This PR fixes the case where groff fails to build if the spack install
path is really long. There are a couple of perl scripts that get built,
and used, during the build phase that will fail when the perl
interpreter line is too long. Filtering the lines will not work because
the files don not exist after the configure phase and patching after the
build phase is too late. This PR runs the scripts explicitly with the
spack perl via the $(PERL) variable in the call to the script.
* Procedure to deprecate old versions of software
* Add documentation
* Fix bug in logic
* Update tab completion
* Deprecate legacy packages
* Deprecate old mxnet as well
* More explicit docs
* py-dvc: new package
* Update var/spack/repos/builtin/packages/py-dvc/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-dvc: add version dependency for py-networkx
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Clarify relaxed double precision option
This is only intended for use on the Fujitsu PRIMEHPC platform
* Fix typo
* Shorten line to keep linter happy
Added conflict for macsio@1.1~mpi after investigating source code. As of
1.1 tag macsio does not properly guard out MPI commands. This is
verified as corrected in @develop
* mxnet: convert to CMakePackage
* Package isn't installed yet, can't find libs
* Fix bug with GCC 8+ and CUDA 10 on PowerPC
* Add space
* Add patch to fix cmake cuda flags
* Space no longer needed
* Add patch to fix OpenBLAS linking
* Add missing CMake flag
* Fix env set, default to Distribution
* Add new version, patch
* added py-python-benedict recipe
* Update var/spack/repos/builtin/packages/py-python-benedict/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
+ Provide optional variant `pythontools` (default False) that adds a run-time dependency on
`py-matplotlib`.
+ Latest versions require `cmake@3.18:` to support cuda features.
+ Enable a cmake option that forcibly disables qt support. Previously, draco would enable qt
support if it was available in the local build environment (outside of spack).
* graphviz: Remove ghostscript requirement when ~ghostscript
* Add doc variant and patch for 2.44.1
* Patch does not apply
* Update graphviz versions, using archives rather than git hash
* Complete implementation of doc variant
* Fix typo
This commit adds an option to the `external find`
command that allows it to search by tags. In this
way group of executables with common purposes can
be grouped under a single name and a simple command
can be used to detect all of them.
As an example introduce the 'build-tools' tag to
search for common development tools on a system
* add to LD_LIBRARY_PATH so that it finds libimf.so
* amrex: fix handling of CUDA arch (#20786)
* amrex: fix handling of CUDA arch
* amrex: fix style
* amrex: fix bug
* Update var/spack/repos/builtin/packages/amrex/package.py
* Update var/spack/repos/builtin/packages/amrex/package.py
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* ecp-data-vis-sdk: Combine the vis and io SDK packages (#20737)
This better enables the collective set to be deployed togethor satisfying
eachothers dependencies
* r-sf: fix dependency error (#20898)
* improve documentation for Rocm (hip amd builds) (#20812)
* improve documentation
* astyle: Fix makefile for install parameter (#20899)
* llvm-doe: added new package (#20719)
The package contains duplicated code from llvm/package.py,
will supersede solve.
* r-e1071: added v1.7-4 (#20891)
* r-diffusionmap: added v1.2.0 (#20881)
* r-covr: added v3.5.1 (#20868)
* r-class: added v7.3-17 (#20856)
* py-h5py: HDF5_DIR is needed for ~mpi too (#20905)
For the `~mpi` variant, the environment variable `HDF5_DIR` is still required. I moved this command out of the `+mpi` conditional.
* py-hovorod: fix typo on variant name in conflicts directive (#20906)
* fujitsu-fftw: Add new package (#20824)
* pocl: added v1.6 (#20932)
Made version 1.5 or lower conflicts with a64fx.
* PCL: add new package (#20933)
* r-rle: new package (#20916)
Common 'base' and 'stats' methods for 'rle' objects, aiming to make it
possible to treat them transparently as vectors.
* r-ellipsis: added v0.3.1 (#20913)
* libconfig: add build dependency on texinfo (#20930)
* r-flexmix: add v2.3-17 (#20924)
* r-fitdistrplus: add v1.1-3 (#20923)
* r-fit-models: add v0.64 (#20922)
* r-fields: add v11.6 (#20921)
* r-fftwtools: add v0.9-9 (#20920)
* r-farver: add v2.0.3 (#20919)
* r-expm: add v0.999-6 (#20918)
* cln: add build dependency on texinfo (#20928)
* r-expint: add v0.1-6 (#20917)
* r-envstats: add v2.4.0 (#20915)
* r-energy: add v1.7-7 (#20914)
* r-ellipse: add v0.4.2 (#20912)
* py-fiscalyear: add v0.3.0 (#20911)
* r-ecp: add v3.1.3 (#20910)
* r-plotmo: add v3.6.0 (#20909)
* Improve gcc detection in llvm. (#20189)
Co-authored-by: Tom Scogland <tom.scogland@gmail.com>
Co-authored-by: Thomas Green <ca-tgreen@gw4a64fxlogin00.head.gw4.metoffice.gov.uk>
* hatchet: updated urls (#20908)
* py-anuga: add new package (#20782)
* libvips: added v8.10.5 (#20902)
* libzmq: add platform conditions to libbsd dependency (#20893)
* r-dtw: add v1.22-3 (#20890)
* r-dt: add v0.17 (#20889)
* r-dosnow: add v1.0.19 (#20888)
* add version 1.0.16 to r-doparallel (#20886)
* add version 1.3.7 to r-domc (#20885)
* add version 0.9-15 to r-diversitree (#20884)
* add version 1.3-3 to r-dismo (#20883)
* add version 0.6.27 to r-digest (#20882)
* add version 1.5 to r-rngtools (#20887)
* add version 1.5.8 to r-dicekriging (#20877)
* add version 1.4.2 to r-httr (#20876)
* add version 1.28 to r-desolve (#20875)
* add version 2.2-5 to r-deoptim (#20874)
* add version 0.2-3 to r-deldir (#20873)
* add version 1.0.0 to r-crul (#20870)
* add version 1.1.0.1 to r-crosstalk (#20869)
* add version 1.0-1 to r-copula (#20867)
* add version 5.0.2 to r-rcppparallel (#20866)
* add version 2.0-1 to r-compositions (#20865)
* add version 0.4.10 to r-rlang (#20796)
* add version 0.3.6 to r-vctrs (#20878)
* amrex: add ROCm support (#20809)
* add version 2.0-0 to r-colorspace (#20864)
* add version 1.3-1 to r-coin (#20863)
* add version 0.19-4 to r-coda (#20862)
* add version 1.3.7 to r-clustergeneration (#20861)
* add version 0.3-58 to r-clue (#20860)
* add version 0.7.1 to r-clipr (#20859)
* add version 2.2.0 to r-cli (#20858)
* add version 0.4-3 to r-classint (#20857)
* add version 0.1.2 to r-globaloptions (#20855)
* add version 2.3-56 to r-chron (#20854)
* add version 0.4.10 to r-checkpoint (#20853)
* add version 2.0.0 to r-checkmate (#20852)
* add version 1.18.1 to r-catools (#20850)
* add version 1.2.2.2 to r-modelmetrics (#20849)
* add version 3.0-4 to r-cardata (#20847)
* add version 1.0.1 to r-caracas (#20846)
* r-lifecycle: new package at v0.2.0 (#20845)
* add version 3.0-10 to r-car (#20844)
* add version 3.4.5 to r-processx (#20843)
* add version 1.5-12.2 to r-cairo (#20842)
* add version 0.2.3 to r-cubist (#20841)
* add version 2.6 to r-rmarkdown (#20838)
* add version 1.2.1 to r-blob (#20819)
* add version 4.0.4 to r-bit (#20818)
* add version 2.4-1 to r-bio3d (#20816)
* add version 0.4.2.3 to r-bibtex (#20815)
* add version 3.1-4 to r-bayesm (#20807)
* add version 1.2.1 to r-backports (#20806)
* add version 2.0.3 to r-argparse (#20805)
* add version 5.4-1 to r-ape (#20804)
* add version 0.8-18 to r-amap (#20803)
* r-pixmap: added new package (#20795)
* zoltan: source code location change (#20787)
* refactor path logic
* added some paths to make compilers and libs discoverable
* add to LD_LIBRARY_PATH so that it finds libimf.so
and cleanup PEP8
* refactor path logic
* adding paths to LIBRARY_PATH so compiler wrappers will find -lmpi
* added vals for CC=icx, CXX=icpx, FC=ifx to generated module
* back out changes to intel-oneapi-mpi, save for separate PR
* Update var/spack/repos/builtin/packages/intel-oneapi-compilers/package.py
path is joined in _ld_library_path()
Co-authored-by: Robert Cohn <rscohn2@gmail.com>
* set absolute paths to icx,icpx,ifx
* dang close parenthesis
Co-authored-by: Robert Cohn <rscohn2@gmail.com>
Co-authored-by: mic84 <mrosso@lbl.gov>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Chuck Atkins <chuck.atkins@kitware.com>
Co-authored-by: darmac <xiaojun2@hisilicon.com>
Co-authored-by: Danny Taller <66029857+dtaller@users.noreply.github.com>
Co-authored-by: Tomoyasu Nojiri <68096132+t-nojiri@users.noreply.github.com>
Co-authored-by: Shintaro Iwasaki <siwasaki@anl.gov>
Co-authored-by: Glenn Johnson <glenn-johnson@uiowa.edu>
Co-authored-by: Kelly (KT) Thompson <KineticTheory@users.noreply.github.com>
Co-authored-by: Henrique Mendonça <henrique@users.noreply.github.com>
Co-authored-by: h-denpo <57649496+h-denpo@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Thomas Green <tomgreen66@hotmail.com>
Co-authored-by: Tom Scogland <tom.scogland@gmail.com>
Co-authored-by: Thomas Green <ca-tgreen@gw4a64fxlogin00.head.gw4.metoffice.gov.uk>
Co-authored-by: Abhinav Bhatele <bhatele@cs.umd.edu>
Co-authored-by: a-saitoh-fj <63334055+a-saitoh-fj@users.noreply.github.com>
Co-authored-by: QuellynSnead <quellyn@lanl.gov>
* py-dictdiffer: fix offline dependencies
* Update var/spack/repos/builtin/packages/py-dictdiffer/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-flatten-dict: new recipe
* Update var/spack/repos/builtin/packages/py-flatten-dict/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-flatten-dict: fix dependencies
* py-flatten-dict: fix dependency
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* clingo/clingo-bootstrap: added a package with option for bootstrapping clingo
package builds in Release mode
uses GCC options to link libstdc++ and libgcc statically
* clingo-bootstrap: apple-clang options to bootstrap statically on darwin
* clingo: fix the path of the Python interpreter
In case multiple Python versions are in the same prefix
(e.g. when clingo is built against an external Python),
it may happen that the Python used by CMake does not
match the corresponding node in the current spec.
This is fixed here by defining "Python_EXECUTABLE"
properly as a hint to CMake.
* clingo: the commit for "spack" version has been updated.
- add variants for build targets, language bindings, backends
- ensure selected variants are compatible with zfp version
- point to GitHub (not LLNL) tar balls
- add dependencies
- update link to homepage
- add maintainers
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Patch provided by @Billae
Avoid the following error:
File "/home/danlipsa/projects/spack/lib/spack/llnl/util/tty/log.py", line 768, in _writer_daemon
line = _retry(in_pipe.readline)()
File "/home/danlipsa/projects/spack/lib/spack/llnl/util/tty/log.py", line 830, in wrapped
return function(*args, **kwargs)
File "/usr/lib/python3.8/codecs.py", line 322, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x97 in position 220: invalid start byte
This PR adds:
1. A patch that fixes a bug in version 2.70
(will be fixed upstream in the next release: https://savannah.gnu.org/support/?110396).
2. A fix for the way we patch shebang in bin/autom4te.in.
For 2, we need to keep the original modification timestamp of the file.
Otherwise, we either get an empty man page for autom4te (versions 2.69 and before)
or a failure at the build time (versions 2.70 and after).
The difference has to do with the update of the missing script: https://git.savannah.gnu.org/cgit/automake.git/commit/lib/missing?id=a22717dffe37f30ef2ad2c355b68c9b3b5e4b8c7
It will take time until developers of Autotools-based packages adjust their scripts
to the new version, therefore, 2.69 is marked as preferred.
* New interface reconstruction package
* forgot to put in CMake option for Jali
* cleanup whitespace
* fix lines with more than 79 chars
* more long line cleanup
* fix typo WONTON_ENABLE_Kokkos ---> TANGRAM_ENABLE_Kokkos
* New interface reconstruction package
* forgot to put in CMake option for Jali
* cleanup whitespace
* fix lines with more than 79 chars
* more long line cleanup
* fix typo WONTON_ENABLE_Kokkos ---> TANGRAM_ENABLE_Kokkos
* fix bugs in CMake section
* more compact cmake block
* update hash for 1.2.10 and add 1.2.11
* update recipe for Portage 3.0.0
* removing old versions - they won't build with the new recipe and the url specification doesn't work for them
* update version to 3.3.6
Co-authored-by: Rao Garimella <rao@abyzou.lanl.gov>
* added pytest-benchmark recipe
* Update var/spack/repos/builtin/packages/py-pytest-benchmark/package.py
Added Python2 dependence.
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* added package py-pytest-cpp
* Update var/spack/repos/builtin/packages/py-pytest-cpp/package.py
package is !=5.4.0 use @:5.3.999
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* added package py-pytest-timeout
* Update var/spack/repos/builtin/packages/py-pytest-timeout/package.py
Added Python2.
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* added package py-openmc
* Update var/spack/repos/builtin/packages/py-openmc/package.py
specify branch when using branch names for versions
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-openmc/package.py
use run after fixture to install openmc lib
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-openmc/package.py
Simplify copying openmc library to py-openmc prefix using install
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-openmc/package.py
NumPy should be 1.9+
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* fix paren missing
* Update var/spack/repos/builtin/packages/py-openmc/package.py
fixed parens
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-openmc/package.py
use v0.11.0 in URL
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Python extensions use CC and LDSHARED from the sysconfig module to
build. When Spack installs Python, it replaces the Spack compiler
wrappers in these values with the underlying compilers (since these
wrappers are not useful outside of the context of running Spack).
In order to use the Spack compiler wrappers when building Python
extensions with Spack, Spack sets the LDSHARED environment variable
when running `Python.setup_py` (which overrides sysconfig). However,
many Python extensions use an alternative method to build (namely
PythonPackage.setup_py), which meant that LDSHARED was not set (and
RPATHs were not inserted for dependencies).
This commit makes the following changes:
* Sets LDSHARED in the environment: this applies to all commands
executed during the build, rather than for a single command
invocation
* Updates the logic to set LDSHARED: this replaces the compiler
executable in LDSHARED with the Spack compiler wrapper. This
means that for some externally-built instances of Python,
Spack will now switch to using the Spack wrappers when building
extensions. The behavior is expected to be the same for Spack-
built instances of Python.
* Performs similar modifications for LDCXXSHARED (to ensure RPATHs
are included for C++ codes)
On ppc64le and aarch64, Spack tries to execute any "config.guess" and
"config.sub" scripts it finds in the source package.
However, in the libsodium tarball, these files are present but not
executable. This causes the following error when trying to install
libsodium with spack:
Error: RuntimeError: Failed to find suitable substitutes for config.sub, config.guess
Fix this by chmod-ing the scripts in the patch() function of libsodium.
* recipe: add version 6.1.1 for pytest
add recipe for new dependency py-iniconfig
recipe: add version 6.1.1 for pytest
add recipe for new dependency py-iniconfig
* fix: 'SyntaxError: invalid syntax' during unittests
* requested changes on the pull request done
* requested changes on dep for py-pytest
* change constaint on python for importlib-metadata
* undo change on py-importlib-metada as requested
* bug fix
* bug fix on py-wcwidth
* fix as requested
* forget @ in when param
* forget a colon
* add new versions py-pytest and py-py
* fix setuptools* version
* add rule for more-itertools
* [py-intel-openmp] created template
* [py-intel-openmp] is wheel
* [py-intel-openmp] fixed version for linux
* [py-intel-openmp] removed fixmes, added homepage and description
* [py-intel-openmp] added macos support
* [py-intel-openmp] style fix
* petsc: add a +mkl-pardiso variant
mkl_pardiso solver is distributed with intel-mkl
* petsc: depend on mkl instead of intel-mkl
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Add version 4.12.6, 5.0.3
I think, the preferred was there to keep version 4.
But that's why we have spack, because people can install
whatever version they want.
And root has a properly versioned dependency.
* mumps: Fix for problematic src/makefile patch (#20590)
Minor change in src/Makefile between 5.2.0 and 5.3.3 causing patch to
break. Split into 2 patchfiles
* mumps: Additional patch for fixing #20590
This is to fix issue wherein build fails on Ubuntu due to undefined
symbols, despite symbols being included in other libraries referenced
on the compilation line. I believe the issue is that the inclusion
of libsmumps.so was (due to my original patch) causing
libmumps_common.so to be automatically loaded, but since libpords.so
was not also required, the error was occuring. I have added libpords.so
along with libmumps_common.so to be explicit dependencies of
libsmumps.so, etc., which seems to resolve the issue.
* ArrayFire: Add version 3.7.2.
* ArrayFire: Allow using MKL as the FFTW provider.
* ArrayFire: Ensure the libraries are properly found.
The required backend(s) can be specified in the library query.
* openssl: remove preprocessor flags incompatible with NVIDIA HPC SDK
* Update var/spack/repos/builtin/packages/openssl/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Scott McMillan <smcmillan@nvidia.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
