 +02:00
Diego Alvarez S
12e249f64e Add nextflow 23.04.1 (#38166) 2023-06-06 12:12:50 -07:00
Tamara Dahlgren
c34cd76f2a perl: convert to new stand-alone test process (#37727) 2023-06-06 12:07:44 -07:00
Tamara Dahlgren
815b210fc8 tests/ginkgo: converted to new stand-alone test process (#35730)
* Ginkgo: converted to new stand-alone test process

* ginkgo: update string formatting, compiler setting
2023-06-06 11:58:53 -07:00
Tamara Dahlgren
e5d5efb4c1 tests/darshan-util: convert to new stand-alone test process (#37836) 2023-06-06 11:56:40 -07:00
Tamara Dahlgren
0aa4b4d990 tests/oommf: convert to new stand-alone test process (#38009)
* oommf: convert to new stand-alone test process

* oommf: Switch build-time tests to documented approach
2023-06-06 11:55:33 -07:00
Tamara Dahlgren
01c1d334ae tests/mfem: convert to new stand-alone test process (#38011)
* mfem: convert to new stand-alone test process
* Restore make target, use config_mk property
2023-06-06 11:42:51 -07:00
Massimiliano Culpo
717fc11a46 Don't build rocky:9 images for ppc64le (#38202)
See https://docs.rockylinux.org/release_notes/9_2/
2023-06-06 17:46:53 +02:00
eugeneswalker
d21c49e329 @develop+stokhos: do not set Stokhos_ENABLE_PCE_Scalar_Type=False (#38187) 2023-06-06 08:32:21 -07:00
Tamara Dahlgren
6937d9dddc eigenexa: convert to new stand-alone test process (#35745) 2023-06-06 15:08:51 +02:00
Thomas Bouvier
4c2531d5fb libraqm: add missing fribidi dependency (#36125)
* `libraqm`: add missing `fribidi` dependency
* `libraqm`: add `sheenbidi` variant
* [@spackbot] updating style on behalf of thomas-bouvier

---------

Co-authored-by: thomas-bouvier <thomas-bouvier@users.noreply.github.com>
2023-06-05 18:13:42 -04:00
Alex Richert
62fd890c52 Rename fpic variant to pic for fms (#38101) 2023-06-05 14:58:52 -07:00
Alex Richert
4772fd7723 Add MADIS package (#38097)
* Add MADIS package
* madis update
* [@spackbot] updating style on behalf of AlexanderRichert-NOAA
* allow arg mismatch for gcc@10: for madis
2023-06-05 14:31:51 -07:00
snehring
7c11faceb0 ninja-phylogeny: adding new package ninja-phylogeny (#38182) 2023-06-05 16:44:51 -04:00
Alec Scott
053550e28a asdcplib: add v2_10_38 (#37971) 2023-06-05 12:46:19 -07:00
Alec Scott
3ed7258447 fjcontrib: add v1.052 (#38116) 2023-06-05 14:25:30 -05:00
Manuela Kuhn
a5cf5baa9e py-jupyterlab: add 4.0.1 incl. new dependencies (#38102) 2023-06-05 13:54:20 -05:00
Alec Scott
ec8039cc74 seal: add v4.1.1 (#38155) 2023-06-05 11:46:40 -07:00
snehring
9bfa840c27 ncbi-rmblastn: adding new version 2.14.0 (#38173)
* ncbi-rmblastn: adding new version 2.14.0
* ncbi-rmblastn: add maintainer
2023-06-05 11:45:15 -07:00
Alec Scott
9865f42335 azcopy: add v10.19.0 (#38106) 2023-06-05 10:56:34 -07:00
Alec Scott
dba2829871 hssp: add v3.1.5 (#38107) 2023-06-05 10:51:30 -07:00
Alec Scott
8c0e1fbed9 diamond: add v2.1.7 (#38115) 2023-06-05 10:46:39 -07:00
Alec Scott
187488b75b optional-lite: add v3.5.0 (#38148) 2023-06-05 10:24:37 -07:00
Alec Scott
2aa35fef3e nccmp: add v1.9.1.0 (#38142) 2023-06-05 10:15:25 -07:00
Nathalie Furmento
d373fc36ae starpu: add release 1.3.11 (#38172) 2023-06-05 09:12:40 -07:00
Massimiliano Culpo
e483762015 Update RtD and Sphinx configuration (#38046) 2023-06-05 17:39:11 +02:00
Houjun Tang
5840a00000 Update package.py require HDF5 1.14+ (#38026) 2023-06-05 11:27:53 -04:00
George Young
110f836927 fastqc: add 0.12.1, update patch files (#37934)
* fastqc: add 0.12.1

* fastqc: add 0.12.1

* Update var/spack/repos/builtin/packages/fastqc/package.py

Yeah, had considered doing the same, I'd just opted to maintain the status quo. All good.

Co-authored-by: Alec Scott <alec@bcs.sh>

* Update package.py

Style fiddles to make the bot contented.

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Alec Scott <alec@bcs.sh>
2023-06-05 11:07:51 -04:00
Weiqun Zhang
d6765f66ae amrex: add version 23.06 (#38056) 2023-06-05 07:44:32 -07:00
Alec Scott
19dac780e8 iozone: add v3_506 (#38118) 2023-06-05 13:00:23 +02:00
Alec Scott
b82b549c59 iqtree2: add v2.2.2 (#38119) 2023-06-05 13:00:06 +02:00
Alec Scott
b376401ece jimtcl: add v0.82 (#38120) 2023-06-05 12:59:48 +02:00
Alec Scott
7d956dbe9e jline3: add v3.22.0 (#38121) 2023-06-05 12:59:32 +02:00
Alec Scott
6db1d84bb0 kubernetes: add v1.27.2 (#38123) 2023-06-05 12:58:47 +02:00
Alec Scott
2094fa3056 simde: add v0.7.6 (#38157) 2023-06-05 06:38:46 -04:00
Alec Scott
3d255bc213 leptonica: add v1.83.1 (#38125) 2023-06-05 12:36:16 +02:00
Alec Scott
5538dda722 libcint: add v5.3.0 (#38127) 2023-06-05 12:36:02 +02:00
Alec Scott
1c0d89bf25 libeatmydata: add v131 (#38128) 2023-06-05 12:35:46 +02:00
Alec Scott
4cc0199fbb libibumad: add v46.0 (#38130) 2023-06-05 12:35:33 +02:00
Alec Scott
edb8226fff librdkafka: add v2.1.1 (#38131) 2023-06-05 12:35:20 +02:00
Alec Scott
ef972cf642 libspiro: add v20221101 (#38132) 2023-06-05 12:35:03 +02:00
Alec Scott
50c13541e4 libgd: add v2.3.3 (#38129) 2023-06-05 06:29:32 -04:00
Alec Scott
fd5d7cea6e perl-math-bigint: add v1.999838 (#38150) 2023-06-05 06:29:15 -04:00
Alec Scott
526314b275 laszip: add v3.4.3 (#38124) 2023-06-05 06:29:00 -04:00
Alec Scott
7b37c30019 libthai: add v0.1.29 (#38133) 2023-06-05 11:28:44 +02:00
Alec Scott
dc03c3ad9e libvori: add v220621 (#38135) 2023-06-05 11:26:58 +02:00
Alec Scott
61b485f75d lsscsi: add v0.32 (#38136) 2023-06-05 11:26:42 +02:00
Alec Scott
e24151783f ltp: add v20230127 (#38137) 2023-06-05 11:25:55 +02:00
Alec Scott
ed9714e5ae mariadb-c-client: add v3.3.5 (#38140) 2023-06-05 11:25:22 +02:00
Alec Scott
ea620a083c nco: add v5.1.6 (#38143) 2023-06-05 11:24:54 +02:00
Alec Scott
504a8be666 nettle: add v3.9.1 (#38144) 2023-06-05 11:24:34 +02:00
Alec Scott
d460870c77 ngmlr: add v0.2.7 (#38145) 2023-06-05 11:24:19 +02:00
Alec Scott
f0f77251b3 nim: add v1.9.3 (#38146) 2023-06-05 11:24:00 +02:00
Alec Scott
bdd454b70b openexr: add v3.1.7 (#38147) 2023-06-05 11:23:26 +02:00
Alec Scott
aea6662774 pgdspider: add v2.1.1.5 (#38151) 2023-06-05 11:22:41 +02:00
Alec Scott
fe6bcb36c7 primer3: add v2.6.1 (#38152) 2023-06-05 11:22:22 +02:00
Alec Scott
2474a2efe1 sbt: add v1.8.3 (#38154) 2023-06-05 11:22:06 +02:00
Alec Scott
4cfd49019c signify: add v31 (#38156) 2023-06-05 11:20:04 +02:00
Alec Scott
7beae8af30 madx: add v5.09.00 (#38139) 2023-06-05 11:19:37 +02:00
Umashankar Sivakumar
22fc5d2039 papi: update git URL (#38042) 2023-06-05 11:13:17 +02:00
Alec Scott
b70fc461a4 at-spi2-core: add v2.48.3 (#38162) 2023-06-05 11:09:57 +02:00
Alec Scott
e756436d7c grep: add v3.11 (#38163) 2023-06-05 11:09:34 +02:00
Alec Scott
8dd87e2572 hugo: add v0.112.7 (#38164) 2023-06-05 11:09:12 +02:00
Manuela Kuhn
853bf95bd2 py-ipython: add 8.14.0 (#38113) 2023-06-04 22:18:00 -04:00
Manuela Kuhn
1c80d07fd2 py-iso8601: add 1.1.0 (#38110) 2023-06-04 22:07:43 -04:00
Manuela Kuhn
6fd8001604 py-ipykernel: add 6.23.1 (#38111) 2023-06-04 21:52:55 -04:00
Pariksheet Nanda
c08f9fd6fc py-jaxlib: patch bazel server cpu limit (#37548) (#38090) 2023-06-04 19:28:41 -04:00
Adam J. Stewart
c3fb998414 GMT: add new versions (#37921)
* GMT: add new versions

* [@spackbot] updating style on behalf of adamjstewart

---------

Co-authored-by: adamjstewart <adamjstewart@users.noreply.github.com>
2023-06-04 18:00:49 -05:00
George Young
3368a98210 py-htseq: add 2.0.3, switch to PyPI (#37935)
* py-htseq: add 0.12.3, switching over to new GitHub repo

* py-htseq: add 0.12.3, switching over to new GitHub repo

Style fixes

* py-htseq: add 2.0.3, switch to PyPI

* py-htseq: add 2.0.3, switch to PyPI

* Update package.py

* Update var/spack/repos/builtin/packages/py-htseq/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Removing SWIG

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-06-04 17:55:16 -05:00
Manuela Kuhn
606b7c7f16 py-hatch-fancy-pypi-readme: add 23.1.0 (#38075) 2023-06-04 17:30:33 -05:00
Manuela Kuhn
2f4e66be09 py-hatchling: add 1.17.0 (#38076) 2023-06-04 17:29:40 -05:00
Manuela Kuhn
9ce3e8707c py-humanize: add 4.6.0 (#38077) 2023-06-04 17:28:45 -05:00
Manuela Kuhn
d6a96745ee py-identify: add 2.5.24 (#38088) 2023-06-04 17:27:47 -05:00
Manuela Kuhn
a0fcdd092b py-imageio: add 2.30.0 (#38089) 2023-06-04 17:27:08 -05:00
Christoph Junghans
e17d09e607 votca: stable branch was removed (#38043) 2023-06-04 17:26:02 -05:00
Manuela Kuhn
847d67f223 py-gast: add 0.5.4 (#38054)
* py-gast: add 0.5.4

* py-pythran: add 0.12.2 and restict upper bound of py-gast
2023-06-04 17:25:35 -05:00
Alec Scott
7ae0e06a62 libbson: add v1.23.4 (#38126) 2023-06-04 16:33:51 -05:00
Alec Scott
d3df97df8b hyperfine: add v1.16.1 (#38108) 2023-06-04 12:45:51 +02:00
Sergey Kosukhin
7d5d075809 llvm: optionally build compiler-rt, libcxx and libunwind as runtimes (#32476)
* llvm: replace +omp_as_runtime with omp=runtime

* llvm: fetch 'libomp-libflags-as-list.patch' from upstream repo

* llvm: replace 'llvm14-hwloc-ompd.patch' with the official fix from upstream repo

* llvm: fix-up for the black reformatting

* llvm: fetch 'constexpr_longdouble.patch' from upstream repo

* llvm: optionally build libcxx as a runtime

* llvm: fetch 'llvm5-sanitizer-ustat.patch' from upstream repo

* llvm: update 'sanitizer-ipc_perm_mode.patch'

* llvm: refactor compiler conflicts when libcxx=project

* llvm: fetch 'llvm_python_path.patch' from upstream repo

* llvm: update comments and condition for 'xray_buffer_queue-cstddef.patch'

* llvm: optionally build compiler-rt as a runtime

* llvm: fetch 'lldb_external_ncurses-10.patch' from upstream repo

* llvm: fetch 'llvm_py37.patch' from upstream repo

* llvm: rename variant 'internal_unwind' to 'libunwind'

* llvm: optionally build libunwind as a runtime

* llvm: extend the list of maintainers

* llvm: allow for explicit '~clang~flang~libomptarget~lldb~omp_debug~z3'

* llvm: fetch 'llvm5-lld-ELF-Symbols.patch' from FreeBSD port repo

* llvm: fetch most of 'missing-includes.patch' from upstream repo and reuse 'llvm-gcc11.patch'

* llvm: regroup patches for missing include directives and drop compiler constraints for them

* llvm: fetch 'llvm-gcc11.patch' from upstream repo

* llvm: fetch 'no_cyclades.patch' from upstream repo

* llvm: update comments and condition for 'no_cyclades9.patch'

* llvm: rename variant 'omp' to 'openmp'

* llvm: constrain and rename variant 'omp_tsan' to 'libomp_tsan'

* llvm: rename variant 'omp_debug' to 'libomptarget_debug'

* llvm: do not apply same patch twice

* llvm: constrain and document the '*-thread.patch' patches

* llvm: document the '~lld+libomptarget' conflict

* llvm: update comments for the 'D133513.diff' patch
2023-06-03 23:08:10 -05:00
Peter Scheibel
237a0d8999 Add explicit CMake .libs implementation that returns an empty list; same for .headers (#35816) 2023-06-03 18:08:02 -07:00
Alec Scott
6952ed9950 c-blosc: add v1.21.4 (#37973) 2023-06-03 13:52:43 -04:00
Thomas Madlener
3e2d1bd413 lcio: Add latest version 2.20 (#38078) 2023-06-03 10:35:17 -07:00
Martin Aumüller
9dfba4659e botan: checksum new versions and enable external find (#38081)
* botan: checksum new versions, including new major

version 3 breaks API

* botan: support external find
2023-06-03 10:33:59 -07:00
Michael Kuhn
7fca252aa4 sqlite: add 3.42.0 (#38091) 2023-06-03 10:30:25 -07:00
Wouter Deconinck
fa23a0228f py-hatch-fancy-pypi-readme: depends_on when typo (#38103) 2023-06-03 09:57:03 -05:00
Massimiliano Culpo
ed76966a3a gnupg: add v2.4.2 (#38059)
* gnupg: add v2.4.2

* [@spackbot] updating style on behalf of alalazo

---------

Co-authored-by: alalazo <alalazo@users.noreply.github.com>
2023-06-02 09:28:54 -07:00
willdunklin
2015a51d1a sz: add versions v2.1.12.5 and v2.1.12.4 (#38060) 2023-06-02 09:28:05 -05:00
Manuela Kuhn
34b8fe827e py-flask: add 2.3.2, py-blinker: add 1.6.2, py-werkzeug: add 2.3.4 (#38025) 2023-06-02 05:57:22 -04:00
Manuela Kuhn
6f1ed9b2e4 py-exceptiongroup: add 1.1.1 (#38018) 2023-06-02 05:47:49 -04:00
M. Eric Irrgang
dd00f50943 Add py-gmxapi version 0.4.2 (#38053) 2023-06-02 03:07:34 -04:00
Sam Grayson
f0ec625321 singularityce: add v3.11.3 (#38055) 2023-06-02 08:04:39 +02:00
Manuela Kuhn
d406c371a8 py-formulaic: add 0.6.1 (#38035) 2023-06-01 19:23:15 -04:00
Sean Koyama
42d374a34d double-batched-fft-library: patch to add search paths to findOpenCL.cmake (#36355)
* double-batched-fft-library: PATCH: add search paths to find libOpenCL

* Apply patch up to version 0.3.6
2023-06-01 16:17:04 -07:00
Sean Koyama
d90e4fcc3d lua-luafilesystem: update source URL and improve rockspec detection (#36692)
* lua-luafilesystem: updated sources to new URL. Changed versioning to dot-separated versions.

* lua-luafilesystem: override install phase to find correct rockspec

* lua-luafilesystem: improved rockspec detection

* lua-luafilesystem: added lua version constraint for older versions
2023-06-01 16:15:42 -07:00
Manuela Kuhn
a44fde9dc9 py-docutils: add 0.20.1 (#38001) 2023-06-01 18:18:29 -04:00
Manuela Kuhn
9ac8841dab py-fonttools: add 4.39.4 (#38027) 2023-06-01 18:13:20 -04:00
Manuela Kuhn
a1f87638ec py-future: add 0.18.3 (#38041)
* py-future: add 0.18.3

* Update var/spack/repos/builtin/packages/py-future/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-06-01 17:48:13 -04:00
Manuela Kuhn
3b55e0a65d py-executing: add 1.2.0 (#38019) 2023-06-01 17:38:09 -04:00
Massimiliano Culpo
42667fe7fa Memoize a few hot functions during module file generation (#37739) 2023-06-01 13:36:42 -07:00
Ted Stern
cd27611d2f Adding libpsm3 package (#37444)
* Adding libpsm3 package
* Make changes suggested by flake8
* Make one more flake8-suggested change, blank line after 'import os'
* Change to standard header to pass flake8 tests
* Update doc string, remove unnecessary comments
* Reviewer-recommende changes
* Alphabetize variants
* Use helper functions
* Change quotes to pass spack style check
2023-06-01 13:01:43 -07:00
Massimiliano Culpo
b111d2172e py-archspec: add v0.2.1 (#38014) 2023-06-01 14:58:45 -05:00
Tobias Ribizel
055263fa3c Fix OpenCV detection on Ubuntu (#35336)
* fix OpenCV detection on Ubuntu

* Update package.py

* Simplify version detection

* remove superfluous `return`
2023-06-01 14:38:17 -05:00
Manuela Kuhn
f34f207bdc py-datalad-neuroimaging: add 0.3.3 (#38017) 2023-06-01 14:31:54 -05:00
snehring
0c9f0fd40d openssh: depend on krb5+shared when +gssapi (#38034) 2023-06-01 13:17:44 -04:00
pauleonix
24d5b1e645 asio: Add stable versions up to 1.28.0 (#38007)
Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>

- Add pkgconfig dependency from 1.23.0 onward.
- Add conflict of old versions with new gcc due to missing includes.
- Deprecate uneven minor versions because they are not regarded as stable.
- Add maintainer
2023-06-01 11:09:27 +02:00
Mikael Simberg
616f7bcaef pika: add 0.16.0 and pika-algorithms 0.1.3 (#38021)
* pika: add 0.16.0

* pika-algorithms: add 0.1.3

---------

Co-authored-by: Alberto Invernizzi <9337627+albestro@users.noreply.github.com>
2023-06-01 04:18:26 -04:00
Greg Becker
dace0316a2 Spec.format: print false attributes if requested (#37932) 2023-06-01 09:08:45 +02:00
Greg Sjaardema
3bb86418b8 seacas: add 2023-05 release, update fmt dependency (#38008)
The fmt dependency for the previous release was incorrect as does not work with latest lib::fmt.  Fixed that specification
2023-06-01 02:48:50 -04:00
Veselin Dobrev
6f6489a2c7 xSDK examples v0.4.0 (#37295)
* [xsdk-examples] Initial commit for v0.4.0

* [xsdk-examples] v0.4.0 depends on xsdk@0.8.0

* add in missing xsdk dependencies

* [xsdk-examples] remove repeated 'depends_on' directive

* [xsdk-examples] simplify and extend a bit the package

[mfem] process more optional dependencies of HiOp

[strumpack, superlu-dist] add a workaround for an issue on Mac

* [mfem] fix the handling of the hiop dependency

* [@spackbot] updating style on behalf of v-dobrev

* [xsdk-examples] enable 'heffte' and 'tasmanian' if enabled in 'xsdk'

* [xsdk-examples] Add PUMI dependency

* [xsdk-examples] Add preCICE dependency

* [xsdk-examples] add +rocm

* heffte: add in a backport fix for building xsdk-examples with cuda

* [xsdk] Remove the explicit requirement for deal.II to be built +hdf5

* ENABLE_ROCM -> ENABLE_HIP

* [hiop] Workaround for CMake not finding Cray's BLAS (libsci)

[xsdk-examples] Set CUDA/HIP architectures; sync cuda/rocm variants with xsdk

* [@spackbot] updating style on behalf of v-dobrev

* [exago] Workaround for CMake not finding Cray's LAPACK/BLAS, libsci

[mfem] Tweaks for running tests under Flux and PBS

* [slate] Pass CUDA/HIP architectures to CMake

* [heffte] For newer CMake versions, set CMAKE_CUDA_ARCHITECTURES

* [hypre] Patch v2.26.0 to fix sequential compilation in 'src/seq_mv'

* [xsdk-examples] Some tweaks in dependencies and compilers used

* [xsdk] Make the 'trilinos' variant sticky

[xsdk-examples] Tweak dependencies

* [slate] Fix copy-paste error

* [xsdk-examples] Workaround for CMakePackage not having the legacy
   property 'build_directory'

* [xsdk-examples] Replace the testing branch used temporarily for v0.4.0 with
                the official release

---------

Co-authored-by: Satish Balay <balay@mcs.anl.gov>
2023-05-31 21:57:53 -04:00
Brian Van Essen
543b697df1 CachedCMakePackage: add CUDA/HIP options and improve independent builds (#37592)
* Add CMake options for building with CUDA/HIP support to
  CachedCMakePackages (intended to reduce duplication across packages
  building with +hip/+cuda and using CachedCMakePackage)
* Define generic variables like CMAKE_PREFIX_PATH for
  CachedCMakePackages (so that a user may invoke "cmake" themselves
  without needing to setthem on the command line).
* Make `lbann` a CachedCMakePackage.

Co-authored-by: Chris White <white238@llnl.gov>
2023-05-31 17:35:11 -07:00
QuellynSnead
042dc2e1d8 libtheora: enforce math library (libm.so) linkage (#37891) 2023-05-31 13:45:11 -07:00
Mosè Giordano
f745e49d9a julia: add patch to fix printing of BigFloat with MPFR v4.2 (#37992) 2023-05-31 15:32:12 -04:00
Michael Kuhn
eda21cdfba gcc: add 11.4.0 (#37988) 2023-05-31 09:15:45 -04:00
Adam J. Stewart
bc8b026072 py-pandas: add v2.0.2 (#38005) 2023-05-30 22:48:51 -04:00
Tiziano Müller
0f84782fcc Bugfix: cray manifest parsing regression (#37909)
fa7719a changed syntax for specifying exact versions, which are
required for some compiler specs (including those read as part
of parsing a Cray manifest). This fixes that and also makes a
couple other improvements to manifest parsing.

* Instantiate compiler specs with exact versions (fixes #37893)
* fix slingshot network detection (CPE 22.10+ has libcxi.so
  in /usr/lib64)
* "spack external find": add arg to ignore default dir for cray
  manifests
2023-05-30 18:03:44 -07:00
AMD Toolchain Support
43b86ce282 HPL: amdalloc with AOCC 4.0 (#37757)
* adding amdalloc when using aocc 4


* adding and libm for aocc3.2
2023-05-30 16:40:41 -07:00
AMD Toolchain Support
d30698d9a8 cp2k fixes for aocc (#37758) 2023-05-30 16:33:00 -07:00
Massimiliano Culpo
8e9efa86c8 Simplify implementation of "get_compiler_config" (#37989) 2023-05-30 15:11:33 -07:00
Jack Morrison
84faf5a6cf intel-mpi-benchmarks: Add MPI implementation check variant (#37363)
* Add MPI implementation check variant to Intel MPI Benchmarks

* [@spackbot] updating style on behalf of jack-morrison
2023-05-30 16:37:58 -05:00
Eric Berquist
9428749a3c Update SST packages to 13.0.0 (#37467)
* add sst-{core,elements,macro} v13.0.0

* Add newest DUMPI versions and remove unavailable ones

* update maintainer lists

* sst-core: tracking and profiling flags

* sst-elements with Pin requires the Pin location

* sst-core: Zoltan integration was removed in version 12

* spack style fixes

* sst-core: ensure Python is in the sst{sim,info}.x rpaths

* sst-macro: update homepage and maintainers

* spack style --fix
2023-05-30 16:35:33 -05:00
Michael Kuhn
efdac68c28 julia: fix build for @1.8.4:1.8.5 (#37990)
julia@1.8.4:1.8.5 fails to build because it does not find libstdc++ (see https://github.com/JuliaLang/julia/issues/47987).
2023-05-30 13:49:15 -07:00
Carlos Bederián
5398c31e82 ucx: add 1.14.1 (#37991) 2023-05-30 13:46:39 -07:00
Thomas Madlener
188168c476 podio: Add 0.16.5 tag (#37994) 2023-05-30 13:39:15 -07:00
Michael Kuhn
4af84ac208 gobject-introspection: add 1.76.1 (#37995) 2023-05-30 13:37:53 -07:00
Manuela Kuhn
deb8b51098 py-dunamai: add 1.17.0 (#38003) 2023-05-30 15:34:15 -04:00
Manuela Kuhn
0d582b2ea9 py-duecredit: add 0.9.2 (#38002) 2023-05-30 15:33:54 -04:00
Manuela Kuhn
f88b01c34b py-datalad-container: add 1.2.0 (#38000) 2023-05-30 15:28:34 -04:00
Manuela Kuhn
0533c6a1b8 py-datalad-metalad: add 0-4-17 and new dep py-datalad-deprecated (#37993)
* py-datalad-metalad: add 0-4-17 and new dep py-datalad-deprecated

* Fix style
2023-05-30 15:18:15 -04:00
Manuela Kuhn
f73d5c2b0e py-cryptography: add 40.0.2 (#37925)
* py-cryptography: add 40.0.2

* Add pkgconfig dependency
2023-05-30 10:26:17 -05:00
Tamara Dahlgren
567d0ee455 tests/hdf5: convert to new stand-alone test process (#35732) 2023-05-29 16:56:17 +02:00
Tamara Dahlgren
577df6f498 sqlite: convert to new stand-alone test process (#37722) 2023-05-29 07:59:23 -04:00
Harmen Stoppels
8790efbcfe Remove patchelf self-relocation (#33834) 2023-05-29 13:14:24 +02:00
Tamara Dahlgren
212b1edb6b tests/biobambam2: convert to new stand-alone test process (#35696) 2023-05-29 12:54:38 +02:00
snehring
d85a27f317 sentieon-genomics: replacing square brackets in help (#37622) 2023-05-29 12:52:36 +02:00
Chris White
5622afbfd1 amgx: add v2.2.0 and v2.3.0 (#37567) 2023-05-29 12:42:36 +02:00
Carlos Bederián
f345038317 nwchem: fix non-fftw fftw-api providers (#37442) 2023-05-29 12:41:41 +02:00
Michael Kuhn
e43d4cfee0 glib: add 2.76.3 and 2.76.2, update build systems (#37226)
This also converts the package to the new way of handling multiple build
systems.

Co-authored-by: michaelkuhn <michaelkuhn@users.noreply.github.com>
2023-05-29 06:38:57 -04:00
Vanessasaurus
7070658e2a Automated deployment to update package flux-core 2023-05-15 (#37684)
Co-authored-by: github-actions <github-actions@users.noreply.github.com>
2023-05-29 12:35:22 +02:00
dependabot[bot]
fc4b032fb4 build(deps): bump codecov/codecov-action from 3.1.3 to 3.1.4 (#37688)
Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 3.1.3 to 3.1.4.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](894ff025c7...eaaf4bedf3)

---
updated-dependencies:
- dependency-name: codecov/codecov-action
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-05-29 12:34:34 +02:00
Vanessasaurus
8c97d8ad3f add flux-security variant to flux-core (#37689)
This will build flux-security separately to have a flux-imp
that can be defined in a flux broker.toml. Note that the user
that wants a multi-user setup is recommended to create a view,
and then a system/broker.toml in flux config directory that
points to it.

Signed-off-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: vsoch <vsoch@users.noreply.github.com>
2023-05-29 12:34:07 +02:00
Alberto Invernizzi
26107fe6b2 highfive: add newer versions + add git repo (#37635)
* add versions
* add develop pointing to git@master
2023-05-29 06:09:02 -04:00
Tamara Dahlgren
9278c0df21 binutils: convert to new stand-alone test process (#37690) 2023-05-29 11:59:09 +02:00
Tamara Dahlgren
37e95713f4 libsigsegv: convert to new stand-alone test process (#37691) 2023-05-29 11:58:39 +02:00
SXS Bot
3ae8a3a517 spectre: add v2023.05.16 (#37716)
Co-authored-by: sxs-bot <sxs-bot@users.noreply.github.com>
2023-05-29 11:56:21 +02:00
Tamara Dahlgren
031af84e90 m4: convert to new stand-alone test process (#37723) 2023-05-29 11:49:28 +02:00
Annop Wongwathanarat
7d4b65491d armpl-gcc: add version 23.04.1 (#37907) 2023-05-29 05:49:19 -04:00
Harmen Stoppels
3038d1e7cd Use @= in some packages (#37737)
Change the pattern @x.y:x.y.0 -> @=x.y

Co-authored-by: haampie <haampie@users.noreply.github.com>
2023-05-29 11:47:00 +02:00
Lehman Garrison
b2e6ef97ce hdfview: add 3.1.4, 3.2.0, 3.3.0. Update dependencies. (#37745) 2023-05-29 11:41:44 +02:00
Tamara Dahlgren
e55236ce5b tests/arborx: convert to new stand-alone test process (#37778)
Co-authored-by: Andrey Prokopenko <andrey.prok@gmail.com>
2023-05-29 11:33:07 +02:00
Alec Scott
68dfd6ba6e hbase: add v2.5.3 (#37518)
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-05-29 11:29:11 +02:00
Jim Galarowicz
38d2459f94 survey: add v1.0.8 (#37385) 2023-05-29 11:26:56 +02:00
Nicolas Cornu
e309f367af catch2: new versions (#37742) 2023-05-29 11:26:06 +02:00
Harmen Stoppels
3b59c95323 fix InternalConcretizerError msg (#37791) 2023-05-29 11:24:43 +02:00
Howard Pritchard
fddaeadff8 OPENMPI: disable use of sphinx (#37717)
Sphinx is used to build Open MPI manpages, etc. as part of the make dist
process to create release tarballs.  There should be no need/use to do
this within Spack.  Also some sites have older Sphinx installs which
aren't compatible with the needs of the Open MPI documentation.
For example, attempts to install openmpi@main fail at NERSC owing to
such a situation.

Since Spack normally is used to build from release tarballs, in which
the docs have already been installed, this should present no issues.

This configuration option will be ignored for older than 5.0.0 Open MPI releases.

Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2023-05-29 11:23:42 +02:00
Joel Falcou
c85eaf9dc5 Add package for KUMI tuple library (#37795) 2023-05-29 11:23:06 +02:00
Brian Vanderwende
ddec7f8aec bbcp: fix cloning "master" version (#37802) 2023-05-29 11:21:48 +02:00
AMD Toolchain Support
f057d7154b NAMD: add AVXTILES support (#37040) 2023-05-29 11:10:09 +02:00
Tamara Dahlgren
a102950d67 berkeley-db: convert to new stand-alone test process (#35702) 2023-05-29 10:56:42 +02:00
Howard Pritchard
783be9b350 dealii - add platform-introspection variant (#37833)
This option is needed for DFT FE - or more accurately the check needs to
be checked off for a number of platforms or else the code doesn't work.

Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2023-05-29 10:56:03 +02:00
Juan Miguel Carceller
27c8135207 xrootd: add patch for when libraries are installed in lib64 (#37858)
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-05-29 10:36:57 +02:00
Tamara Dahlgren
77ce4701b9 Bugfix/tests: add slash to test log message (#37874) 2023-05-29 10:36:36 +02:00
Juan Miguel Carceller
73ad3f729e dd4hep: add patch to fix missing hits when using LCIO (#37854)
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-05-29 10:35:14 +02:00
Jim Edwards
1e7a64ad85 parallelio: add v2.6.0 release and ncint variant (#37805) 2023-05-29 10:19:15 +02:00
Tamara Dahlgren
3a5864bcdb tests/sip: convert to new stand-alone test process (#35693) 2023-05-29 10:16:35 +02:00
Alec Scott
7e13a7dccb cbc: add v2.10.9 (#37974) 2023-05-29 04:04:28 -04:00
Alec Scott
e3249fa155 bedops: add v2.4.41 (#37972) 2023-05-29 04:04:06 -04:00
Thomas-Ulrich
0c20760576 pumi: fix simmodsuite base variant, and mpi lib name (#37401) 2023-05-29 09:59:32 +02:00
Alec Scott
7ee7995493 cracklib: add v2.9.9 (#37976) 2023-05-29 03:59:13 -04:00
Alec Scott
ba1fac1c31 cpio: add v2.14 (#37975) 2023-05-29 03:58:53 -04:00
Adam J. Stewart
b05f0ecb6f py-segmentation-models-pytorch: add v0.3.3 (#37970) 2023-05-29 09:48:32 +02:00
Alec Scott
d5c66b75c3 cyrus-sasl: add v2.1.28 (#37978) 2023-05-29 09:31:54 +02:00
Alec Scott
98303d6956 double-conversion: add v3.3.0 (#37979) 2023-05-29 09:31:38 +02:00
Alec Scott
4622d638a6 elfio: add v3.11 (#37980) 2023-05-29 09:31:23 +02:00
Alec Scott
02023265fc erfa: add v2.0.0 (#37981) 2023-05-29 09:31:09 +02:00
Alec Scott
8a075998f8 erlang: add v26.0 (#37982) 2023-05-29 09:30:28 +02:00
Alec Scott
f2f48b1872 fasttransforms: add v0.6.2 (#37983) 2023-05-29 09:30:10 +02:00
Alec Scott
168d63c447 glog: add v0.6.0 (#37985) 2023-05-29 09:29:34 +02:00
Alec Scott
c25d4cbc1d gradle: add v8.1.1 (#37986) 2023-05-29 09:29:07 +02:00
snehring
ccb07538f7 Beast2: add v2.7.4, add javafx (#37419) 2023-05-29 09:28:32 +02:00
Alec Scott
1356b13b2f form: add v4.3.1 (#37984) 2023-05-29 09:24:34 +02:00
Tamara Dahlgren
935f862863 tests/flibcpp: convert to new stand-alone test process (#37782) 2023-05-28 10:47:23 +02:00
Tamara Dahlgren
9f6d9df302 patchelf: convert to new stand-alone test process (#37831) 2023-05-28 10:46:23 +02:00
Tamara Dahlgren
65d33c02a1 gasnet: convert to new stand-alone test process (#35727) 2023-05-28 10:45:11 +02:00
Tamara Dahlgren
40073e7b21 hdf: convert to new stand-alone test process (#37843) 2023-05-28 10:44:42 +02:00
Tamara Dahlgren
752e02e2f2 tests/upcxx: convert to new stand-alone test process (#37832)
Co-authored-by: Dan Bonachea <dobonachea@lbl.gov>
2023-05-28 10:44:04 +02:00
Vanessasaurus
d717b3a33f Automated deployment to update package flux-core 2023-05-04 (#37421)
Co-authored-by: github-actions <github-actions@users.noreply.github.com>
2023-05-28 10:42:44 +02:00
Bruno Turcksin
9817f24c9a kokkos-nvcc-wrapper: Remove unnecessary dependencies (#37794) 2023-05-28 10:19:30 +02:00
Bruno Turcksin
1f7c4b0557 Kokkos: remove unused variants (#37800) 2023-05-28 10:18:53 +02:00
Xavier Delaruelle
6c42d2b7f7 modules: improve default naming scheme (#37808)
Change default naming scheme for tcl modules for a more user-friendly
experience. 

Change from flat projection to "per software name" projection.

Flat naming scheme restrains module selection capabilities. The
`{name}/{version}...` scheme make possible to use user-friendly
mechanisms:

* implicit defaults (`module load git`)
* extended default (`module load git/2`)
* advanced version specifiers (`module load git@2:`)
2023-05-28 10:06:30 +02:00
Tamara Dahlgren
8df036a5a5 tests/cmake: convert to new stand-alone test process (#37724) 2023-05-28 09:59:21 +02:00
dependabot[bot]
582ebee74c build(deps): bump actions/setup-python from 4.6.0 to 4.6.1 (#37894)
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.6.0 to 4.6.1.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](57ded4d7d5...bd6b4b6205)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-05-28 09:58:14 +02:00
Annop Wongwathanarat
1017b9ddde acfl: add version 23.04.1 and fix checksums for 22.1 (#37908)
Checksums for 22.1 need updates due to an IT incident at developer.arm.com. The package tarballs needed to be recreated.
2023-05-28 09:57:31 +02:00
Thomas Madlener
80ae73119d whizard: Fix parallel build race condition (#37890) 2023-05-28 09:55:52 +02:00
Tamara Dahlgren
1d88f690a4 tests/darshan-runtime: convert to new stand-alone test process (#37838) 2023-05-28 09:46:31 +02:00
Filippo Spiga
fbb271d804 Adding NVIDIA HPC SDK 23.5 (#37913) 2023-05-28 09:45:08 +02:00
Hao Lyu
d6aac873b7 copy namelist and xml to ./bin (#37933) 2023-05-28 09:43:27 +02:00
Tamara Dahlgren
ab3ffd9361 archer: convert to new stand-alone test process (#35697) 2023-05-28 09:41:38 +02:00
Tamara Dahlgren
3b9454a5cc tests/bolt: convert to new stand-alone test process (#35695)
* bolt: convert to new stand-alone test process
* Remove redundant test_requires_compiler (so above directives)
2023-05-27 18:46:11 -07:00
Tamara Dahlgren
c8eb0f9361 tests/amrex: convert to new stand-alone test process (#35698)
* amrex: convert to new stand-alone test process
* smoke->stand-alone
2023-05-27 18:44:06 -07:00
George Young
fb0f14eb06 py-macs2: add 2.2.8, updated dependencies (#37944)
* py-macs2: add 2.2.8, updated dependencies

* Update package.py

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-05-27 14:29:12 -05:00
George Young
e489ee4e2e py-cutadapt: add 4.4, 4.3, 4.2 versions (#37929)
* py-cutadapt: add 4.4, 4.3, 4.2 versions

* Update var/spack/repos/builtin/packages/py-cutadapt/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-cutadapt/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>
2023-05-27 14:27:43 -05:00
Alex Richert
fcd49f2f08 Add shared and pic variants to libtiff (#37965)
* Add static-only option for libtiff

* update libtiff to add pic variant

* fix libtiff pic setting
2023-05-27 11:24:27 -05:00
Alex Richert
b3268c2703 freetype: add pic and shared variants (#37898) 2023-05-27 01:05:10 +02:00
George Young
d1bfcfafe3 py-multiqc: add 1.14, bump dependencies (#37946)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-05-26 17:55:03 -05:00
Manuela Kuhn
490c9f5e16 py-datalad-metadata-model: add 0.3.10 (#37937) 2023-05-26 17:28:36 -05:00
Manuela Kuhn
85628d1474 py-debugpy: add 1.6.7 (#37941) 2023-05-26 17:27:50 -05:00
Manuela Kuhn
720c34d18d py-distro: add 1.8.0 (#37942) 2023-05-26 17:27:06 -05:00
mschouler
cd175377ca Update melissa build (#37609)
* Remove deprecated package

* Add up-to-date melissa builds

* Remove blank lines and FIXME comments

* Use directive syntax for maintainers and remove unnecessary comments

* Remove unused function

* Deprecate former melissa recipe

* Change melissa python package name

* Update setuptools and rapidjson dependencies versions

* Fix mypy error

* Restore rapidjson version

* Variant simplification

* Make variants lower case

* Deprecate former omitted version

* Make torch version consistent with requirement file

* Fix variants definition

* Fix style error

---------

Co-authored-by: Marc Schouler <marc.schouler@inria.fr>
2023-05-26 17:26:29 -05:00
Manuela Kuhn
b91ec05e13 py-coloredlogs: add 15.0.1 and py-humanfriendly: add 10.0 (#37905) 2023-05-26 17:22:02 -05:00
Manuela Kuhn
3bb15f420b py-contourpy: add 1.0.7 (#37914) 2023-05-26 17:19:40 -05:00
Manuela Kuhn
124a81df5b py-coverage: add 5.5 (#37922) 2023-05-26 17:06:39 -05:00
Lee James O'Riordan
d9472c083d Update py-pennylane ecosystem to support v0.30.0 (#37763)
* Update PennyLane ecosystem for 0.30 release

* Update package dep versions

* Fix formatting

* Update dep versions

* Remove PL hard pin and rely on PLQ to define version

* Update var/spack/repos/builtin/packages/py-pennylane-lightning-kokkos/package.py

Co-authored-by: Vincent Michaud-Rioux <vincent.michaud-rioux@xanadu.ai>

* Convert pybind11 from build to link dep, and PL ver limit

---------

Co-authored-by: Vincent Michaud-Rioux <vincent.michaud-rioux@xanadu.ai>
2023-05-26 16:55:21 -05:00
Manuela Kuhn
ac2a5ef4dd py-beautifulsoup4: add 4.12.2 (#37820) 2023-05-26 16:54:43 -05:00
Manuela Kuhn
ea210a6acf py-chardet: add 5.1.0 (#37879)
* py-chardet: add 5.1.0

* Remove py-setuptools as run dependency
2023-05-26 16:51:54 -05:00
kwryankrattiger
afb3bef7af CI: Use relative path in default script (#36649) 2023-05-26 14:28:48 -06:00
George Young
b5b5881426 picard: add 3.0.0, switch to java@17: (#37948)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-05-26 15:38:26 -04:00
George Young
76fc7915a8 minimap2: adding 2.26 (#37945)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-05-26 10:12:14 -07:00
George Young
e7798b619b hyphy: add 2.5.51hf, update dependencies for switch to MPI (#37938)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-05-26 09:48:26 -07:00
Kai Torben Ohlhus
8ecef12a20 Strip inactive maintainer. (#36048) 2023-05-26 10:47:39 -04:00
Brian Spilner
694292ebbf cdo: add 2.2.0 (#37244) 2023-05-26 10:01:49 +02:00
Howard Pritchard
7f18f6f8a1 PMIx and PRRTe: disabled use of sphinx (#37750)
Related to https://github.com/spack/spack/pull/37717

No need to be rebuilding openmpi man pages and other docs in
spack as it almost always is used with release tarballs.

See #37717 for more details.

Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2023-05-26 09:49:02 +02:00
John W. Parent
0b12a480eb Windows MSVC: do not set sdk version if installing sdk (#37930)
Note the win-sdk package is not installable and reports an error
which instructs the user how to add it. Without this fix, a
(more confusing) error occurs before this message can be generated.
2023-05-25 21:38:04 -04:00
George Young
2d91a79af3 fastp: add version 0.23.3, add build dependencies (#37931)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-05-25 21:28:13 -04:00
Leonard-Anderson-NNL
72fcee7227 gradle:add 7.3 (#37928)
Co-authored-by: Cloud User <leonardanderson@leonardander001.hzterscemazurawp3xenxzahla.bx.internal.cloudapp.net>
2023-05-25 20:55:09 -04:00
John W. Parent
d147ef231f Windows: fix "spack build-env" (#37923)
"spack build-env" was not generating proper environment variable
definitions on Windows; this commit updates the generated commands
to succeed with batch/PowerShell.
2023-05-25 17:08:15 -07:00
eugeneswalker
1c7af83d32 update ci ml darwin keypath (#37927) 2023-05-25 16:27:56 -07:00
John W. Parent
b982dfc071 Windows CI: add paraview deps nightly build (#37924)
Add a nightly job to attempt building all Paraview dependencies and
upload the results to cdash. This check doesn't affect the reported
build/test status of Spack. We are using this to monitor the state of
Windows support while working on more-robust checks (eventually the
Windows build will have to succeed to merge PRs to Spack).
2023-05-25 16:13:41 -07:00
H. Joe Lee
c0da8a00fc fix(protobuf-c): set version bound for protobuf dependency (#37917)
Fix #37887 GitLab CI failure.
2023-05-25 19:08:54 -04:00
H. Joe Lee
3f18f689d8 fix(dpdk): add a new version 23.03. (#37919)
Fix E4S GitLab CI issue #37887.
2023-05-25 18:58:41 -04:00
Simon Pintarelli
9dc4553cf3 sirius: add rocsolver/wannier90 (#37900)
* sirius: add rocsolver dependency for 7.5:
* add wannier90
2023-05-25 15:58:04 -07:00
Tim Haines
9a99c94b75 Dyninst: add standalone test (#37876)
* Dyninst: add standalone test
* Add docstring with description
* Don't use join_path for builtin path objects
* Whitespace
* Update format of docstring
2023-05-25 18:48:52 -04:00
John W. Parent
682f0b2a54 Protobuf package: CMake fix for Windows build (#37926)
Qualify reference with namespace. A pending upstream PR will eventually
make this unnecessary, so the patch is only applied for 3.22. versions.
2023-05-25 15:41:16 -07:00
Richard Berger
dbab0c1ff5 flecsi: disable cinch dependency for v1 release (#37857)
* flecsi: disable cinch dependency for v1 releases
* [@spackbot] updating style on behalf of rbberger

---------

Co-authored-by: rbberger <rbberger@users.noreply.github.com>
2023-05-25 14:59:45 -07:00
Xavier Delaruelle
2bf95f5340 environment-modules: fix @main version requirements (#37807)
Some requirements for @main version of environment-modules were missing:

* python (to build ChangeLog documentation file)
* py-sphinx@1.0: (to build man-pages, etc)

Also adding gzip, which is now required to build ChangeLog.gz (which is
now shipped instead of ChangeLog).

Other versions are not requiring these tools (as documentation is
pre-built in dist tarball).
2023-05-25 22:29:26 +02:00
Tamara Dahlgren
55561405b8 Bugfix/tests: write not append stand-alone test status (#37841) 2023-05-25 12:36:24 -07:00
H. Joe Lee
8eef458cea fix(pmdk): add pkconfig as dependency (#37896)
Fix #37887 failure.
2023-05-25 10:35:48 -07:00
Stephen Sachs
64eea9d996 [devito] Move to version 4.8.1 (#37915)
* [devito] Move to version 4.8.1

* Fix: Adding patch file

* Update var/spack/repos/builtin/packages/py-devito/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-devito/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Addressing @adamjstewart comments

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-05-25 13:33:10 -04:00
Alex Richert
60b4e2128b Add shared variant to geos package (#37899)
Co-authored-by: alexrichert <alexrichert@gmail.com>
2023-05-25 11:42:51 -04:00
Adam J. Stewart
2f8cea2792 Add macOS ML CI stacks (#36586)
* Add macOS ML CI stacks

* torchmeta is no longer maintained and requires ancient PyTorch

* Add MXNet

* update darwin aarch64 stacks

* add darwin-aarch64 scoped config.yaml

* remove unnecessary cleanup job

* fix specifications

* fix labels

* fix labels

* fix indent on tags specification

* no tags for trigger jobs

* try overriding tags in stack spack.yaml

* do not use CI_STACK_CONFIG_SCOPES

* incorporate config:install_tree:root: overrides and compiler defs

* copy relevant ci-scoped config settings directly into stack spack.yaml

* remove build-job-remove

* spack ci generate: add debug flag

* include cdash config directly in stack spack.yaml

* customize build-job script section to avoid absolute paths

* add any-job specification

* tags: use aarch64-macos instead of aarch64

* generate tags: use aarch64-macos instead of aarch64

* do not add morepadding

* use shared mirror; comment out known failures

* remove any-job

* nproc || true

* comment out specs failing due to bazel from cache codesign issue

---------

Co-authored-by: eugeneswalker <eugenesunsetwalker@gmail.com>
2023-05-25 01:12:54 -04:00
M. Eric Irrgang
06f9bcf734 Update for py-gmxapi for 0.4.1. (#37834)
* Update for py-gmxapi for 0.4.1.

* Note 0.4.1 hash from PyPI.
* Note relaxed dependencies for future versions.

* Update var/spack/repos/builtin/packages/py-gmxapi/package.py
2023-05-24 22:03:10 -05:00
Manuela Kuhn
ee2725762f py-charset-normalizer: add 3.1.0 (#37880) 2023-05-24 21:57:29 -05:00
Manuela Kuhn
eace0a177c py-bids-validator: add 1.11.0 (#37845) 2023-05-24 21:36:45 -05:00
Manuela Kuhn
80c7d74707 py-bottleneck: add 1.3.7 (#37847) 2023-05-24 21:36:01 -05:00
Manuela Kuhn
a6f5bf821d py-certifi: add 2023.5.7 (#37848) 2023-05-24 21:35:13 -05:00
Manuela Kuhn
b214406253 py-attrs: add 23.1.0 (#37817)
* py-attrs: add 23.1.0

* Add missing dependency
2023-05-24 20:21:31 -05:00
Manuela Kuhn
5b003d80e5 py-babel: add 2.12.1 (#37818)
* py-babel: add 2.12.1

* Update var/spack/repos/builtin/packages/py-babel/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-05-24 20:13:02 -05:00
Adam J. Stewart
185b2d3ee7 py-rasterio: add v1.3.7 (#37886) 2023-05-24 18:48:16 -04:00
Adam J. Stewart
71bb2a1899 py-lightly: add v1.4.6 (#37885) 2023-05-24 16:43:07 -04:00
Nathalie Furmento
785c31b730 starpu: add release 1.4.1 (#37883) 2023-05-24 09:36:56 -07:00
QuellynSnead
175da4a88a paraview (protobuf failure) #37437 (#37440)
When attempting to build paraview@5.10.1 using a recent Intel
compiler (Classic or OneAPI) or the IBM XL compiler, the build
fails if the version of protobuf used is > 3.18
2023-05-24 11:09:48 -05:00
willdunklin
73fc1ef11c sensei: Allow Paraview 5.11 for sensei develop version (#37719) 2023-05-24 11:00:35 -05:00
Stephen Sachs
2d77e44f6f Pcluster local buildcache (#37852)
* [pcluster pipeline] Use local buildcache instead of upstream spack

Spack currently does not relocate compiler references from upstream spack
installations. When using a buildcache we don't need an upstream spack.

* gcc needs to be installed via postinstall to get correct deps

* quantum-espresso@gcc@12.3.0 returns ICE on neoverse_{n,v}1

* Force gitlab to pull the new container

* Revert "Force gitlab to pull the new container"

This reverts commit 3af5f4cd88.

Seems the gitlab version does not yet support "pull_policy" in .gitlab-ci.yml

* Gitlab keeps picking up wrong container. Renaming

* Update containers once more after failed build
2023-05-24 06:55:00 -07:00
Greg Becker
033599c4cd bugfix: env concretize after remove (#37877) 2023-05-24 15:41:57 +02:00
Harmen Stoppels
8096ed4b22 spack remove: fix traversal when user specs intersect (#37882)
drop unnecessary double loop over the matching user specs.
2023-05-24 09:23:46 -04:00
Simon Pintarelli
b49bfe25af update nlcglib package (#37578) 2023-05-24 11:17:15 +02:00
Houjun Tang
8b2f34d802 Add async vol v1.6 (#37875) 2023-05-24 01:47:46 -04:00
H. Joe Lee
3daed0d6a7 hdf5-vol-daos: add a new package (#35653)
* hdf5-vol-daos: add a new package
* hdf5-vol-daos: address @soumagne review

---------

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-05-23 23:42:42 -04:00
Glenn Johnson
d6c1f75e8d julia: remove myself from maintainers list (#37868) 2023-05-23 16:22:56 -05:00
Laura Weber
c80a4c1ddc Updated hash for latest maintenance release (2022.2.1) (#37842) 2023-05-23 14:08:55 -07:00
Glenn Johnson
466abcb62d gate: remove myself as maintainer (#37862) 2023-05-23 14:03:52 -07:00
Glenn Johnson
69e99f0c16 Remove myself as maintainer of R packages (#37859)
* Remove myself as maintainer of R packages
  I will no longer have the time to properly maintain these packages.
* fix flake8 test for import
2023-05-23 15:35:32 -05:00
Glenn Johnson
bbee6dfc58 bart: remove myself as maintainer (#37860) 2023-05-23 16:08:07 -04:00
Glenn Johnson
2d60cf120b heasoft: remove myself as maintainer (#37866) 2023-05-23 14:37:57 -05:00
Glenn Johnson
db17fc2f33 opencv: remove myself from maintainers list (#37870) 2023-05-23 14:34:52 -05:00
eugeneswalker
c62080d498 e4s ci: add dealii (#32484) 2023-05-23 21:34:31 +02:00
Glenn Johnson
f9bbe549fa gatetools: remove myself as maintainer (#37863) 2023-05-23 15:32:54 -04:00
H. Joe Lee
55d7fec69c daos: add a new package (#35649) 2023-05-23 21:30:23 +02:00
Glenn Johnson
e938907150 reditools: remove myself as maintainer (#37871) 2023-05-23 15:28:16 -04:00
Glenn Johnson
0c40b86e96 itk: remove myself as maintainer (#37867) 2023-05-23 15:27:55 -04:00
Glenn Johnson
3d4cf0d8eb mumax: remove myself as maintainer (#37869) 2023-05-23 15:23:28 -04:00
Glenn Johnson
966e19d278 gurobi: remove myself as maintainer (#37865) 2023-05-23 15:23:05 -04:00
Glenn Johnson
8f930462bd fplo: remove myself as maintainer (#37861) 2023-05-23 15:17:50 -04:00
kjrstory
bf4fccee15 New package: FDS (#37850) 2023-05-23 11:59:05 -07:00
Manuela Kuhn
784771a008 py-bleach: add 6.0.0 (#37846) 2023-05-23 11:50:53 -07:00
Glenn Johnson
e4a9d9ae5b Bioc updates (#37297)
* add version 1.48.0 to bioconductor package r-a4
* add version 1.48.0 to bioconductor package r-a4base
* add version 1.48.0 to bioconductor package r-a4classif
* add version 1.48.0 to bioconductor package r-a4core
* add version 1.48.0 to bioconductor package r-a4preproc
* add version 1.48.0 to bioconductor package r-a4reporting
* add version 1.54.0 to bioconductor package r-absseq
* add version 1.30.0 to bioconductor package r-acde
* add version 1.78.0 to bioconductor package r-acgh
* add version 2.56.0 to bioconductor package r-acme
* add version 1.70.0 to bioconductor package r-adsplit
* add version 1.72.0 to bioconductor package r-affxparser
* add version 1.78.0 to bioconductor package r-affy
* add version 1.76.0 to bioconductor package r-affycomp
* add version 1.58.0 to bioconductor package r-affycontam
* add version 1.72.0 to bioconductor package r-affycoretools
* add version 1.48.0 to bioconductor package r-affydata
* add version 1.52.0 to bioconductor package r-affyilm
* add version 1.70.0 to bioconductor package r-affyio
* add version 1.76.0 to bioconductor package r-affyplm
* add version 1.46.0 to bioconductor package r-affyrnadegradation
* add version 1.48.0 to bioconductor package r-agdex
* add version 3.32.0 to bioconductor package r-agilp
* add version 2.50.0 to bioconductor package r-agimicrorna
* add version 1.32.0 to bioconductor package r-aims
* add version 1.32.0 to bioconductor package r-aldex2
* add version 1.38.0 to bioconductor package r-allelicimbalance
* add version 1.26.0 to bioconductor package r-alpine
* add version 2.62.0 to bioconductor package r-altcdfenvs
* add version 2.24.0 to bioconductor package r-anaquin
* add version 1.28.0 to bioconductor package r-aneufinder
* add version 1.28.0 to bioconductor package r-aneufinderdata
* add version 1.72.0 to bioconductor package r-annaffy
* add version 1.78.0 to bioconductor package r-annotate
* add version 1.62.0 to bioconductor package r-annotationdbi
* add version 1.24.0 to bioconductor package r-annotationfilter
* add version 1.42.0 to bioconductor package r-annotationforge
* add version 3.8.0 to bioconductor package r-annotationhub
* add version 3.30.0 to bioconductor package r-aroma-light
* add version 1.32.0 to bioconductor package r-bamsignals
* add version 2.16.0 to bioconductor package r-beachmat
* add version 2.60.0 to bioconductor package r-biobase
* add version 2.8.0 to bioconductor package r-biocfilecache
* add version 0.46.0 to bioconductor package r-biocgeneric
* add version 1.10.0 to bioconductor package r-biocio
* add version 1.18.0 to bioconductor package r-biocneighbors
* add version 1.34.0 to bioconductor package r-biocparallel
* add version 1.16.0 to bioconductor package r-biocsingular
* add version 2.28.0 to bioconductor package r-biocstyle
* add version 3.17.1 to bioconductor package r-biocversion
* add version 2.56.0 to bioconductor package r-biomart
* add version 1.28.0 to bioconductor package r-biomformat
* add version 2.68.0 to bioconductor package r-biostrings
* add version 1.48.0 to bioconductor package r-biovizbase
* add version 1.10.0 to bioconductor package r-bluster
* add version 1.68.0 to bioconductor package r-bsgenome
* add version 1.36.0 to bioconductor package r-bsseq
* add version 1.42.0 to bioconductor package r-bumphunter
* add version 2.66.0 to bioconductor package r-category
* add version 2.30.0 to bioconductor package r-champ
* add version 2.32.0 to bioconductor package r-champdata
* add version 1.50.0 to bioconductor package r-chipseq
* add version 4.8.0 to bioconductor package r-clusterprofiler
* add version 1.36.0 to bioconductor package r-cner
* add version 1.32.0 to bioconductor package r-codex
* add version 2.16.0 to bioconductor package r-complexheatmap
* add version 1.74.0 to bioconductor package r-ctc
* add version 2.28.0 to bioconductor package r-decipher
* add version 0.26.0 to bioconductor package r-delayedarray
* add version 1.22.0 to bioconductor package r-delayedmatrixstats
* add version 1.40.0 to bioconductor package r-deseq2
* add version 1.46.0 to bioconductor package r-dexseq
* add version 1.42.0 to bioconductor package r-dirichletmultinomial
* add version 2.14.0 to bioconductor package r-dmrcate
* add version 1.74.0 to bioconductor package r-dnacopy
* add version 3.26.0 to bioconductor package r-dose
* add version 2.48.0 to bioconductor package r-dss
* add version 3.42.0 to bioconductor package r-edger
* add version 1.20.0 to bioconductor package r-enrichplot
* add version 2.24.0 to bioconductor package r-ensembldb
* add version 1.46.0 to bioconductor package r-exomecopy
* add version 2.8.0 to bioconductor package r-experimenthub
* add version 1.26.0 to bioconductor package r-fgsea
* add version 2.72.0 to bioconductor package r-gcrma
* add version 1.36.0 to bioconductor package r-gdsfmt
* add version 1.82.0 to bioconductor package r-genefilter
* add version 1.36.0 to bioconductor package r-genelendatabase
* add version 1.72.0 to bioconductor package r-genemeta
* add version 1.78.0 to bioconductor package r-geneplotter
* add version 1.22.0 to bioconductor package r-genie3
* add version 1.36.0 to bioconductor package r-genomeinfodb
* update r-genomeinfodbdata
* add version 1.36.0 to bioconductor package r-genomicalignments
* add version 1.52.0 to bioconductor package r-genomicfeatures
* add version 1.52.0 to bioconductor package r-genomicranges
* add version 2.68.0 to bioconductor package r-geoquery
* add version 1.48.0 to bioconductor package r-ggbio
* add version 3.8.0 to bioconductor package r-ggtree
* add version 2.10.0 to bioconductor package r-glimma
* add version 1.12.0 to bioconductor package r-glmgampoi
* add version 5.54.0 to bioconductor package r-globaltest
* update r-go-db
* add version 1.20.0 to bioconductor package r-gofuncr
* add version 2.26.0 to bioconductor package r-gosemsim
* add version 1.52.0 to bioconductor package r-goseq
* add version 2.66.0 to bioconductor package r-gostats
* add version 1.78.0 to bioconductor package r-graph
* add version 1.62.0 to bioconductor package r-gseabase
* add version 1.32.0 to bioconductor package r-gtrellis
* add version 1.44.0 to bioconductor package r-gviz
* add version 1.28.0 to bioconductor package r-hdf5array
* add version 1.72.0 to bioconductor package r-hypergraph
* add version 1.36.0 to bioconductor package r-illumina450probevariants-db
* add version 0.42.0 to bioconductor package r-illuminaio
* add version 1.74.0 to bioconductor package r-impute
* add version 1.38.0 to bioconductor package r-interactivedisplaybase
* add version 2.34.0 to bioconductor package r-iranges
* add version 1.60.0 to bioconductor package r-kegggraph
* add version 1.40.0 to bioconductor package r-keggrest
* add version 3.56.0 to bioconductor package r-limma
* add version 2.52.0 to bioconductor package r-lumi
* add version 1.76.0 to bioconductor package r-makecdfenv
* add version 1.78.0 to bioconductor package r-marray
* add version 1.12.0 to bioconductor package r-matrixgenerics
* add version 1.8.0 to bioconductor package r-metapod
* add version 2.46.0 to bioconductor package r-methylumi
* add version 1.46.0 to bioconductor package r-minfi
* add version 1.34.0 to bioconductor package r-missmethyl
* add version 1.80.0 to bioconductor package r-mlinterfaces
* add version 1.12.0 to bioconductor package r-mscoreutils
* add version 2.26.0 to bioconductor package r-msnbase
* add version 2.56.0 to bioconductor package r-multtest
* add version 1.38.0 to bioconductor package r-mzid
* add version 2.34.0 to bioconductor package r-mzr
* add version 1.62.0 to bioconductor package r-oligoclasses
* update r-org-hs-eg-db
* add version 1.42.0 to bioconductor package r-organismdbi
* add version 1.40.0 to bioconductor package r-pathview
* add version 1.92.0 to bioconductor package r-pcamethods
* update r-pfam-db
* add version 1.44.0 to bioconductor package r-phyloseq
* add version 1.62.0 to bioconductor package r-preprocesscore
* add version 1.32.0 to bioconductor package r-protgenerics
* add version 1.34.0 to bioconductor package r-quantro
* add version 2.32.0 to bioconductor package r-qvalue
* add version 1.76.0 to bioconductor package r-rbgl
* add version 2.40.0 to bioconductor package r-reportingtools
* add version 2.44.0 to bioconductor package r-rgraphviz
* add version 2.44.0 to bioconductor package r-rhdf5
* add version 1.12.0 to bioconductor package r-rhdf5filters
* add version 1.22.0 to bioconductor package r-rhdf5lib
* add version 1.76.0 to bioconductor package r-roc
* add version 1.28.0 to bioconductor package r-rots
* add version 2.16.0 to bioconductor package r-rsamtools
* add version 1.60.0 to bioconductor package r-rtracklayer
* add version 0.38.0 to bioconductor package r-s4vectors
* add version 1.8.0 to bioconductor package r-scaledmatrix
* add version 1.28.0 to bioconductor package r-scater
* add version 1.14.0 to bioconductor package r-scdblfinder
* add version 1.28.0 to bioconductor package r-scran
* add version 1.10.0 to bioconductor package r-scuttle
* add version 1.66.0 to bioconductor package r-seqlogo
* add version 1.58.0 to bioconductor package r-shortread
* add version 1.74.0 to bioconductor package r-siggenes
* add version 1.22.0 to bioconductor package r-singlecellexperiment
* add version 1.34.0 to bioconductor package r-snprelate
* add version 1.50.0 to bioconductor package r-snpstats
* add version 2.36.0 to bioconductor package r-somaticsignatures
* add version 1.12.0 to bioconductor package r-sparsematrixstats
* add version 1.40.0 to bioconductor package r-spem
* add version 1.38.0 to bioconductor package r-sseq
* add version 1.30.0 to bioconductor package r-summarizedexperiment
* add version 3.48.0 to bioconductor package r-sva
* add version 1.38.0 to bioconductor package r-tfbstools
* add version 1.22.0 to bioconductor package r-tmixclust
* add version 2.52.0 to bioconductor package r-topgo
* add version 1.24.0 to bioconductor package r-treeio
* add version 1.28.0 to bioconductor package r-tximport
* add version 1.28.0 to bioconductor package r-tximportdata
* add version 1.46.0 to bioconductor package r-variantannotation
* add version 3.68.0 to bioconductor package r-vsn
* add version 2.6.0 to bioconductor package r-watermelon
* add version 2.46.0 to bioconductor package r-xde
* add version 1.58.0 to bioconductor package r-xmapbridge
* add version 0.40.0 to bioconductor package r-xvector
* add version 1.26.0 to bioconductor package r-yapsa
* add version 1.26.0 to bioconductor package r-yarn
* add version 1.46.0 to bioconductor package r-zlibbioc
* Revert "add version 1.82.0 to bioconductor package r-genefilter"
  This reverts commit 1702071c6d.
* Revert "add version 0.38.0 to bioconductor package r-s4vectors"
  This reverts commit 58a7df2387.
* add version 0.38.0 to bioconductor package r-s4vectors
* Revert "add version 1.28.0 to bioconductor package r-aneufinder"
  This reverts commit 0a1f59de6c.
* add version 1.28.0 to bioconductor package r-aneufinder
* Revert "add version 2.16.0 to bioconductor package r-beachmat"
  This reverts commit cd49fb8e4c.
* add version 2.16.0 to bioconductor package r-beachmat
* Revert "add version 4.8.0 to bioconductor package r-clusterprofiler"
  This reverts commit 6e9a951cbe.
* add version 4.8.0 to bioconductor package r-clusterprofiler
* Fix syntax error
* r-genefilter: add version 1.82.0
* new package: r-basilisk-utils
* new package: r-basilisk
* new package: r-densvis
* new package: r-dir-expiry
* r-affyplm: add zlib dependency
* r-cner: add zlib dependency
* r-mzr: add zlib dependency
* r-rhdf5filters: add zstd dependency
* r-shortread: add zlib dependency
* r-snpstats: add zlib dependency

---------

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-05-23 11:40:00 -07:00
snehring
a6886983dc usalign: new package (#37646)
* usalign: adding new package
* usalign: updating shasum, adding note about distribution
2023-05-23 11:30:40 -07:00
Andrey Parfenov
93a34a9635 hpcg: apply patch with openmp pragma changes for intel and oneapi compilers (#37856)
Signed-off-by: Andrey Parfenov <andrey.parfenov@intel.com>
2023-05-23 11:52:45 -04:00
Todd Gamblin
91a54029f9 libgcrypt: patch 1.10.2 on macos (#37844)
macOS doesn't have `getrandom`, and 1.10.2 fails to compile because of this.

There's an upstream fix at https://dev.gnupg.org/T6442 that will be in the next
`libgcrypt` release, but the patch is available now.
2023-05-23 06:03:13 -04:00
Juan Miguel Carceller
5400b49ed6 dd4hep: add LD_LIBRARY_PATH for plugins for Gaudi (#37824)
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-05-23 10:28:26 +01:00
Juan Miguel Carceller
c17fc3c0c1 gaudi: add gaudi to LD_LIBRARY_PATH (#37821)
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-05-23 10:27:55 +01:00
Juan Miguel Carceller
6f248836ea dd4hep: restrict podio versions (#37699)
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-05-23 10:20:31 +01:00
snehring
693c1821b0 py-pastml: adding version for compatibility with py-topiary-asr (#37828) 2023-05-22 14:44:00 -05:00
Manuela Kuhn
62afe3bd5a py-asttokens: add 2.2.1 (#37816) 2023-05-22 14:40:08 -05:00
genric
53a756d045 py-dask: add v2023.4.1 (#37550)
* py-dask: add v2023.4.1

* address review comments
2023-05-22 14:29:23 -05:00
Adam J. Stewart
321b687ae6 py-huggingface-hub: add v0.14.1, cli variant (#37815) 2023-05-22 11:19:41 -07:00
Adam J. Stewart
c8617f0574 py-fiona: add v1.9.4 (#37780) 2023-05-22 13:17:13 -05:00
Adam J. Stewart
7843e2ead0 azcopy: add new package (#37693) 2023-05-22 11:09:06 -07:00
Juan Miguel Carceller
dca3d071d7 gaudi: fix issue with fmt::format (#37810)
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-05-22 10:33:05 -07:00
eugeneswalker
436f077482 tau %oneapi: -Wno-error=implicit-function-declaration (#37829) 2023-05-22 13:13:02 -04:00
simonleary-umass-edu
ab3f705019 deleted package.py better error message (#37814)
adds the namespace to the exception object's string representation
2023-05-22 09:59:07 -07:00
Tamara Dahlgren
d739989ec8 swig: convert to new stand-alone test process (#37786) 2023-05-22 09:39:30 -07:00
Jordan Galby
52ee1967d6 llvm: Fix hwloc@1 and hwloc@:2.3 compatibility (#35387) 2023-05-22 10:28:57 -05:00
Andrey Prokopenko
1af7284b5d arborx: new version 1.4 (#37809) 2023-05-21 12:25:53 -07:00
658 changed files with 6751 additions and 3264 deletions

View File

@@ -5,3 +5,8 @@ updates:
directory: "/"
schedule:
interval: "daily"
# Requirements to build documentation
- package-ecosystem: "pip"
directory: "/lib/spack/docs"
schedule:
interval: "daily"

View File

@@ -20,7 +20,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # @v2
- uses: actions/setup-python@57ded4d7d5e986d7296eab16560982c6dd7c923b # @v2
- uses: actions/setup-python@bd6b4b6205c4dbad673328db7b31b7fab9e241c0 # @v2
with:
python-version: ${{inputs.python_version}}
- name: Install Python packages
@@ -38,7 +38,7 @@ jobs:
run: |
. share/spack/setup-env.sh
$(which spack) audit packages
- uses: codecov/codecov-action@894ff025c7b54547a9a2a1e9f228beae737ad3c2 # @v2.1.0
- uses: codecov/codecov-action@eaaf4bedf32dbdc6b720b63067d99c4d77d6047d # @v2.1.0
if: ${{ inputs.with_coverage == 'true' }}
with:
flags: unittests,linux,audits

View File

@@ -49,7 +49,7 @@ jobs:
[almalinux8, 'linux/amd64,linux/arm64,linux/ppc64le', 'almalinux:8'],
[almalinux9, 'linux/amd64,linux/arm64,linux/ppc64le', 'almalinux:9'],
[rockylinux8, 'linux/amd64,linux/arm64', 'rockylinux:8'],
[rockylinux9, 'linux/amd64,linux/arm64,linux/ppc64le', 'rockylinux:9'],
[rockylinux9, 'linux/amd64,linux/arm64', 'rockylinux:9'],
[fedora37, 'linux/amd64,linux/arm64,linux/ppc64le', 'fedora:37'],
[fedora38, 'linux/amd64,linux/arm64,linux/ppc64le', 'fedora:38']]
name: Build ${{ matrix.dockerfile[0] }}

View File

@@ -0,0 +1,31 @@
name: Windows Paraview Nightly
on:
schedule:
- cron: '0 2 * * *' # Run at 2 am
defaults:
run:
shell:
powershell Invoke-Expression -Command "./share/spack/qa/windows_test_setup.ps1"; {0}
jobs:
build-paraview-deps:
runs-on: windows-latest
steps:
- uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab
with:
fetch-depth: 0
- uses: actions/setup-python@bd6b4b6205c4dbad673328db7b31b7fab9e241c0
with:
python-version: 3.9
- name: Install Python packages
run: |
python -m pip install --upgrade pip six pywin32 setuptools coverage
- name: Build Test
run: |
spack compiler find
spack external find cmake ninja win-sdk win-wdk wgl msmpi
spack -d install -y --cdash-upload-url https://cdash.spack.io/submit.php?project=Spack+on+Windows --cdash-track Nightly --only dependencies paraview
exit 0

View File

@@ -50,7 +50,7 @@ jobs:
- uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # @v2
with:
fetch-depth: 0
- uses: actions/setup-python@57ded4d7d5e986d7296eab16560982c6dd7c923b # @v2
- uses: actions/setup-python@bd6b4b6205c4dbad673328db7b31b7fab9e241c0 # @v2
with:
python-version: ${{ matrix.python-version }}
- name: Install System packages
@@ -87,7 +87,7 @@ jobs:
UNIT_TEST_COVERAGE: ${{ matrix.python-version == '3.11' }}
run: |
share/spack/qa/run-unit-tests
- uses: codecov/codecov-action@894ff025c7b54547a9a2a1e9f228beae737ad3c2
- uses: codecov/codecov-action@eaaf4bedf32dbdc6b720b63067d99c4d77d6047d
with:
flags: unittests,linux,${{ matrix.concretizer }}
# Test shell integration
@@ -97,7 +97,7 @@ jobs:
- uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # @v2
with:
fetch-depth: 0
- uses: actions/setup-python@57ded4d7d5e986d7296eab16560982c6dd7c923b # @v2
- uses: actions/setup-python@bd6b4b6205c4dbad673328db7b31b7fab9e241c0 # @v2
with:
python-version: '3.11'
- name: Install System packages
@@ -118,7 +118,7 @@ jobs:
COVERAGE: true
run: |
share/spack/qa/run-shell-tests
- uses: codecov/codecov-action@894ff025c7b54547a9a2a1e9f228beae737ad3c2
- uses: codecov/codecov-action@eaaf4bedf32dbdc6b720b63067d99c4d77d6047d
with:
flags: shelltests,linux
@@ -155,7 +155,7 @@ jobs:
- uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # @v2
with:
fetch-depth: 0
- uses: actions/setup-python@57ded4d7d5e986d7296eab16560982c6dd7c923b # @v2
- uses: actions/setup-python@bd6b4b6205c4dbad673328db7b31b7fab9e241c0 # @v2
with:
python-version: '3.11'
- name: Install System packages
@@ -176,7 +176,7 @@ jobs:
SPACK_TEST_SOLVER: clingo
run: |
share/spack/qa/run-unit-tests
- uses: codecov/codecov-action@894ff025c7b54547a9a2a1e9f228beae737ad3c2 # @v2.1.0
- uses: codecov/codecov-action@eaaf4bedf32dbdc6b720b63067d99c4d77d6047d # @v2.1.0
with:
flags: unittests,linux,clingo
# Run unit tests on MacOS
@@ -189,7 +189,7 @@ jobs:
- uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # @v2
with:
fetch-depth: 0
- uses: actions/setup-python@57ded4d7d5e986d7296eab16560982c6dd7c923b # @v2
- uses: actions/setup-python@bd6b4b6205c4dbad673328db7b31b7fab9e241c0 # @v2
with:
python-version: ${{ matrix.python-version }}
- name: Install Python packages
@@ -211,6 +211,6 @@ jobs:
$(which spack) solve zlib
common_args=(--dist loadfile --tx '4*popen//python=./bin/spack-tmpconfig python -u ./bin/spack python' -x)
$(which spack) unit-test --cov --cov-config=pyproject.toml --cov-report=xml:coverage.xml "${common_args[@]}"
- uses: codecov/codecov-action@894ff025c7b54547a9a2a1e9f228beae737ad3c2
- uses: codecov/codecov-action@eaaf4bedf32dbdc6b720b63067d99c4d77d6047d
with:
flags: unittests,macos

View File

@@ -19,7 +19,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # @v2
- uses: actions/setup-python@57ded4d7d5e986d7296eab16560982c6dd7c923b # @v2
- uses: actions/setup-python@bd6b4b6205c4dbad673328db7b31b7fab9e241c0 # @v2
with:
python-version: '3.11'
cache: 'pip'
@@ -38,7 +38,7 @@ jobs:
- uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # @v2
with:
fetch-depth: 0
- uses: actions/setup-python@57ded4d7d5e986d7296eab16560982c6dd7c923b # @v2
- uses: actions/setup-python@bd6b4b6205c4dbad673328db7b31b7fab9e241c0 # @v2
with:
python-version: '3.11'
cache: 'pip'

View File

@@ -18,7 +18,7 @@ jobs:
- uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab
with:
fetch-depth: 0
- uses: actions/setup-python@57ded4d7d5e986d7296eab16560982c6dd7c923b
- uses: actions/setup-python@bd6b4b6205c4dbad673328db7b31b7fab9e241c0
with:
python-version: 3.9
- name: Install Python packages
@@ -33,7 +33,7 @@ jobs:
./share/spack/qa/validate_last_exit.ps1
coverage combine -a
coverage xml
- uses: codecov/codecov-action@894ff025c7b54547a9a2a1e9f228beae737ad3c2
- uses: codecov/codecov-action@eaaf4bedf32dbdc6b720b63067d99c4d77d6047d
with:
flags: unittests,windows
unit-tests-cmd:
@@ -42,7 +42,7 @@ jobs:
- uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab
with:
fetch-depth: 0
- uses: actions/setup-python@57ded4d7d5e986d7296eab16560982c6dd7c923b
- uses: actions/setup-python@bd6b4b6205c4dbad673328db7b31b7fab9e241c0
with:
python-version: 3.9
- name: Install Python packages
@@ -57,7 +57,7 @@ jobs:
./share/spack/qa/validate_last_exit.ps1
coverage combine -a
coverage xml
- uses: codecov/codecov-action@894ff025c7b54547a9a2a1e9f228beae737ad3c2
- uses: codecov/codecov-action@eaaf4bedf32dbdc6b720b63067d99c4d77d6047d
with:
flags: unittests,windows
build-abseil:
@@ -66,7 +66,7 @@ jobs:
- uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab
with:
fetch-depth: 0
- uses: actions/setup-python@57ded4d7d5e986d7296eab16560982c6dd7c923b
- uses: actions/setup-python@bd6b4b6205c4dbad673328db7b31b7fab9e241c0
with:
python-version: 3.9
- name: Install Python packages

View File

@@ -1,10 +1,16 @@
version: 2
build:
os: "ubuntu-22.04"
apt_packages:
- graphviz
tools:
python: "3.11"
sphinx:
configuration: lib/spack/docs/conf.py
fail_on_warning: true
python:
version: 3.7
install:
- requirements: lib/spack/docs/requirements.txt

View File

@@ -0,0 +1,16 @@
# Copyright 2013-2023 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)
# The name of the Pygments (syntax highlighting) style to use.
# We use our own extension of the default style with a few modifications
from pygments.styles.default import DefaultStyle
from pygments.token import Generic
class SpackStyle(DefaultStyle):
styles = DefaultStyle.styles.copy()
background_color = "#f4f4f8"
styles[Generic.Output] = "#355"
styles[Generic.Prompt] = "bold #346ec9"

View File

@@ -149,7 +149,6 @@ def setup(sphinx):
# Get nice vector graphics
graphviz_output_format = "svg"
# Add any paths that contain templates here, relative to this directory.
templates_path = ["_templates"]
@@ -233,30 +232,8 @@ def setup(sphinx):
# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
# show_authors = False
# The name of the Pygments (syntax highlighting) style to use.
# We use our own extension of the default style with a few modifications
from pygments.style import Style
from pygments.styles.default import DefaultStyle
from pygments.token import Comment, Generic, Text
class SpackStyle(DefaultStyle):
styles = DefaultStyle.styles.copy()
background_color = "#f4f4f8"
styles[Generic.Output] = "#355"
styles[Generic.Prompt] = "bold #346ec9"
import pkg_resources
dist = pkg_resources.Distribution(__file__)
sys.path.append(".") # make 'conf' module findable
ep = pkg_resources.EntryPoint.parse("spack = conf:SpackStyle", dist=dist)
dist._ep_map = {"pygments.styles": {"plugin1": ep}}
pkg_resources.working_set.add(dist)
pygments_style = "spack"
sys.path.append("./_pygments")
pygments_style = "style.SpackStyle"
# A list of ignored prefixes for module index sorting.
# modindex_common_prefix = []
@@ -341,16 +318,15 @@ class SpackStyle(DefaultStyle):
# Output file base name for HTML help builder.
htmlhelp_basename = "Spackdoc"
# -- Options for LaTeX output --------------------------------------------------
latex_elements = {
# The paper size ('letterpaper' or 'a4paper').
#'papersize': 'letterpaper',
# 'papersize': 'letterpaper',
# The font size ('10pt', '11pt' or '12pt').
#'pointsize': '10pt',
# 'pointsize': '10pt',
# Additional stuff for the LaTeX preamble.
#'preamble': '',
# 'preamble': '',
}
# Grouping the document tree into LaTeX files. List of tuples

View File

@@ -636,7 +636,7 @@ to customize the generation of container recipes:
- No
* - ``os_packages:command``
- Tool used to manage system packages
- ``apt``, ``yum``, ``zypper``, ``apk``, ``yum_amazon``
- ``apt``, ``yum``, ``dnf``, ``dnf_epel``, ``zypper``, ``apk``, ``yum_amazon``
- Only with custom base images
* - ``os_packages:update``
- Whether or not to update the list of available packages

View File

@@ -317,7 +317,7 @@ installed, but you know that new compilers have been added to your
.. code-block:: console
$ module load gcc-4.9.0
$ module load gcc/4.9.0
$ spack compiler find
==> Added 1 new compiler to ~/.spack/linux/compilers.yaml
gcc@4.9.0

View File

@@ -76,6 +76,7 @@ or refer to the full manual below.
chain
extensions
pipelines
signing
.. toctree::
:maxdepth: 2

View File

@@ -35,27 +35,27 @@ showing lots of installed packages:
$ module avail
--------------------------------------------------------------- ~/spack/share/spack/modules/linux-ubuntu14-x86_64 ---------------------------------------------------------------
autoconf-2.69-gcc-4.8-qextxkq hwloc-1.11.6-gcc-6.3.0-akcisez m4-1.4.18-gcc-4.8-ev2znoc openblas-0.2.19-gcc-6.3.0-dhkmed6 py-setuptools-34.2.0-gcc-6.3.0-fadur4s
automake-1.15-gcc-4.8-maqvukj isl-0.18-gcc-4.8-afi6taq m4-1.4.18-gcc-6.3.0-uppywnz openmpi-2.1.0-gcc-6.3.0-go2s4z5 py-six-1.10.0-gcc-6.3.0-p4dhkaw
binutils-2.28-gcc-4.8-5s7c6rs libiconv-1.15-gcc-4.8-at46wg3 mawk-1.3.4-gcc-4.8-acjez57 openssl-1.0.2k-gcc-4.8-dkls5tk python-2.7.13-gcc-6.3.0-tyehea7
bison-3.0.4-gcc-4.8-ek4luo5 libpciaccess-0.13.4-gcc-6.3.0-gmufnvh mawk-1.3.4-gcc-6.3.0-ostdoms openssl-1.0.2k-gcc-6.3.0-gxgr5or readline-7.0-gcc-4.8-xhufqhn
bzip2-1.0.6-gcc-4.8-iffrxzn libsigsegv-2.11-gcc-4.8-pp2cvte mpc-1.0.3-gcc-4.8-g5mztc5 pcre-8.40-gcc-4.8-r5pbrxb readline-7.0-gcc-6.3.0-zzcyicg
bzip2-1.0.6-gcc-6.3.0-bequudr libsigsegv-2.11-gcc-6.3.0-7enifnh mpfr-3.1.5-gcc-4.8-o7xm7az perl-5.24.1-gcc-4.8-dg5j65u sqlite-3.8.5-gcc-6.3.0-6zoruzj
cmake-3.7.2-gcc-6.3.0-fowuuby libtool-2.4.6-gcc-4.8-7a523za mpich-3.2-gcc-6.3.0-dmvd3aw perl-5.24.1-gcc-6.3.0-6uzkpt6 tar-1.29-gcc-4.8-wse2ass
curl-7.53.1-gcc-4.8-3fz46n6 libtool-2.4.6-gcc-6.3.0-n7zmbzt ncurses-6.0-gcc-4.8-dcpe7ia pkg-config-0.29.2-gcc-4.8-ib33t75 tcl-8.6.6-gcc-4.8-tfxzqbr
expat-2.2.0-gcc-4.8-mrv6bd4 libxml2-2.9.4-gcc-4.8-ryzxnsu ncurses-6.0-gcc-6.3.0-ucbhcdy pkg-config-0.29.2-gcc-6.3.0-jpgubk3 util-macros-1.19.1-gcc-6.3.0-xorz2x2
flex-2.6.3-gcc-4.8-yf345oo libxml2-2.9.4-gcc-6.3.0-rltzsdh netlib-lapack-3.6.1-gcc-6.3.0-js33dog py-appdirs-1.4.0-gcc-6.3.0-jxawmw7 xz-5.2.3-gcc-4.8-mew4log
gcc-6.3.0-gcc-4.8-24puqve lmod-7.4.1-gcc-4.8-je4srhr netlib-scalapack-2.0.2-gcc-6.3.0-5aidk4l py-numpy-1.12.0-gcc-6.3.0-oemmoeu xz-5.2.3-gcc-6.3.0-3vqeuvb
gettext-0.19.8.1-gcc-4.8-yymghlh lua-5.3.4-gcc-4.8-im75yaz netlib-scalapack-2.0.2-gcc-6.3.0-hjsemcn py-packaging-16.8-gcc-6.3.0-i2n3dtl zip-3.0-gcc-4.8-rwar22d
gmp-6.1.2-gcc-4.8-5ub2wu5 lua-luafilesystem-1_6_3-gcc-4.8-wkey3nl netlib-scalapack-2.0.2-gcc-6.3.0-jva724b py-pyparsing-2.1.10-gcc-6.3.0-tbo6gmw zlib-1.2.11-gcc-4.8-pgxsxv7
help2man-1.47.4-gcc-4.8-kcnqmau lua-luaposix-33.4.0-gcc-4.8-mdod2ry netlib-scalapack-2.0.2-gcc-6.3.0-rgqfr6d py-scipy-0.19.0-gcc-6.3.0-kr7nat4 zlib-1.2.11-gcc-6.3.0-7cqp6cj
autoconf/2.69-gcc-4.8-qextxkq hwloc/1.11.6-gcc-6.3.0-akcisez m4/1.4.18-gcc-4.8-ev2znoc openblas/0.2.19-gcc-6.3.0-dhkmed6 py-setuptools/34.2.0-gcc-6.3.0-fadur4s
automake/1.15-gcc-4.8-maqvukj isl/0.18-gcc-4.8-afi6taq m4/1.4.18-gcc-6.3.0-uppywnz openmpi/2.1.0-gcc-6.3.0-go2s4z5 py-six/1.10.0-gcc-6.3.0-p4dhkaw
binutils/2.28-gcc-4.8-5s7c6rs libiconv/1.15-gcc-4.8-at46wg3 mawk/1.3.4-gcc-4.8-acjez57 openssl/1.0.2k-gcc-4.8-dkls5tk python/2.7.13-gcc-6.3.0-tyehea7
bison/3.0.4-gcc-4.8-ek4luo5 libpciaccess/0.13.4-gcc-6.3.0-gmufnvh mawk/1.3.4-gcc-6.3.0-ostdoms openssl/1.0.2k-gcc-6.3.0-gxgr5or readline/7.0-gcc-4.8-xhufqhn
bzip2/1.0.6-gcc-4.8-iffrxzn libsigsegv/2.11-gcc-4.8-pp2cvte mpc/1.0.3-gcc-4.8-g5mztc5 pcre/8.40-gcc-4.8-r5pbrxb readline/7.0-gcc-6.3.0-zzcyicg
bzip2/1.0.6-gcc-6.3.0-bequudr libsigsegv/2.11-gcc-6.3.0-7enifnh mpfr/3.1.5-gcc-4.8-o7xm7az perl/5.24.1-gcc-4.8-dg5j65u sqlite/3.8.5-gcc-6.3.0-6zoruzj
cmake/3.7.2-gcc-6.3.0-fowuuby libtool/2.4.6-gcc-4.8-7a523za mpich/3.2-gcc-6.3.0-dmvd3aw perl/5.24.1-gcc-6.3.0-6uzkpt6 tar/1.29-gcc-4.8-wse2ass
curl/7.53.1-gcc-4.8-3fz46n6 libtool/2.4.6-gcc-6.3.0-n7zmbzt ncurses/6.0-gcc-4.8-dcpe7ia pkg-config/0.29.2-gcc-4.8-ib33t75 tcl/8.6.6-gcc-4.8-tfxzqbr
expat/2.2.0-gcc-4.8-mrv6bd4 libxml2/2.9.4-gcc-4.8-ryzxnsu ncurses/6.0-gcc-6.3.0-ucbhcdy pkg-config/0.29.2-gcc-6.3.0-jpgubk3 util-macros/1.19.1-gcc-6.3.0-xorz2x2
flex/2.6.3-gcc-4.8-yf345oo libxml2/2.9.4-gcc-6.3.0-rltzsdh netlib-lapack/3.6.1-gcc-6.3.0-js33dog py-appdirs/1.4.0-gcc-6.3.0-jxawmw7 xz/5.2.3-gcc-4.8-mew4log
gcc/6.3.0-gcc-4.8-24puqve lmod/7.4.1-gcc-4.8-je4srhr netlib-scalapack/2.0.2-gcc-6.3.0-5aidk4l py-numpy/1.12.0-gcc-6.3.0-oemmoeu xz/5.2.3-gcc-6.3.0-3vqeuvb
gettext/0.19.8.1-gcc-4.8-yymghlh lua/5.3.4-gcc-4.8-im75yaz netlib-scalapack/2.0.2-gcc-6.3.0-hjsemcn py-packaging/16.8-gcc-6.3.0-i2n3dtl zip/3.0-gcc-4.8-rwar22d
gmp/6.1.2-gcc-4.8-5ub2wu5 lua-luafilesystem/1_6_3-gcc-4.8-wkey3nl netlib-scalapack/2.0.2-gcc-6.3.0-jva724b py-pyparsing/2.1.10-gcc-6.3.0-tbo6gmw zlib/1.2.11-gcc-4.8-pgxsxv7
help2man/1.47.4-gcc-4.8-kcnqmau lua-luaposix/33.4.0-gcc-4.8-mdod2ry netlib-scalapack/2.0.2-gcc-6.3.0-rgqfr6d py-scipy/0.19.0-gcc-6.3.0-kr7nat4 zlib/1.2.11-gcc-6.3.0-7cqp6cj
The names should look familiar, as they resemble the output from ``spack find``.
For example, you could type the following command to load the ``cmake`` module:
.. code-block:: console
$ module load cmake-3.7.2-gcc-6.3.0-fowuuby
$ module load cmake/3.7.2-gcc-6.3.0-fowuuby
Neither of these is particularly pretty, easy to remember, or easy to
type. Luckily, Spack offers many facilities for customizing the module
@@ -779,35 +779,35 @@ cut-and-pasted into a shell script. For example:
$ spack module tcl loads --dependencies py-numpy git
# bzip2@1.0.6%gcc@4.9.3=linux-x86_64
module load bzip2-1.0.6-gcc-4.9.3-ktnrhkrmbbtlvnagfatrarzjojmkvzsx
module load bzip2/1.0.6-gcc-4.9.3-ktnrhkrmbbtlvnagfatrarzjojmkvzsx
# ncurses@6.0%gcc@4.9.3=linux-x86_64
module load ncurses-6.0-gcc-4.9.3-kaazyneh3bjkfnalunchyqtygoe2mncv
module load ncurses/6.0-gcc-4.9.3-kaazyneh3bjkfnalunchyqtygoe2mncv
# zlib@1.2.8%gcc@4.9.3=linux-x86_64
module load zlib-1.2.8-gcc-4.9.3-v3ufwaahjnviyvgjcelo36nywx2ufj7z
module load zlib/1.2.8-gcc-4.9.3-v3ufwaahjnviyvgjcelo36nywx2ufj7z
# sqlite@3.8.5%gcc@4.9.3=linux-x86_64
module load sqlite-3.8.5-gcc-4.9.3-a3eediswgd5f3rmto7g3szoew5nhehbr
module load sqlite/3.8.5-gcc-4.9.3-a3eediswgd5f3rmto7g3szoew5nhehbr
# readline@6.3%gcc@4.9.3=linux-x86_64
module load readline-6.3-gcc-4.9.3-se6r3lsycrwxyhreg4lqirp6xixxejh3
module load readline/6.3-gcc-4.9.3-se6r3lsycrwxyhreg4lqirp6xixxejh3
# python@3.5.1%gcc@4.9.3=linux-x86_64
module load python-3.5.1-gcc-4.9.3-5q5rsrtjld4u6jiicuvtnx52m7tfhegi
module load python/3.5.1-gcc-4.9.3-5q5rsrtjld4u6jiicuvtnx52m7tfhegi
# py-setuptools@20.5%gcc@4.9.3=linux-x86_64
module load py-setuptools-20.5-gcc-4.9.3-4qr2suj6p6glepnedmwhl4f62x64wxw2
module load py-setuptools/20.5-gcc-4.9.3-4qr2suj6p6glepnedmwhl4f62x64wxw2
# py-nose@1.3.7%gcc@4.9.3=linux-x86_64
module load py-nose-1.3.7-gcc-4.9.3-pwhtjw2dvdvfzjwuuztkzr7b4l6zepli
module load py-nose/1.3.7-gcc-4.9.3-pwhtjw2dvdvfzjwuuztkzr7b4l6zepli
# openblas@0.2.17%gcc@4.9.3+shared=linux-x86_64
module load openblas-0.2.17-gcc-4.9.3-pw6rmlom7apfsnjtzfttyayzc7nx5e7y
module load openblas/0.2.17-gcc-4.9.3-pw6rmlom7apfsnjtzfttyayzc7nx5e7y
# py-numpy@1.11.0%gcc@4.9.3+blas+lapack=linux-x86_64
module load py-numpy-1.11.0-gcc-4.9.3-mulodttw5pcyjufva4htsktwty4qd52r
module load py-numpy/1.11.0-gcc-4.9.3-mulodttw5pcyjufva4htsktwty4qd52r
# curl@7.47.1%gcc@4.9.3=linux-x86_64
module load curl-7.47.1-gcc-4.9.3-ohz3fwsepm3b462p5lnaquv7op7naqbi
module load curl/7.47.1-gcc-4.9.3-ohz3fwsepm3b462p5lnaquv7op7naqbi
# autoconf@2.69%gcc@4.9.3=linux-x86_64
module load autoconf-2.69-gcc-4.9.3-bkibjqhgqm5e3o423ogfv2y3o6h2uoq4
module load autoconf/2.69-gcc-4.9.3-bkibjqhgqm5e3o423ogfv2y3o6h2uoq4
# cmake@3.5.0%gcc@4.9.3~doc+ncurses+openssl~qt=linux-x86_64
module load cmake-3.5.0-gcc-4.9.3-x7xnsklmgwla3ubfgzppamtbqk5rwn7t
module load cmake/3.5.0-gcc-4.9.3-x7xnsklmgwla3ubfgzppamtbqk5rwn7t
# expat@2.1.0%gcc@4.9.3=linux-x86_64
module load expat-2.1.0-gcc-4.9.3-6pkz2ucnk2e62imwakejjvbv6egncppd
module load expat/2.1.0-gcc-4.9.3-6pkz2ucnk2e62imwakejjvbv6egncppd
# git@2.8.0-rc2%gcc@4.9.3+curl+expat=linux-x86_64
module load git-2.8.0-rc2-gcc-4.9.3-3bib4hqtnv5xjjoq5ugt3inblt4xrgkd
module load git/2.8.0-rc2-gcc-4.9.3-3bib4hqtnv5xjjoq5ugt3inblt4xrgkd
The script may be further edited by removing unnecessary modules.
@@ -826,12 +826,12 @@ For example, consider the following on one system:
.. code-block:: console
$ module avail
linux-SuSE11-x86_64/antlr-2.7.7-gcc-5.3.0-bdpl46y
linux-SuSE11-x86_64/antlr/2.7.7-gcc-5.3.0-bdpl46y
$ spack module tcl loads antlr # WRONG!
# antlr@2.7.7%gcc@5.3.0~csharp+cxx~java~python arch=linux-SuSE11-x86_64
module load antlr-2.7.7-gcc-5.3.0-bdpl46y
module load antlr/2.7.7-gcc-5.3.0-bdpl46y
$ spack module tcl loads --prefix linux-SuSE11-x86_64/ antlr
# antlr@2.7.7%gcc@5.3.0~csharp+cxx~java~python arch=linux-SuSE11-x86_64
module load linux-SuSE11-x86_64/antlr-2.7.7-gcc-5.3.0-bdpl46y
module load linux-SuSE11-x86_64/antlr/2.7.7-gcc-5.3.0-bdpl46y

View File

@@ -1,13 +1,8 @@
# These dependencies should be installed using pip in order
# to build the documentation.
sphinx>=3.4,!=4.1.2,!=5.1.0
sphinxcontrib-programoutput
sphinx-design
sphinx-rtd-theme
python-levenshtein
# Restrict to docutils <0.17 to workaround a list rendering issue in sphinx.
# https://stackoverflow.com/questions/67542699
docutils <0.17
pygments <2.13
urllib3 <2
sphinx==6.2.1
sphinxcontrib-programoutput==0.17
sphinx_design==0.4.1
sphinx-rtd-theme==1.2.1
python-levenshtein==0.21.0
docutils==0.18.1
pygments==2.15.1
urllib3==2.0.2

484
lib/spack/docs/signing.rst Normal file
View File

@@ -0,0 +1,484 @@
.. Copyright 2013-2022 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)
.. _signing:
=====================
Spack Package Signing
=====================
The goal of package signing in Spack is to provide data integrity
assurances around official packages produced by the automated Spack CI
pipelines. These assurances directly address the security of Spacks
software supply chain by explaining why a security-conscious user can
be reasonably justified in the belief that packages installed via Spack
have an uninterrupted auditable trail back to change management
decisions judged to be appropriate by the Spack maintainers. This is
achieved through cryptographic signing of packages built by Spack CI
pipelines based on code that has been transparently reviewed and
approved on GitHub. This document describes the signing process for
interested users.
.. _risks:
------------------------------
Risks, Impact and Threat Model
------------------------------
This document addresses the approach taken to safeguard Spacks
reputation with regard to the integrity of the package data produced by
Spacks CI pipelines. It does not address issues of data confidentiality
(Spack is intended to be largely open source) or availability (efforts
are described elsewhere). With that said the main reputational risk can
be broadly categorized as a loss of faith in the data integrity due to a
breach of the private key used to sign packages. Remediation of a
private key breach would require republishing the public key with a
revocation certificate, generating a new signing key, an assessment and
potential rebuild/resigning of all packages since the key was breached,
and finally direct intervention by every spack user to update their copy
of Spacks public keys used for local verification.
The primary threat model used in mitigating the risks of these stated
impacts is one of individual error not malicious intent or insider
threat. The primary objective is to avoid the above impacts by making a
private key breach nearly impossible due to oversight or configuration
error. Obvious and straightforward measures are taken to mitigate issues
of malicious interference in data integrity and insider threats but
these attack vectors are not systematically addressed. It should be hard
to exfiltrate the private key intentionally, and almost impossible to
leak the key by accident.
.. _overview:
-----------------
Pipeline Overview
-----------------
Spack pipelines build software through progressive stages where packages
in later stages nominally depend on packages built in earlier stages.
For both technical and design reasons these dependencies are not
implemented through the default GitLab artifacts mechanism; instead
built packages are uploaded to AWS S3 mirrors (buckets) where they are
retrieved by subsequent stages in the pipeline. Two broad categories of
pipelines exist: Pull Request (PR) pipelines and Develop/Release
pipelines.
- PR pipelines are launched in response to pull requests made by
trusted and untrusted users. Packages built on these pipelines upload
code to quarantined AWS S3 locations which cache the built packages
for the purposes of review and iteration on the changes proposed in
the pull request. Packages built on PR pipelines can come from
untrusted users so signing of these pipelines is not implemented.
Jobs in these pipelines are executed via normal GitLab runners both
within the AWS GitLab infrastructure and at affiliated institutions.
- Develop and Release pipelines **sign** the packages they produce and carry
strong integrity assurances that trace back to auditable change management
decisions. These pipelines only run after members from a trusted group of
reviewers verify that the proposed changes in a pull request are appropriate.
Once the PR is merged, or a release is cut, a pipeline is run on protected
GitLab runners which provide access to the required signing keys within the
job. Intermediary keys are used to sign packages in each stage of the
pipeline as they are built and a final job officially signs each package
external to any specific packages build environment. An intermediate key
exists in the AWS infrastructure and for each affiliated instritution that
maintains protected runners. The runners that execute these pipelines
exclusively accept jobs from protected branches meaning the intermediate keys
are never exposed to unreviewed code and the official keys are never exposed
to any specific build environment.
.. _key_architecture:
----------------
Key Architecture
----------------
Spacks CI process uses public-key infrastructure (PKI) based on GNU Privacy
Guard (gpg) keypairs to sign public releases of spack package metadata, also
called specs. Two classes of GPG keys are involved in the process to reduce the
impact of an individual private key compromise, these key classes are the
*Intermediate CI Key* and *Reputational Key*. Each of these keys has signing
sub-keys that are used exclusively for signing packages. This can be confusing
so for the purpose of this explanation well refer to Root and Signing keys.
Each key has a private and a public component as well as one or more identities
and zero or more signatures.
-------------------
Intermediate CI Key
-------------------
The Intermediate key class is used to sign and verify packages between stages
within a develop or release pipeline. An intermediate key exists for the AWS
infrastructure as well as each affiliated institution that maintains protected
runners. These intermediate keys are made available to the GitLab execution
environment building the package so that the packages dependencies may be
verified by the Signing Intermediate CI Public Key and the final package may be
signed by the Signing Intermediate CI Private Key.
+---------------------------------------------------------------------------------------------------------+
| **Intermediate CI Key (GPG)** |
+==================================================+======================================================+
| Root Intermediate CI Private Key (RSA 4096)# | Root Intermediate CI Public Key (RSA 4096) |
+--------------------------------------------------+------------------------------------------------------+
| Signing Intermediate CI Private Key (RSA 4096) | Signing Intermediate CI Public Key (RSA 4096) |
+--------------------------------------------------+------------------------------------------------------+
| Identity: “Intermediate CI Key <maintainers@spack.io>” |
+---------------------------------------------------------------------------------------------------------+
| Signatures: None |
+---------------------------------------------------------------------------------------------------------+
The *Root intermediate CI Private Key*\ Is stripped out of the GPG key and
stored offline completely separate from Spacks infrastructure. This allows the
core development team to append revocation certificates to the GPG key and
issue new sub-keys for use in the pipeline. It is our expectation that this
will happen on a semi regular basis. A corollary of this is that *this key
should not be used to verify package integrity outside the internal CI process.*
----------------
Reputational Key
----------------
The Reputational Key is the public facing key used to sign complete groups of
development and release packages. Only one key pair exsits in this class of
keys. In contrast to the Intermediate CI Key the Reputational Key *should* be
used to verify package integrity. At the end of develop and release pipeline a
final pipeline job pulls down all signed package metadata built by the pipeline,
verifies they were signed with an Intermediate CI Key, then strips the
Intermediate CI Key signature from the package and re-signs them with the
Signing Reputational Private Key. The officially signed packages are then
uploaded back to the AWS S3 mirror. Please note that separating use of the
reputational key into this final job is done to prevent leakage of the key in a
spack package. Because the Signing Reputational Private Key is never exposed to
a build job it cannot accidentally end up in any built package.
+---------------------------------------------------------------------------------------------------------+
| **Reputational Key (GPG)** |
+==================================================+======================================================+
| Root Reputational Private Key (RSA 4096)# | Root Reputational Public Key (RSA 4096) |
+--------------------------------------------------+------------------------------------------------------+
| Signing Reputational Private Key (RSA 4096) | Signing Reputational Public Key (RSA 4096) |
+--------------------------------------------------+------------------------------------------------------+
| Identity: “Spack Project <maintainers@spack.io>” |
+---------------------------------------------------------------------------------------------------------+
| Signatures: Signed by core development team [#f1]_ |
+---------------------------------------------------------------------------------------------------------+
The Root Reputational Private Key is stripped out of the GPG key and stored
offline completely separate from Spacks infrastructure. This allows the core
development team to append revocation certificates to the GPG key in the
unlikely event that the Signing Reputation Private Key is compromised. In
general it is the expectation that rotating this key will happen infrequently if
at all. This should allow relatively transparent verification for the end-user
community without needing deep familiarity with GnuPG or Public Key
Infrastructure.
.. _build_cache_format:
------------------
Build Cache Format
------------------
A binary package consists of a metadata file unambiguously defining the
built package (and including other details such as how to relocate it)
and the installation directory of the package stored as a compressed
archive file. The metadata files can either be unsigned, in which case
the contents are simply the json-serialized concrete spec plus metadata,
or they can be signed, in which case the json-serialized concrete spec
plus metadata is wrapped in a gpg cleartext signature. Built package
metadata files are named to indicate the operating system and
architecture for which the package was built as well as the compiler
used to build it and the packages name and version. For example::
linux-ubuntu18.04-haswell-gcc-7.5.0-zlib-1.2.12-llv2ysfdxnppzjrt5ldybb5c52qbmoow.spec.json.sig
would contain the concrete spec and binary metadata for a binary package
of ``zlib@1.2.12``, built for the ``ubuntu`` operating system and ``haswell``
architecture. The id of the built package exists in the name of the file
as well (after the package name and version) and in this case begins
with ``llv2ys``. The id distinguishes a particular built package from all
other built packages with the same os/arch, compiler, name, and version.
Below is an example of a signed binary package metadata file. Such a
file would live in the ``build_cache`` directory of a binary mirror::
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
{
"spec": {
<concrete-spec-contents-omitted>
},
"buildcache_layout_version": 1,
"binary_cache_checksum": {
"hash_algorithm": "sha256",
"hash": "4f1e46452c35a5e61bcacca205bae1bfcd60a83a399af201a29c95b7cc3e1423"
},
"buildinfo": {
"relative_prefix":
"linux-ubuntu18.04-haswell/gcc-7.5.0/zlib-1.2.12-llv2ysfdxnppzjrt5ldybb5c52qbmoow",
"relative_rpaths": false
}
}
-----BEGIN PGP SIGNATURE-----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=3gvm
-----END PGP SIGNATURE-----
If a user has trusted the public key associated with the private key
used to sign the above spec file, the signature can be verified with
gpg, as follows::
$ gpg verify linux-ubuntu18.04-haswell-gcc-7.5.0-zlib-1.2.12-llv2ysfdxnppzjrt5ldybb5c52qbmoow.spec.json.sig
The metadata (regardless whether signed or unsigned) contains the checksum
of the ``.spack`` file containing the actual installation. The checksum should
be compared to a checksum computed locally on the ``.spack`` file to ensure the
contents have not changed since the binary spec plus metadata were signed. The
``.spack`` files are actually tarballs containing the compressed archive of the
install tree. These files, along with the metadata files, live within the
``build_cache`` directory of the mirror, and together are organized as follows::
build_cache/
# unsigned metadata (for indexing, contains sha256 of .spack file)
<arch>-<compiler>-<name>-<ver>-24zvipcqgg2wyjpvdq2ajy5jnm564hen.spec.json
# clearsigned metadata (same as above, but signed)
<arch>-<compiler>-<name>-<ver>-24zvipcqgg2wyjpvdq2ajy5jnm564hen.spec.json.sig
<arch>/
<compiler>/
<name>-<ver>/
# tar.gz-compressed prefix (may support more compression formats later)
<arch>-<compiler>-<name>-<ver>-24zvipcqgg2wyjpvdq2ajy5jnm564hen.spack
Uncompressing and extracting the ``.spack`` file results in the install tree.
This is in contrast to previous versions of spack, where the ``.spack`` file
contained a (duplicated) metadata file, a signature file and a nested tarball
containing the install tree.
.. _internal_implementation:
-----------------------
Internal Implementation
-----------------------
The technical implementation of the pipeline signing process includes components
defined in Amazon Web Services, the Kubernetes cluster, at affilicated
institutions, and the GitLab/GitLab Runner deployment. We present the techincal
implementation in two interdependent sections. The first addresses how secrets
are managed through the lifecycle of a develop or release pipeline. The second
section describes how Gitlab Runner and pipelines are configured and managed to
support secure automated signing.
Secrets Management
^^^^^^^^^^^^^^^^^^
As stated above the Root Private Keys (intermediate and reputational)
are stripped from the GPG keys and stored outside Spacks
infrastructure.
.. warning::
**TODO**
- Explanation here about where and how access is handled for these keys.
- Both Root private keys are protected with strong passwords
- Who has access to these and how?
**Intermediate CI Key**
-----------------------
Multiple intermediate CI signing keys exist, one Intermediate CI Key for jobs
run in AWS, and one key for each affiliated institution (e.g. Univerity of
Oregon). Here we describe how the Intermediate CI Key is managed in AWS:
The Intermediate CI Key (including the Signing Intermediate CI Private Key is
exported as an ASCII armored file and stored in a Kubernetes secret called
``spack-intermediate-ci-signing-key``. For convenience sake, this same secret
contains an ASCII-armored export of just the *public* components of the
Reputational Key. This secret also contains the *public* components of each of
the affiliated institutions' Intermediate CI Key. These are potentially needed
to verify dependent packages which may have been found in the public mirror or
built by a protected job running on an affiliated institution's infrastrcuture
in an earlier stage of the pipeline.
Procedurally the ``spack-intermediate-ci-signing-key`` secret is used in
the following way:
1. A ``large-arm-prot`` or ``large-x86-prot`` protected runner picks up
a job tagged ``protected`` from a protected GitLab branch. (See
`Protected Runners and Reserved Tags <#_8bawjmgykv0b>`__).
2. Based on its configuration, the runner creates a job Pod in the
pipeline namespace and mounts the spack-intermediate-ci-signing-key
Kubernetes secret into the build container
3. The Intermediate CI Key, affiliated institutions' public key and the
Reputational Public Key are imported into a keyring by the ``spack gpg …``
sub-command. This is initiated by the jobs build script which is created by
the generate job at the beginning of the pipeline.
4. Assuming the package has dependencies those specs are verified using
the keyring.
5. The package is built and the spec.json is generated
6. The spec.json is signed by the keyring and uploaded to the mirrors
build cache.
**Reputational Key**
--------------------
Because of the increased impact to end users in the case of a private
key breach, the Reputational Key is managed separately from the
Intermediate CI Keys and has additional controls. First, the Reputational
Key was generated outside of Spacks infrastructure and has been signed
by the core development team. The Reputational Key (along with the
Signing Reputational Private Key) was then ASCII armor exported to a
file. Unlike the Intermediate CI Key this exported file is not stored as
a base64 encoded secret in Kubernetes. Instead\ *the key file
itself*\ is encrypted and stored in Kubernetes as the
``spack-signing-key-encrypted`` secret in the pipeline namespace.
The encryption of the exported Reputational Key (including the Signing
Reputational Private Key) is handled by `AWS Key Management Store (KMS) data
keys
<https://docs.aws.amazon.com/kms/latest/developerguide/concepts.html#data-keys>`__.
The private key material is decrypted and imported at the time of signing into a
memory mounted temporary directory holding the keychain. The signing job uses
the `AWS Encryption SDK
<https://docs.aws.amazon.com/encryption-sdk/latest/developer-guide/crypto-cli.html>`__
(i.e. ``aws-encryption-cli``) to decrypt the Reputational Key. Permission to
decrypt the key is granted to the job Pod through a Kubernetes service account
specifically used for this, and only this, function. Finally, for convenience
sake, this same secret contains an ASCII-armored export of the *public*
components of the Intermediate CI Keys and the Reputational Key. This allows the
signing script to verify that packages were built by the pipeline (both on AWS
or at affiliated institutions), or signed previously as a part of a different
pipeline. This is is done *before* importing decrypting and importing the
Signing Reputational Private Key material and officially signing the packages.
Procedurally the ``spack-singing-key-encrypted`` secret is used in the
following way:
1. The ``spack-package-signing-gitlab-runner`` protected runner picks
up a job tagged ``notary`` from a protected GitLab branch (See
`Protected Runners and Reserved Tags <#_8bawjmgykv0b>`__).
2. Based on its configuration, the runner creates a job pod in the
pipeline namespace. The job is run in a stripped down purpose-built
image ``ghcr.io/spack/notary:latest`` Docker image. The runner is
configured to only allow running jobs with this image.
3. The runner also mounts the ``spack-signing-key-encrypted`` secret to
a path on disk. Note that this becomes several files on disk, the
public components of the Intermediate CI Keys, the public components
of the Reputational CI, and an AWS KMS encrypted file containing the
Singing Reputational Private Key.
4. In addition to the secret, the runner creates a tmpfs memory mounted
directory where the GnuPG keyring will be created to verify, and
then resign the package specs.
5. The job script syncs all spec.json.sig files from the build cache to
a working directory in the jobs execution environment.
6. The job script then runs the ``sign.sh`` script built into the
notary Docker image.
7. The ``sign.sh`` script imports the public components of the
Reputational and Intermediate CI Keys and uses them to verify good
signatures on the spec.json.sig files. If any signed spec does not
verify the job immediately fails.
8. Assuming all specs are verified, the ``sign.sh`` script then unpacks
the spec json data from the signed file in preparation for being
re-signed with the Reputational Key.
9. The private components of the Reputational Key are decrypted to
standard out using ``aws-encryption-cli`` directly into a ``gpg
import …`` statement which imports the key into the
keyring mounted in-memory.
10. The private key is then used to sign each of the json specs and the
keyring is removed from disk.
11. The re-signed json specs are resynced to the AWS S3 Mirror and the
public signing of the packages for the develop or release pipeline
that created them is complete.
Non service-account access to the private components of the Reputational
Key that are managed through access to the symmetric secret in KMS used
to encrypt the data key (which in turn is used to encrypt the GnuPG key
- See:\ `Encryption SDK
Documentation <https://docs.aws.amazon.com/encryption-sdk/latest/developer-guide/crypto-cli-examples.html#cli-example-encrypt-file>`__).
A small trusted subset of the core development team are the only
individuals with access to this symmetric key.
.. _protected_runners:
Protected Runners and Reserved Tags
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Spack has a large number of Gitlab Runners operating in its build farm.
These include runners deployed in the AWS Kubernetes cluster as well as
runners deployed at affiliated institutions. The majority of runners are
shared runners that operate across projects in gitlab.spack.io. These
runners pick up jobs primarily from the spack/spack project and execute
them in PR pipelines.
A small number of runners operating on AWS and at affiliated institutions are
registered as specific *protected* runners on the spack/spack project. In
addition to protected runners there are protected branches on the spack/spack
project. These are the ``develop`` branch, any release branch (i.e. managed with
the ``releases/v*`` wildcard) and any tag branch (managed with the ``v*``
wildcard) Finally Spacks pipeline generation code reserves certain tags to make
sure jobs are routed to the correct runners, these tags are ``public``,
``protected``, and ``notary``. Understanding how all this works together to
protect secrets and provide integrity assurances can be a little confusing so
lets break these down:
- **Protected Branches**- Protected branches in Spack prevent anyone
other than Maintainers in GitLab from pushing code. In the case of
Spack the only Maintainer level entity pushing code to protected
branches is Spack bot. Protecting branches also marks them in such a
way that Protected Runners will only run jobs from those branches
- **Protected Runners**- Protected Runners only run jobs from protected
branches. Because protected runners have access to secrets, it's critical
that they not run Jobs from untrusted code (i.e. PR branches). If they did it
would be possible for a PR branch to tag a job in such a way that a protected
runner executed that job and mounted secrets into a code execution
environment that had not been reviewed by Spack maintainers. Note however
that in the absence of tagging used to route jobs, public runners *could* run
jobs from protected branches. No secrets would be at risk of being breached
because non-protected runners do not have access to those secrets; lack of
secrets would, however, cause the jobs to fail.
- **Reserved Tags**- To mitigate the issue of public runners picking up
protected jobs Spack uses a small set of “reserved” job tags (Note that these
are *job* tags not git tags). These tags are “public”, “private”, and
“notary.” The majority of jobs executed in Spacks GitLab instance are
executed via a ``generate`` job. The generate job code systematically ensures
that no user defined configuration sets these tags. Instead, the ``generate``
job sets these tags based on rules related to the branch where this pipeline
originated. If the job is a part of a pipeline on a PR branch it sets the
``public`` tag. If the job is part of a pipeline on a protected branch it
sets the ``protected`` tag. Finally if the job is the package signing job and
it is running on a pipeline that is part of a protected branch then it sets
the ``notary`` tag.
Protected Runners are configured to only run jobs from protected branches. Only
jobs running in pipelines on protected branches are tagged with ``protected`` or
``notary`` tags. This tightly couples jobs on protected branches to protected
runners that provide access to the secrets required to sign the built packages.
The secrets are can **only** be accessed via:
1. Runners under direct control of the core development team.
2. Runners under direct control of trusted maintainers at affiliated institutions.
3. By code running the automated pipeline that has been reviewed by the
Spack maintainers and judged to be appropriate.
Other attempts (either through malicious intent or incompetence) can at
worst grab jobs intended for protected runners which will cause those
jobs to fail alerting both Spack maintainers and the core development
team.
.. [#f1]
The Reputational Key has also cross signed core development team
keys.

View File

@@ -1373,7 +1373,7 @@ def long_message(self):
test_log = join_path(os.path.dirname(self.log_name), spack_install_test_log)
if os.path.isfile(test_log):
out.write("\nSee test log for details:\n")
out.write(" {0}n".format(test_log))
out.write(" {0}\n".format(test_log))
return out.getvalue()

View File

@@ -2,6 +2,7 @@
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import collections.abc
import os
from typing import Tuple
@@ -13,21 +14,24 @@
from .cmake import CMakeBuilder, CMakePackage
def cmake_cache_path(name, value, comment=""):
def cmake_cache_path(name, value, comment="", force=False):
"""Generate a string for a cmake cache variable"""
return 'set({0} "{1}" CACHE PATH "{2}")\n'.format(name, value, comment)
force_str = " FORCE" if force else ""
return 'set({0} "{1}" CACHE PATH "{2}"{3})\n'.format(name, value, comment, force_str)
def cmake_cache_string(name, value, comment=""):
def cmake_cache_string(name, value, comment="", force=False):
"""Generate a string for a cmake cache variable"""
return 'set({0} "{1}" CACHE STRING "{2}")\n'.format(name, value, comment)
force_str = " FORCE" if force else ""
return 'set({0} "{1}" CACHE STRING "{2}"{3})\n'.format(name, value, comment, force_str)
def cmake_cache_option(name, boolean_value, comment=""):
def cmake_cache_option(name, boolean_value, comment="", force=False):
"""Generate a string for a cmake configuration option"""
value = "ON" if boolean_value else "OFF"
return 'set({0} {1} CACHE BOOL "{2}")\n'.format(name, value, comment)
force_str = " FORCE" if force else ""
return 'set({0} {1} CACHE BOOL "{2}"{3})\n'.format(name, value, comment, force_str)
class CachedCMakeBuilder(CMakeBuilder):
@@ -63,6 +67,34 @@ def cache_name(self):
def cache_path(self):
return os.path.join(self.pkg.stage.source_path, self.cache_name)
# Implement a version of the define_from_variant for Cached packages
def define_cmake_cache_from_variant(self, cmake_var, variant=None, comment=""):
"""Return a Cached CMake field from the given variant's value.
See define_from_variant in lib/spack/spack/build_systems/cmake.py package
"""
if variant is None:
variant = cmake_var.lower()
if variant not in self.pkg.variants:
raise KeyError('"{0}" is not a variant of "{1}"'.format(variant, self.pkg.name))
if variant not in self.pkg.spec.variants:
return ""
value = self.pkg.spec.variants[variant].value
field = None
if isinstance(value, bool):
field = cmake_cache_option(cmake_var, value, comment)
else:
if isinstance(value, collections.abc.Sequence) and not isinstance(value, str):
value = ";".join(str(v) for v in value)
else:
value = str(value)
field = cmake_cache_string(cmake_var, value, comment)
return field
def initconfig_compiler_entries(self):
# This will tell cmake to use the Spack compiler wrappers when run
# through Spack, but use the underlying compiler when run outside of
@@ -130,6 +162,17 @@ def initconfig_compiler_entries(self):
libs_string = libs_format_string.format(lang)
entries.append(cmake_cache_string(libs_string, libs_flags))
# Set the generator in the cached config
if self.spec.satisfies("generator=make"):
entries.append(cmake_cache_string("CMAKE_GENERATOR", "Unix Makefiles"))
if self.spec.satisfies("generator=ninja"):
entries.append(cmake_cache_string("CMAKE_GENERATOR", "Ninja"))
entries.append(
cmake_cache_string(
"CMAKE_MAKE_PROGRAM", "{0}/ninja".format(spec["ninja"].prefix.bin)
)
)
return entries
def initconfig_mpi_entries(self):
@@ -195,26 +238,57 @@ def initconfig_hardware_entries(self):
"#------------------{0}\n".format("-" * 60),
]
# Provide standard CMake arguments for dependent CachedCMakePackages
if spec.satisfies("^cuda"):
entries.append("#------------------{0}".format("-" * 30))
entries.append("# Cuda")
entries.append("#------------------{0}\n".format("-" * 30))
cudatoolkitdir = spec["cuda"].prefix
entries.append(cmake_cache_path("CUDA_TOOLKIT_ROOT_DIR", cudatoolkitdir))
cudacompiler = "${CUDA_TOOLKIT_ROOT_DIR}/bin/nvcc"
entries.append(cmake_cache_path("CMAKE_CUDA_COMPILER", cudacompiler))
entries.append(cmake_cache_path("CUDAToolkit_ROOT", cudatoolkitdir))
entries.append(cmake_cache_path("CMAKE_CUDA_COMPILER", "${CUDAToolkit_ROOT}/bin/nvcc"))
entries.append(cmake_cache_path("CMAKE_CUDA_HOST_COMPILER", "${CMAKE_CXX_COMPILER}"))
# Include the deprecated CUDA_TOOLKIT_ROOT_DIR for supporting BLT packages
entries.append(cmake_cache_path("CUDA_TOOLKIT_ROOT_DIR", cudatoolkitdir))
archs = spec.variants["cuda_arch"].value
if archs[0] != "none":
arch_str = ";".join(archs)
entries.append(
cmake_cache_string("CMAKE_CUDA_ARCHITECTURES", "{0}".format(arch_str))
)
if "+rocm" in spec:
entries.append("#------------------{0}".format("-" * 30))
entries.append("# ROCm")
entries.append("#------------------{0}\n".format("-" * 30))
# Explicitly setting HIP_ROOT_DIR may be a patch that is no longer necessary
entries.append(cmake_cache_path("HIP_ROOT_DIR", "{0}".format(spec["hip"].prefix)))
entries.append(
cmake_cache_path("HIP_CXX_COMPILER", "{0}".format(self.spec["hip"].hipcc))
)
archs = self.spec.variants["amdgpu_target"].value
if archs[0] != "none":
arch_str = ";".join(archs)
entries.append(
cmake_cache_string("CMAKE_HIP_ARCHITECTURES", "{0}".format(arch_str))
)
entries.append(cmake_cache_string("AMDGPU_TARGETS", "{0}".format(arch_str)))
entries.append(cmake_cache_string("GPU_TARGETS", "{0}".format(arch_str)))
return entries
def std_initconfig_entries(self):
cmake_prefix_path_env = os.environ["CMAKE_PREFIX_PATH"]
cmake_prefix_path = cmake_prefix_path_env.replace(os.pathsep, ";")
return [
"#------------------{0}".format("-" * 60),
"# !!!! This is a generated file, edit at own risk !!!!",
"#------------------{0}".format("-" * 60),
"# CMake executable path: {0}".format(self.pkg.spec["cmake"].command.path),
"#------------------{0}\n".format("-" * 60),
cmake_cache_path("CMAKE_PREFIX_PATH", cmake_prefix_path),
]
def initconfig_package_entries(self):

View File

@@ -5,6 +5,7 @@
import collections.abc
import inspect
import os
import pathlib
import platform
import re
import sys
@@ -15,7 +16,6 @@
import spack.build_environment
import spack.builder
import spack.package_base
import spack.util.path
from spack.directives import build_system, conflicts, depends_on, variant
from spack.multimethod import when
@@ -271,7 +271,7 @@ def std_args(pkg, generator=None):
args = [
"-G",
generator,
define("CMAKE_INSTALL_PREFIX", pkg.prefix),
define("CMAKE_INSTALL_PREFIX", pathlib.Path(pkg.prefix).as_posix()),
define("CMAKE_BUILD_TYPE", build_type),
define("BUILD_TESTING", pkg.run_tests),
]

View File

@@ -7,7 +7,7 @@
import llnl.util.lang as lang
from spack.directives import extends, maintainers
from spack.directives import extends
from .generic import GenericBuilder, Package
@@ -71,8 +71,6 @@ class RPackage(Package):
GenericBuilder = RBuilder
maintainers("glennpj")
#: This attribute is used in UI queries that need to know the build
#: system base class
build_system_class = "RPackage"

View File

@@ -10,6 +10,7 @@
from llnl.util.filesystem import find, join_path, working_dir
import spack.builder
import spack.install_test
import spack.package_base
from spack.directives import build_system, depends_on, extends
from spack.multimethod import when
@@ -30,8 +31,8 @@ class SIPPackage(spack.package_base.PackageBase):
#: Name of private sip module to install alongside package
sip_module = "sip"
#: Callback names for install-time test
install_time_test_callbacks = ["test"]
#: Callback names for install-time testing
install_time_test_callbacks = ["test_imports"]
#: Legacy buildsystem attribute used to deserialize and install old specs
legacy_buildsystem = "sip"
@@ -87,18 +88,20 @@ def python(self, *args, **kwargs):
"""The python ``Executable``."""
inspect.getmodule(self).python(*args, **kwargs)
def test(self):
def test_imports(self):
"""Attempts to import modules of the installed package."""
# Make sure we are importing the installed modules,
# not the ones in the source directory
python = inspect.getmodule(self).python
for module in self.import_modules:
self.run_test(
inspect.getmodule(self).python.path,
["-c", "import {0}".format(module)],
with spack.install_test.test_part(
self,
"test_imports_{0}".format(module),
purpose="checking import of {0}".format(module),
work_dir="spack-test",
)
):
python("-c", "import {0}".format(module))
@spack.builder.builder("sip")

View File

@@ -751,7 +751,7 @@ def generate_gitlab_ci_yaml(
env.concretize()
env.write()
yaml_root = ev.config_dict(env.manifest)
yaml_root = env.manifest[ev.TOP_LEVEL_KEY]
# Get the joined "ci" config with all of the current scopes resolved
ci_config = cfg.get("ci")
@@ -946,7 +946,7 @@ def generate_gitlab_ci_yaml(
# Add config scopes to environment
env_includes = env_yaml_root["spack"].get("include", [])
cli_scopes = [
os.path.abspath(s.path)
os.path.relpath(s.path, concrete_env_dir)
for s in cfg.scopes().values()
if type(s) == cfg.ImmutableConfigScope
and s.path not in env_includes
@@ -1095,7 +1095,7 @@ def generate_gitlab_ci_yaml(
raise AttributeError
def main_script_replacements(cmd):
return cmd.replace("{env_dir}", concrete_env_dir)
return cmd.replace("{env_dir}", rel_concrete_env_dir)
job_object["script"] = _unpack_script(
job_object["script"], op=main_script_replacements

View File

@@ -228,7 +228,7 @@ def ci_reindex(args):
Use the active, gitlab-enabled environment to rebuild the buildcache
index for the associated mirror."""
env = spack.cmd.require_active_env(cmd_name="ci rebuild-index")
yaml_root = ev.config_dict(env.manifest)
yaml_root = env.manifest[ev.TOP_LEVEL_KEY]
if "mirrors" not in yaml_root or len(yaml_root["mirrors"].values()) < 1:
tty.die("spack ci rebuild-index requires an env containing a mirror")

View File

@@ -349,7 +349,7 @@ def install_status():
"-I",
"--install-status",
action="store_true",
default=False,
default=True,
help="show install status of packages. packages can be: "
"installed [+], missing and needed by an installed package [-], "
"installed in and upstream instance [^], "
@@ -357,6 +357,17 @@ def install_status():
)
@arg
def no_install_status():
return Args(
"--no-install-status",
dest="install_status",
action="store_false",
default=True,
help="do not show install status annotations",
)
@arg
def no_checksum():
return Args(

View File

@@ -53,7 +53,7 @@ def setup_parser(subparser):
"--scope",
choices=scopes,
metavar=scopes_metavar,
default=spack.config.default_modify_scope("compilers"),
default=None,
help="configuration scope to modify",
)
@@ -106,19 +106,21 @@ def compiler_find(args):
def compiler_remove(args):
cspec = spack.spec.CompilerSpec(args.compiler_spec)
compilers = spack.compilers.compilers_for_spec(cspec, scope=args.scope)
if not compilers:
tty.die("No compilers match spec %s" % cspec)
elif not args.all and len(compilers) > 1:
tty.error("Multiple compilers match spec %s. Choose one:" % cspec)
colify(reversed(sorted([c.spec.display_str for c in compilers])), indent=4)
compiler_spec = spack.spec.CompilerSpec(args.compiler_spec)
candidate_compilers = spack.compilers.compilers_for_spec(compiler_spec, scope=args.scope)
if not candidate_compilers:
tty.die("No compilers match spec %s" % compiler_spec)
if not args.all and len(candidate_compilers) > 1:
tty.error(f"Multiple compilers match spec {compiler_spec}. Choose one:")
colify(reversed(sorted([c.spec.display_str for c in candidate_compilers])), indent=4)
tty.msg("Or, use `spack compiler remove -a` to remove all of them.")
sys.exit(1)
for compiler in compilers:
spack.compilers.remove_compiler_from_config(compiler.spec, scope=args.scope)
tty.msg("Removed compiler %s" % compiler.spec.display_str)
for current_compiler in candidate_compilers:
spack.compilers.remove_compiler_from_config(current_compiler.spec, scope=args.scope)
tty.msg(f"{current_compiler.spec.display_str} has been removed")
def compiler_info(args):

View File

@@ -79,6 +79,12 @@ def setup_parser(subparser):
read_cray_manifest.add_argument(
"--directory", default=None, help="specify a directory storing a group of manifest files"
)
read_cray_manifest.add_argument(
"--ignore-default-dir",
action="store_true",
default=False,
help="ignore the default directory of manifest files",
)
read_cray_manifest.add_argument(
"--dry-run",
action="store_true",
@@ -177,11 +183,16 @@ def external_read_cray_manifest(args):
manifest_directory=args.directory,
dry_run=args.dry_run,
fail_on_error=args.fail_on_error,
ignore_default_dir=args.ignore_default_dir,
)
def _collect_and_consume_cray_manifest_files(
manifest_file=None, manifest_directory=None, dry_run=False, fail_on_error=False
manifest_file=None,
manifest_directory=None,
dry_run=False,
fail_on_error=False,
ignore_default_dir=False,
):
manifest_files = []
if manifest_file:
@@ -191,7 +202,7 @@ def _collect_and_consume_cray_manifest_files(
if manifest_directory:
manifest_dirs.append(manifest_directory)
if os.path.isdir(cray_manifest.default_path):
if not ignore_default_dir and os.path.isdir(cray_manifest.default_path):
tty.debug(
"Cray manifest path {0} exists: collecting all files to read.".format(
cray_manifest.default_path

View File

@@ -44,7 +44,11 @@ def setup_parser(subparser):
)
# Below are arguments w.r.t. spec display (like spack spec)
arguments.add_common_arguments(subparser, ["long", "very_long", "install_status"])
arguments.add_common_arguments(subparser, ["long", "very_long"])
install_status_group = subparser.add_mutually_exclusive_group()
arguments.add_common_arguments(install_status_group, ["install_status", "no_install_status"])
subparser.add_argument(
"-y",
"--yaml",

View File

@@ -31,7 +31,11 @@ def setup_parser(subparser):
for further documentation regarding the spec syntax, see:
spack help --spec
"""
arguments.add_common_arguments(subparser, ["long", "very_long", "install_status"])
arguments.add_common_arguments(subparser, ["long", "very_long"])
install_status_group = subparser.add_mutually_exclusive_group()
arguments.add_common_arguments(install_status_group, ["install_status", "no_install_status"])
format_group = subparser.add_mutually_exclusive_group()
format_group.add_argument(
"-y",

View File

@@ -37,7 +37,6 @@
"implicit_rpaths",
"extra_rpaths",
]
_cache_config_file = []
# TODO: Caches at module level make it difficult to mock configurations in
# TODO: unit tests. It might be worth reworking their implementation.
@@ -112,36 +111,26 @@ def _to_dict(compiler):
def get_compiler_config(scope=None, init_config=True):
"""Return the compiler configuration for the specified architecture."""
def init_compiler_config():
"""Compiler search used when Spack has no compilers."""
compilers = find_compilers()
compilers_dict = []
for compiler in compilers:
compilers_dict.append(_to_dict(compiler))
spack.config.set("compilers", compilers_dict, scope=scope)
config = spack.config.get("compilers", scope=scope) or []
if config or not init_config:
return config
merged_config = spack.config.get("compilers")
if merged_config:
return config
_init_compiler_config(scope=scope)
config = spack.config.get("compilers", scope=scope)
# Update the configuration if there are currently no compilers
# configured. Avoid updating automatically if there ARE site
# compilers configured but no user ones.
if not config and init_config:
if scope is None:
# We know no compilers were configured in any scope.
init_compiler_config()
config = spack.config.get("compilers", scope=scope)
elif scope == "user":
# Check the site config and update the user config if
# nothing is configured at the site level.
site_config = spack.config.get("compilers", scope="site")
sys_config = spack.config.get("compilers", scope="system")
if not site_config and not sys_config:
init_compiler_config()
config = spack.config.get("compilers", scope=scope)
return config
elif config:
return config
else:
return [] # Return empty list which we will later append to.
return config
def _init_compiler_config(*, scope):
"""Compiler search used when Spack has no compilers."""
compilers = find_compilers()
compilers_dict = []
for compiler in compilers:
compilers_dict.append(_to_dict(compiler))
spack.config.set("compilers", compilers_dict, scope=scope)
def compiler_config_files():
@@ -165,52 +154,65 @@ def add_compilers_to_config(compilers, scope=None, init_config=True):
compiler_config = get_compiler_config(scope, init_config)
for compiler in compilers:
compiler_config.append(_to_dict(compiler))
global _cache_config_file
_cache_config_file = compiler_config
spack.config.set("compilers", compiler_config, scope=scope)
@_auto_compiler_spec
def remove_compiler_from_config(compiler_spec, scope=None):
"""Remove compilers from the config, by spec.
"""Remove compilers from configuration by spec.
If scope is None, all the scopes are searched for removal.
Arguments:
compiler_specs: a list of CompilerSpec objects.
scope: configuration scope to modify.
compiler_spec: compiler to be removed
scope: configuration scope to modify
"""
# Need a better way for this
global _cache_config_file
candidate_scopes = [scope]
if scope is None:
candidate_scopes = spack.config.config.scopes.keys()
removal_happened = False
for current_scope in candidate_scopes:
removal_happened |= _remove_compiler_from_scope(compiler_spec, scope=current_scope)
return removal_happened
def _remove_compiler_from_scope(compiler_spec, scope):
"""Removes a compiler from a specific configuration scope.
Args:
compiler_spec: compiler to be removed
scope: configuration scope under consideration
Returns:
True if one or more compiler entries were actually removed, False otherwise
"""
assert scope is not None, "a specific scope is needed when calling this function"
compiler_config = get_compiler_config(scope)
config_length = len(compiler_config)
filtered_compiler_config = [
comp
for comp in compiler_config
compiler_entry
for compiler_entry in compiler_config
if not spack.spec.parse_with_version_concrete(
comp["compiler"]["spec"], compiler=True
compiler_entry["compiler"]["spec"], compiler=True
).satisfies(compiler_spec)
]
# Update the cache for changes
_cache_config_file = filtered_compiler_config
if len(filtered_compiler_config) == config_length: # No items removed
CompilerSpecInsufficientlySpecificError(compiler_spec)
spack.config.set("compilers", filtered_compiler_config, scope=scope)
if len(filtered_compiler_config) == len(compiler_config):
return False
# We need to preserve the YAML type for comments, hence we are copying the
# items in the list that has just been retrieved
compiler_config[:] = filtered_compiler_config
spack.config.set("compilers", compiler_config, scope=scope)
return True
def all_compilers_config(scope=None, init_config=True):
"""Return a set of specs for all the compiler versions currently
available to build with. These are instances of CompilerSpec.
"""
# Get compilers for this architecture.
# Create a cache of the config file so we don't load all the time.
global _cache_config_file
if not _cache_config_file:
_cache_config_file = get_compiler_config(scope, init_config)
return _cache_config_file
else:
return _cache_config_file
return get_compiler_config(scope, init_config)
def all_compiler_specs(scope=None, init_config=True):

View File

@@ -151,7 +151,11 @@ def setup_custom_environment(self, pkg, env):
arch = arch.replace("-", "_")
# vcvars can target specific sdk versions, force it to pick up concretized sdk
# version, if needed by spec
sdk_ver = "" if "win-sdk" not in pkg.spec else pkg.spec["win-sdk"].version.string + ".0"
sdk_ver = (
""
if "win-sdk" not in pkg.spec or pkg.name == "win-sdk"
else pkg.spec["win-sdk"].version.string + ".0"
)
# provide vcvars with msvc version selected by concretization,
# not whatever it happens to pick up on the system (highest available version)
out = subprocess.check_output( # novermin

View File

@@ -81,7 +81,7 @@
# Same as above, but including keys for environments
# this allows us to unify config reading between configs and environments
all_schemas = copy.deepcopy(section_schemas)
all_schemas.update(dict((key, spack.schema.env.schema) for key in spack.schema.env.keys))
all_schemas.update({spack.schema.env.TOP_LEVEL_KEY: spack.schema.env.schema})
#: Path to the default configuration
configuration_defaults_path = ("defaults", os.path.join(spack.paths.etc_path, "defaults"))
@@ -111,14 +111,6 @@
overrides_base_name = "overrides-"
def first_existing(dictionary, keys):
"""Get the value of the first key in keys that is in the dictionary."""
try:
return next(k for k in keys if k in dictionary)
except StopIteration:
raise KeyError("None of %s is in dict!" % str(keys))
class ConfigScope(object):
"""This class represents a configuration scope.
@@ -838,12 +830,10 @@ def _config():
def add_from_file(filename, scope=None):
"""Add updates to a config from a filename"""
import spack.environment as ev
# Get file as config dict
# Extract internal attributes, if we are dealing with an environment
data = read_config_file(filename)
if any(k in data for k in spack.schema.env.keys):
data = ev.config_dict(data)
if spack.schema.env.TOP_LEVEL_KEY in data:
data = data[spack.schema.env.TOP_LEVEL_KEY]
# update all sections from config dict
# We have to iterate on keys to keep overrides from the file
@@ -1353,17 +1343,11 @@ def use_configuration(*scopes_or_paths):
configuration = _config_from(scopes_or_paths)
config.clear_caches(), configuration.clear_caches()
# Save and clear the current compiler cache
saved_compiler_cache = spack.compilers._cache_config_file
spack.compilers._cache_config_file = []
saved_config, config = config, configuration
try:
yield configuration
finally:
# Restore previous config files
spack.compilers._cache_config_file = saved_compiler_cache
config = saved_config

View File

@@ -37,7 +37,7 @@ def validate(configuration_file):
config = syaml.load(f)
# Ensure we have a "container" attribute with sensible defaults set
env_dict = ev.config_dict(config)
env_dict = config[ev.TOP_LEVEL_KEY]
env_dict.setdefault(
"container", {"format": "docker", "images": {"os": "ubuntu:22.04", "spack": "develop"}}
)

View File

@@ -17,7 +17,7 @@
"template": "container/fedora_38.dockerfile",
"image": "docker.io/fedora:38"
},
"os_package_manager": "yum",
"os_package_manager": "dnf",
"build": "spack/fedora38",
"build_tags": {
"develop": "latest"
@@ -31,7 +31,7 @@
"template": "container/fedora_37.dockerfile",
"image": "docker.io/fedora:37"
},
"os_package_manager": "yum",
"os_package_manager": "dnf",
"build": "spack/fedora37",
"build_tags": {
"develop": "latest"
@@ -45,7 +45,7 @@
"template": "container/rockylinux_9.dockerfile",
"image": "docker.io/rockylinux:9"
},
"os_package_manager": "yum",
"os_package_manager": "dnf_epel",
"build": "spack/rockylinux9",
"build_tags": {
"develop": "latest"
@@ -59,7 +59,7 @@
"template": "container/rockylinux_8.dockerfile",
"image": "docker.io/rockylinux:8"
},
"os_package_manager": "yum",
"os_package_manager": "dnf_epel",
"build": "spack/rockylinux8",
"build_tags": {
"develop": "latest"
@@ -73,7 +73,7 @@
"template": "container/almalinux_9.dockerfile",
"image": "quay.io/almalinux/almalinux:9"
},
"os_package_manager": "yum",
"os_package_manager": "dnf_epel",
"build": "spack/almalinux9",
"build_tags": {
"develop": "latest"
@@ -87,7 +87,7 @@
"template": "container/almalinux_8.dockerfile",
"image": "quay.io/almalinux/almalinux:8"
},
"os_package_manager": "yum",
"os_package_manager": "dnf_epel",
"build": "spack/almalinux8",
"build_tags": {
"develop": "latest"
@@ -101,7 +101,7 @@
"template": "container/centos_stream.dockerfile",
"image": "quay.io/centos/centos:stream"
},
"os_package_manager": "yum",
"os_package_manager": "dnf_epel",
"build": "spack/centos-stream",
"final": {
"image": "quay.io/centos/centos:stream"
@@ -185,6 +185,16 @@
"install": "apt-get -yqq install",
"clean": "rm -rf /var/lib/apt/lists/*"
},
"dnf": {
"update": "dnf update -y",
"install": "dnf install -y",
"clean": "rm -rf /var/cache/dnf && dnf clean all"
},
"dnf_epel": {
"update": "dnf update -y && dnf install -y epel-release && dnf update -y",
"install": "dnf install -y",
"clean": "rm -rf /var/cache/dnf && dnf clean all"
},
"yum": {
"update": "yum update -y && yum install -y epel-release && yum update -y",
"install": "yum install -y",

View File

@@ -50,7 +50,7 @@ def create(configuration, last_phase=None):
configuration (dict): how to generate the current recipe
last_phase (str): last phase to be printed or None to print them all
"""
name = ev.config_dict(configuration)["container"]["format"]
name = configuration[ev.TOP_LEVEL_KEY]["container"]["format"]
return _writer_factory[name](configuration, last_phase)
@@ -138,7 +138,7 @@ class PathContext(tengine.Context):
template_name: Optional[str] = None
def __init__(self, config, last_phase):
self.config = ev.config_dict(config)
self.config = config[ev.TOP_LEVEL_KEY]
self.container_config = self.config["container"]
# Operating system tag as written in the configuration file

View File

@@ -48,7 +48,8 @@ def translated_compiler_name(manifest_compiler_name):
def compiler_from_entry(entry):
compiler_name = translated_compiler_name(entry["name"])
paths = entry["executables"]
version = entry["version"]
# to instantiate a compiler class we may need a concrete version:
version = "={}".format(entry["version"])
arch = entry["arch"]
operating_system = arch["os"]
target = arch["target"]

View File

@@ -337,6 +337,7 @@
"""
from .environment import (
TOP_LEVEL_KEY,
Environment,
SpackEnvironmentError,
SpackEnvironmentViewError,
@@ -345,7 +346,6 @@
active_environment,
all_environment_names,
all_environments,
config_dict,
create,
create_in_dir,
deactivate,
@@ -369,6 +369,7 @@
)
__all__ = [
"TOP_LEVEL_KEY",
"Environment",
"SpackEnvironmentError",
"SpackEnvironmentViewError",
@@ -377,7 +378,6 @@
"active_environment",
"all_environment_names",
"all_environments",
"config_dict",
"create",
"create_in_dir",
"deactivate",

View File

@@ -53,6 +53,7 @@
import spack.version
from spack.filesystem_view import SimpleFilesystemView, inverse_view_func_parser, view_func_parser
from spack.installer import PackageInstaller
from spack.schema.env import TOP_LEVEL_KEY
from spack.spec import Spec
from spack.spec_list import InvalidSpecConstraintError, SpecList
from spack.util.path import substitute_path_variables
@@ -361,19 +362,6 @@ def ensure_env_root_path_exists():
fs.mkdirp(env_root_path())
def config_dict(yaml_data):
"""Get the configuration scope section out of an spack.yaml"""
# TODO (env:): Remove env: as a possible top level keyword in v0.21
key = spack.config.first_existing(yaml_data, spack.schema.env.keys)
if key == "env":
msg = (
"using 'env:' as a top-level attribute of a Spack environment is deprecated and "
"will be removed in Spack v0.21. Please use 'spack:' instead."
)
warnings.warn(msg)
return yaml_data[key]
def all_environment_names():
"""List the names of environments that currently exist."""
# just return empty if the env path does not exist. A read-only
@@ -821,8 +809,8 @@ def write_transaction(self):
def _construct_state_from_manifest(self):
"""Read manifest file and set up user specs."""
self.spec_lists = collections.OrderedDict()
for item in config_dict(self.manifest).get("definitions", []):
env_configuration = self.manifest[TOP_LEVEL_KEY]
for item in env_configuration.get("definitions", []):
entry = copy.deepcopy(item)
when = _eval_conditional(entry.pop("when", "True"))
assert len(entry) == 1
@@ -834,13 +822,13 @@ def _construct_state_from_manifest(self):
else:
self.spec_lists[name] = user_specs
spec_list = config_dict(self.manifest).get(user_speclist_name, [])
spec_list = env_configuration.get(user_speclist_name, [])
user_specs = SpecList(
user_speclist_name, [s for s in spec_list if s], self.spec_lists.copy()
)
self.spec_lists[user_speclist_name] = user_specs
enable_view = config_dict(self.manifest).get("view")
enable_view = env_configuration.get("view")
# enable_view can be boolean, string, or None
if enable_view is True or enable_view is None:
self.views = {default_view_name: ViewDescriptor(self.path, self.view_path_default)}
@@ -855,14 +843,11 @@ def _construct_state_from_manifest(self):
else:
self.views = {}
# Retrieve the current concretization strategy
configuration = config_dict(self.manifest)
# Retrieve unification scheme for the concretizer
self.unify = spack.config.get("concretizer:unify", False)
# Retrieve dev-build packages:
self.dev_specs = copy.deepcopy(configuration.get("develop", {}))
self.dev_specs = copy.deepcopy(env_configuration.get("develop", {}))
for name, entry in self.dev_specs.items():
# spec must include a concrete version
assert Spec(entry["spec"]).versions.concrete_range_as_version
@@ -982,7 +967,7 @@ def included_config_scopes(self):
# load config scopes added via 'include:', in reverse so that
# highest-precedence scopes are last.
includes = config_dict(self.manifest).get("include", [])
includes = self.manifest[TOP_LEVEL_KEY].get("include", [])
missing = []
for i, config_path in enumerate(reversed(includes)):
# allow paths to contain spack config/environment variables, etc.
@@ -1075,10 +1060,7 @@ def env_file_config_scope(self):
"""Get the configuration scope for the environment's manifest file."""
config_name = self.env_file_config_scope_name()
return spack.config.SingleFileScope(
config_name,
self.manifest_path,
spack.schema.env.schema,
[spack.config.first_existing(self.manifest, spack.schema.env.keys)],
config_name, self.manifest_path, spack.schema.env.schema, [TOP_LEVEL_KEY]
)
def config_scopes(self):
@@ -1221,28 +1203,27 @@ def remove(self, query_spec, list_name=user_speclist_name, force=False):
old_specs = set(self.user_specs)
new_specs = set()
for spec in matches:
if spec in list_to_change:
try:
list_to_change.remove(spec)
self.update_stale_references(list_name)
new_specs = set(self.user_specs)
except spack.spec_list.SpecListError:
# define new specs list
new_specs = set(self.user_specs)
msg = f"Spec '{spec}' is part of a spec matrix and "
msg += f"cannot be removed from list '{list_to_change}'."
if force:
msg += " It will be removed from the concrete specs."
# Mock new specs, so we can remove this spec from concrete spec lists
new_specs.remove(spec)
tty.warn(msg)
if spec not in list_to_change:
continue
try:
list_to_change.remove(spec)
self.update_stale_references(list_name)
new_specs = set(self.user_specs)
except spack.spec_list.SpecListError:
# define new specs list
new_specs = set(self.user_specs)
msg = f"Spec '{spec}' is part of a spec matrix and "
msg += f"cannot be removed from list '{list_to_change}'."
if force:
msg += " It will be removed from the concrete specs."
# Mock new specs, so we can remove this spec from concrete spec lists
new_specs.remove(spec)
tty.warn(msg)
else:
if list_name == user_speclist_name:
self.manifest.remove_user_spec(str(spec))
else:
if list_name == user_speclist_name:
for user_spec in matches:
self.manifest.remove_user_spec(str(user_spec))
else:
for user_spec in matches:
self.manifest.remove_definition(str(user_spec), list_name=list_name)
self.manifest.remove_definition(str(spec), list_name=list_name)
# If force, update stale concretized specs
for spec in old_specs - new_specs:
@@ -1352,6 +1333,10 @@ def concretize(self, force=False, tests=False):
self.concretized_order = []
self.specs_by_hash = {}
# Remove concrete specs that no longer correlate to a user spec
for spec in set(self.concretized_user_specs) - set(self.user_specs):
self.deconcretize(spec)
# Pick the right concretization strategy
if self.unify == "when_possible":
return self._concretize_together_where_possible(tests=tests)
@@ -1365,6 +1350,16 @@ def concretize(self, force=False, tests=False):
msg = "concretization strategy not implemented [{0}]"
raise SpackEnvironmentError(msg.format(self.unify))
def deconcretize(self, spec):
# spec has to be a root of the environment
index = self.concretized_user_specs.index(spec)
dag_hash = self.concretized_order.pop(index)
del self.concretized_user_specs[index]
# If this was the only user spec that concretized to this concrete spec, remove it
if dag_hash not in self.concretized_order:
del self.specs_by_hash[dag_hash]
def _get_specs_to_concretize(
self,
) -> Tuple[Set[spack.spec.Spec], Set[spack.spec.Spec], List[spack.spec.Spec]]:
@@ -2671,8 +2666,8 @@ def add_user_spec(self, user_spec: str) -> None:
Args:
user_spec: user spec to be appended
"""
config_dict(self.pristine_yaml_content).setdefault("specs", []).append(user_spec)
config_dict(self.yaml_content).setdefault("specs", []).append(user_spec)
self.pristine_configuration.setdefault("specs", []).append(user_spec)
self.configuration.setdefault("specs", []).append(user_spec)
self.changed = True
def remove_user_spec(self, user_spec: str) -> None:
@@ -2685,8 +2680,8 @@ def remove_user_spec(self, user_spec: str) -> None:
SpackEnvironmentError: when the user spec is not in the list
"""
try:
config_dict(self.pristine_yaml_content)["specs"].remove(user_spec)
config_dict(self.yaml_content)["specs"].remove(user_spec)
self.pristine_configuration["specs"].remove(user_spec)
self.configuration["specs"].remove(user_spec)
except ValueError as e:
msg = f"cannot remove {user_spec} from {self}, no such spec exists"
raise SpackEnvironmentError(msg) from e
@@ -2703,8 +2698,8 @@ def override_user_spec(self, user_spec: str, idx: int) -> None:
SpackEnvironmentError: when the user spec cannot be overridden
"""
try:
config_dict(self.pristine_yaml_content)["specs"][idx] = user_spec
config_dict(self.yaml_content)["specs"][idx] = user_spec
self.pristine_configuration["specs"][idx] = user_spec
self.configuration["specs"][idx] = user_spec
except ValueError as e:
msg = f"cannot override {user_spec} from {self}"
raise SpackEnvironmentError(msg) from e
@@ -2720,14 +2715,14 @@ def add_definition(self, user_spec: str, list_name: str) -> None:
Raises:
SpackEnvironmentError: is no valid definition exists already
"""
defs = config_dict(self.pristine_yaml_content).get("definitions", [])
defs = self.pristine_configuration.get("definitions", [])
msg = f"cannot add {user_spec} to the '{list_name}' definition, no valid list exists"
for idx, item in self._iterate_on_definitions(defs, list_name=list_name, err_msg=msg):
item[list_name].append(user_spec)
break
config_dict(self.yaml_content)["definitions"][idx][list_name].append(user_spec)
self.configuration["definitions"][idx][list_name].append(user_spec)
self.changed = True
def remove_definition(self, user_spec: str, list_name: str) -> None:
@@ -2741,7 +2736,7 @@ def remove_definition(self, user_spec: str, list_name: str) -> None:
SpackEnvironmentError: if the user spec cannot be removed from the list,
or the list does not exist
"""
defs = config_dict(self.pristine_yaml_content).get("definitions", [])
defs = self.pristine_configuration.get("definitions", [])
msg = (
f"cannot remove {user_spec} from the '{list_name}' definition, "
f"no valid list exists"
@@ -2754,7 +2749,7 @@ def remove_definition(self, user_spec: str, list_name: str) -> None:
except ValueError:
pass
config_dict(self.yaml_content)["definitions"][idx][list_name].remove(user_spec)
self.configuration["definitions"][idx][list_name].remove(user_spec)
self.changed = True
def override_definition(self, user_spec: str, *, override: str, list_name: str) -> None:
@@ -2769,7 +2764,7 @@ def override_definition(self, user_spec: str, *, override: str, list_name: str)
Raises:
SpackEnvironmentError: if the user spec cannot be overridden
"""
defs = config_dict(self.pristine_yaml_content).get("definitions", [])
defs = self.pristine_configuration.get("definitions", [])
msg = f"cannot override {user_spec} with {override} in the '{list_name}' definition"
for idx, item in self._iterate_on_definitions(defs, list_name=list_name, err_msg=msg):
@@ -2780,7 +2775,7 @@ def override_definition(self, user_spec: str, *, override: str, list_name: str)
except ValueError:
pass
config_dict(self.yaml_content)["definitions"][idx][list_name][sub_index] = override
self.configuration["definitions"][idx][list_name][sub_index] = override
self.changed = True
def _iterate_on_definitions(self, definitions, *, list_name, err_msg):
@@ -2812,24 +2807,24 @@ def set_default_view(self, view: Union[bool, str, pathlib.Path, Dict[str, str]])
True the default view is used for the environment, if False there's no view.
"""
if isinstance(view, dict):
config_dict(self.pristine_yaml_content)["view"][default_view_name].update(view)
config_dict(self.yaml_content)["view"][default_view_name].update(view)
self.pristine_configuration["view"][default_view_name].update(view)
self.configuration["view"][default_view_name].update(view)
self.changed = True
return
if not isinstance(view, bool):
view = str(view)
config_dict(self.pristine_yaml_content)["view"] = view
config_dict(self.yaml_content)["view"] = view
self.pristine_configuration["view"] = view
self.configuration["view"] = view
self.changed = True
def remove_default_view(self) -> None:
"""Removes the default view from the manifest file"""
view_data = config_dict(self.pristine_yaml_content).get("view")
view_data = self.pristine_configuration.get("view")
if isinstance(view_data, collections.abc.Mapping):
config_dict(self.pristine_yaml_content)["view"].pop(default_view_name)
config_dict(self.yaml_content)["view"].pop(default_view_name)
self.pristine_configuration["view"].pop(default_view_name)
self.configuration["view"].pop(default_view_name)
self.changed = True
return
@@ -2846,12 +2841,10 @@ def add_develop_spec(self, pkg_name: str, entry: Dict[str, str]) -> None:
if entry["path"] == pkg_name:
entry.pop("path")
config_dict(self.pristine_yaml_content).setdefault("develop", {}).setdefault(
pkg_name, {}
).update(entry)
config_dict(self.yaml_content).setdefault("develop", {}).setdefault(pkg_name, {}).update(
self.pristine_configuration.setdefault("develop", {}).setdefault(pkg_name, {}).update(
entry
)
self.configuration.setdefault("develop", {}).setdefault(pkg_name, {}).update(entry)
self.changed = True
def remove_develop_spec(self, pkg_name: str) -> None:
@@ -2864,11 +2857,11 @@ def remove_develop_spec(self, pkg_name: str) -> None:
SpackEnvironmentError: if there is nothing to remove
"""
try:
del config_dict(self.pristine_yaml_content)["develop"][pkg_name]
del self.pristine_configuration["develop"][pkg_name]
except KeyError as e:
msg = f"cannot remove '{pkg_name}' from develop specs in {self}, entry does not exist"
raise SpackEnvironmentError(msg) from e
del config_dict(self.yaml_content)["develop"][pkg_name]
del self.configuration["develop"][pkg_name]
self.changed = True
def absolutify_dev_paths(self, init_file_dir: Union[str, pathlib.Path]) -> None:
@@ -2879,11 +2872,11 @@ def absolutify_dev_paths(self, init_file_dir: Union[str, pathlib.Path]) -> None:
init_file_dir: directory with the "spack.yaml" used to initialize the environment.
"""
init_file_dir = pathlib.Path(init_file_dir).absolute()
for _, entry in config_dict(self.pristine_yaml_content).get("develop", {}).items():
for _, entry in self.pristine_configuration.get("develop", {}).items():
expanded_path = os.path.normpath(str(init_file_dir / entry["path"]))
entry["path"] = str(expanded_path)
for _, entry in config_dict(self.yaml_content).get("develop", {}).items():
for _, entry in self.configuration.get("develop", {}).items():
expanded_path = os.path.normpath(str(init_file_dir / entry["path"]))
entry["path"] = str(expanded_path)
self.changed = True
@@ -2897,6 +2890,16 @@ def flush(self) -> None:
_write_yaml(self.pristine_yaml_content, f)
self.changed = False
@property
def pristine_configuration(self):
"""Return the dictionaries in the pristine YAML, without the top level attribute"""
return self.pristine_yaml_content[TOP_LEVEL_KEY]
@property
def configuration(self):
"""Return the dictionaries in the YAML, without the top level attribute"""
return self.yaml_content[TOP_LEVEL_KEY]
def __len__(self):
return len(self.yaml_content)

View File

@@ -460,7 +460,8 @@ def write_tested_status(self):
elif self.counts[TestStatus.PASSED] > 0:
status = TestStatus.PASSED
_add_msg_to_file(self.tested_file, f"{status.value}")
with open(self.tested_file, "w") as f:
f.write(f"{status.value}\n")
@contextlib.contextmanager

View File

@@ -170,11 +170,9 @@ def merge_config_rules(configuration, spec):
Returns:
dict: actions to be taken on the spec passed as an argument
"""
# Construct a dictionary with the actions we need to perform on the spec passed as a parameter
spec_configuration = {}
# The keyword 'all' is always evaluated first, all the others are
# evaluated in order of appearance in the module file
spec_configuration.update(copy.deepcopy(configuration.get("all", {})))
spec_configuration = copy.deepcopy(configuration.get("all", {}))
for constraint, action in configuration.items():
if spec.satisfies(constraint):
if hasattr(constraint, "override") and constraint.override:
@@ -395,7 +393,7 @@ class BaseConfiguration(object):
querying easier. It needs to be sub-classed for specific module types.
"""
default_projections = {"all": "{name}-{version}-{compiler.name}-{compiler.version}"}
default_projections = {"all": "{name}/{version}-{compiler.name}-{compiler.version}"}
def __init__(self, spec, module_set_name, explicit=None):
# Module where type(self) is defined

View File

@@ -134,6 +134,7 @@ def filter_hierarchy_specs(self):
return configuration(self.name).get("filter_hierarchy_specs", {})
@property
@lang.memoized
def hierarchy_tokens(self):
"""Returns the list of tokens that are part of the modulefile
hierarchy. 'compiler' is always present.
@@ -158,6 +159,7 @@ def hierarchy_tokens(self):
return tokens
@property
@lang.memoized
def requires(self):
"""Returns a dictionary mapping all the requirements of this spec
to the actual provider. 'compiler' is always present among the
@@ -224,6 +226,7 @@ def available(self):
return available
@property
@lang.memoized
def missing(self):
"""Returns the list of tokens that are not available."""
return [x for x in self.hierarchy_tokens if x not in self.available]
@@ -317,6 +320,7 @@ def available_path_parts(self):
return parts
@property
@lang.memoized
def unlocked_paths(self):
"""Returns a dictionary mapping conditions to a list of unlocked
paths.
@@ -428,6 +432,7 @@ def missing(self):
return self.conf.missing
@tengine.context_property
@lang.memoized
def unlocked_paths(self):
"""Returns the list of paths that are unlocked unconditionally."""
layout = make_layout(self.spec, self.conf.name, self.conf.explicit)

View File

@@ -37,7 +37,9 @@
def slingshot_network():
return os.path.exists("/opt/cray/pe") and os.path.exists("/lib64/libcxi.so")
return os.path.exists("/opt/cray/pe") and (
os.path.exists("/lib64/libcxi.so") or os.path.exists("/usr/lib64/libcxi.so")
)
def _target_name_from_craype_target_name(name):

View File

@@ -6,7 +6,6 @@
import itertools
import os
import re
import shutil
from collections import OrderedDict
import macholib.mach_o
@@ -356,13 +355,7 @@ def _set_elf_rpaths(target, rpaths):
# Join the paths using ':' as a separator
rpaths_str = ":".join(rpaths)
# If we're relocating patchelf itself, make a copy and use it
bak_path = None
if target.endswith("/bin/patchelf"):
bak_path = target + ".bak"
shutil.copy(target, bak_path)
patchelf, output = executable.Executable(bak_path or _patchelf()), None
patchelf, output = executable.Executable(_patchelf()), None
try:
# TODO: revisit the use of --force-rpath as it might be conditional
# TODO: if we want to support setting RUNPATH from binary packages
@@ -371,9 +364,6 @@ def _set_elf_rpaths(target, rpaths):
except executable.ProcessError as e:
msg = "patchelf --force-rpath --set-rpath {0} failed with error {1}"
tty.warn(msg.format(target, e))
finally:
if bak_path and os.path.exists(bak_path):
os.remove(bak_path)
return output

View File

@@ -1239,7 +1239,7 @@ def get_pkg_class(self, pkg_name):
try:
module = importlib.import_module(fullname)
except ImportError:
raise UnknownPackageError(pkg_name)
raise UnknownPackageError(fullname)
except Exception as e:
msg = f"cannot load package '{pkg_name}' from the '{self.namespace}' repository: {e}"
raise RepoError(msg) from e

View File

@@ -209,7 +209,7 @@ def update(data):
# Warn if deprecated section is still in the environment
ci_env = ev.active_environment()
if ci_env:
env_config = ev.config_dict(ci_env.manifest)
env_config = ci_env.manifest[ev.TOP_LEVEL_KEY]
if "gitlab-ci" in env_config:
tty.die("Error: `gitlab-ci` section detected with `ci`, these are not compatible")

View File

@@ -15,8 +15,8 @@
import spack.schema.packages
import spack.schema.projections
#: legal first keys in the schema
keys = ("spack", "env")
#: Top level key in a manifest file
TOP_LEVEL_KEY = "spack"
spec_list_schema = {
"type": "array",
@@ -47,8 +47,8 @@
"title": "Spack environment file schema",
"type": "object",
"additionalProperties": False,
"patternProperties": {
"^env|spack$": {
"properties": {
"spack": {
"type": "object",
"default": {},
"additionalProperties": False,

View File

@@ -2836,12 +2836,13 @@ class InternalConcretizerError(spack.error.UnsatisfiableSpecError):
"""
def __init__(self, provided, conflicts):
indented = [" %s\n" % conflict for conflict in conflicts]
error_msg = "".join(indented)
msg = "Spack concretizer internal error. Please submit a bug report"
msg += "\n Please include the command, environment if applicable,"
msg += "\n and the following error message."
msg = "\n %s is unsatisfiable, errors are:\n%s" % (provided, error_msg)
msg = (
"Spack concretizer internal error. Please submit a bug report and include the "
"command, environment if applicable and the following error message."
f"\n {provided} is unsatisfiable, errors are:"
)
msg += "".join([f"\n {conflict}" for conflict in conflicts])
super(spack.error.UnsatisfiableSpecError, self).__init__(msg)

View File

@@ -4333,7 +4333,7 @@ def write_attribute(spec, attribute, color):
if callable(current):
raise SpecFormatStringError("Attempted to format callable object")
if not current:
if current is None:
# We're not printing anything
return

View File

@@ -4,7 +4,7 @@
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import itertools
import textwrap
from typing import List
from typing import List, Optional, Tuple
import llnl.util.lang
@@ -66,17 +66,17 @@ def to_dict(self):
return dict(d)
def make_environment(dirs=None):
"""Returns an configured environment for template rendering."""
@llnl.util.lang.memoized
def make_environment(dirs: Optional[Tuple[str, ...]] = None):
"""Returns a configured environment for template rendering."""
# Import at this scope to avoid slowing Spack startup down
import jinja2
if dirs is None:
# Default directories where to search for templates
builtins = spack.config.get("config:template_dirs", ["$spack/share/spack/templates"])
extensions = spack.extensions.get_template_dirs()
dirs = [canonicalize_path(d) for d in itertools.chain(builtins, extensions)]
# avoid importing this at the top level as it's used infrequently and
# slows down startup a bit.
import jinja2
dirs = tuple(canonicalize_path(d) for d in itertools.chain(builtins, extensions))
# Loader for the templates
loader = jinja2.FileSystemLoader(dirs)

View File

@@ -115,9 +115,6 @@ def default_config(tmpdir, config_directory, monkeypatch, install_mockery_mutabl
spack.config.config, old_config = cfg, spack.config.config
spack.config.config.set("repos", [spack.paths.mock_packages_path])
# This is essential, otherwise the cache will create weird side effects
# that will compromise subsequent tests if compilers.yaml is modified
monkeypatch.setattr(spack.compilers, "_cache_config_file", [])
njobs = spack.config.get("config:build_jobs")
if not njobs:
spack.config.set("config:build_jobs", 4, scope="user")

View File

@@ -3,6 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import pickle
import sys
import pytest
@@ -39,7 +40,10 @@ def test_dump(tmpdir):
with tmpdir.as_cwd():
build_env("--dump", _out_file, "zlib")
with open(_out_file) as f:
assert any(line.startswith("PATH=") for line in f.readlines())
if sys.platform == "win32":
assert any(line.startswith('set "PATH=') for line in f.readlines())
else:
assert any(line.startswith("PATH=") for line in f.readlines())
@pytest.mark.usefixtures("config", "mock_packages", "working_env")

View File

@@ -8,8 +8,6 @@
import pytest
import llnl.util.filesystem
import spack.compilers
import spack.main
import spack.version
@@ -18,124 +16,8 @@
@pytest.fixture
def mock_compiler_version():
return "4.5.3"
@pytest.fixture()
def mock_compiler_dir(tmpdir, mock_compiler_version):
"""Return a directory containing a fake, but detectable compiler."""
tmpdir.ensure("bin", dir=True)
bin_dir = tmpdir.join("bin")
gcc_path = bin_dir.join("gcc")
gxx_path = bin_dir.join("g++")
gfortran_path = bin_dir.join("gfortran")
gcc_path.write(
"""\
#!/bin/sh
for arg in "$@"; do
if [ "$arg" = -dumpversion ]; then
echo '%s'
fi
done
"""
% mock_compiler_version
)
# Create some mock compilers in the temporary directory
llnl.util.filesystem.set_executable(str(gcc_path))
gcc_path.copy(gxx_path, mode=True)
gcc_path.copy(gfortran_path, mode=True)
return str(tmpdir)
@pytest.mark.skipif(
sys.platform == "win32",
reason="Cannot execute bash \
script on Windows",
)
@pytest.mark.regression("11678,13138")
def test_compiler_find_without_paths(no_compilers_yaml, working_env, tmpdir):
with tmpdir.as_cwd():
with open("gcc", "w") as f:
f.write(
"""\
#!/bin/sh
echo "0.0.0"
"""
)
os.chmod("gcc", 0o700)
os.environ["PATH"] = str(tmpdir)
output = compiler("find", "--scope=site")
assert "gcc" in output
@pytest.mark.regression("17589")
def test_compiler_find_no_apple_gcc(no_compilers_yaml, working_env, tmpdir):
with tmpdir.as_cwd():
# make a script to emulate apple gcc's version args
with open("gcc", "w") as f:
f.write(
"""\
#!/bin/sh
if [ "$1" = "-dumpversion" ]; then
echo "4.2.1"
elif [ "$1" = "--version" ]; then
echo "Configured with: --prefix=/dummy"
echo "Apple clang version 11.0.0 (clang-1100.0.33.16)"
echo "Target: x86_64-apple-darwin18.7.0"
echo "Thread model: posix"
echo "InstalledDir: /dummy"
else
echo "clang: error: no input files"
fi
"""
)
os.chmod("gcc", 0o700)
os.environ["PATH"] = str(tmpdir)
output = compiler("find", "--scope=site")
assert "gcc" not in output
def test_compiler_remove(mutable_config, mock_packages):
assert spack.spec.CompilerSpec("gcc@=4.5.0") in spack.compilers.all_compiler_specs()
args = spack.util.pattern.Bunch(all=True, compiler_spec="gcc@4.5.0", add_paths=[], scope=None)
spack.cmd.compiler.compiler_remove(args)
assert spack.spec.CompilerSpec("gcc@=4.5.0") not in spack.compilers.all_compiler_specs()
@pytest.mark.skipif(
sys.platform == "win32",
reason="Cannot execute bash \
script on Windows",
)
def test_compiler_add(mutable_config, mock_packages, mock_compiler_dir, mock_compiler_version):
# Compilers available by default.
old_compilers = set(spack.compilers.all_compiler_specs())
args = spack.util.pattern.Bunch(
all=None, compiler_spec=None, add_paths=[mock_compiler_dir], scope=None
)
spack.cmd.compiler.compiler_find(args)
# Ensure new compiler is in there
new_compilers = set(spack.compilers.all_compiler_specs())
new_compiler = new_compilers - old_compilers
assert any(c.version == spack.version.Version(mock_compiler_version) for c in new_compiler)
@pytest.fixture
def clangdir(tmpdir):
"""Create a directory with some dummy compiler scripts in it.
def compilers_dir(mock_executable):
"""Create a directory with some mock compiler scripts in it.
Scripts are:
- clang
@@ -145,11 +27,9 @@ def clangdir(tmpdir):
- gfortran-8
"""
with tmpdir.as_cwd():
with open("clang", "w") as f:
f.write(
"""\
#!/bin/sh
clang_path = mock_executable(
"clang",
output="""
if [ "$1" = "--version" ]; then
echo "clang version 11.0.0 (clang-1100.0.33.16)"
echo "Target: x86_64-apple-darwin18.7.0"
@@ -159,12 +39,11 @@ def clangdir(tmpdir):
echo "clang: error: no input files"
exit 1
fi
"""
)
shutil.copy("clang", "clang++")
""",
)
shutil.copy(clang_path, clang_path.parent / "clang++")
gcc_script = """\
#!/bin/sh
gcc_script = """
if [ "$1" = "-dumpversion" ]; then
echo "8"
elif [ "$1" = "-dumpfullversion" ]; then
@@ -178,30 +57,111 @@ def clangdir(tmpdir):
exit 1
fi
"""
with open("gcc-8", "w") as f:
f.write(gcc_script.format("gcc", "gcc-8"))
with open("g++-8", "w") as f:
f.write(gcc_script.format("g++", "g++-8"))
with open("gfortran-8", "w") as f:
f.write(gcc_script.format("GNU Fortran", "gfortran-8"))
os.chmod("clang", 0o700)
os.chmod("clang++", 0o700)
os.chmod("gcc-8", 0o700)
os.chmod("g++-8", 0o700)
os.chmod("gfortran-8", 0o700)
mock_executable("gcc-8", output=gcc_script.format("gcc", "gcc-8"))
mock_executable("g++-8", output=gcc_script.format("g++", "g++-8"))
mock_executable("gfortran-8", output=gcc_script.format("GNU Fortran", "gfortran-8"))
yield tmpdir
return clang_path.parent
@pytest.mark.skipif(
sys.platform == "win32",
reason="Cannot execute bash \
script on Windows",
)
@pytest.mark.skipif(sys.platform == "win32", reason="Cannot execute bash script on Windows")
@pytest.mark.regression("11678,13138")
def test_compiler_find_without_paths(no_compilers_yaml, working_env, mock_executable):
"""Tests that 'spack compiler find' looks into PATH by default, if no specific path
is given.
"""
gcc_path = mock_executable("gcc", output='echo "0.0.0"')
os.environ["PATH"] = str(gcc_path.parent)
output = compiler("find", "--scope=site")
assert "gcc" in output
@pytest.mark.regression("17589")
def test_compiler_find_no_apple_gcc(no_compilers_yaml, working_env, mock_executable):
"""Tests that Spack won't mistake Apple's GCC as a "real" GCC, since it's really
Clang with a few tweaks.
"""
gcc_path = mock_executable(
"gcc",
output="""
if [ "$1" = "-dumpversion" ]; then
echo "4.2.1"
elif [ "$1" = "--version" ]; then
echo "Configured with: --prefix=/dummy"
echo "Apple clang version 11.0.0 (clang-1100.0.33.16)"
echo "Target: x86_64-apple-darwin18.7.0"
echo "Thread model: posix"
echo "InstalledDir: /dummy"
else
echo "clang: error: no input files"
fi
""",
)
os.environ["PATH"] = str(gcc_path.parent)
output = compiler("find", "--scope=site")
assert "gcc" not in output
@pytest.mark.regression("37996")
def test_compiler_remove(mutable_config, mock_packages):
"""Tests that we can remove a compiler from configuration."""
assert spack.spec.CompilerSpec("gcc@=4.5.0") in spack.compilers.all_compiler_specs()
args = spack.util.pattern.Bunch(all=True, compiler_spec="gcc@4.5.0", add_paths=[], scope=None)
spack.cmd.compiler.compiler_remove(args)
assert spack.spec.CompilerSpec("gcc@=4.5.0") not in spack.compilers.all_compiler_specs()
@pytest.mark.regression("37996")
def test_removing_compilers_from_multiple_scopes(mutable_config, mock_packages):
# Duplicate "site" scope into "user" scope
site_config = spack.config.get("compilers", scope="site")
spack.config.set("compilers", site_config, scope="user")
assert spack.spec.CompilerSpec("gcc@=4.5.0") in spack.compilers.all_compiler_specs()
args = spack.util.pattern.Bunch(all=True, compiler_spec="gcc@4.5.0", add_paths=[], scope=None)
spack.cmd.compiler.compiler_remove(args)
assert spack.spec.CompilerSpec("gcc@=4.5.0") not in spack.compilers.all_compiler_specs()
@pytest.mark.skipif(sys.platform == "win32", reason="Cannot execute bash script on Windows")
def test_compiler_add(mutable_config, mock_packages, mock_executable):
"""Tests that we can add a compiler to configuration."""
expected_version = "4.5.3"
gcc_path = mock_executable(
"gcc",
output=f"""\
for arg in "$@"; do
if [ "$arg" = -dumpversion ]; then
echo '{expected_version}'
fi
done
""",
)
bin_dir = gcc_path.parent
root_dir = bin_dir.parent
compilers_before_find = set(spack.compilers.all_compiler_specs())
args = spack.util.pattern.Bunch(
all=None, compiler_spec=None, add_paths=[str(root_dir)], scope=None
)
spack.cmd.compiler.compiler_find(args)
compilers_after_find = set(spack.compilers.all_compiler_specs())
compilers_added_by_find = compilers_after_find - compilers_before_find
assert len(compilers_added_by_find) == 1
new_compiler = compilers_added_by_find.pop()
assert new_compiler.version == spack.version.Version(expected_version)
@pytest.mark.skipif(sys.platform == "win32", reason="Cannot execute bash script on Windows")
@pytest.mark.regression("17590")
def test_compiler_find_mixed_suffixes(no_compilers_yaml, working_env, clangdir):
def test_compiler_find_mixed_suffixes(no_compilers_yaml, working_env, compilers_dir):
"""Ensure that we'll mix compilers with different suffixes when necessary."""
os.environ["PATH"] = str(clangdir)
os.environ["PATH"] = str(compilers_dir)
output = compiler("find", "--scope=site")
assert "clang@11.0.0" in output
@@ -211,39 +171,33 @@ def test_compiler_find_mixed_suffixes(no_compilers_yaml, working_env, clangdir):
clang = next(c["compiler"] for c in config if c["compiler"]["spec"] == "clang@=11.0.0")
gcc = next(c["compiler"] for c in config if c["compiler"]["spec"] == "gcc@=8.4.0")
gfortran_path = str(clangdir.join("gfortran-8"))
gfortran_path = str(compilers_dir / "gfortran-8")
assert clang["paths"] == {
"cc": str(clangdir.join("clang")),
"cxx": str(clangdir.join("clang++")),
"cc": str(compilers_dir / "clang"),
"cxx": str(compilers_dir / "clang++"),
# we only auto-detect mixed clang on macos
"f77": gfortran_path if sys.platform == "darwin" else None,
"fc": gfortran_path if sys.platform == "darwin" else None,
}
assert gcc["paths"] == {
"cc": str(clangdir.join("gcc-8")),
"cxx": str(clangdir.join("g++-8")),
"cc": str(compilers_dir / "gcc-8"),
"cxx": str(compilers_dir / "g++-8"),
"f77": gfortran_path,
"fc": gfortran_path,
}
@pytest.mark.skipif(
sys.platform == "win32",
reason="Cannot execute bash \
script on Windows",
)
@pytest.mark.skipif(sys.platform == "win32", reason="Cannot execute bash script on Windows")
@pytest.mark.regression("17590")
def test_compiler_find_prefer_no_suffix(no_compilers_yaml, working_env, clangdir):
def test_compiler_find_prefer_no_suffix(no_compilers_yaml, working_env, compilers_dir):
"""Ensure that we'll pick 'clang' over 'clang-gpu' when there is a choice."""
with clangdir.as_cwd():
shutil.copy("clang", "clang-gpu")
shutil.copy("clang++", "clang++-gpu")
os.chmod("clang-gpu", 0o700)
os.chmod("clang++-gpu", 0o700)
clang_path = compilers_dir / "clang"
shutil.copy(clang_path, clang_path.parent / "clang-gpu")
shutil.copy(clang_path, clang_path.parent / "clang++-gpu")
os.environ["PATH"] = str(clangdir)
os.environ["PATH"] = str(compilers_dir)
output = compiler("find", "--scope=site")
assert "clang@11.0.0" in output
@@ -252,46 +206,38 @@ def test_compiler_find_prefer_no_suffix(no_compilers_yaml, working_env, clangdir
config = spack.compilers.get_compiler_config("site", False)
clang = next(c["compiler"] for c in config if c["compiler"]["spec"] == "clang@=11.0.0")
assert clang["paths"]["cc"] == str(clangdir.join("clang"))
assert clang["paths"]["cxx"] == str(clangdir.join("clang++"))
assert clang["paths"]["cc"] == str(compilers_dir / "clang")
assert clang["paths"]["cxx"] == str(compilers_dir / "clang++")
@pytest.mark.skipif(
sys.platform == "win32",
reason="Cannot execute bash \
script on Windows",
)
def test_compiler_find_path_order(no_compilers_yaml, working_env, clangdir):
"""Ensure that we find compilers that come first in the PATH first"""
with clangdir.as_cwd():
os.mkdir("first_in_path")
shutil.copy("gcc-8", "first_in_path/gcc-8")
shutil.copy("g++-8", "first_in_path/g++-8")
shutil.copy("gfortran-8", "first_in_path/gfortran-8")
# the first_in_path folder should be searched first
os.environ["PATH"] = "{0}:{1}".format(str(clangdir.join("first_in_path")), str(clangdir))
@pytest.mark.skipif(sys.platform == "win32", reason="Cannot execute bash script on Windows")
def test_compiler_find_path_order(no_compilers_yaml, working_env, compilers_dir):
"""Ensure that we look for compilers in the same order as PATH, when there are duplicates"""
new_dir = compilers_dir / "first_in_path"
new_dir.mkdir()
for name in ("gcc-8", "g++-8", "gfortran-8"):
shutil.copy(compilers_dir / name, new_dir / name)
# Set PATH to have the new folder searched first
os.environ["PATH"] = "{}:{}".format(str(new_dir), str(compilers_dir))
compiler("find", "--scope=site")
config = spack.compilers.get_compiler_config("site", False)
gcc = next(c["compiler"] for c in config if c["compiler"]["spec"] == "gcc@=8.4.0")
assert gcc["paths"] == {
"cc": str(clangdir.join("first_in_path", "gcc-8")),
"cxx": str(clangdir.join("first_in_path", "g++-8")),
"f77": str(clangdir.join("first_in_path", "gfortran-8")),
"fc": str(clangdir.join("first_in_path", "gfortran-8")),
"cc": str(new_dir / "gcc-8"),
"cxx": str(new_dir / "g++-8"),
"f77": str(new_dir / "gfortran-8"),
"fc": str(new_dir / "gfortran-8"),
}
def test_compiler_list_empty(no_compilers_yaml, working_env, clangdir):
# Spack should not automatically search for compilers when listing them and none
# are available. And when stdout is not a tty like in tests, there should be no
# output and no error exit code.
os.environ["PATH"] = str(clangdir)
def test_compiler_list_empty(no_compilers_yaml, working_env, compilers_dir):
"""Spack should not automatically search for compilers when listing them and none are
available. And when stdout is not a tty like in tests, there should be no output and
no error exit code.
"""
os.environ["PATH"] = str(compilers_dir)
out = compiler("list")
assert not out
assert compiler.returncode == 0

View File

@@ -32,7 +32,7 @@ def check_develop(self, env, spec, path=None):
assert dev_specs_entry["spec"] == str(spec)
# check yaml representation
yaml = ev.config_dict(env.manifest)
yaml = env.manifest[ev.TOP_LEVEL_KEY]
assert spec.name in yaml["develop"]
yaml_entry = yaml["develop"][spec.name]
assert yaml_entry["spec"] == str(spec)

View File

@@ -390,6 +390,19 @@ def test_remove_after_concretize():
assert not any(s.name == "mpileaks" for s in env_specs)
def test_remove_before_concretize():
e = ev.create("test")
e.unify = True
e.add("mpileaks")
e.concretize()
e.remove("mpileaks")
e.concretize()
assert not list(e.concretized_specs())
def test_remove_command():
env("create", "test")
assert "test" in env("list")
@@ -2675,7 +2688,7 @@ def test_modules_relative_to_views(environment_from_manifest, install_mockery, m
spec = e.specs_by_hash[e.concretized_order[0]]
view_prefix = e.default_view.get_projection_for_spec(spec)
modules_glob = "%s/modules/**/*" % e.path
modules_glob = "%s/modules/**/*/*" % e.path
modules = glob.glob(modules_glob)
assert len(modules) == 1
module = modules[0]
@@ -2711,12 +2724,12 @@ def test_multiple_modules_post_env_hook(environment_from_manifest, install_mocke
spec = e.specs_by_hash[e.concretized_order[0]]
view_prefix = e.default_view.get_projection_for_spec(spec)
modules_glob = "%s/modules/**/*" % e.path
modules_glob = "%s/modules/**/*/*" % e.path
modules = glob.glob(modules_glob)
assert len(modules) == 1
module = modules[0]
full_modules_glob = "%s/full_modules/**/*" % e.path
full_modules_glob = "%s/full_modules/**/*/*" % e.path
full_modules = glob.glob(full_modules_glob)
assert len(full_modules) == 1
full_module = full_modules[0]

View File

@@ -44,9 +44,8 @@ def define_plat_exe(exe):
def test_find_external_single_package(mock_executable, executables_found, _platform_executables):
pkgs_to_check = [spack.repo.path.get_pkg_class("cmake")]
executables_found(
{mock_executable("cmake", output="echo cmake version 1.foo"): define_plat_exe("cmake")}
)
cmake_path = mock_executable("cmake", output="echo cmake version 1.foo")
executables_found({str(cmake_path): define_plat_exe("cmake")})
pkg_to_entries = spack.detection.by_executable(pkgs_to_check)
@@ -71,7 +70,7 @@ def test_find_external_two_instances_same_package(
"cmake", output="echo cmake version 3.17.2", subdir=("base2", "bin")
)
cmake_exe = define_plat_exe("cmake")
executables_found({cmake_path1: cmake_exe, cmake_path2: cmake_exe})
executables_found({str(cmake_path1): cmake_exe, str(cmake_path2): cmake_exe})
pkg_to_entries = spack.detection.by_executable(pkgs_to_check)
@@ -107,7 +106,7 @@ def test_get_executables(working_env, mock_executable):
cmake_path1 = mock_executable("cmake", output="echo cmake version 1.foo")
path_to_exe = spack.detection.executables_in_path([os.path.dirname(cmake_path1)])
cmake_exe = define_plat_exe("cmake")
assert path_to_exe[cmake_path1] == cmake_exe
assert path_to_exe[str(cmake_path1)] == cmake_exe
external = SpackCommand("external")
@@ -334,7 +333,7 @@ def test_packages_yaml_format(mock_executable, mutable_config, monkeypatch, _pla
assert "extra_attributes" in external_gcc
extra_attributes = external_gcc["extra_attributes"]
assert "prefix" not in extra_attributes
assert extra_attributes["compilers"]["c"] == gcc_exe
assert extra_attributes["compilers"]["c"] == str(gcc_exe)
def test_overriding_prefix(mock_executable, mutable_config, monkeypatch, _platform_executables):

View File

@@ -157,7 +157,7 @@ def _parse_types(string):
def test_spec_deptypes_nodes():
output = spec("--types", "--cover", "nodes", "dt-diamond")
output = spec("--types", "--cover", "nodes", "--no-install-status", "dt-diamond")
types = _parse_types(output)
assert types["dt-diamond"] == [" "]
@@ -167,7 +167,7 @@ def test_spec_deptypes_nodes():
def test_spec_deptypes_edges():
output = spec("--types", "--cover", "edges", "dt-diamond")
output = spec("--types", "--cover", "edges", "--no-install-status", "dt-diamond")
types = _parse_types(output)
assert types["dt-diamond"] == [" "]

View File

@@ -337,8 +337,6 @@ def test_compiler_flags_differ_identical_compilers(self):
# Get the compiler that matches the spec (
compiler = spack.compilers.compiler_for_spec("clang@=12.2.0", spec.architecture)
# Clear cache for compiler config since it has its own cache mechanism outside of config
spack.compilers._cache_config_file = []
# Configure spack to have two identical compilers with different flags
default_dict = spack.compilers._to_dict(compiler)
@@ -2137,7 +2135,7 @@ def test_compiler_with_custom_non_numeric_version(self, mock_executable):
{
"compiler": {
"spec": "gcc@foo",
"paths": {"cc": gcc_path, "cxx": gcc_path, "f77": None, "fc": None},
"paths": {"cc": str(gcc_path), "cxx": str(gcc_path), "f77": None, "fc": None},
"operating_system": "debian6",
"modules": [],
}

View File

@@ -1669,22 +1669,21 @@ def clear_directive_functions():
@pytest.fixture
def mock_executable(tmpdir):
def mock_executable(tmp_path):
"""Factory to create a mock executable in a temporary directory that
output a custom string when run.
"""
import jinja2
shebang = "#!/bin/sh\n" if sys.platform != "win32" else "@ECHO OFF"
def _factory(name, output, subdir=("bin",)):
f = tmpdir.ensure(*subdir, dir=True).join(name)
executable_dir = tmp_path.joinpath(*subdir)
executable_dir.mkdir(parents=True, exist_ok=True)
executable_path = executable_dir / name
if sys.platform == "win32":
f += ".bat"
t = jinja2.Template("{{ shebang }}{{ output }}\n")
f.write(t.render(shebang=shebang, output=output))
f.chmod(0o755)
return str(f)
executable_path = executable_dir / (name + ".bat")
executable_path.write_text(f"{ shebang }{ output }\n")
executable_path.chmod(0o755)
return executable_path
return _factory

View File

@@ -62,7 +62,7 @@ def source_file(tmpdir, is_relocatable):
src = tmpdir.join("relocatable.c")
shutil.copy(template_src, str(src))
else:
template_dirs = [os.path.join(spack.paths.test_path, "data", "templates")]
template_dirs = (os.path.join(spack.paths.test_path, "data", "templates"),)
env = spack.tengine.make_environment(template_dirs)
template = env.get_template("non_relocatable.c")
text = template.render({"prefix": spack.store.layout.root})
@@ -173,14 +173,6 @@ def test_ensure_binary_is_relocatable(source_file, is_relocatable):
assert relocatable == is_relocatable
@pytest.mark.requires_executables("patchelf", "strings", "file")
@skip_unless_linux
def test_patchelf_is_relocatable():
patchelf = os.path.realpath(spack.relocate._patchelf())
assert llnl.util.filesystem.is_exe(patchelf)
spack.relocate.ensure_binary_is_relocatable(patchelf)
@skip_unless_linux
def test_ensure_binary_is_relocatable_errors(tmpdir):
# The file passed in as argument must exist...
@@ -241,30 +233,6 @@ def test_normalize_relative_paths(start_path, relative_paths, expected):
assert normalized == expected
def test_set_elf_rpaths(mock_patchelf):
# Try to relocate a mock version of patchelf and check
# the call made to patchelf itself
patchelf = mock_patchelf("echo $@")
rpaths = ["/usr/lib", "/usr/lib64", "/opt/local/lib"]
output = spack.relocate._set_elf_rpaths(patchelf, rpaths)
# Assert that the arguments of the call to patchelf are as expected
assert "--force-rpath" in output
assert "--set-rpath " + ":".join(rpaths) in output
assert patchelf in output
@skip_unless_linux
def test_set_elf_rpaths_warning(mock_patchelf):
# Mock a failing patchelf command and ensure it warns users
patchelf = mock_patchelf("exit 1")
rpaths = ["/usr/lib", "/usr/lib64", "/opt/local/lib"]
# To avoid using capfd in order to check if the warning was triggered
# here we just check that output is not set
output = spack.relocate._set_elf_rpaths(patchelf, rpaths)
assert output is None
@pytest.mark.requires_executables("patchelf", "strings", "file", "gcc")
@skip_unless_linux
def test_relocate_text_bin(binary_with_rpaths, prefix_like):

View File

@@ -660,6 +660,7 @@ def test_spec_formatting(self, default_mock_concretization):
("{architecture.os}", "", "os", lambda spec: spec.architecture),
("{architecture.target}", "", "target", lambda spec: spec.architecture),
("{prefix}", "", "prefix", lambda spec: spec),
("{external}", "", "external", lambda spec: spec), # test we print "False"
]
hash_segments = [

View File

@@ -71,7 +71,7 @@ def test_template_retrieval(self):
"""Tests the template retrieval mechanism hooked into config files"""
# Check the directories are correct
template_dirs = spack.config.get("config:template_dirs")
template_dirs = [canonicalize_path(x) for x in template_dirs]
template_dirs = tuple([canonicalize_path(x) for x in template_dirs])
assert len(template_dirs) == 3
env = tengine.make_environment(template_dirs)

View File

@@ -441,6 +441,30 @@ def test_write_tested_status(
assert TestStatus(status) == expected
@pytest.mark.regression("37840")
def test_write_tested_status_no_repeats(
tmpdir, install_mockery_mutable_config, mock_fetch, mock_test_stage
):
"""Emulate re-running the same stand-alone tests a second time."""
s = spack.spec.Spec("trivial-smoke-test").concretized()
pkg = s.package
statuses = [TestStatus.PASSED, TestStatus.PASSED]
for i, status in enumerate(statuses):
pkg.tester.test_parts[f"test_{i}"] = status
pkg.tester.counts[status] += 1
pkg.tester.tested_file = tmpdir.join("test-log.txt")
pkg.tester.write_tested_status()
pkg.tester.write_tested_status()
# The test should NOT result in a ValueError: invalid literal for int()
# with base 10: '2\n2' (i.e., the results being appended instead of
# written to the file).
with open(pkg.tester.tested_file, "r") as f:
status = int(f.read().strip("\n"))
assert TestStatus(status) == TestStatus.PASSED
def test_check_special_outputs(tmpdir):
"""This test covers two related helper methods"""
contents = """CREATE TABLE packages (

View File

@@ -119,7 +119,10 @@ def test_dump_environment(prepare_environment_for_tests, tmpdir):
dumpfile_path = str(tmpdir.join("envdump.txt"))
envutil.dump_environment(dumpfile_path)
with open(dumpfile_path, "r") as dumpfile:
assert "TEST_ENV_VAR={0}; export TEST_ENV_VAR\n".format(test_paths) in list(dumpfile)
if sys.platform == "win32":
assert 'set "TEST_ENV_VAR={}"\n'.format(test_paths) in list(dumpfile)
else:
assert "TEST_ENV_VAR={0}; export TEST_ENV_VAR\n".format(test_paths) in list(dumpfile)
def test_reverse_environment_modifications(working_env):

View File

@@ -935,7 +935,7 @@ def test_inclusion_upperbound():
@pytest.mark.skipif(sys.platform == "win32", reason="Not supported on Windows (yet)")
def test_git_version_repo_attached_after_serialization(
mock_git_version_info, mock_packages, monkeypatch
mock_git_version_info, mock_packages, config, monkeypatch
):
"""Test that a GitVersion instance can be serialized and deserialized
without losing its repository reference.
@@ -954,7 +954,9 @@ def test_git_version_repo_attached_after_serialization(
@pytest.mark.skipif(sys.platform == "win32", reason="Not supported on Windows (yet)")
def test_resolved_git_version_is_shown_in_str(mock_git_version_info, mock_packages, monkeypatch):
def test_resolved_git_version_is_shown_in_str(
mock_git_version_info, mock_packages, config, monkeypatch
):
"""Test that a GitVersion from a commit without a user supplied version is printed
as <hash>=<version>, and not just <hash>."""
repo_path, _, commits = mock_git_version_info
@@ -968,7 +970,7 @@ def test_resolved_git_version_is_shown_in_str(mock_git_version_info, mock_packag
assert str(spec.version) == f"{commit}=1.0-git.1"
def test_unresolvable_git_versions_error(mock_packages):
def test_unresolvable_git_versions_error(config, mock_packages):
"""Test that VersionLookupError is raised when a git prop is not set on a package."""
with pytest.raises(VersionLookupError):
# The package exists, but does not have a git property set. When dereferencing

View File

@@ -171,7 +171,11 @@ def path_put_first(var_name: str, directories: List[Path]):
BASH_FUNCTION_FINDER = re.compile(r"BASH_FUNC_(.*?)\(\)")
def _env_var_to_source_line(var: str, val: str) -> str:
def _win_env_var_to_set_line(var: str, val: str) -> str:
return f'set "{var}={val}"'
def _nix_env_var_to_source_line(var: str, val: str) -> str:
if var.startswith("BASH_FUNC"):
source_line = "function {fname}{decl}; export -f {fname}".format(
fname=BASH_FUNCTION_FINDER.sub(r"\1", var), decl=val
@@ -181,6 +185,13 @@ def _env_var_to_source_line(var: str, val: str) -> str:
return source_line
def _env_var_to_source_line(var: str, val: str) -> str:
if sys.platform == "win32":
return _win_env_var_to_set_line(var, val)
else:
return _nix_env_var_to_source_line(var, val)
@system_path_filter(arg_slice=slice(1))
def dump_environment(path: Path, environment: Optional[MutableMapping[str, str]] = None):
"""Dump an environment dictionary to a source-able file.

View File

@@ -4,6 +4,11 @@ default:
image: { "name": "ghcr.io/spack/e4s-ubuntu-18.04:v2021-10-18", "entrypoint": [""] }
# CI Platform-Arch
.cray_zen4:
variables:
SPACK_TARGET_PLATFORM: "cray"
SPACK_TARGET_ARCH: "zen4"
.darwin_x86_64:
variables:
SPACK_TARGET_PLATFORM: "darwin"
@@ -128,6 +133,38 @@ default:
extends: [ ".base-job", ".generate-base" ]
tags: ["spack", "public", "medium", "x86_64"]
.darwin-generate-base:
stage: generate
script:
- export SPACK_DISABLE_LOCAL_CONFIG=1
- export SPACK_USER_CACHE_PATH=$(pwd)/_user_cache
- uname -a || true
- grep -E 'vendor|model name' /proc/cpuinfo 2>/dev/null | sort -u || head -n10 /proc/cpuinfo 2>/dev/null || true
- nproc || true
- . "./share/spack/setup-env.sh"
- spack --version
- cd share/spack/gitlab/cloud_pipelines/stacks/${SPACK_CI_STACK_NAME}
- spack env activate --without-view .
- spack -d ci generate --check-index-only
--buildcache-destination "${SPACK_BUILDCACHE_DESTINATION}"
--artifacts-root "${CI_PROJECT_DIR}/jobs_scratch_dir"
--output-file "${CI_PROJECT_DIR}/jobs_scratch_dir/cloud-ci-pipeline.yml"
after_script:
- cat /proc/loadavg || true
artifacts:
paths:
- "${CI_PROJECT_DIR}/jobs_scratch_dir"
interruptible: true
timeout: 60 minutes
retry:
max: 2
when:
- always
.darwin-generate:
extends: [ ".base-job", ".darwin-generate-base" ]
.generate-deprecated:
extends: [ ".base-job" ]
stage: generate
@@ -236,124 +273,6 @@ protected-publish:
# - artifacts: True
# job: my-super-cool-stack-generate
########################################
# E4S Mac Stack
#
# With no near-future plans to have
# protected aws runners running mac
# builds, it seems best to decouple
# them from the rest of the stacks for
# the time being. This way they can
# still run on UO runners and be signed
# using the previous approach.
########################################
# .e4s-mac:
# variables:
# SPACK_CI_STACK_NAME: e4s-mac
# allow_failure: True
# .mac-pr:
# only:
# - /^pr[\d]+_.*$/
# - /^github\/pr[\d]+_.*$/
# variables:
# SPACK_BUILDCACHE_DESTINATION: "s3://spack-binaries-prs/${CI_COMMIT_REF_NAME}"
# SPACK_PRUNE_UNTOUCHED: "True"
# .mac-protected:
# only:
# - /^develop$/
# - /^releases\/v.*/
# - /^v.*/
# - /^github\/develop$/
# variables:
# SPACK_BUILDCACHE_DESTINATION: "s3://spack-binaries/${CI_COMMIT_REF_NAME}/${SPACK_CI_STACK_NAME}"
# .mac-pr-build:
# extends: [ ".mac-pr", ".build" ]
# variables:
# AWS_ACCESS_KEY_ID: ${PR_MIRRORS_AWS_ACCESS_KEY_ID}
# AWS_SECRET_ACCESS_KEY: ${PR_MIRRORS_AWS_SECRET_ACCESS_KEY}
# .mac-protected-build:
# extends: [ ".mac-protected", ".build" ]
# variables:
# AWS_ACCESS_KEY_ID: ${PROTECTED_MIRRORS_AWS_ACCESS_KEY_ID}
# AWS_SECRET_ACCESS_KEY: ${PROTECTED_MIRRORS_AWS_SECRET_ACCESS_KEY}
# SPACK_SIGNING_KEY: ${PACKAGE_SIGNING_KEY}
# e4s-mac-pr-generate:
# extends: [".e4s-mac", ".mac-pr"]
# stage: generate
# script:
# - tmp="$(mktemp -d)"; export SPACK_USER_CONFIG_PATH="$tmp"; export SPACK_USER_CACHE_PATH="$tmp"
# - . "./share/spack/setup-env.sh"
# - spack --version
# - cd share/spack/gitlab/cloud_pipelines/stacks/${SPACK_CI_STACK_NAME}
# - spack env activate --without-view .
# - spack ci generate --check-index-only
# --buildcache-destination "${SPACK_BUILDCACHE_DESTINATION}"
# --artifacts-root "${CI_PROJECT_DIR}/jobs_scratch_dir"
# --output-file "${CI_PROJECT_DIR}/jobs_scratch_dir/cloud-ci-pipeline.yml"
# artifacts:
# paths:
# - "${CI_PROJECT_DIR}/jobs_scratch_dir"
# tags:
# - lambda
# interruptible: true
# retry:
# max: 2
# when:
# - runner_system_failure
# - stuck_or_timeout_failure
# timeout: 60 minutes
# e4s-mac-protected-generate:
# extends: [".e4s-mac", ".mac-protected"]
# stage: generate
# script:
# - tmp="$(mktemp -d)"; export SPACK_USER_CONFIG_PATH="$tmp"; export SPACK_USER_CACHE_PATH="$tmp"
# - . "./share/spack/setup-env.sh"
# - spack --version
# - cd share/spack/gitlab/cloud_pipelines/stacks/${SPACK_CI_STACK_NAME}
# - spack env activate --without-view .
# - spack ci generate --check-index-only
# --artifacts-root "${CI_PROJECT_DIR}/jobs_scratch_dir"
# --output-file "${CI_PROJECT_DIR}/jobs_scratch_dir/cloud-ci-pipeline.yml"
# artifacts:
# paths:
# - "${CI_PROJECT_DIR}/jobs_scratch_dir"
# tags:
# - omicron
# interruptible: true
# retry:
# max: 2
# when:
# - runner_system_failure
# - stuck_or_timeout_failure
# timeout: 60 minutes
# e4s-mac-pr-build:
# extends: [ ".e4s-mac", ".mac-pr-build" ]
# trigger:
# include:
# - artifact: jobs_scratch_dir/cloud-ci-pipeline.yml
# job: e4s-mac-pr-generate
# strategy: depend
# needs:
# - artifacts: True
# job: e4s-mac-pr-generate
# e4s-mac-protected-build:
# extends: [ ".e4s-mac", ".mac-protected-build" ]
# trigger:
# include:
# - artifact: jobs_scratch_dir/cloud-ci-pipeline.yml
# job: e4s-mac-protected-generate
# strategy: depend
# needs:
# - artifacts: True
# job: e4s-mac-protected-generate
########################################
# E4S pipeline
########################################
@@ -410,7 +329,7 @@ gpu-tests-build:
e4s-oneapi-generate:
extends: [ ".e4s-oneapi", ".generate"]
image: ecpe4s/ubuntu20.04-runner-x86_64-oneapi:2023-01-01
image: ecpe4s/ubuntu20.04-runner-x86_64-oneapi:2023.06.01
e4s-oneapi-build:
extends: [ ".e4s-oneapi", ".build" ]
@@ -762,6 +681,28 @@ ml-linux-x86_64-rocm-build:
- artifacts: True
job: ml-linux-x86_64-rocm-generate
########################################
# Machine Learning - Darwin aarch64 (MPS)
########################################
.ml-darwin-aarch64-mps:
variables:
SPACK_CI_STACK_NAME: ml-darwin-aarch64-mps
ml-darwin-aarch64-mps-generate:
tags: [ "macos-ventura", "apple-clang-14", "aarch64-macos" ]
extends: [ ".ml-darwin-aarch64-mps", ".darwin-generate"]
ml-darwin-aarch64-mps-build:
extends: [ ".ml-darwin-aarch64-mps", ".build" ]
trigger:
include:
- artifact: jobs_scratch_dir/cloud-ci-pipeline.yml
job: ml-darwin-aarch64-mps-generate
strategy: depend
needs:
- artifacts: True
job: ml-darwin-aarch64-mps-generate
########################################
# Deprecated CI testing
########################################
@@ -788,22 +729,22 @@ deprecated-ci-build:
########################################
.aws-pcluster-generate-image:
image: { "name": "ghcr.io/spack/pcluster-amazonlinux-2:latest", "entrypoint": [""] }
image: { "name": "ghcr.io/spack/pcluster-amazonlinux-2:v2023-05-25", "entrypoint": [""] }
.aws-pcluster-generate:
before_script:
# Setup postinstall Spack as upstream installation
# Use gcc from local container buildcache
- - . "./share/spack/setup-env.sh"
- . /etc/profile.d/modules.sh
- if [[ -f /bootstrap/spack/etc/spack/packages.yaml ]]; then cp /bootstrap/spack/etc/spack/packages.yaml ./etc/spack/; fi
- if [[ -f /bootstrap/spack/etc/spack/config.yaml ]]; then cp /bootstrap/spack/etc/spack/config.yaml ./etc/spack/; fi
- if [[ -f /bootstrap/spack/etc/spack/modules.xyaml ]]; then cp /bootstrap/spack/etc/spack/modules.yaml ./etc/spack/; fi
- if [[ -f /bootstrap/spack/etc/spack/mirrors.yaml ]]; then cp /bootstrap/spack/etc/spack/mirrors.yaml ./etc/spack/; fi
- if [[ -d /bootstrap/spack/opt/spack ]]; then spack config add "upstreams:postinstall:install_tree:/bootstrap/spack/opt/spack"; fi
- spack buildcache rebuild-index /bootstrap/local-cache/
- spack mirror add local-cache /bootstrap/local-cache
- spack gpg trust /bootstrap/public-key
- cd "${CI_PROJECT_DIR}" && curl -sOL https://raw.githubusercontent.com/spack/spack-configs/main/AWS/parallelcluster/postinstall.sh
- sed -i -e '/nohup/s/&$//' -e 's/nohup//' -e "s/spack arch -t/echo ${SPACK_TARGET_ARCH}/g" postinstall.sh
- sed -i -e "s/spack arch -t/echo ${SPACK_TARGET_ARCH}/g" postinstall.sh
- sed -i.bkp s/"spack install gcc"/"spack install --cache-only --reuse gcc"/ postinstall.sh
- diff postinstall.sh postinstall.sh.bkp || echo Done
- /bin/bash postinstall.sh -fg
- spack config --scope site add "packages:all:target:\"target=${SPACK_TARGET_ARCH}\""
- spack config --scope site add "packages:all:target:\"${SPACK_TARGET_ARCH}\""
after_script:
- - mv "${CI_PROJECT_DIR}/postinstall.sh" "${CI_PROJECT_DIR}/jobs_scratch_dir/"
@@ -882,3 +823,89 @@ aws-pcluster-build-neoverse_v1:
needs:
- artifacts: True
job: aws-pcluster-generate-neoverse_v1
# Cray definitions
.base-cray-job:
variables:
SPACK_BUILDCACHE_DESTINATION: "s3://spack-binaries-cray/${CI_COMMIT_REF_NAME}/${SPACK_CI_STACK_NAME}"
AWS_ACCESS_KEY_ID: ${CRAY_MIRRORS_AWS_ACCESS_KEY_ID}
AWS_SECRET_ACCESS_KEY: ${CRAY_MIRRORS_AWS_SECRET_ACCESS_KEY}
rules:
- if: $CI_COMMIT_REF_NAME == "develop"
# Pipelines on develop only rebuild what is missing from the mirror
when: always
variables:
SPACK_PIPELINE_TYPE: "spack_protected_branch"
- if: $CI_COMMIT_REF_NAME =~ /^pr[\d]+_.*$/
# Pipelines on PR branches rebuild only what's missing, and do extra pruning
when: always
variables:
SPACK_PIPELINE_TYPE: "spack_pull_request"
SPACK_BUILDCACHE_DESTINATION: "s3://spack-binaries-cray/prs/${CI_COMMIT_REF_NAME}/${SPACK_CI_STACK_NAME}"
SPACK_PRUNE_UNTOUCHED: "True"
SPACK_PRUNE_UNTOUCHED_DEPENDENT_DEPTH: "1"
.generate-cray:
tags: [ "cce@15.0.1", "cray-zen4", "public" ]
extends: [ ".base-cray-job" ]
stage: generate
script:
- echo $PATH
- module avail
- module list
- export SPACK_DISABLE_LOCAL_CONFIG=1
- export SPACK_USER_CACHE_PATH=$(pwd)/_user_cache
- uname -a || true
- grep -E 'vendor|model name' /proc/cpuinfo 2>/dev/null | sort -u || head -n10 /proc/cpuinfo 2>/dev/null || true
- nproc || true
- . "./share/spack/setup-env.sh"
- spack --version
- cd share/spack/gitlab/cloud_pipelines/stacks/${SPACK_CI_STACK_NAME}
- spack env activate --without-view .
- export SPACK_CI_CONFIG_ROOT="${SPACK_ROOT}/share/spack/gitlab/cloud_pipelines/configs"
- spack
--config-scope "${SPACK_CI_CONFIG_ROOT}"
--config-scope "${SPACK_CI_CONFIG_ROOT}/${SPACK_TARGET_PLATFORM}"
--config-scope "${SPACK_CI_CONFIG_ROOT}/${SPACK_TARGET_PLATFORM}/${SPACK_TARGET_ARCH}"
${CI_STACK_CONFIG_SCOPES}
ci generate --check-index-only
--buildcache-destination "${SPACK_BUILDCACHE_DESTINATION}"
--artifacts-root "${CI_PROJECT_DIR}/jobs_scratch_dir"
--output-file "${CI_PROJECT_DIR}/jobs_scratch_dir/cloud-ci-pipeline.yml"
after_script:
- cat /proc/loadavg || true
artifacts:
paths:
- "${CI_PROJECT_DIR}/jobs_scratch_dir"
interruptible: true
timeout: 60 minutes
retry:
max: 2
when:
- always
.build-cray:
extends: [ ".base-cray-job" ]
stage: build
#######################################
# E4S - Cray
#######################################
.e4s-cray:
extends: [ ".cray_zen4" ]
variables:
SPACK_CI_STACK_NAME: e4s-cray
e4s-cray-generate:
extends: [ ".generate-cray", ".e4s-cray" ]
e4s-cray-build:
extends: [ ".build-cray", ".e4s-cray" ]
trigger:
include:
- artifact: jobs_scratch_dir/cloud-ci-pipeline.yml
job: e4s-cray-generate
strategy: depend
needs:
- artifacts: True
job: e4s-cray-generate

View File

@@ -0,0 +1,295 @@
ci:
pipeline-gen:
- build-job-remove:
image: no-image
- build-job:
script+:
# AWS runners mount E4S public key (verification), UO runners mount public/private (signing/verification)
- if [[ -r /etc/protected-runner/e4s.gpg ]]; then spack gpg trust /etc/protected-runner/e4s.gpg; fi
# UO runners mount intermediate ci public key (verification), AWS runners mount public/private (signing/verification)
- if [[ -r /etc/protected-runner/intermediate_ci_signing_key.gpg ]]; then spack gpg trust /etc/protected-runner/intermediate_ci_signing_key.gpg; fi
- if [[ -r /etc/protected-runner/spack_public_key.gpg ]]; then spack gpg trust /etc/protected-runner/spack_public_key.gpg; fi
- match_behavior: first
submapping:
- match:
- hipblas
- llvm
- llvm-amdgpu
- pango
- paraview
- py-tensorflow
- py-torch
- qt
- rocblas
- visit
build-job:
tags: [ "spack", "huge" ]
variables:
CI_JOB_SIZE: huge
SPACK_BUILD_JOBS: "12"
- match:
- ascent
- atk
- axom
- cistem
- cmake
- ctffind
- cuda
- dealii
- dray
- dyninst
- ecp-data-vis-sdk
- gcc
- ginkgo
- hdf5
- hpx
- kokkos-kernels
- kokkos-nvcc-wrapper
- lbann
- magma
- mesa
- mfem
- mpich
- netlib-lapack
- nvhpc
- oce
- openblas
- openfoam
- openturns
- parallelio
- plumed
- precice
#- py-tensorflow
#- qt
- raja
- relion
#- rocblas
- rocfft
- rocsolver
- rocsparse
- rust
- slate
- strumpack
- sundials
- trilinos
- umpire
#- visit
- vtk
- vtk-h
- vtk-m
- warpx
- wrf
- wxwidgets
build-job:
tags: [ "spack", "large" ]
variables:
CI_JOB_SIZE: large
SPACK_BUILD_JOBS: "8"
- match:
- adios2
- amrex
- archer
- ascent
- autoconf-archive
- axom
- binutils
- blaspp
- blt
- boost
- butterflypack
- cabana
- caliper
- camp
- chai
- conduit
- curl
- datatransferkit
- double-conversion
- dray
- eigen
- faodel
- ffmpeg
- fftw
- fortrilinos
- gettext
- gperftools
- gptune
- hdf5
- heffte
- hpctoolkit
- hwloc
- hydrogen
- hypre
- kokkos
- lammps
- lapackpp
- legion
- libtool
- libxml2
- libzmq
- llvm-openmp-ompt
- mbedtls
- mfem
- mpich
- mvapich2
- nasm
- netlib-scalapack
- omega-h
- openblas
- openjpeg
- openmpi
- openpmd-api
- pagmo2
- papyrus
- parsec
- pdt
- pegtl
- petsc
- pumi
- py-beniget
- py-cinemasci
- pygmo
- py-ipython-genutils
- py-packaging
- py-petsc4py
- py-scipy
- py-statsmodels
- py-warlock
- py-warpx
- raja
- samrai
- slepc
- slurm
- sqlite
- strumpack
- sundials
- superlu-dist
- tasmanian
- tau
- upcxx
- vtk
- vtk-h
- vtk-m
- zfp
build-job:
tags: [ "spack", "medium" ]
variables:
CI_JOB_SIZE: "medium"
SPACK_BUILD_JOBS: "2"
- match:
- alsa-lib
- ant
- antlr
- argobots
- autoconf-archive
- automake
- berkeley-db
- bison
- blt
- bzip2
- camp
- cmake
- curl
- czmq
- darshan-util
- diffutils
- docbook-xml
- exmcutils
- expat
- findutils
- flit
- freetype
- gawk
- gdbm
- gettext
- glib
- gmake
- gotcha
- hpcviewer
- hwloc
- jansson
- json-c
- libbsd
- libedit
- libevent
- libfabric
- libffi
- libgcrypt
- libiconv
- libidn2
- libjpeg-turbo
- libmd
- libnrm
- libpciaccess
- libpng
- libsigsegv
- libsodium
- libunistring
- libunwind
- libxml2
- libyaml
- libzmq
- lua
- lua-luaposix
- lz4
- m4
- meson
- metis
- mpfr
- ncurses
- ninja
- numactl
- openblas
- openjdk
- openssh
- openssl
- papi
- parallel-netcdf
- pcre
- pcre2
- pdsh
- perl
- perl-data-dumper
- pkgconf
- py-alembic
- py-cffi
- py-cycler
- py-decorator
- py-idna
- py-jsonschema
- py-kiwisolver
- py-mistune
- py-pycparser
- py-setuptools
- py-setuptools-scm
- py-six
- py-testpath
- py-wheel
- qhull
- readline
- sed
- slurm
- snappy
- sqlite
- superlu
- swig
- tar
- tcl
- texinfo
- tut
- unzip
- util-linux-uuid
- util-macros
- xz
- yaml-cpp
- zfp
- zlib
- zstd
build-job:
tags: [ "spack", "small" ]
variables:
CI_JOB_SIZE: "small"
SPACK_BUILD_JOBS: "1"

View File

@@ -0,0 +1,9 @@
config:
concretizer: clingo
db_lock_timeout: 120
install_tree:
root: $spack/opt/spack
padded_length: 256
projections:
all: '{architecture}/{compiler.name}-{compiler.version}/{name}-{version}-{hash}'

View File

@@ -0,0 +1,4 @@
ci:
pipeline-gen:
- build-job:
tags: ["cce@15.0.1", "cray-zen4"]

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@@ -0,0 +1,27 @@
compilers:
- compiler:
spec: apple-clang@14.0.0
paths:
cc: /usr/bin/clang
cxx: /usr/bin/clang++
f77: /opt/homebrew/bin/gfortran
fc: /opt/homebrew/bin/gfortran
flags: {}
operating_system: ventura
target: aarch64
modules: []
environment: {}
extra_rpaths: []
- compiler:
spec: gcc@12.2.0
paths:
cc: /opt/homebrew/bin/gcc-12
cxx: /opt/homebrew/bin/g++-12
f77: /opt/homebrew/bin/gfortran-12
fc: /opt/homebrew/bin/gfortran-12
flags: {}
operating_system: ventura
target: aarch64
modules: []
environment: {}
extra_rpaths: []

View File

@@ -0,0 +1,3 @@
config:
install_tree:
root: $spack/opt/spack

View File

@@ -1,14 +0,0 @@
ci:
pipeline-gen:
- build-job:
script: |
- tmp="$(mktemp -d)"; export SPACK_USER_CONFIG_PATH="$tmp"; export SPACK_USER_CACHE_PATH="$tmp"
- . "./share/spack/setup-env.sh"
- spack --version
- spack arch
- cd ${SPACK_CONCRETE_ENV_DIR}
- spack env activate --without-view .
- spack config add "config:install_tree:projections:${SPACK_JOB_SPEC_PKG_NAME}:'morepadding/{architecture}/{compiler.name}-{compiler.version}/{name}-{version}-{hash}'"
- mkdir -p ${SPACK_ARTIFACTS_ROOT}/user_data
- spack --color=always --backtrace ci rebuild > >(tee ${SPACK_ARTIFACTS_ROOT}/user_data/pipeline_out.txt) 2> >(tee ${SPACK_ARTIFACTS_ROOT}/user_data/pipeline_err.txt >&2)
tags: ["lambda"]

View File

@@ -35,18 +35,18 @@ spack:
ci:
pipeline-gen:
- build-job:
image: { "name": "ghcr.io/spack/pcluster-amazonlinux-2:latest", "entrypoint": [""] }
image: { "name": "ghcr.io/spack/pcluster-amazonlinux-2:v2023-05-25", "entrypoint": [""] }
before_script:
- - . "./share/spack/setup-env.sh"
- . /etc/profile.d/modules.sh
- spack --version
- spack arch
# Setup postinstall Spack as upstream installation
- - if [[ -f /bootstrap/spack/etc/spack/packages.yaml ]]; then cp /bootstrap/spack/etc/spack/packages.yaml ./etc/spack/; fi
- if [[ -f /bootstrap/spack/etc/spack/config.yaml ]]; then cp /bootstrap/spack/etc/spack/config.yaml ./etc/spack/; fi
- if [[ -f /bootstrap/spack/etc/spack/modules.yaml ]]; then cp /bootstrap/spack/etc/spack/modules.yaml ./etc/spack/; fi
- if [[ -f /bootstrap/spack/etc/spack/mirrors.yaml ]]; then cp /bootstrap/spack/etc/spack/mirrors.yaml ./etc/spack/; fi
- if [[ -d /bootstrap/spack/opt/spack ]]; then spack config add "upstreams:postinstall:install_tree:/bootstrap/spack/opt/spack"; fi
# Use gcc from local container buildcache
- - spack buildcache rebuild-index /bootstrap/local-cache/
- sed -i.bkp s/"spack install gcc"/"spack install --cache-only --reuse gcc"/ /bootstrap/postinstall.sh
- spack mirror add local-cache /bootstrap/local-cache
- spack gpg trust /bootstrap/public-key
- diff /bootstrap/postinstall.sh /bootstrap/postinstall.sh.bkp || echo Done
- - /bin/bash "${SPACK_ARTIFACTS_ROOT}/postinstall.sh" -fg
- spack config --scope site add "packages:all:target:\"target=${SPACK_TARGET_ARCH}\""
- signing-job:

View File

@@ -16,7 +16,7 @@ spack:
- openfoam
- palace
# - py-devito
- quantum-espresso
# - quantum-espresso
# - wrf
- optimized_libs:
@@ -36,19 +36,19 @@ spack:
ci:
pipeline-gen:
- build-job:
image: { "name": "ghcr.io/spack/pcluster-amazonlinux-2:latest", "entrypoint": [""] }
image: { "name": "ghcr.io/spack/pcluster-amazonlinux-2:v2023-05-25", "entrypoint": [""] }
tags: ["aarch64"]
before_script:
- - . "./share/spack/setup-env.sh"
- . /etc/profile.d/modules.sh
- spack --version
- spack arch
# Setup postinstall Spack as upstream installation
- - if [[ -f /bootstrap/spack/etc/spack/packages.yaml ]]; then cp /bootstrap/spack/etc/spack/packages.yaml ./etc/spack/; fi
- if [[ -f /bootstrap/spack/etc/spack/config.yaml ]]; then cp /bootstrap/spack/etc/spack/config.yaml ./etc/spack/; fi
- if [[ -f /bootstrap/spack/etc/spack/modules.yaml ]]; then cp /bootstrap/spack/etc/spack/modules.yaml ./etc/spack/; fi
- if [[ -f /bootstrap/spack/etc/spack/mirrors.yaml ]]; then cp /bootstrap/spack/etc/spack/mirrors.yaml ./etc/spack/; fi
- if [[ -d /bootstrap/spack/opt/spack ]]; then spack config add "upstreams:postinstall:install_tree:/bootstrap/spack/opt/spack"; fi
# Use gcc from local container buildcache
- - spack buildcache rebuild-index /bootstrap/local-cache/
- sed -i.bkp s/"spack install gcc"/"spack install --cache-only --reuse gcc"/ /bootstrap/postinstall.sh
- spack mirror add local-cache /bootstrap/local-cache
- spack gpg trust /bootstrap/public-key
- diff /bootstrap/postinstall.sh /bootstrap/postinstall.sh.bkp || echo Done
- - /bin/bash "${SPACK_ARTIFACTS_ROOT}/postinstall.sh" -fg
- spack config --scope site add "packages:all:target:\"target=${SPACK_TARGET_ARCH}\""
- signing-job:

View File

@@ -16,7 +16,7 @@ spack:
- openfoam
- palace
# - py-devito
- quantum-espresso
# - quantum-espresso
# - wrf
- optimized_libs:
@@ -36,19 +36,19 @@ spack:
ci:
pipeline-gen:
- build-job:
image: { "name": "ghcr.io/spack/pcluster-amazonlinux-2:latest", "entrypoint": [""] }
image: { "name": "ghcr.io/spack/pcluster-amazonlinux-2:v2023-05-25", "entrypoint": [""] }
tags: ["aarch64"]
before_script:
- - . "./share/spack/setup-env.sh"
- . /etc/profile.d/modules.sh
- spack --version
- spack arch
# Setup postinstall Spack as upstream installation
- - if [[ -f /bootstrap/spack/etc/spack/packages.yaml ]]; then cp /bootstrap/spack/etc/spack/packages.yaml ./etc/spack/; fi
- if [[ -f /bootstrap/spack/etc/spack/config.yaml ]]; then cp /bootstrap/spack/etc/spack/config.yaml ./etc/spack/; fi
- if [[ -f /bootstrap/spack/etc/spack/modules.yaml ]]; then cp /bootstrap/spack/etc/spack/modules.yaml ./etc/spack/; fi
- if [[ -f /bootstrap/spack/etc/spack/mirrors.yaml ]]; then cp /bootstrap/spack/etc/spack/mirrors.yaml ./etc/spack/; fi
- if [[ -d /bootstrap/spack/opt/spack ]]; then spack config add "upstreams:postinstall:install_tree:/bootstrap/spack/opt/spack"; fi
# Use gcc from local container buildcache
- - spack buildcache rebuild-index /bootstrap/local-cache/
- sed -i.bkp s/"spack install gcc"/"spack install --cache-only --reuse gcc"/ /bootstrap/postinstall.sh
- spack mirror add local-cache /bootstrap/local-cache
- spack gpg trust /bootstrap/public-key
- diff /bootstrap/postinstall.sh /bootstrap/postinstall.sh.bkp || echo Done
- - /bin/bash "${SPACK_ARTIFACTS_ROOT}/postinstall.sh" -fg
- spack config --scope site add "packages:all:target:\"target=${SPACK_TARGET_ARCH}\""
- signing-job:

View File

@@ -35,18 +35,18 @@ spack:
ci:
pipeline-gen:
- build-job:
image: { "name": "ghcr.io/spack/pcluster-amazonlinux-2:latest", "entrypoint": [""] }
image: { "name": "ghcr.io/spack/pcluster-amazonlinux-2:v2023-05-25", "entrypoint": [""] }
before_script:
- - . "./share/spack/setup-env.sh"
- . /etc/profile.d/modules.sh
- spack --version
- spack arch
# Setup postinstall Spack as upstream installation
- - if [[ -f /bootstrap/spack/etc/spack/packages.yaml ]]; then cp /bootstrap/spack/etc/spack/packages.yaml ./etc/spack/; fi
- if [[ -f /bootstrap/spack/etc/spack/config.yaml ]]; then cp /bootstrap/spack/etc/spack/config.yaml ./etc/spack/; fi
- if [[ -f /bootstrap/spack/etc/spack/modules.yaml ]]; then cp /bootstrap/spack/etc/spack/modules.yaml ./etc/spack/; fi
- if [[ -f /bootstrap/spack/etc/spack/mirrors.yaml ]]; then cp /bootstrap/spack/etc/spack/mirrors.yaml ./etc/spack/; fi
- if [[ -d /bootstrap/spack/opt/spack ]]; then spack config add "upstreams:postinstall:install_tree:/bootstrap/spack/opt/spack"; fi
# Use gcc from local container buildcache
- - spack buildcache rebuild-index /bootstrap/local-cache/
- sed -i.bkp s/"spack install gcc"/"spack install --cache-only --reuse gcc"/ /bootstrap/postinstall.sh
- spack mirror add local-cache /bootstrap/local-cache
- spack gpg trust /bootstrap/public-key
- diff /bootstrap/postinstall.sh /bootstrap/postinstall.sh.bkp || echo Done
- - /bin/bash "${SPACK_ARTIFACTS_ROOT}/postinstall.sh" -fg
- spack config --scope site add "packages:all:target:\"target=${SPACK_TARGET_ARCH}\""
- signing-job:

View File

@@ -14,7 +14,7 @@ spack:
llvm:
require: "@14:"
# Minimize LLVM
variants: ~lldb~lld~internal_unwind~polly~compiler-rt~gold
variants: "~lldb~lld~polly~gold libunwind=none compiler-rt=none"
all:
require: target=x86_64_v3

View File

@@ -0,0 +1,102 @@
spack:
view: false
concretizer:
reuse: false
unify: false
compilers:
- compiler:
spec: cce@15.0.1
paths:
cc: cc
cxx: CC
f77: ftn
fc: ftn
flags: {}
operating_system: rhel8
target: any
modules:
- PrgEnv-cray/8.3.3
- cce/15.0.1
environment:
set:
MACHTYPE: x86_64
- compiler:
spec: gcc@11.2.0
paths:
cc: gcc
cxx: g++
f77: gfortran
fc: gfortran
flags: {}
operating_system: rhel8
target: any
modules:
- PrgEnv-gnu
- gcc/11.2.0
environment: {}
packages:
all:
require: '%cce@15.0.1'
compiler: [cce@15.0.1]
providers:
blas: [cray-libsci]
lapack: [cray-libsci]
mpi: [cray-mpich]
tbb: [intel-tbb]
scalapack: [netlib-scalapack]
target: [zen4]
variants: +mpi
binutils:
variants: +ld +gold +headers +libiberty ~nls
hdf5:
variants: +fortran +hl +shared
libunwind:
variants: +pic +xz
ncurses:
require: '@6.3 +termlib'
openblas:
require: '@0.3.20'
variants: threads=openmp
python:
require: '@3.7.15'
xz:
variants: +pic
elfutils:
variants: +bzip2 ~nls +xz
require: '%gcc'
# EXTERNALS
cray-mpich:
buildable: false
externals:
- spec: cray-mpich@8.1.25 %cce@15.0.1
prefix: /opt/cray/pe/mpich/8.1.25/ofi/cray/10.0
modules:
- cray-mpich/8.1.25
cray-libsci:
buildable: false
externals:
- spec: cray-libsci@23.02.1.1 %cce@15.0.1
prefix: /opt/cray/pe/libsci/23.02.1.1/CRAY/9.0/x86_64/
modules:
- cray-libsci/23.02.1.1
specs:
- butterflypack
- hypre
- kokkos
- kokkos-kernels
- petsc
- raja
- slepc
- superlu-dist
- tau
mirrors: { "mirror": "s3://spack-binaries-cray/develop/e4s-cray" }
cdash:
build-group: E4S Cray

View File

@@ -1,40 +0,0 @@
spack:
view: false
packages:
all:
compiler: [apple-clang@13.1.6]
target: [m1]
definitions:
- easy_specs:
- berkeley-db
- ncurses
- gcc
- py-jupyterlab
- py-scipy
- py-matplotlib
- py-pandas
- arch:
- '%apple-clang@13.1.6 target=m1'
specs:
- matrix:
- - $easy_specs
- - $arch
mirrors: { "mirror": "s3://spack-binaries/develop/e4s-mac" }
ci:
pipeline-gen:
- cleanup-job:
before_script: |
- export SPACK_USER_CACHE_PATH=$(pwd)/.spack-user-cache
- export SPACK_USER_CONFIG_PATH=$(pwd)/.spack-user-config
- . "./share/spack/setup-env.sh"
- spack --version
tags: [lambda]
cdash:
build-group: E4S Mac

View File

@@ -1,35 +1,87 @@
spack:
view: false
concretizer:
reuse: false
unify: false
packages:
all:
require: '%oneapi'
providers:
blas: [openblas]
mpi: [mpich]
tbb: [intel-tbb]
target: [x86_64]
variants: +mpi
elfutils:
variants: +bzip2 ~nls +xz
libfabric:
variants: fabrics=sockets,tcp,udp,rxm
libunwind:
variants: +pic +xz
ncurses:
variants: +termlib
openblas:
variants: threads=openmp
trilinos:
variants: +amesos +amesos2 +anasazi +aztec +belos +boost +epetra +epetraext
+ifpack +ifpack2 +intrepid +intrepid2 +isorropia +kokkos +ml +minitensor +muelu
+nox +piro +phalanx +rol +rythmos +sacado +stk +shards +shylu +stokhos +stratimikos
+teko +tempus +tpetra +trilinoscouplings +zoltan +zoltan2 +superlu-dist gotype=long_long
xz:
variants: +pic
mesa:
version: [21.3.8]
hdf5:
require: "%gcc"
variants: +fortran +hl +shared
mpi:
require: mpich
mpich:
require: '@4.1.1 ~wrapperrpath ~hwloc'
python:
require: '@3.7.15'
py-cryptography:
require: '@38.0.1'
unzip:
require: '%gcc'
binutils:
require: '%gcc'
variants: +ld +gold +headers +libiberty ~nls
llvm:
require: '%gcc'
ruby:
require: '%gcc'
rust:
require: '%gcc'
krb5:
require: '%gcc'
papi:
require: '%gcc'
openssh:
require: '%gcc'
bison:
require: '%gcc'
libffi:
require: "@3.4.4"
dyninst:
require: "%gcc"
compilers:
- compiler:
spec: dpcpp@2023.0.0
spec: oneapi@2023.1.0
paths:
cc: /opt/intel/oneapi/compiler/2023.0.0/linux/bin/icx
cxx: /opt/intel/oneapi/compiler/2023.0.0/linux/bin/dpcpp
f77: /opt/intel/oneapi/compiler/2023.0.0/linux/bin/ifx
fc: /opt/intel/oneapi/compiler/2023.0.0/linux/bin/ifx
cc: /opt/intel/oneapi/compiler/2023.1.0/linux/bin/icx
cxx: /opt/intel/oneapi/compiler/2023.1.0/linux/bin/icpx
f77: /opt/intel/oneapi/compiler/2023.1.0/linux/bin/ifx
fc: /opt/intel/oneapi/compiler/2023.1.0/linux/bin/ifx
flags: {}
operating_system: ubuntu20.04
target: x86_64
modules: [compiler]
environment:
prepend_path:
LD_LIBRARY_PATH: /opt/intel/oneapi/compiler/2023.0.0/linux/compiler/lib/intel64_lin
extra_rpaths: []
- compiler:
spec: oneapi@2023.0.0
paths:
cc: /opt/intel/oneapi/compiler/2023.0.0/linux/bin/icx
cxx: /opt/intel/oneapi/compiler/2023.0.0/linux/bin/icpx
f77: /opt/intel/oneapi/compiler/2023.0.0/linux/bin/ifx
fc: /opt/intel/oneapi/compiler/2023.0.0/linux/bin/ifx
flags: {}
operating_system: ubuntu20.04
target: x86_64
modules: [compiler]
environment:
prepend_path:
LD_LIBRARY_PATH: /opt/intel/oneapi/compiler/2023.0.0/linux/compiler/lib/intel64_lin
modules: []
environment: {}
extra_rpaths: []
- compiler:
spec: gcc@11.1.0
@@ -45,108 +97,53 @@ spack:
environment: {}
extra_rpaths: []
packages:
all:
require: '%oneapi'
providers:
blas: [openblas]
mpi: [mpich]
target: [x86_64]
variants: +mpi
elfutils:
variants: +bzip2 ~nls +xz
hdf5:
variants: +fortran +hl +shared
libfabric:
variants: fabrics=sockets,tcp,udp,rxm
libunwind:
variants: +pic +xz
mpich:
variants: ~wrapperrpath
ncurses:
variants: +termlib
openblas:
variants: threads=openmp
python:
version: [3.8.13]
trilinos:
variants: +amesos +amesos2 +anasazi +aztec +belos +boost +epetra +epetraext
+ifpack +ifpack2 +intrepid +intrepid2 +isorropia +kokkos +ml +minitensor +muelu
+nox +piro +phalanx +rol +rythmos +sacado +stk +shards +shylu +stokhos +stratimikos
+teko +tempus +tpetra +trilinoscouplings +zoltan +zoltan2 +superlu-dist gotype=long_long
vtk-m:
require: ~openmp
xz:
variants: +pic
mesa:
version: [21.3.8]
binutils:
require: '%gcc'
variants: +ld +gold +headers +libiberty ~nls
bison:
require: '%gcc'
krb5:
require: '%gcc'
llvm:
require: '%gcc'
m4:
require: '%gcc'
openssh:
require: '%gcc'
papi:
require: '%gcc'
py-scipy:
require: '%gcc'
ruby:
require: '%gcc'
rust:
require: '%gcc'
unzip:
require: '%gcc'
specs:
# CPU
- adios
- adios2
- alquimia
- aml
- amrex
- arborx
- archer
- argobots
- ascent
- amrex
- axom
- bolt
- boost
- bricks ~cuda
- butterflypack
- cabana
- caliper
- chai ~benchmarks ~tests
- charliecloud
- conduit
- darshan-runtime
- darshan-util
- datatransferkit
- faodel
- exaworks
- flecsi
- flit
- flux-core
- fortrilinos
- gasnet
- globalarrays
- gmp
- gotcha
- hdf5 +fortran +hl +shared
- h5bench
- hdf5-vol-async
- hdf5-vol-log
- heffte +fftw
- hpx networking=mpi
- hypre
- kokkos-kernels +openmp
- kokkos +openmp
- kokkos-kernels +openmp
- lammps
- lbann
- legion
- libnrm
- libnrm
- libquo
- libunwind
- loki
- mercury
- metall
- mfem
- mgard +serial +openmp +timing +unstructured ~cuda
- mpark-variant
- mpifileutils ~xattr
- nccmp
@@ -157,17 +154,19 @@ spack:
- openpmd-api
- papi
- papyrus
- parallel-netcdf
- parsec ~cuda
- pdt
- petsc
- phist
- plasma
- plumed
- precice
- pumi
- py-h5py
- py-libensemble
- py-petsc4py
- qthreads scheduler=distrib
- quantum-espresso
- raja
- rempi
- slate ~cuda
@@ -175,104 +174,80 @@ spack:
- stc
- strumpack ~slate
- sundials
- superlu-dist
- superlu
- swig
- sz
- superlu-dist
- swig@4.0.2-fortran
- sz3
- tasmanian
- trilinos@13.0.1 +amesos +amesos2 +anasazi +aztec +belos +boost +epetra +epetraext
+ifpack +ifpack2 +intrepid +intrepid2 +isorropia +kokkos +ml +minitensor +muelu
+nox +piro +phalanx +rol +rythmos +sacado +stk +shards +shylu +stokhos +stratimikos
+teko +tempus +tpetra +trilinoscouplings +zoltan +zoltan2 +superlu-dist gotype=long_long
- trilinos@13.0.1 +amesos +amesos2 +anasazi +aztec +belos +boost +epetra +epetraext +ifpack +ifpack2 +intrepid +intrepid2 +isorropia +kokkos +ml +minitensor +muelu +nox +piro +phalanx +rol +rythmos +sacado +stk +shards +shylu +stokhos +stratimikos +teko +tempus +tpetra +trilinoscouplings +zoltan +zoltan2 +superlu-dist gotype=long_long
- turbine
- umap
- umpire
- unifyfs
- upcxx
- veloc
- vtk-m ~openmp # can't build +openmp w/ %oneapi: https://github.com/spack/spack/issues/31830
- variorum
- wannier90
- zfp
# INCLUDED IN ECP DAV CPU
# - adios2
# - ascent
# - darshan-runtime
# - darshan-util
# - faodel
# - hdf5
# - libcatalyst
# - parallel-netcdf
# - paraview
# - py-cinemasci
# - sz
# - unifyfs
# - veloc
# - visit
# - vtk-m ~openmp # https://github.com/spack/spack/issues/31830
# - zfp
# --
# - alquimia # pflotran: pflotran/hdf5_aux.F90(5): error #7013: This module file was not generated by any release of this compiler. [HDF5]
# - dealii # intel-tbb: icpx: error: unknown argument: '-flifetime-dse=1'
# - ecp-data-vis-sdk ~cuda ~rocm +adios2 +ascent +cinema +darshan +faodel +hdf5 +paraview +pnetcdf +sz +unifyfs +veloc +visit +vtkm +zfp # sz: hdf5-filter/H5Z-SZ/src/H5Z_SZ.c:24:9: error: call to undeclared function 'gettimeofday'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
# - geopm # geopm: In file included from src/ProfileTable.cpp:34: ./src/ProfileTable.hpp:79:45: error: no type named 'string' in namespace 'std'
# - ginkgo # ginkgo: icpx: error: clang frontend command failed with exit code 139 (use -v to see invocation)
# - gptune ~mpispawn # py-scipy: for_main.c:(.text+0x19): undefined reference to `MAIN__'
# - hdf5-vol-cache # /H5VLcache_ext.c:580:9: error: incompatible function pointer types initializing 'herr_t (*)(const void *, uint64_t *)' (aka 'int (*)(const void *, unsigned long *)') with an expression of type 'herr_t (const void *, unsigned int *)' (aka 'int (const void *, unsigned int *)') [-Wincompatible-function-pointer-types]
# - hpctoolkit # intel-tbb: icpx: error: unknown argument: '-flifetime-dse=1'
# - libpressio +bitgrooming +bzip2 ~cuda ~cusz +fpzip +hdf5 +libdistributed +lua +openmp +python +sz +sz3 +unix +zfp # py-numcodecs: c-blosc/internal-complibs/zlib-1.2.8/gzread.c:30:15: error: call to undeclared function 'read'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
# - nrm # py-scipy: for_main.c:(.text+0x19): undefined reference to `MAIN__'
# - openfoam # adios2: patch failed
# - pruners-ninja # pruners-ninja: ninja_test_pingpong.c:79:5: error: call to undeclared library function 'memset' with type 'void *(void *, int, unsigned long)'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
# - py-jupyterhub # py-ruamel-yaml-clib: setuptools/dist.py:287: SetuptoolsDeprecationWarning: The namespace_packages parameter is deprecated, consider using implicit namespaces instead (PEP 420). See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
# - py-warpx ^warpx dims=2 # py-scipy: for_main.c:(.text+0x19): undefined reference to `MAIN__'
# - py-warpx ^warpx dims=3 # py-scipy: for_main.c:(.text+0x19): undefined reference to `MAIN__'
# - py-warpx ^warpx dims=rz # py-scipy: for_main.c:(.text+0x19): undefined reference to `MAIN__'
# - scr # libyogrt: configure: error: slurm is not in specified location!
# - tau +mpi +python # tau: x86_64/lib/Makefile.tau-icpx-papi-mpi-pthread-python-pdt: No such file or directory
# - upcxx # upcxx: /opt/intel/oneapi/mpi/2021.9.0//libfabric/bin/fi_info: error while loading shared libraries: libfabric.so.1: cannot open shared object file: No such file or directory
# - xyce +mpi +shared +pymi +pymi_static_tpls ^trilinos~shylu # cmake/tps.cmake:220 (message): Unable to compile against Trilinos. It is possible Trilinos was not properly configured, or the environment has changed since Trilinos was installed. See the CMake log files for more information.
# GPU
- aml +ze
- amrex +sycl
- arborx +sycl ^kokkos +sycl +openmp std=17 +tests +examples
- cabana +sycl ^kokkos +sycl +openmp std=17 +tests +examples
- kokkos +sycl +openmp std=17 +tests +examples %oneapi
- kokkos-kernels build_type=Release ^kokkos +sycl +openmp std=17 +tests +examples %oneapi
# CPU FAILURES
# - bricks # bricks
# - charliecloud # charliecloud
# - dyninst # old intel-tbb
# - exaworks # py-setuptools-scm
# - flux-core # py-setuptools-scm
# - geopm # geopm
# - ginkgo # ginkgo
# - gptune # py-scipy@1.3.3
# - h5bench # h5bench
# - hpctoolkit # dyninst
# - hpx max_cpu_count=512 networking=mpi # boost cxxstd=17
# - nrm # py-scipy
# - paraview +qt # qt
# - phist # phist
# - pruners-ninja # pruners-ninja
# - py-cinemasci # py-scipy@1.3.3, py-setuptools-scm
# - py-jupyterhub # py-setuptools-scm
# - py-warpx ^warpx dims=2 # py-scipy@1.5.4
# - py-warpx ^warpx dims=3 # py-scipy@1.5.4
# - py-warpx ^warpx dims=rz # py-scipy@1.5.4
# - scr # libyogrt
# - swig@4.0.2-fortran # swig
# - tau +mpi +python # tau
# - variorum # variorum
# --
# amrex: /opt/intel/oneapi/compiler/2023.0.0/linux/bin-llvm/../include/sycl/detail/defines_elementary.hpp:52:40: note: expanded from macro '__SYCL2020_DEPRECATED'
# amrex: /opt/intel/oneapi/compiler/2023.0.0/linux/bin-llvm/../include/sycl/detail/defines_elementary.hpp:52:40: note: expanded from macro '__SYCL2020_DEPRECATED'
# binutils: gold/powerpc.cc:3590: undefined reference to `gold::Sized_symbol<64>::Value_type gold::Symbol_table::compute_final_value<64>(gold::Sized_symbol<64> const*, gold::Symbol_table::Compute_final_value_status*) const'
# boost cxxstd=17: ./boost/mpl/aux_/integral_wrapper.hpp:73:31: error: integer value -1 is outside the valid range of values [0, 3] for this enumeration type [-Wenum-constexpr-conversion]
# bricks: cc1plus: error: bad value ('OFF') for '-mtune=' switch
# charliecloud: autoreconf phase: RuntimeError: configure script not found in ...
# flux-sched: include/yaml-cpp/emitter.h:164:9: error: comparison with NaN always evaluates to false in fast floating point modes [-Werror,-Wtautological-constant-compare]
# flux-sched: include/yaml-cpp/emitter.h:171:24: error: comparison with infinity always evaluates to false in fast floating point modes [-Werror,-Wtautological-constant-compare]
# ginkgo: icpx: error: clang frontend command failed with exit code 139
# h5bench: commons/h5bench_util.h:196: multiple definition of `has_vol_async';
# intel-tbb: clang++clang++clang++clang++clang++clang++clang++: : : : : : : clang++error: : unknown argument: '-flifetime-dse=1'
# libyogrt: configure: error: slurm is not in specified location!
# phist: fortran_bindings/test/kernels.F90(63): error #8284: If the actual argument is scalar, the dummy argument shall be scalar unless the actual argument is of type character or is an element of an array that is not assumed shape, pointer, or polymorphic. [ARGV]
# pruners-ninja: test/ninja_test_util.c:34: multiple definition of `a';
# py-cryptography: ??
# py-scipy@1.3.3: gcc: error: unrecognized command-line option '-fp-model=strict'
# py-scipy@1.5.4: gcc: error: unrecognized command-line option '-fp-model=strict'
# py-setuptools-scm: ??
# ruby: limits.c:415:34: error: invalid suffix 'D' on floating constant
# rust: /usr/bin/ld: /opt/intel/oneapi/compiler/2022.1.0/linux/bin-llvm/../compiler/lib/intel64_lin/libimf.a(libm_feature_flag.o): in function `__libm_feature_flag_init': libm_feature_flag.c:(.text+0x25): undefined reference to `__intel_cpu_feature_indicator_x'
# swig@4.0.2-fortran: /spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/m4-1.4.19-p3otmjixpi6zibdsyoqib5dpzfshq3nj/bin/m4:/spack/opt/spack/linux-ubuntu20.04-x86_64/oneapi-2023.0.0/bison-3.8.2-xca2sot4jhd72hvj2m2b3ajchagczvau/share/bison/skeletons/yacc.c:420: undefined macro `b4_symbol(103, tag)'
# tau: Error: Unable to identify ifort lib directory
# variorum: ld: Intel/CMakeFiles/variorum_intel.dir/msr_core.c.o:(.bss+0x0): multiple definition of `g_platform'; CMakeFiles/variorum.dir/config_architecture.c.o:(.bss+0x0): first defined here
# vtk-m +openmp: clang++: error: clang frontend command failed with exit code 139 (use -v to see invocation)
# GPU FAILURES
# - amrex +sycl # amrex
# - ginkgo +oneapi # ginkgo
# - hpctoolkit +level_zero # dyninst
# - sundials +sycl cxxstd=17 # sundials
# - tau +mpi +opencl +level_zero ~pdt # tau
- kokkos +sycl +openmp std=17 +tests +examples
- kokkos-kernels build_type=Release %oneapi ^kokkos +sycl +openmp std=17 +tests +examples
# --
# - ginkgo +oneapi # InstallError: Ginkgo's oneAPI backend requires theDPC++ compiler as main CXX compiler.
# - hpctoolkit +level_zero # intel-tbb: icpx: error: unknown argument: '-flifetime-dse=1'
# - sundials +sycl cxxstd=17 # sundials: include/sunmemory/sunmemory_sycl.h:20:10: fatal error: 'CL/sycl.hpp' file not found
# - tau +mpi +opencl +level_zero ~pdt # builds ok in container, but needs libdrm, will update container
# SKIPPED
# - flecsi # dependency pfunit marks oneapi as an unsupported compiler
# - nvhpc
# - dyninst # only %gcc
mirrors: { "mirror": "s3://spack-binaries/develop/e4s-oneapi" }
ci:
pipeline-gen:
- build-job:
image: ecpe4s/ubuntu20.04-runner-x86_64-oneapi:2023-01-01
before_script:
- - . /bootstrap/runner/view/lmod/lmod/init/bash
- module use /opt/intel/oneapi/modulefiles
- module load compiler
image: ecpe4s/ubuntu20.04-runner-x86_64-oneapi:2023.06.01
cdash:
build-group: E4S OneAPI
build-group: E4S OneAPI

View File

@@ -70,6 +70,7 @@ spack:
- charliecloud
- conduit
- datatransferkit
- dealii
- dyninst
- ecp-data-vis-sdk ~cuda ~rocm +adios2 +ascent +cinema +darshan +faodel +hdf5 +paraview +pnetcdf +sz +unifyfs +veloc ~visit +vtkm +zfp ^hdf5@1.14
- exaworks

View File

@@ -0,0 +1,139 @@
spack:
view: false
concretizer:
unify: false
reuse: false
config:
concretizer: clingo
db_lock_timeout: 120
install_tree:
root: $spack/opt/spack
padded_length: 256
projections:
all: '{architecture}/{compiler.name}-{compiler.version}/{name}-{version}-{hash}'
packages:
all:
require: target=aarch64
variants: +mps~cuda~rocm
mpi:
require: openmpi
specs:
# Hugging Face
- py-transformers
# JAX
# - py-jax # bazel codesign
# - py-jaxlib # bazel codesign
# Keras
- py-keras-applications
- py-keras-preprocessing
- py-keras2onnx
# - py-keras # bazel codesign
# MXNet
- mxnet
# PyTorch
- py-botorch
- py-gpytorch
- py-pytorch-gradual-warmup-lr
- py-segmentation-models-pytorch
- py-timm
- py-torch
- py-torch-cluster
- py-torch-geometric
- py-torch-sparse
- py-torchdata
- py-torchfile
- py-torchgeo
- py-torchvision
# scikit-learn
- py-scikit-learn
- py-scikit-learn-extra
# TensorBoard
- py-tensorboard
- py-tensorboard-data-server
- py-tensorboard-plugin-wit
- py-tensorboardx
# TensorFlow
# - py-tensorflow # bazel codesign
# - py-tensorflow-datasets # bazel codesign
# - py-tensorflow-hub # bazel codesign
# - py-tensorflow-metadata # bazel codesign
# - py-tensorflow-estimator # bazel codesign
# - py-tensorflow-probability # py-dm-tree due to bazel codesign
# XGBoost
- py-xgboost
- xgboost
# ERRORS
# - py-efficientnet-pytorch # py-torch
# - py-horovod # py-torch
# - py-kornia # py-torch
# - py-lightning # py-torch
# - py-pytorch-lightning # py-torch
# - py-torch-nvidia-apex # py-torch
# - py-torch-scatter # py-torch
# - py-torch-spline-conv # py-torch
# - py-torchaudio # py-torchaudio
# - py-torchmetrics # py-torch
# - py-torchtext # py-torchtext
# - py-vector-quantize-pytorch # py-torch
# - r-xgboost # r
mirrors: { "mirror": "s3://spack-binaries/develop/ml-darwin-aarch64-cpu" }
ci:
pipeline-gen:
- build-job-remove:
image: no-image
tags: [spack, public]
- build-job:
tags: [ "macos-ventura", "apple-clang-14", "aarch64-macos" ]
script::
- - spack compiler find
- cd ${SPACK_CONCRETE_ENV_DIR}
- spack env activate --without-view .
- if [ -n "$SPACK_BUILD_JOBS" ]; then spack config add "config:build_jobs:$SPACK_BUILD_JOBS"; fi
- mkdir -p ${SPACK_ARTIFACTS_ROOT}/user_data
# AWS runners mount E4S public key (verification), UO runners mount public/private (signing/verification)
- if [[ -r /etc/protected-runner/e4s.gpg ]]; then spack gpg trust /etc/protected-runner/e4s.gpg; fi
# UO runners mount intermediate ci public key (verification), AWS runners mount public/private (signing/verification)
- if [[ -r /etc/protected-runner/intermediate_ci_signing_key.gpg ]]; then spack gpg trust /etc/protected-runner/intermediate_ci_signing_key.gpg; fi
- if [[ -r /etc/protected-runner/spack_public_key.gpg ]]; then spack gpg trust /etc/protected-runner/spack_public_key.gpg; fi
- spack --color=always --backtrace ci rebuild --tests > >(tee ${SPACK_ARTIFACTS_ROOT}/user_data/pipeline_out.txt) 2> >(tee ${SPACK_ARTIFACTS_ROOT}/user_data/pipeline_err.txt >&2)
after_script:
- - cat /proc/loadavg || true
- signing-job:
image: { "name": "ghcr.io/spack/notary:latest", "entrypoint": [""] }
tags: ["aws"]
script:
- - aws s3 sync --exclude "*" --include "*spec.json*" ${SPACK_REMOTE_MIRROR_OVERRIDE}/build_cache /tmp
- /sign.sh
- aws s3 sync --exclude "*" --include "*spec.json.sig*" /tmp ${SPACK_REMOTE_MIRROR_OVERRIDE}/build_cache
- aws s3 cp /tmp/public_keys ${SPACK_REMOTE_MIRROR_OVERRIDE}/build_cache/_pgp --recursive --exclude "*" --include "*.pub"
- any-job:
image: "ghcr.io/spack/e4s-ubuntu-18.04:v2021-10-18"
tags: ["spack"]
before_script:
- - uname -a || true
- grep -E "vendor|model name" /proc/cpuinfo 2>/dev/null | sort -u || head -n10 /proc/cpuinfo 2>/dev/null || true
- nproc || true
- - . "./share/spack/setup-env.sh"
- spack --version
- spack arch
cdash:
build-group: Machine Learning MPS
url: https://cdash.spack.io
project: Spack Testing
site: Cloud Gitlab Infrastructure

View File

@@ -1060,7 +1060,7 @@ _spack_external_list() {
}
_spack_external_read_cray_manifest() {
SPACK_COMPREPLY="-h --help --file --directory --dry-run --fail-on-error"
SPACK_COMPREPLY="-h --help --file --directory --ignore-default-dir --dry-run --fail-on-error"
}
_spack_fetch() {
@@ -1695,7 +1695,7 @@ _spack_restage() {
_spack_solve() {
if $list_options
then
SPACK_COMPREPLY="-h --help --show -l --long -L --very-long -I --install-status -y --yaml -j --json -c --cover -N --namespaces -t --types --timers --stats -U --fresh --reuse --reuse-deps"
SPACK_COMPREPLY="-h --help --show -l --long -L --very-long -I --install-status --no-install-status -y --yaml -j --json -c --cover -N --namespaces -t --types --timers --stats -U --fresh --reuse --reuse-deps"
else
_all_packages
fi
@@ -1704,7 +1704,7 @@ _spack_solve() {
_spack_spec() {
if $list_options
then
SPACK_COMPREPLY="-h --help -l --long -L --very-long -I --install-status -y --yaml -j --json --format -c --cover -N --namespaces -t --types -U --fresh --reuse --reuse-deps"
SPACK_COMPREPLY="-h --help -l --long -L --very-long -I --install-status --no-install-status -y --yaml -j --json --format -c --cover -N --namespaces -t --types -U --fresh --reuse --reuse-deps"
else
_all_packages
fi

View File

@@ -37,7 +37,7 @@ RUN find -L {{ paths.view }}/* -type f -exec readlink -f '{}' \; | \
# Modifications to the environment that are necessary to run
RUN cd {{ paths.environment }} && \
spack env activate --sh -d . >> /etc/profile.d/z10_spack_environment.sh
spack env activate --sh -d . > activate.sh
{% if extra_instructions.build %}
{{ extra_instructions.build }}
@@ -53,7 +53,13 @@ COPY --from=builder {{ paths.environment }} {{ paths.environment }}
COPY --from=builder {{ paths.store }} {{ paths.store }}
COPY --from=builder {{ paths.hidden_view }} {{ paths.hidden_view }}
COPY --from=builder {{ paths.view }} {{ paths.view }}
COPY --from=builder /etc/profile.d/z10_spack_environment.sh /etc/profile.d/z10_spack_environment.sh
RUN { \
echo '#!/bin/sh' \
&& echo '.' {{ paths.environment }}/activate.sh \
&& echo 'exec "$@"'; \
} > /entrypoint.sh \
&& chmod a+x /entrypoint.sh
{% block final_stage %}
@@ -70,6 +76,6 @@ RUN {% if os_package_update %}{{ os_packages_final.update }} \
{% for label, value in labels.items() %}
LABEL "{{ label }}"="{{ value }}"
{% endfor %}
ENTRYPOINT ["/bin/bash", "--rcfile", "/etc/profile", "-l", "-c", "$*", "--" ]
ENTRYPOINT [ "/entrypoint.sh" ]
CMD [ "/bin/bash" ]
{% endif %}

View File

@@ -1,7 +1,7 @@
{% extends "container/bootstrap-base.dockerfile" %}
{% block install_os_packages %}
RUN yum update -y \
&& yum install -y \
RUN dnf update -y \
&& dnf install -y \
bzip2 \
curl \
file \
@@ -23,6 +23,6 @@ RUN yum update -y \
unzip \
zstd \
&& pip3 install boto3 \
&& rm -rf /var/cache/yum \
&& yum clean all
&& rm -rf /var/cache/dnf \
&& dnf clean all
{% endblock %}

View File

@@ -1,9 +1,9 @@
{% extends "container/bootstrap-base.dockerfile" %}
{% block install_os_packages %}
RUN yum update -y \
&& yum install -y epel-release \
&& yum update -y \
&& yum --enablerepo epel install -y \
RUN dnf update -y \
&& dnf install -y epel-release \
&& dnf update -y \
&& dnf --enablerepo epel install -y \
bzip2 \
curl-minimal \
file \
@@ -25,6 +25,6 @@ RUN yum update -y \
unzip \
zstd \
&& pip3 install boto3 \
&& rm -rf /var/cache/yum \
&& yum clean all
&& rm -rf /var/cache/dnf \
&& dnf clean all
{% endblock %}

View File

@@ -1,13 +1,13 @@
{% extends "container/bootstrap-base.dockerfile" %}
{% block install_os_packages %}
RUN yum update -y \
RUN dnf update -y \
# See https://fedoraproject.org/wiki/EPEL#Quickstart for powertools
&& yum install -y dnf-plugins-core \
&& dnf install -y dnf-plugins-core \
&& dnf config-manager --set-enabled powertools \
&& yum install -y epel-release \
&& yum update -y \
&& yum --enablerepo epel groupinstall -y "Development Tools" \
&& yum --enablerepo epel install -y \
&& dnf install -y epel-release \
&& dnf update -y \
&& dnf --enablerepo epel groupinstall -y "Development Tools" \
&& dnf --enablerepo epel install -y \
curl \
findutils \
gcc-c++ \
@@ -24,6 +24,6 @@ RUN yum update -y \
python38-setuptools \
unzip \
&& pip3 install boto3 \
&& rm -rf /var/cache/yum \
&& yum clean all
&& rm -rf /var/cache/dnf \
&& dnf clean all
{% endblock %}

View File

@@ -1,7 +1,7 @@
{% extends "container/bootstrap-base.dockerfile" %}
{% block install_os_packages %}
RUN yum update -y \
&& yum install -y \
RUN dnf update -y \
&& dnf install -y \
bzip2 \
curl \
file \
@@ -24,6 +24,6 @@ RUN yum update -y \
zstd \
xz \
&& pip3 install boto3 \
&& rm -rf /var/cache/yum \
&& yum clean all
&& rm -rf /var/cache/dnf \
&& dnf clean all
{% endblock %}

View File

@@ -1,7 +1,7 @@
{% extends "container/bootstrap-base.dockerfile" %}
{% block install_os_packages %}
RUN yum update -y \
&& yum install -y \
RUN dnf update -y \
&& dnf install -y \
bzip2 \
curl \
file \
@@ -24,6 +24,6 @@ RUN yum update -y \
xz \
zstd \
&& pip3 install boto3 \
&& rm -rf /var/cache/yum \
&& yum clean all
&& rm -rf /var/cache/dnf \
&& dnf clean all
{% endblock %}

View File

@@ -1,7 +1,7 @@
{% extends "container/bootstrap-base.dockerfile" %}
{% block install_os_packages %}
RUN yum update -y \
&& yum install -y \
RUN dnf update -y \
&& dnf install -y \
bzip2 \
curl \
file \
@@ -24,6 +24,6 @@ RUN yum update -y \
xz \
zstd \
&& pip3 install boto3 \
&& rm -rf /var/cache/yum \
&& yum clean all
&& rm -rf /var/cache/dnf \
&& dnf clean all
{% endblock %}

View File

@@ -1,9 +1,9 @@
{% extends "container/bootstrap-base.dockerfile" %}
{% block install_os_packages %}
RUN yum update -y \
&& yum install -y epel-release \
&& yum update -y \
&& yum --enablerepo epel install -y \
RUN dnf update -y \
&& dnf install -y epel-release \
&& dnf update -y \
&& dnf --enablerepo epel install -y \
bzip2 \
curl-minimal \
file \
@@ -26,6 +26,6 @@ RUN yum update -y \
xz \
zstd \
&& pip3 install boto3 \
&& rm -rf /var/cache/yum \
&& yum clean all
&& rm -rf /var/cache/dnf \
&& dnf clean all
{% endblock %}

View File

@@ -27,7 +27,8 @@ class Abinit(AutotoolsPackage):
homepage = "https://www.abinit.org/"
url = "https://www.abinit.org/sites/default/files/packages/abinit-8.6.3.tar.gz"
version("9.8.3", sha256="65fb93217336a72d1554cc6991127203958cc7df59921782251a86569e33a357")
version("9.8.4", sha256="a086d5045f0093b432e6a044d5f71f7edf5a41a62d67b3677cb0751d330c564a")
version("9.8.3", sha256="de823878aea2c20098f177524fbb4b60de9b1b5971b2e835ec244dfa3724589b")
version("9.6.1", sha256="b6a12760fd728eb4aacca431ae12150609565bedbaa89763f219fcd869f79ac6")
version("9.4.2", sha256="d40886f5c8b138bb4aa1ca05da23388eb70a682790cfe5020ecce4db1b1a76bc")
version("8.10.3", sha256="ed626424b4472b93256622fbb9c7645fa3ffb693d4b444b07d488771ea7eaa75")

View File

@@ -36,6 +36,40 @@
}
_versions = {
"23.04.1": {
"RHEL-7": (
"5e84daaf0510f73c235723112f9241bbd744ed89eb4f70f089bac05cf2aad2c4",
"https://developer.arm.com/-/media/Files/downloads/hpc/arm-compiler-for-linux/23-04-1/arm-compiler-for-linux_23.04.1_RHEL-7_aarch64.tar",
),
"RHEL-8": (
"6ec1f2c7338ea8a2831a7ff353ab44f87804f56716d1f3686576fb950c2f730f",
"https://developer.arm.com/-/media/Files/downloads/hpc/arm-compiler-for-linux/23-04-1/arm-compiler-for-linux_23.04.1_RHEL-8_aarch64.tar",
),
"RHEL-9": (
"dbd6493ea762b9b4c6cb54a76ad42e2223360882165ee3c223c1b7d1ebe927e2",
"https://developer.arm.com/-/media/Files/downloads/hpc/arm-compiler-for-linux/23-04-1/arm-compiler-for-linux_23.04.1_RHEL-9_aarch64.tar",
),
"SLES-15": (
"74c29890d47556114922c77e5a9797b055f8fe49f0c8665d17102465fca766b4",
"https://developer.arm.com/-/media/Files/downloads/hpc/arm-compiler-for-linux/23-04-1/arm-compiler-for-linux_23.04.1_SLES-15_aarch64.tar",
),
"Ubuntu-20.04": (
"78015ff5a246facfe45219a03a3774221b2f3b58db6fa3d9840d2574d103310c",
"https://developer.arm.com/-/media/Files/downloads/hpc/arm-compiler-for-linux/23-04-1/arm-compiler-for-linux_23.04.1_Ubuntu-20.04_aarch64.tar",
),
"Ubuntu-22.04": (
"19213db67aa11de44b617255e9e32efd294f930c6b6145192acf9ee331452ea6",
"https://developer.arm.com/-/media/Files/downloads/hpc/arm-compiler-for-linux/23-04-1/arm-compiler-for-linux_23.04.1_Ubuntu-22.04_aarch64.tar",
),
"AmazonLinux-2": (
"31ba559302a2889e5f0897f1c07563b20a5a8eaa671e623bef406b6490d1f4f2",
"https://developer.arm.com/-/media/Files/downloads/hpc/arm-compiler-for-linux/23-04-1/arm-compiler-for-linux_23.04.1_AmazonLinux-2_aarch64.tar",
),
"AmazonLinux-2023": (
"fa38f3d79775e9a537c59c8ba39c3b10505e895a3602bbd93c09445170db571f",
"https://developer.arm.com/-/media/Files/downloads/hpc/arm-compiler-for-linux/23-04-1/arm-compiler-for-linux_23.04.1_AmazonLinux-2023_aarch64.tar",
),
},
"23.04": {
"RHEL-7": (
"6526218484e87c195c1145f60536552fabbd25ba98c05cf096f54de18381a422",
@@ -72,23 +106,23 @@
},
"22.1": {
"RHEL-7": (
"bfbfef9099bf0e90480d48b3a1a741d583fc939284f869958e9c09e177098c73",
"367b9a60fa13b5fcf2fa787122c12d4bfb14d6f3e3e7b0460efc7627484a56a4",
"https://developer.arm.com/-/media/Files/downloads/hpc/arm-compiler-for-linux/22-1/arm-compiler-for-linux_22.1_RHEL-7_aarch64.tar",
),
"RHEL-8": (
"28116f6030c95ee8f69eba89023966974d6b44d4a686098f5c3c03e34f7495f6",
"f03ad3381a74df73a4c25baf5f1c15bd466cfd6286498c38b37ddeaa85c9965e",
"https://developer.arm.com/-/media/Files/downloads/hpc/arm-compiler-for-linux/22-1/arm-compiler-for-linux_22.1_RHEL-8_aarch64.tar",
),
"SLES-15": (
"6616dba1af4a73300ce822b645a0f1dfd363f507db5ea44cab1c6051ea388554",
"8a1c5bd570bd195982c342da8dafb7075f8f6b373b44539d4c810e69e8157c1f",
"https://developer.arm.com/-/media/Files/downloads/hpc/arm-compiler-for-linux/22-1/arm-compiler-for-linux_22.1_SLES-15_aarch64.tar",
),
"Ubuntu-18.04": (
"3b3dd6f416299fbd14fbaf0b1bddf7e2f4445a186de7a87e9efdae0b9d0dc3d5",
"4628599d389efcee07d0986cc3e791931e6a37eddb6e4b93c7846e17efe2148f",
"https://developer.arm.com/-/media/Files/downloads/hpc/arm-compiler-for-linux/22-1/arm-compiler-for-linux_22.1_Ubuntu-18.04_aarch64.tar",
),
"Ubuntu-20.04": (
"e6361a08f75817c8dbfb56dc72578810eaf5ffb65591215e394cb3ec6bdd9c10",
"20d950d16e6bb0b3a4c4f3c8ad393aae2356d4c998303b319da9e9833d4a6d12",
"https://developer.arm.com/-/media/Files/downloads/hpc/arm-compiler-for-linux/22-1/arm-compiler-for-linux_22.1_Ubuntu-20.04_aarch64.tar",
),
},
@@ -199,8 +233,8 @@ class Acfl(Package):
with a modern LLVM-based compiler framework.
"""
homepage = "https://developer.arm.com/tools-and-software/server-and-hpc/arm-allinea-studio"
url = "https://developer.arm.com/-/media/Files/downloads/hpc/arm-compiler-for-linux/22-1/arm-compiler-for-linux_22.1_Ubuntu-20.04_aarch64.tar"
homepage = "https://developer.arm.com/Tools%20and%20Software/Arm%20Compiler%20for%20Linux"
url = "https://developer.arm.com/-/media/Files/downloads/hpc/arm-compiler-for-linux/23-04-1/arm-compiler-for-linux_23.04.1_Ubuntu-22.04_aarch64.tar"
maintainers("annop-w")

View File

@@ -21,6 +21,8 @@ class Amgx(CMakePackage, CudaPackage):
maintainers("js947")
version("2.3.0", sha256="419b3cd5bd3eb3469cbef79d64a8d19d5db88dd5cce809e49cac6fc4fc2edff1")
version("2.2.0", sha256="dac78516bb528135cad903399fe0093aa0904e304565ef2d3da4fae05eda7928")
version("2.1.0", sha256="6245112b768a1dc3486b2b3c049342e232eb6281a6021fffa8b20c11631f63cc")
version("2.0.1", sha256="6f9991f1836fbf4ba2114ce9f49febd0edc069a24f533bd94fd9aa9be72435a7")
version("2.0.0", sha256="8ec7ea8412be3de216fcf7243c4e2a8bcf76878e6865468e4238630a082a431b")

View File

@@ -24,6 +24,7 @@ class Amrex(CMakePackage, CudaPackage, ROCmPackage):
maintainers("WeiqunZhang", "asalmgren", "etpalmer63")
version("develop", branch="development")
version("23.06", sha256="3bddcb07cce3e65e06cac35005c30820d311ce47ae54b46e4af333fa272b236b")
version("23.05", sha256="a4bf5ad5322e706b9fae46ff52043e2cca5ddba81479647816251e9ab21c0027")
version("23.04", sha256="b070949611abd2156208e675e40e5e73ed405bf83e3b1e8ba70fbb451a9e7dd7")
version("23.03", sha256="e17c721b1aba4f66e467723f61b59e56c02cf1b72cab5a2680b13ff6e79ef903")
@@ -314,43 +315,20 @@ def cmake_args(self):
return args
# TODO: Replace this method and its 'get' use for cmake path with
# join_path(self.spec['cmake'].prefix.bin, 'cmake') once stand-alone
# tests can access build dependencies through self.spec['cmake'].
def cmake_bin(self, set=True):
"""(Hack) Set/get cmake dependency path."""
filepath = join_path(self.install_test_root, "cmake_bin_path.txt")
if set:
with open(filepath, "w") as out_file:
cmake_bin = join_path(self.spec["cmake"].prefix.bin, "cmake")
out_file.write("{0}\n".format(cmake_bin))
else:
with open(filepath, "r") as in_file:
return in_file.read().strip()
@run_after("build")
def setup_smoke_test(self):
"""Skip setup smoke tests for AMReX versions less than 21.12."""
def setup_standalone_test(self):
"""Setup stand-alonetests for AMReX versions from 21.12 on."""
if self.spec.satisfies("@:21.11"):
return
self.cache_extra_test_sources(["Tests"])
# TODO: Remove once self.spec['cmake'] is available here
self.cmake_bin(set=True)
def test(self):
"""Skip smoke tests for AMReX versions less than 21.12."""
def test_run_install_test(self):
"""build and run AmrCore test"""
if self.spec.satisfies("@:21.11"):
print("SKIPPED: Stand-alone tests not supported for this version of AMReX.")
return
raise SkipTest("Test is not supported for versions @:21.11")
"""Perform smoke tests on installed package."""
# TODO: Remove/replace once self.spec['cmake'] is available here
cmake_bin = self.cmake_bin(set=False)
args = []
args.append("-S./cache/amrex/Tests/SpackSmokeTest")
args = ["-S{0}".format(join_path(".", "cache", "amrex", "Tests", "SpackSmokeTest"))]
args.append("-DAMReX_ROOT=" + self.prefix)
if "+mpi" in self.spec:
args.append("-DMPI_C_COMPILER=" + self.spec["mpi"].mpicc)
@@ -360,15 +338,15 @@ def test(self):
args.append("-DCMAKE_CUDA_COMPILER=" + join_path(self.spec["cuda"].prefix.bin, "nvcc"))
args.extend(self.cmake_args())
self.run_test(cmake_bin, args, purpose="Configure with CMake")
cmake = which(self.spec["cmake"].prefix.bin.cmake)
cmake(*args)
self.run_test("make", [], purpose="Compile")
make = which("make")
make()
self.run_test(
"install_test",
["./cache/amrex/Tests/Amr/Advection_AmrCore/Exec/inputs-ci"],
["finalized"],
installed=False,
purpose="AMReX Stand-Alone Smoke Test -- AmrCore",
skip_missing=False,
install_test = which("install_test")
inputs_path = join_path(
".", "cache", "amrex", "Tests", "Amr", "Advection_AmrCore", "Exec", "inputs-ci"
)
out = install_test(inputs_path, output=str.split, error=str.split)
assert "finalized" in out

View File

@@ -2,6 +2,7 @@
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import os
from spack.package import *
@@ -17,7 +18,10 @@ class Arborx(CMakePackage, CudaPackage, ROCmPackage):
maintainers("aprokop")
test_requires_compiler = True
version("master", branch="master")
version("1.4", sha256="803a1018a6305cf3fea161172b3ada49537f59261279d91c2abbcce9492ee7af")
version("1.3", sha256="3f1e17f029a460ab99f8396e2772cec908eefc4bf3868c8828907624a2d0ce5d")
version("1.2", sha256="ed1939110b2330b7994dcbba649b100c241a2353ed2624e627a200a398096c20")
version("1.1", sha256="2b5f2d2d5cec57c52f470c2bf4f42621b40271f870b4f80cb57e52df1acd90ce")
@@ -61,7 +65,8 @@ class Arborx(CMakePackage, CudaPackage, ROCmPackage):
# Standalone Kokkos
depends_on("kokkos@3.1.00:", when="~trilinos")
depends_on("kokkos@3.4.00:", when="@1.2~trilinos")
depends_on("kokkos@3.6.00:", when="@1.3:~trilinos")
depends_on("kokkos@3.6.00:", when="@1.3~trilinos")
depends_on("kokkos@3.7.01:", when="@1.4:~trilinos")
for backend in kokkos_backends:
depends_on("kokkos+%s" % backend.lower(), when="~trilinos+%s" % backend.lower())
@@ -83,7 +88,8 @@ class Arborx(CMakePackage, CudaPackage, ROCmPackage):
depends_on("trilinos+kokkos", when="+trilinos")
depends_on("trilinos+openmp", when="+trilinos+openmp")
depends_on("trilinos@13.2.0:", when="@1.2+trilinos")
depends_on("trilinos@13.4.0:", when="@1.3:+trilinos")
depends_on("trilinos@13.4.0:", when="@1.3+trilinos")
depends_on("trilinos@14.0.0:", when="@1.4:+trilinos")
conflicts("~serial", when="+trilinos")
conflicts("+cuda", when="+trilinos")
@@ -117,18 +123,18 @@ def cached_tests_work_dir(self):
"""The working directory for cached test sources."""
return join_path(self.test_suite.current_test_cache_dir, self.examples_src_dir)
def build_tests(self):
"""Build the stand-alone/smoke test."""
def test_run_ctest(self):
"""run ctest tests on the installed package"""
arborx_dir = self.spec["arborx"].prefix
cmake_prefix_path = "-DCMAKE_PREFIX_PATH={0}".format(arborx_dir)
cmake_prefix_path = f"-DCMAKE_PREFIX_PATH={arborx_dir}"
if "+mpi" in self.spec:
cmake_prefix_path += ";{0}".format(self.spec["mpi"].prefix)
cmake_prefix_path += f";{self.spec['mpi'].prefix}"
cmake_args = [
".",
cmake_prefix_path,
"-DCMAKE_CXX_COMPILER={0}".format(self.compiler.cxx),
f"-DCMAKE_CXX_COMPILER={os.environ['CXX']}",
self.define(
"Kokkos_ROOT",
self.spec["kokkos"].prefix
@@ -136,23 +142,11 @@ def build_tests(self):
else self.spec["trilinos"].prefix,
),
]
cmake = which(self.spec["cmake"].prefix.bin.cmake)
make = which("make")
ctest = which("ctest")
self.run_test(
"cmake", cmake_args, purpose="test: calling cmake", work_dir=self.cached_tests_work_dir
)
self.run_test(
"make", [], purpose="test: building the tests", work_dir=self.cached_tests_work_dir
)
def test(self):
"""Perform stand-alone/smoke tests on the installed package."""
self.build_tests()
self.run_test(
"ctest",
["-V"],
purpose="test: running the tests",
installed=False,
work_dir=self.cached_tests_work_dir,
)
with working_dir(self.cached_tests_work_dir):
cmake(*cmake_args)
make()
ctest("-V")

View File

@@ -3,7 +3,6 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import os
from spack.package import *
@@ -50,25 +49,17 @@ def cache_test_sources(self):
install test subdirectory for use during `spack test run`."""
self.cache_extra_test_sources(["test"])
def run_parallel_example_test(self):
"""Run stand alone test: parallel-simple"""
def test_run_parallel_example(self):
"""build and run parallel-simple"""
test_dir = join_path(self.test_suite.current_test_cache_dir, "test", "parallel")
if not os.path.exists(test_dir):
print("Skipping archer test")
return
raise SkipTest("Parallel test directory does not exist")
exe = "parallel-simple"
test_exe = "parallel-simple"
test_src = "{0}.c".format(test_exe)
with working_dir(test_dir):
clang = which("clang-archer")
clang("-o", test_exe, test_src)
self.run_test(
"clang-archer",
options=["-o", exe, "{0}".format(join_path(test_dir, "parallel-simple.c"))],
purpose="test: compile {0} example".format(exe),
work_dir=test_dir,
)
self.run_test(exe, purpose="test: run {0} example".format(exe), work_dir=test_dir)
def test(self):
self.run_parallel_example_test()
parallel_simple = which(test_exe)
parallel_simple()

View File

@@ -14,6 +14,7 @@ class Armadillo(CMakePackage):
homepage = "http://arma.sourceforge.net/"
url = "http://sourceforge.net/projects/arma/files/armadillo-8.100.1.tar.xz"
version("12.4.0", sha256="9905282781ced3f99769b0e45a705ecb50192ca1622300707b3302ea167dc883")
version("12.2.0", sha256="b0dce042297e865add3351dad77f78c2c7638d6632f58357b015e50edcbd2186")
version("12.0.1", sha256="230a5c75daad52dc47e1adce8f5a50f9aa4e4354e0f1bb18ea84efa2e70e20df")
version("10.5.0", sha256="ea990c34dc6d70d7c95b4354d9f3b0819bde257dbb67796348e91e196082cb87")

View File

@@ -36,6 +36,50 @@
}
_versions = {
"23.04.1_gcc-12.2": {
"RHEL-7": ("789cc093cb7e0d9294aff0fdf94b74987435a09cdff4c1b7118a03350548d03c"),
"RHEL-8": ("1b668baec6d3df2d48c5aedc70baa6a9b638983b94bf2cd58d378859a1da49f0"),
"RHEL-9": ("8a4d7aec2fe109aedcb9e8fdec566dc1ba3adcb3ba79e5c08b78b9717578db1c"),
"SLES-15": ("9c8aa114907d3ac9311301b991d732d535422e73516e0f337395637ce6a14c4a"),
"Ubuntu-20.04": ("c0a67afb6989b2bdb172052ff7d20a9e3197356714df06c862edd3ac71ef62f0"),
"Ubuntu-22.04": ("02e59d834c341164f5acf633555024bf614726aed8a85c1b0b46d024ce7840e2"),
"AmazonLinux-2": ("1cbb9a3d777353b42bfb5af327419c231640e7744ab46ab3a13e97802b1ce227"),
"AmazonLinux-2023": ("ee9b0b6ee0d881280e473390007020504a147b75bf6076d245832f101b01653e"),
},
"23.04.1_gcc-11.3": {
"RHEL-7": ("522e0269ca03d6251c10ee3aa8d94ceec4618887f47847defb535849434439a5"),
"RHEL-8": ("00f6fee4ba4bbff5be6d5ad34137973ab89505fc61a23d8e0c302b8860c70484"),
"RHEL-9": ("2402165267b25d07fd64b6d444b3120354dfd27594b11a1f082e85e76465e712"),
"SLES-15": ("a928539efe5af760fc86a009e3d87c9648e4d4e91490c13bc136a837591549c3"),
"Ubuntu-20.04": ("5754d8a6040bb6d0b1df326c9ab61901a72e5cc6d2d4195e52ca9271e55fb9f6"),
"Ubuntu-22.04": ("8af5aca7512a604b051a7808701a5c0285e92d88232138612d8caf973b7b1252"),
"AmazonLinux-2": ("8c710cb7bb21694130b915cc2650cfb85fb00cfca7e5fca9bbdec5c59a09c007"),
"AmazonLinux-2023": ("8b9c69a72c5b1ed5814e28ddd122ab09dbe5dd3585e4c395242ed590eea6ea79"),
},
"23.04.1_gcc-10.2": {
"RHEL-7": ("40d62517bd978516c308b2e57ab88772699fd8bb579d98bbc10ea397c0bab431"),
"RHEL-8": ("76554ea1f3d143f1236afea67e33eea74660f57718ef57c12986843da75e03d3"),
"SLES-15": ("63a6acb00300a9e85cfafd2141515ecb28dac82c1f441778d74e8add038724e2"),
"Ubuntu-20.04": ("7b6bcb8d1b9ca8be2d29e7620862fa961d965f479fa04873616ac8cc9bb399fc"),
"AmazonLinux-2": ("c6410ce2c109ae72568186bb7e162fcf4a9b05ea89da36d17db695b7df34f506"),
},
"23.04.1_gcc-9.3": {
"RHEL-7": ("782bbc27c77c230426086c226a78b8951501066d631947438e65ca51d33f24c3"),
"RHEL-8": ("8d3be6381b3e5032c5068a1d2e3d0e69c308a93496f85af42d43a579f9f7d9a3"),
"SLES-15": ("abe2245674a66ec93cff3c93dac7ae04a99c6c7e43e2733de214ec188e0d6cae"),
"Ubuntu-20.04": ("a7d385b901f2d1c07f243c816030ad19543e00667615dea1969ce16d29759271"),
"AmazonLinux-2": ("7113b6e2c795933ce8d18d468889168732d3a52a0df4a48ef4bf4497e891083a"),
},
"23.04.1_gcc-8.2": {
"RHEL-7": ("4e077813121c1cbd8abd1afe5348cafcce5b70f96affa725c7c2d8671e2d5eed"),
"RHEL-8": ("772aaab9304191e3a398cba2dec21ec22fd0abadcaf44d44f32114968bd3b59d"),
"SLES-15": ("33766ac351fb4628c6b39f16d6bdb310ad09d88b6a6f43740349405c960d4d21"),
"AmazonLinux-2": ("c215ed8de77b5144a60b6552f79ef2b59ccbfac5350f083ef135305ddf643a4e"),
},
"23.04.1_gcc-7.5": {
"RHEL-7": ("7b2239b2ce5315e1be14dbd8fe15aff2d3b07968d64b5c80c8ab57140b6a17a8"),
"AmazonLinux-2": ("a2e0f176df627c50f851924ac57994f582f63b0f3d42ad0b65c915ea04dc0467"),
},
"23.04_gcc-12.2": {
"RHEL-7": ("e159f84f14d885aa5e47ca17c16ef3d95128f834a655827bf6b48fcf8d6ec459"),
"RHEL-8": ("6ac1974ec9bd814d3a4eecf330cefd67cf2c878f026a8b04bc2928368948671a"),
@@ -225,6 +269,13 @@ class ArmplGcc(Package):
conflicts("target=ppc64:", msg="Only available on Aarch64")
conflicts("target=ppc64le:", msg="Only available on Aarch64")
conflicts("%gcc@:11", when="@23.04.1_gcc-12.2")
conflicts("%gcc@:10", when="@23.04.1_gcc-11.3")
conflicts("%gcc@:9", when="@23.04.1_gcc-10.2")
conflicts("%gcc@:8", when="@23.04.1_gcc-9.3")
conflicts("%gcc@:7", when="@23.04.1_gcc-8.2")
conflicts("%gcc@:6", when="@23.04.1_gcc-7.5")
conflicts("%gcc@:11", when="@23.04_gcc-12.2")
conflicts("%gcc@:10", when="@23.04_gcc-11.3")
conflicts("%gcc@:9", when="@23.04_gcc-10.2")

View File

@@ -12,6 +12,7 @@ class Asdcplib(AutotoolsPackage):
homepage = "https://github.com/cinecert/asdcplib"
url = "https://github.com/cinecert/asdcplib/archive/rel_2_10_35.tar.gz"
version("2_10_38", sha256="f8cb3b1fecfe18f1a64e12e96e5696480631509e9088e29f5a259eb25b1b1656")
version("2_10_35", sha256="a68eec9ae0cc363f75331dc279c6dd6d3a9999a9e5f0a4405fd9afa8a29ca27b")
version("2_10_34", sha256="faa54ee407c1afceb141e08dae9ebf83b3f839e9c49a1793ac741ec6cdee5c3c")
version("2_10_33", sha256="16fafb5da3d46b0f44570ef9780c85dd82cca60106a9e005e538809ea1a95373")

View File

@@ -14,17 +14,44 @@ class Asio(AutotoolsPackage):
homepage = "https://think-async.com/Asio/"
url = "https://github.com/chriskohlhoff/asio/archive/asio-1-18-2.tar.gz"
git = "https://github.com/chriskohlhoff/asio.git"
maintainers("msimberg")
maintainers("msimberg", "pauleonix")
version("1.21.0", sha256="5d2d2dcb7bfb39bff941cabbfc8c27ee322a495470bf0f3a7c5238648cf5e6a9")
# As uneven minor versions of asio are not considered stable, they wont be added anymore
version("1.28.0", sha256="226438b0798099ad2a202563a83571ce06dd13b570d8fded4840dbc1f97fa328")
version("1.26.0", sha256="935583f86825b7b212479277d03543e0f419a55677fa8cb73a79a927b858a72d")
version("1.24.0", sha256="cbcaaba0f66722787b1a7c33afe1befb3a012b5af3ad7da7ff0f6b8c9b7a8a5b")
version("1.22.2", sha256="985fc2d522f32d232d8386d2fa4ac6f2b25a0cad30495bf2e2e7997bce743f0b")
version("1.22.1", sha256="30cb54a5de5e465d10ec0c2026d6b5917f5e89fffabdbabeb1475846fc9a2cf0")
version("1.22.0", sha256="17bfd506f6d55c85a33603277a256b42ca5883bf290930040489ffeeed23724a")
version(
"1.21.0",
sha256="5d2d2dcb7bfb39bff941cabbfc8c27ee322a495470bf0f3a7c5238648cf5e6a9",
deprecated=True, # non-stable
)
version("1.20.0", sha256="34a8f07be6f54e3753874d46ecfa9b7ab7051c4e3f67103c52a33dfddaea48e6")
version("1.19.2", sha256="5ee191aee825dfb1325cbacf643d599b186de057c88464ea98f1bae5ba4ff47a")
version("1.19.1", sha256="2555e0a29256de5c77d6a34b14faefd28c76555e094ba0371acb0b91d483520e")
version("1.19.0", sha256="11bc0e22fcdfb3f0b77574ac33760a3592c0dac7e7eece7668b823c158243629")
version(
"1.19.2",
sha256="5ee191aee825dfb1325cbacf643d599b186de057c88464ea98f1bae5ba4ff47a",
deprecated=True, # non-stable
)
version(
"1.19.1",
sha256="2555e0a29256de5c77d6a34b14faefd28c76555e094ba0371acb0b91d483520e",
deprecated=True, # non-stable
)
version(
"1.19.0",
sha256="11bc0e22fcdfb3f0b77574ac33760a3592c0dac7e7eece7668b823c158243629",
deprecated=True, # non-stable
)
version("1.18.2", sha256="8d67133b89e0f8b212e9f82fdcf1c7b21a978d453811e2cd941c680e72c2ca32")
version("1.18.1", sha256="39c721b987b7a0d2fe2aee64310bd128cd8cc10f43481604d18cb2d8b342fd40")
version("1.18.0", sha256="820688d1e0387ff55194ae20036cbae0fb3c7d11b7c3f46492369723c01df96f")
version("1.17.0", sha256="46406a830f8334b3789e7352ed7309a39c7c30b685b0499d289eda4fd4ae2067")
version(
"1.17.0",
sha256="46406a830f8334b3789e7352ed7309a39c7c30b685b0499d289eda4fd4ae2067",
deprecated=True, # non-stable
)
version("1.16.1", sha256="e40bbd531530f08318b7c7d7e84e457176d8eae6f5ad2e3714dc27b9131ecd35")
version("1.16.0", sha256="c87410ea62de6245aa239b9ed2057edf01d7f66acc3f5e50add9a29343c87512")
@@ -32,6 +59,15 @@ class Asio(AutotoolsPackage):
depends_on("automake", type="build")
depends_on("m4", type="build")
depends_on("libtool", type="build")
depends_on("pkgconfig", type="build", when="@1.23:")
# See https://github.com/chriskohlhoff/asio/issues/944 and
# https://github.com/chriskohlhoff/asio/pull/995
conflicts(
"%gcc@12:",
when="@:1.22.0",
msg="asio v1.22.1 fixed missing includes necessary for gcc v12 and above",
)
stds = ("11", "14", "17", "2a")
variant(

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