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2020-01-28intel-tbb: Fix install names on Darwin (#14650)Ben Morgan1-0/+7
* intel-tbb: Fix install names on Darwin Intel-TBB's libraries on Darwin are installed with "@rpath" prefixed to their install names. This was found to cause issues building the root package on Darwin due to libtbb not being found when running some of the generated tools linking to it. Follow example from other packages with the same issue and fixup up install names for intel-tbb post install. * intel-tbb: fix flake8 errors
2020-01-28Note about Intel compiler segfault with long paths (#14652)Glenn Johnson1-5/+15
This PR adds a note about segfaults with the Intel compiler when the install paths are long and the dependencies many.
2020-01-28Fix handling of filter_file exceptions (#14651)Greg Becker1-1/+0
2020-01-28Fix for #14148 (#14595)iarspider1-20/+28
* Dirty hack to fix #14148 * A better way of checking if a package is taken from system * Update var/spack/repos/builtin/packages/qt/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update qt/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-01-28ninja: add v1.10.0 (#14647)Christoph Junghans1-0/+1
2020-01-27make the new 'spack load' faster (#14628)Andrew W Elble1-10/+13
before, a 'time spack load singularity' 4.129u 0.346s 0:04.47 99.7% 0+0k 0+8io 0pf+0w after, a 'time spack load singularity' 0.844u 0.319s 0:01.16 99.1% 0+0k 0+16io 0pf+0w
2020-01-27fix spack env loads example (#14558)Owen Solberg1-2/+3
2020-01-27mpifileutils: add v0.10 (#14644)Adam Moody1-6/+7
Signed-off-by: Adam Moody <moody20@llnl.gov>
2020-01-27Fix: hash-based references to upstream specs (#14629)Andrew W Elble2-36/+56
Spack commands referring to upstream-installed specs by hash have been broken since 6b619da (merged September 2019), which added a new Database function specifically for parsing hashes from command-line specs; this function was inappropriately attempting to acquire locks on upstream databases. This PR updates the offending function to avoid locking upstream databases and also updates associated tests to catch regression errors: the upstream database created for these tests was not explicitly set as an upstream (i.e. initialized with upstream=True) so it was not guarding against inappropriate accesses.
2020-01-27Package source ID cannot be determined when the url can't be extrapolated ↵Patrick Gartung1-1/+4
for older version. (#14237)
2020-01-27Follow the example of spack arch (#14642)Patrick Gartung1-4/+8
2020-01-27Add the py-merlinwf package (#14622)Joe Koning1-0/+38
* Add the py-merlinwf package * Fix importlib-resources package name for spack naming convention. * Add build to dependencies and add updated versions. * Remove pytest-runner dependency. * Fix typo. * Add the py-tabulate dependency. * Add sha256 for version 1.0.0 * Change to maestro version 1.1.5. * Increase to version 1.0.4. * Bump maestrowf version and prepare for new pypi version. * Add sha256sum for version 1.1.5 * Add version 1.1.1. Update maestrowf version to 1.1.7 * Add versions 1.0.5, 1.1.0, 1.1.1 and potential 1.2.0. * Add version 1.2.0 and when on maestrowf@1.1.6. * Add version 1.2.2 , remove 1.2.1 and 1.1.0. * Update var/spack/repos/builtin/packages/py-merlinwf/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-merlinwf/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Remove mysql variant until new mysql interface module is enabled. The mysql code may be removed. Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-01-27Only set tcl default. Remove lmod default. (#14640)Patrick Gartung1-1/+0
2020-01-27Fix bug introduced by pull request 14467 being merged (#14639)Patrick Gartung1-2/+8
* Fix bug introduced by pull request 14467 being merged * Only filter on platform and OS
2020-01-27Set module_roots in test/config/config.yaml to defaults. (#14517)Patrick Gartung1-0/+3
2020-01-27Unified environment modifications in config files (#14372)Massimiliano Culpo8-183/+169
* Unified environment modifications in config files fixes #13357 This commit factors all the code that is involved in the validation (schema) and parsing of environment modifications from configuration files in a single place. The factored out code is then used for module files and compiler configuration. Attributes were separated by dashes in `compilers.yaml` files and by underscores in `modules.yaml` files. This PR unifies the syntax on attributes separated by underscores. Unit testing of environment modifications in compilers has been refactored and simplified.
2020-01-27asdf-cxx: new package (#14637)Erik Schnetter1-0/+47
2020-01-27amrex: Update to version 20.01 (#14635)Erik Schnetter1-0/+2
Now using Github releases instead of git commits.
2020-01-26Fix Python version compatibility tests for vermin 0.10.0 (#14632)Adam J. Stewart2-4/+4
2020-01-26pygdal and gdal versions should be in lockstep (#14630)Sinan1-1/+4
2020-01-26Add py-vermin package (#14631)Adam J. Stewart1-0/+23
2020-01-26simulationio: Correct HDF5 dependency bounds (#14626)Erik Schnetter1-1/+1
The HDF5 dependency bound was inverted. (How did this ever compile? There is a cmake check.)
2020-01-26hwloc: New version 2.1.0 (#14627)Erik Schnetter1-0/+1
2020-01-26curl: New version 7.68.0 (#14625)Erik Schnetter1-0/+1
2020-01-26Add TensorFlow 1.15.2 (#14624)Adam J. Stewart1-0/+1
2020-01-25When spack install checks for buildcaches only add urls for current arch. ↵Patrick Gartung2-4/+10
(#14467)
2020-01-25h5cpp: Download from github release instead of git repo (#14573)Erik Schnetter1-3/+4
* h5cpp: Download from github release instead of git repo * Correct typo in package description
2020-01-25Add TensorFlow 2.0.1 (#14623)Adam J. Stewart1-0/+1
2020-01-25Get vtk-8.2.0 to build (#14562)Glenn Johnson1-2/+17
This PR adds some extra dependencies needed for vtk-8.2.0. It also handles the variable name changes to turn off some of the external libraries.
2020-01-25acts-core: Add and adapt to ACTS v0.14.0 and v0.15.0 (#14580)Hadrien G1-1/+7
* Add and adapt to ACTS v0.14.0 * Add v0.15.0 too
2020-01-25Removing flang variant from llvm package (#14600)Brian Homerding1-83/+6
2020-01-25libcircle: add v0.3 (#14611)Adam Moody1-0/+1
2020-01-24configure z3+python to build python libraries in its own prefix (#14604)Greg Becker1-3/+13
2020-01-24Get py-torch to build caffe2 (#14619)Glenn Johnson1-2/+31
* Get py-torch to build caffe2 This PR gets the py-torch package to build with caffe2, and closes issue #14576. If building on a machine with CUDA but no GPU the build will try to build with all compute capabilities. Older compute capabilities are not supported so the build will fail. The list of capabilities can be passed to the build using values set in the cuda_arch variant. Likewise, conflicts are also set to catch if the unsupported capabilities are listed in cuda_arch. This PR also sets version constraints on using an external mkldnn for newer versions. Currenly, only versions up to 0.4 use an external mkldnn library. Also, the cuda variant is set to True, which restores previous behavior. * Update var/spack/repos/builtin/packages/py-torch/package.py Fix typo. Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Adjust conflicts This commit adjusts the conflicts. There is an issue with the cuda_arch=20 conflicts directive as there is a conflicting dependency with any version >=1.1 and a cuda_arch=20 dependency specified in CudaPackage that gets trapped first. * Use a common message for conflicts This commit adds a variable to contain the bulk of the message stringi for the cuda_arch conflicts. This is used along with a version string in the conflicts directives messages. * Fix the strings - Use a multiline string for the cuda_arch_conflict variable. - No need for format() in the msg value. Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-01-24py-opppy package: add version 0_1_2 (#14229)Mathew Cleveland1-1/+2
2020-01-24py-pygdal package: 2.4.0 depends on gdal 2.4.1 (#14075)iarspider1-0/+1
2020-01-24libhio: remove autoreconf method (#14283)plamborn1-4/+0
The autoreconf is not necessary and can cause errors.
2020-01-24New package: MBDyn (#14438)健美猞猁1-0/+19
2020-01-24harfbuzz package: add conflict for @2.3.1: with intel compiler (#14386)Glenn Johnson1-0/+3
harfbuzz 2.3.1 (and presumably all future versions after it) does not build with the Intel compiler
2020-01-24Add spack config list command for tab completion (#14474)Adam J. Stewart4-8/+29
* Add spack config list command for tab completion * Update tab completion scripts
2020-01-24New package: p3dfft3 (#14508)Sajid Ali1-0/+103
2020-01-24sbang: Fix perl binary detectionMichael Kuhn1-3/+3
The perl binary can also be called `perlX.Y.Z` if using a development build or simply using the versioned binary. We were also dropping all sbang arguments, since `exec $interpreter_v` was only using the first element of the `interpreter_v` array.
2020-01-24Fixing GCC compiler setting for PDT packageKevin Huck1-0/+4
2020-01-24IOR package: add version 3.2.1 (#14582)Kevin Manalo1-2/+3
2020-01-24charliecloud package: add version 0.13; remove older versions (#14591)Jordan Ogas1-23/+12
* Add version 0.13 and update to use Autotools build system * Remove all versions prior to 0.13 (which do not use Autotools)
2020-01-24bugfix: make `_source_single_file` work in venvs (#14569)Massimiliano Culpo2-6/+10
Using `sys.executable` to run Python in a sub-shell doesn't always work in a virtual environment as the `sys.executable` Python is not necessarily compatible with any loaded spack/other virtual environment. - revert use of sys.executable to print out subshell environment (#14496) - try instead to use an available python, then if there *is not* one, use `sys.executable` - this addresses RHEL8 (where there is no `python` and `PYTHONHOME` issue in a simpler way
2020-01-24magma: add new version 2.5.2Piotr Luszczek1-0/+1
2020-01-24Add version 0.6.3 of yaml-cpp.Jon Rood1-0/+1
2020-01-24Updated and cleaned up the recipe for the LBANN and Hydrogen packages. (#14612)Brian Van Essen2-9/+16
* Updated and cleaned up the recipe for the LBANN and Hydrogen packages. * Flake8 * Added type test for catch2
2020-01-24Added version for 10.2 compatibility (#14613)Brian Van Essen1-2/+7
* Added version for 10.2 compatibility * Updated the preferred version