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2022-04-27openmpi: add toggle for rsh plm (#30251)Harmen Stoppels1-1/+6
By default `openmpi` needs `rsh` from `openssh`, which is a somewhat redundant dependency for clusters using slurm. This PR adds a toggle to allow users to disable the ssh/rsh plm altogether.
2022-04-27gcta: rework package recipe (#30286)snehring2-10/+85
2022-04-27py-pil: deprecate package (#30308)Adam J. Stewart1-1/+1
2022-04-27relion: add altcpu variant and fix fftw (#30097)Glenn Johnson1-16/+53
This package was not setting FFTW when +mklfft was used with +cuda. Since both were set to 'True', the default build was not linked to any FFTW, leading to a run time error. It seems MKL support was conflated with alternative CPU acceleration support. This PR does the following: - adds the altcpu variant to specify non-GPU/CPU acceleration - sets a conflict between +altcpu and +cuda - sets an FFTW implementation - sets fltk+xft when +gui to get a decent looking GUI interface - sets tbb dependency only when +altcpu - adds dependency on ctffind - adds variant and dependency on motioncor2 - sets defaults for - qsub template location - ctffind location - motioncor2 location Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2022-04-27bucky: fix compile errors with newer gccs (#30314)snehring1-2/+10
2022-04-27ASP-based solver: handle installed specs from unknown namespaces (#30092)Massimiliano Culpo2-0/+44
fixes #28259 This commit discard specs from unknown namespaces from the ones that can be "reused" during concretization. Previously Spack would just error out when encountering them.
2022-04-27reprimand: update requests on boost (#30109)Erik Schnetter1-1/+1
2022-04-27suntans: add new package (#30149)Lhxone1-0/+46
2022-04-26py-cryptography@35: tell cargo to use cli git, not cargo internal git… ↵eugeneswalker1-0/+10
(#30307)
2022-04-26libgit2: add 1.4.3 and 1.3.1 (#30122)Michael Kuhn1-0/+2
2022-04-27fossil: New package (#30311)Erik Schnetter1-0/+25
* fossil: new package * fossil: Format code
2022-04-26Feature: Allow re-use of run_test() in install_time_test_callbacks (#26594)Tamara Dahlgren6-54/+167
Allow re-use of run_test() in install_time_test_callbacks Co-authored-by: Greg Becker <becker33@llnl.gov>
2022-04-27New package: CaNS (#30218)Lhxone1-0/+45
2022-04-26hadoop: Update url and add version 3.3.2 (#29812)haralmha1-1/+2
* hadoop: Update url and add version 3.3.2 * Update url
2022-04-26arrow: Add version 7.0.0 (#29962)haralmha1-0/+1
2022-04-26New package: Swan (#30217)Lhxone1-0/+40
2022-04-26gnuplot: Add version 5.4.3 and add workaround for not found DSO (#30163)haralmha1-0/+2
2022-04-26docs: Fix ROCmPackage example syntax (#30168)Ken Raffenetti1-1/+1
2022-04-26Add g2tmpl versions 1.10.2 and 1.10.1 (#30202)Kyle Gerheiser1-0/+2
2022-04-26Power9 build fix for ctffind4 (#30300)John Hodrien2-0/+17
Only tested against the latest version, which is why it only applies the patch when using 4.1.14. Fix comes from: https://grigoriefflab.umassmed.edu/forum/software/ctffind_ctftilt/installing_ctffind_4114_ibm_power9
2022-04-26EVE now use main instead of develop as main branch (#30220)Joel Falcou1-1/+1
2022-04-26old concretizer: update deprecation warning (#30227)Greg Becker1-2/+2
2022-04-26intel-xed: add version 2022.04.17 (#30239)Mark W. Krentel2-3/+17
1. Add version 2022.04.17 (new numbering scheme) and update mbuild resource. 2. Branch 'master' is now 'main'. 3. Old rev 10.2019.03 needs a patch for python vs python3.
2022-04-26Add NCIO v1.1.0 (#30306)Kyle Gerheiser1-0/+1
See release notes https://github.com/NOAA-EMC/NCEPLIBS-ncio/releases/tag/v1.1.0
2022-04-26Windows: fix termination of process output redirection (#29923)John W. Parent2-25/+20
The parent thread in the process stdout redirection logic on Windows was closing a file that was being read in child thread, which lead to error-based termination of the reader thread. This updates the interaction to avoid the error.
2022-04-26Add checksum for py-ipywidgets@7.7.0 (#30155)Andrea Valenzuela2-1/+5
* Add checksum for py-ipywidgets@7.7.0 * Correct py-widgetsnbextension and py-ipython dependencies * Update widgetsnbextension dependency to 3.6 Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Allow requirement to next versions Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Revert ipyhton dependencies * Add widgetsnbextension@3.6.0 checksum Co-authored-by: aandvalenzuela <andrea.valenzuela.ramirez@cern.ch> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-04-26thrust: added version 1.12.1-1.16.0 (#30292)Lucas Frérot1-0/+6
2022-04-26py-uvw: updated versions (#30297)Lucas Frérot1-0/+4
2022-04-26opendatadetector: add new package (#30298)Valentin Volkl1-0/+36
* opendatadetector: add new package * style * opendatadetector: add hep tag
2022-04-26ginkgo: fix stand-alone test directory / install_test (#28412)Tamara Dahlgren1-3/+11
2022-04-26spack spec: add '--format' argument (#27908)lorddavidiii3-4/+15
2022-04-26exabayes: specify c++11 (#30282)snehring1-0/+6
2022-04-26boost: update list of modules (#30104)Erik Schnetter1-5/+28
Co-authored-by: Tim Haines <thaines.astro@gmail.com>
2022-04-26setup_package: don't unload modules on Cray when run with --dirty (#30261)Mark W. Krentel2-1/+40
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2022-04-26spfft: pass cuda_arch to cmake (#30295)Simon Pintarelli1-0/+4
2022-04-26express: specify patch version range (#30283)snehring1-2/+2
2022-04-26googletest: change "master" to "main" (#30285)H. Joe Lee1-1/+1
There's no master branch on GitHub for googletest.
2022-04-26snpeff: change jdk dependency to java (#30048)dlkuehn1-1/+1
Co-authored-by: David Kuehn <las_dkuehn@iastate.edu>
2022-04-26apex: add v2.5.1 (#30287)Kevin Huck1-0/+1
2022-04-26hiop: add v0.6.1, add new variant "cusolver" (#30288)Asher Mancinelli2-2/+7
2022-04-26glib: add 2.72.1 and 2.70.5 (#30274)Michael Kuhn1-2/+4
2022-04-26gawk: drop gettext by default (#30290)Harmen Stoppels1-1/+6
Reduces the number of packages to bootstrap gcc (which actually has --disable-nls).
2022-04-25ASP-based solver: allow configuring target selection (#29835)Massimiliano Culpo6-43/+162
* ASP-based solver: allow configuring target selection This commit adds a new "concretizer:targets" configuration section, and two options under it. - "concretizer:targets:granularity" allows switching from considering only generic targets to consider all possible microarchitectures. - "concretizer:targets:host_compatible" instead controls whether we can concretize for microarchitectures that are incompatible with the current host. * Add documentation * Add unit-tests
2022-04-25Environments: add flag to skip printing concretized specs (#30272)iarspider2-2/+6
With an active environment, you can now run "spack concretize --quiet" and it will suppress printing the concretized specs.
2022-04-25MAINT: Add a debug variant to PyTorch (#30267)Rohit Goswami1-0/+6
* MAINT: Add a debug flag * MAINT: Apply suggestions from code review Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-04-25exago +cuda, +rocm: pass amdgpu_target, cuda_arch to dependencies, as ↵eugeneswalker2-13/+22
appropriate (#30259) * exago +rocm: pass amdgpu_target to raja, hiop dependencies * +cuda builds: pass cuda_arch to dependencies * hiop: pass cuda_arch to dependencies
2022-04-25gcc: Make gcc 11.3 build on Darwin (#30278)Erik Schnetter0-0/+0
Don't apply a Darwin-specific patch that doesn't work on 11.3 any more. Closes https://github.com/spack/spack/issues/30264.
2022-04-25gcc: Make gcc 11.3 build on Darwin (#30278)Erik Schnetter1-1/+1
Don't apply a Darwin-specific patch that doesn't work on 11.3 any more. Closes https://github.com/spack/spack/issues/30264.
2022-04-25OpenMPI: improve PMix handling (#29449)Seth R. Johnson2-105/+87
* openmpi: always require pmix for 4: `~pmix` is not applicable to version 4+, since it always builds a vendored copy of pmix (currently 3.2.3). * pmix: relax version requirements When the version range was specified, newer versions didn't exist. Also use normalized spack versions rather than artificial .9.9 /.0.0. * openmpi: restrict pmix versions pmix option isn't available for OpenMPI@1, and according to https://github.com/open-mpi/ompi/issues/7988 , OpenMPI 4.0.1 will not build with pmix@3.1.5. * pmix: add newer versions * OpenMPI: re-express conflicts/configure logic as conditional variants This relies partly on `self.enable_or_disable` and its ilk to emit an empty list when the variant isn't applicable.
2022-04-25ASP-based solver: always consider version of installed packages (#29933)Massimiliano Culpo3-19/+115
* ASP-based solver: always consider version of installed packages fixes #29201 Explicitly add facts for versions of installed software when using the --reuse option, so that we could consider versions that are not declared in package.py
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