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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
2020-10-23Update asciidoc-py3 and fix build problem (#19491)lorddavidiii1-0/+3
* asciidoc-py3: add new version 9.0.3 * asciidoc-py3: fix build - add libxml2 and libxslt as dependency
2020-10-23modified:var/spack/repos/builtin/packages/ppopen-appl-fem/package.py (#19489)daichi-nishi1-2/+3
2020-10-23modified:var/spack/repos/builtin/packages/ppopen-appl-fdm/package.py (#19488)daichi-nishi1-3/+2
2020-10-23gaussian-src: initial commit, gaussian-view: update to 6.1.1 (#17711)Tiziano Müller7-8/+1237
* gaussian-src: initial commit to build from source * do not install the source to ensure to not accidentally distribute it to users * set required runtime env vars based on the login.profile * gaussian-view: update to 6.1.1
2020-10-23gcc: Fix zstd patch version range (#19490)Michael Kuhn1-1/+1
PR #19482 updated gcc to only apply the zstd patch until @10.2 but the releases/gcc-10 branch actually does not contain the patch yet, that is, gcc@10.3 will most likely have the same problem. Apply the patch for all 10.x releases instead.
2020-10-23Add new package: acpica-tools (#18739)darmac1-0/+22
* Add new package: acpica-tools * refine build dependencies
2020-10-23gcc: fix build of gcc@master by limiting the version range of a patch (#19482)Thomas Green1-1/+1
Co-authored-by: Thomas Green <ca-tgreen@gw4a64fxlogin00.head.gw4.metoffice.gov.uk>
2020-10-23graphviz: add patch for XCode 12 (#19485)Todd Gamblin2-0/+26
- [x] Add a patch to fix an implicit declaration error with apple-clang 12
2020-10-23openipmi: added new package at v2.0.28 (#18790)darmac1-0/+30
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-10-22modified:var/spack/repos/builtin/packages/ppopen-appl-fvm/package.py (#19487)daichi-nishi1-3/+5
2020-10-22Bcolz (#19331)manifest1-0/+27
* gemini dep -py-bcolz + * Update var/spack/repos/builtin/packages/py-bcolz/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-bcolz/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * py-bcolz URL fix * Update var/spack/repos/builtin/packages/py-bcolz/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-10-22Syscalc hash (#19323)iarspider1-2/+3
* Update syscalc hash * Tiny fix * Change URL and update hash as advised by the devs Co-authored-by: iarspider <iarpsider@gmail.com>
2020-10-22New package: py-dominate (#19483)Jen Herting1-0/+24
* [py-dominate] created template * [py-dominate] added dependencies * [py-dominate] added homepage and description. removed fixmes * [py-dominate] fixed url format
2020-10-22Enable packages to use the NVIDIA HPC SDK (#19452)Scott McMillan85-18/+1824
* Enable packages to use the NVIDIA HPC SDK * fix linter and review items * fix linter issue Co-authored-by: Scott McMillan <smcmillan@nvidia.com>
2020-10-22New package: py-torchfile (#19481)Jen Herting1-0/+22
* [py-torchfile] created template * [py-torchfile] set python versions * [py-torchfile] depends on py-numpy * [py-torchfile] fixed url format * [py-torchfile] added homepage and description. removed fixmes * [py-torchfile] fixed url format
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