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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
2020-10-26fujitsu-ssl2: update package.py (#19519)takanori-ihara1-60/+68
2020-10-26abseil-cpp: add versions 20200923.{1,2} (#19517)Geoffrey Gunter1-1/+3
2020-10-26New package: py-visdom (#19479)Jen Herting1-0/+30
* [py-visdom] created template * [py-visdom] added dependencies * [py-visdom] added homepage and description. removed fixmes * [py-visdom] added dependency on py-torchfile * [py-visdom] py-pillow -> pil * [py-visdom] fixed url format * [py-visdom] fixed url format
2020-10-26Add BLT package (#19410)David Beckingsale1-0/+30
* Add BLT package * Switch install function Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Add type='run' to cmake dependency Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Add git attribute to BLT Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-10-26cp2k, libxc, libint: fix builds with %intel, resp. intel-parallel-studio+mkl ↵Tiziano Müller3-39/+23
(#19522) * cp2k: locate correct include dir when using intel-parallel-studio+mkl for fftw-api * libxc: drop arch-specific intel opt. flags fixes #17794 * libint: drop arch-specific intel opt. flags, always build Fortran example with FC fixes #17509
2020-10-26bugfix: test_push_and_fetch_keys should be skipped w/o gpg (#19511)Todd Gamblin1-0/+2
- [x] add a `@pytest.skipif` decorator
2020-10-25package/pmdk add variants, version 1.9 (#19512)Sinan1-4/+13
* package/pmdk add variants, version 1.9 * add dependency * Update var/spack/repos/builtin/packages/pmdk/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>
2020-10-25phist: two new versions and disable ccache because we don't have a ↵jthies1-1/+4
dependency on ccache. (#19510) Otherwise, phist would look for ccache via cmake, which is not the spack way to do it. Co-authored-by: Thies <thie_jo@be-cpu03.sc.bs.dlr.de>
2020-10-24bugfix: fix config merge order for OrderdDicts (#18482)Todd Gamblin5-30/+67
The logic in `config.py` merges lists correctly so that list elements from higher-precedence config files come first, but the way we merge `dict` elements reverses the precedence. Since `mirrors.yaml` relies on `OrderedDict` for precedence, this bug causes mirrors in lower-precedence config scopes to be checked before higher-precedence scopes. We should probably convert `mirrors.yaml` to use a list at some point, but in the meantie here's a fix for `OrderedDict`. - [x] ensuring that keys are ordered correctly in `OrderedDict` by re-inserting keys from the destination `dict` after adding the keys from the source `dict`. - [x] also simplify the logic in `merge_yaml` by always reinserting common keys -- this preserves mark information without all the special cases, and makes it simpler to preserve insertion order. Assuming a default spack configuration, if we run this: ```console $ spack mirror add foo https://bar.com ``` Results before this change: ```console $ spack config blame mirrors --- mirrors: /Users/gamblin2/src/spack/etc/spack/defaults/mirrors.yaml:2 spack-public: https://spack-llnl-mirror.s3-us-west-2.amazonaws.com/ /Users/gamblin2/.spack/mirrors.yaml:2 foo: https://bar.com ``` Results after: ```console $ spack config blame mirrors --- mirrors: /Users/gamblin2/.spack/mirrors.yaml:2 foo: https://bar.com /Users/gamblin2/src/spack/etc/spack/defaults/mirrors.yaml:2 spack-public: https://spack-llnl-mirror.s3-us-west-2.amazonaws.com/ ```
2020-10-24py-coverage: added v5.3 (#19509)Massimiliano Culpo1-0/+1
2020-10-23docs: update docs on shell support and using packages (#19486)Todd Gamblin3-337/+344
Shell integration no longer requires setting `SPACK_ROOT`, so we can simplify the documentation on it. The docs on shell support and using packages are getting a bit old, and information on `spack load` (which seems to be everyone's most common way of using packages) is hard to find. This PR simplifies the shell documentation to remove SPACK_ROOT, and also moves some sections around for clearer organization. - [x] make docs on sourcing setup scripts clearer and simpler - [x] introduce `spack load` early in the basic usage guide instead of burying it in the module docs - [x] clean up module docs so that spack module tcl loads comes later - [x] be clear about the different ways to use packages so that the users can find the docs better. Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2020-10-23csh: don't require SPACK_ROOT for sourcing setup-env.csh (#18225)Todd Gamblin15-122/+242
Don't require SPACK_ROOT for sourcing setup-env.csh and make output more consistent
2020-10-23Fix GROMACS to require FFTW when using cuda (#19505)Marty Kandes1-1/+1
GROMACS still requires a version of FFTW when compiling it to utilize NVIDIA GPUs. In fact, the type of calculation that depends on FFTW -- Particle-Mesh Ewald (PME) -- is generally run on the host system's CPUs, even when GPUs are available.
2020-10-23New package: py-rise (#19496)iarspider1-0/+19
* New package: py-rise * Fix URL and add description * Update var/spack/repos/builtin/packages/py-rise/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-10-23let intel-parallel-studio provide fftw-api for +mkl (#19497)Tiziano Müller1-0/+4
2020-10-23CMake fix: narrow versions that the PGI patch is applied to (#19495)Scott McMillan1-1/+1
Co-authored-by: Scott McMillan <smcmillan@nvidia.com>
2020-10-23New package: py-gsi (#19494)iarspider1-0/+19
* New package: py-gsi * Add dependency on py-setuptools
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