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2020-10-29Oneapi add compiler (#19330)Frank Willmore7-3/+164
* enable flatcc to be built with gcc/9.X.X * add static option for building libyogrt * cleanup * Initial working version * rework new oneapi wrappers * tested and removed my initials from source * cleanup * Update __init__.py * remove whitespace * working now with mods for testing, detection. Detection for oneapi is working, but entry needs to be modified to add link path for libimf.so. Cleared cruft for old Intel versions * fixed some formatting * cleanup * flake8 cleanup * flake8 * fixed syntax of compiler version detection tests * fixed syntax of compiler version detection tests modified: detection.py * fix typo * fixes for compilers tests * remove erroneous tests for outdated -std= flags, remove ifx version check (output won't parse) Co-authored-by: Frank Willmore <willmore@anl.gov>
2020-10-29Suite-sparse: Fix Darwin install name (#19507)Jean-Paul Pelteret1-0/+7
2020-10-29yapf: add version 0.30.0 (#19598)Geoffrey Oxberry1-0/+1
2020-10-29Adds a package for LvArray (#19221)Ben Corbett3-8/+347
* RAJA and CHAI changes. * Added LvArray package.
2020-10-29Patch CMake version check in Umpire (#19590)David Beckingsale2-0/+16
* Patch CMake version check in Umpire * Update version constraint for cmake_version_check patch Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Add maintainers to Umpire Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-10-29[py-torch-nvidia-apex] added version 201019 and added dependency on p… ↵Jen Herting1-0/+2
(#19548) * [py-torch-nvidia-apex] added version 201019 and added dependency on py-pybind11 * [py-torch-nvidia-apex] changed versioning format * [py-torch-nvidia-apex] removed redundent version condition * [py-torch-nvidia-apex] removed condition on dependency
2020-10-29New package: py-cupy (#19468)Jen Herting1-0/+27
* [py-cupy] created template * [py-cupy] added dependencies * [py-cupy] switched to git based download for submodules * [py-cupy] added dependencies * [py-cupy] added homepage and description. removed fixmes * [py-cupy] updated to tarball from pypi
2020-10-29plplot:fix:　add: depends_on('libsm', type='link') (#19594)h-denpo1-0/+1
2020-10-29Gromacs: Remove a dependency that could never be enabled. (#19599)Rémi Lacroix1-1/+0
The `fft` variant was removed but not the associated dependency.
2020-10-29clingo+python extends python (#19585)Greg Becker1-0/+1
2020-10-29Adding AOCC support for M4 (#19572)AMD Toolchain Support1-7/+4
* Adding AOCC support for M4 * combining 4 if-statements into a single if-statement with or conditions * keeping parentheses around the or expressions * fixing flake8 test failures Co-authored-by: mohan babu <mohbabul@amd.com>
2020-10-29SLATE package: New versions of slate, blaspp, and lapackpp with CMake build ↵G-Ragghianti3-36/+32
support (#19587) * New versions of slate, blaspp, and lapackpp with CMake build support * Fixing formatting
2020-10-28launchmon: Fix for aarch64 (#19562)t-nojiri2-0/+1295
2020-10-28qt: Silence build and force `xmlpatterns` library on for Qt4 (#19591)Seth R. Johnson1-3/+7
For some mysterious reason Qt4 stopped building the xmlpatterns component, needed by some downstream packages. With this patch, the component successfully builds with ``` qt@4.8.7~dbus~debug~examples~framework~gtk~opengl~phonon+shared~sql~ssl~tools~webkit freetype=none arch=linux-rhel7-haswell %gcc@10.2.0 ```
2020-10-28pest suit + (#19458)manifest1-0/+27
* pestpp + * build -f default
2020-10-28PopLDdecay package + (#17802)manifest1-0/+28
* poplddecay bio * flake8 debug * bin PATH correction * build step opt * BUILD_PATH fix * retro implementation + style fix
2020-10-28Pbbam debug (#17803)manifest1-1/+1
* pbbam path fix * pbbam flake8 fix * sys var build_directory sub * pbbam flake8 fix
2020-10-28sbang: vendor sbangTodd Gamblin4-164/+24
`sbang` now lives at https://github.com/spack/sbang, and it has its own test suite that's more extensive than what's in Spack. We'll leave sbang tests to sbang from now on, and just vendor `bin/sbang` directly. Remaining `sbang` tests have to do with patching files, not with `sbang`'s functionality. This update also fixes a bug with `sbang` and multiple command line arguments that was introduced in #19529. See: * https://github.com/spack/sbang/pull/1 * https://github.com/spack/sbang/pull/2 - [x] include latest `sbang` from https://github.com/spack/sbang - [x] remove old `sbang` tests from Spack - [x] update `COPYRIGHT` and `cmd/license.py`
2020-10-28RAJA package: Don't set both CUDA_ARCH and CMAKE_CUDA_FLAGS (#19589)David Beckingsale1-2/+0
2020-10-28Update strelka (#19565)dunatotatos1-47/+13
* Update package.py Remove breaking patch. Patching the shebang is useless is the dependencies are properly loaded before execution. Furthermore, the long paths which can be generated when installing with Spack can exceed the maximum length of the shebang. * Add newer versions of strelka.
2020-10-28Remove unused dependency. (#19566)dunatotatos1-1/+0
Boost is not used to build Manta.
2020-10-28py-mmcv: fix Opencv detection. (#19567)Toyohisa Kameyama2-0/+30
2020-10-28Do not build XCFun tests (#19568)Roberto Di Remigio1-0/+1
2020-10-28Do not build MRCPP tests (#19569)Roberto Di Remigio1-0/+1
2020-10-28Add new package: mrchem (#19571)Roberto Di Remigio1-0/+47
2020-10-28openssl: Add version 1.1.1h (#19574)Dr. Christian Tacke1-0/+1
2020-10-27Add new minor version 1.2.1 for ButterflyPACK (#19554)Pieter Ghysels1-0/+1
2020-10-27asciidoc-py3 add docbook dependency and fix a enviroment variable problem ↵lorddavidiii3-3/+13
for docbook-{xml,xsl} (#19547) * asciidoc-py3: add docbook-{xml,xsl} dependency * docbook-{xsl,xml}: fix XML_CATALOG_FILES enviroment variable
2020-10-27New package: libcudf (#19110)Jen Herting1-0/+36
* [libcudf] created template * [libcudf] depends on cuda * [libcudf] set cmake dir * [libcudf] depends on boost * [libcudf] depends on py-pyarrow * [libcudf] depends on librmm * [libcudf] depends on dlpack * [libcudf] added more dependency information from https://github.com/rapidsai/libcudf/blob/v0.15.0/CONTRIBUTING.md#customizing-the-build * [libcudf] removed python dependencies * [libcudf] fixed url that got mangled in package renaming * [libcudf] added default build options from build.sh * [libcudf] added version 0.16.0a * [libcudf] removed version 0.16.0a as it's an alpha version * [libcudf] added homepage and description. removed fixmes * [libcudf] flake8 * [libcudf] arrow requires +orc * [libcudf] requires +parquet * [libcudf] checksum changed
2020-10-27New Package: py-rmm (#19104)Jen Herting1-0/+30
* [py-rmm] created template * [py-rmm] added dependencies * [py-rmm] setting build_directory * [py-rmm] added dependencies cuda and spdlog * [py-rmm] added homepage and description. removed fixmes * [py-rmm] added for loop for dependency versions * [py-rmm] flake8 * [py-rmm] updating upper range of python version * [py-rmm] removing python upper limit
2020-10-27bowtie2: Add version 2.4.2 (#19537)t-nojiri1-0/+2
2020-10-27sbang: use bashcov in sbang on LinuxTodd Gamblin1-2/+7
2020-10-27sbang: convert sbang script to POSIX shellTodd Gamblin3-55/+181
`sbang` was previously a bash script but did not need to be. This converts it to a plain old POSIX shell script and adds some options. This also allows us to simplify sbang shebangs to `#!/bin/sh /path/to/sbang` instead of `#!/bin/bash /path/to/sbang`. The new script passes shellcheck (with a few exceptions noted in the file) - [x] `SBANG_DEBUG` env var enables printing what *would* be executed - [x] `sbang` checks whether it has been passed an option and fails gracefully - [x] `sbang` will now fail if it can't find a second shebang line, or if the second line happens to be sbang (avoid infinite loops) - [x] add more rigorous tests for `sbang` behavior using `SBANG_DEBUG`
2020-10-27Update package.py (#19513)adityakavalur1-3/+3
On Cori(Cray-XC40), I need to pass the entire path for the compilers, this is what is saved in c_compiler, cpp_compiler, f_compiler. Therefore, when for the MPI wrappers only the binary name is provided I run into the same issue. There is no drawback of passing the entire path, this is set by the user through the compiler path anyways.
2020-10-27Update MRCPP package.py (#19541)Roberto Di Remigio1-1/+3
2020-10-27ghostscript: fix: add: depends_on('krb5', type='link') (#19536)h-denpo1-0/+1
2020-10-27diamond: Add version 2.0.4 (#19535)t-nojiri1-1/+5
2020-10-27added -lpthread flag in kv/tests/CMakeLists.txt (#19533)Jungwon Kim1-2/+3
* added -lpthread flag in kv/tests/CMakeLists.txt * Update var/spack/repos/builtin/packages/papyrus/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-10-27modified:var/spack/repos/builtin/packages/ppopen-appl-bem-at/package.py (#19538)daichi-nishi1-4/+3
2020-10-27camp: Add missing checksum (#19543)Chuck Atkins1-1/+2
2020-10-26sbang: add support for php (#18299)Toyohisa Kameyama5-7/+105
PHP supports an initial shebang, but its comment syntax can't handle our 2-line shebangs. So, we need to embed the 2nd-line shebang comment to look like a PHP comment: <?php #!/path/to/php ?> This adds patching support to the sbang hook and support for instrumenting php shebangs. This also patches `phar`, which is a tool used to create php packages. `phar` itself has to add sbangs to those packages (as phar archives apparently contain UTF-8, as well as binary blobs), and `phar` sets a checksum based on the contents of the package. Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
2020-10-26netgauge: Fix for aarch64 (#19462)t-nojiri1-0/+7
* netgauge: Fix for aarch64 * netgauge: Revise the points indicated by the review.
2020-10-26New package: date (#19515)Geoffrey Gunter1-0/+49
* Add new package: date * date: resolve style conformance issues * date: explicitly disable some cmake options Explicitly disable CMake options corresponding to variant 'tzdb=download' * date: make more cmake options explicit * date: simplify defining cmake cli args
2020-10-26coverage: add bin directory to coverage (#19530)Todd Gamblin1-1/+3
2020-10-26New package: py-minrpc (#19524)iarspider1-0/+18
* New package: py-minrpc * Delete package.py.save * Update var/spack/repos/builtin/packages/py-minrpc/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-10-26packages/phist: fix incorrect git url (#19527)jthies1-1/+1
Co-authored-by: Thies <thie_jo@fe-store01.sc.bs.dlr.de>
2020-10-26package/gunrock add v1.2 (#19516)Sinan1-3/+3
* package/gunrock add v1.2 * Update var/spack/repos/builtin/packages/gunrock/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: sbulut <sbulut@3vgeomatics.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-10-26Add camp & BLT dependencies to Umpire (#19411)David Beckingsale2-1/+11
* Add camp & BLT dependencies to Umpire * Remove tests variant
2020-10-26sbang: put sbang in the install_tree (#11598)Patrick Gartung4-17/+90
`sbang` is not always accessible to users of packages, e.g., if Spack is installed in someone's home directory and they deploy software for others. Avoid this by: 1. Always installing the `sbang` script in the `install_tree` 2. Relocating binaries to point to the copy in the `install_tree` and not the one in the Spack installation. This PR also: - ensures that `sbang` is reinstalled if it is modified in Spack - adds tests - updates the way `gobject-introspection` patches Makefiles to support `sbang` Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
2020-10-26Update GATK versions. (#19521)dunatotatos1-0/+40
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