Commit graph

13216 commits

Author SHA1 Message Date
manifest
3243e904a8
Pbbam debug (#17803)
* pbbam path fix

* pbbam flake8 fix

* sys var build_directory sub

* pbbam flake8 fix
2020-10-28 20:44:38 -05:00
David Beckingsale
44bacefb27
RAJA package: Don't set both CUDA_ARCH and CMAKE_CUDA_FLAGS (#19589) 2020-10-28 16:54:23 -07:00
dunatotatos
f028079564
Update strelka (#19565)
* 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.
2020-10-28 10:58:30 -05:00
dunatotatos
1dd7370885
Remove unused dependency. (#19566)
Boost is not used to build Manta.
2020-10-28 10:57:19 -05:00
Toyohisa Kameyama
f320a650d8
py-mmcv: fix Opencv detection. (#19567) 2020-10-28 10:56:52 -05:00
Roberto Di Remigio
98a1771590
Do not build XCFun tests (#19568) 2020-10-28 10:56:11 -05:00
Roberto Di Remigio
f4b63db78f
Do not build MRCPP tests (#19569) 2020-10-28 10:55:46 -05:00
Roberto Di Remigio
85e6334d6f
Add new package: mrchem (#19571) 2020-10-28 10:55:19 -05:00
Dr. Christian Tacke
674fb16828
openssl: Add version 1.1.1h (#19574) 2020-10-28 10:53:33 -05:00
Pieter Ghysels
9b809e01b4
Add new minor version 1.2.1 for ButterflyPACK (#19554) 2020-10-27 20:28:24 -05:00
lorddavidiii
6a5d399f55
asciidoc-py3 add docbook dependency and fix a enviroment variable problem for docbook-{xml,xsl} (#19547)
* asciidoc-py3: add docbook-{xml,xsl} dependency

* docbook-{xsl,xml}: fix XML_CATALOG_FILES enviroment variable
2020-10-27 20:11:37 -05:00
Jen Herting
79b0eab2af
New package: libcudf (#19110)
* [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
2020-10-27 20:11:06 -05:00
Jen Herting
7bd5397aca
New Package: py-rmm (#19104)
* [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
2020-10-27 20:10:40 -05:00
t-nojiri
429f49a1e4
bowtie2: Add version 2.4.2 (#19537) 2020-10-27 20:09:05 -05:00
adityakavalur
9f89a7e9f7
Update package.py (#19513)
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.
2020-10-27 13:24:09 -05:00
Roberto Di Remigio
7313cf5ea5
Update MRCPP package.py (#19541) 2020-10-27 09:58:24 -05:00
h-denpo
78a759129a
ghostscript: fix: add: depends_on('krb5', type='link') (#19536) 2020-10-27 09:54:33 -05:00
t-nojiri
f6c51efa85
diamond: Add version 2.0.4 (#19535) 2020-10-27 09:53:38 -05:00
Jungwon Kim
64974c43c7
added -lpthread flag in kv/tests/CMakeLists.txt (#19533)
* 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>
2020-10-27 09:53:22 -05:00
daichi-nishi
e214deec5b
modified:var/spack/repos/builtin/packages/ppopen-appl-bem-at/package.py (#19538) 2020-10-27 09:53:04 -05:00
Chuck Atkins
57200f01fd
camp: Add missing checksum (#19543) 2020-10-27 09:52:28 -05:00
Toyohisa Kameyama
bb00b1a7c9
sbang: add support for php (#18299)
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>
2020-10-26 22:11:43 -07:00
t-nojiri
cb07d9ddb1
netgauge: Fix for aarch64 (#19462)
* netgauge: Fix for aarch64

* netgauge: Revise the points indicated by the review.
2020-10-26 20:20:18 -05:00
Geoffrey Gunter
e9223062a8
New package: date (#19515)
* 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
2020-10-26 20:18:34 -05:00
iarspider
93c985e5a9
New package: py-minrpc (#19524)
* 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>
2020-10-26 16:20:45 -05:00
jthies
5d5711621a
packages/phist: fix incorrect git url (#19527)
Co-authored-by: Thies <thie_jo@fe-store01.sc.bs.dlr.de>
2020-10-26 16:19:53 -05:00
Sinan
4f720fb9ba
package/gunrock add v1.2 (#19516)
* 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>
2020-10-26 16:17:27 -05:00
David Beckingsale
4f9c621284
Add camp & BLT dependencies to Umpire (#19411)
* Add camp & BLT dependencies to Umpire

* Remove tests variant
2020-10-26 16:12:03 -05:00
Patrick Gartung
1c2c30a139
sbang: put sbang in the install_tree (#11598)
`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>
2020-10-26 12:37:54 -07:00
dunatotatos
718150b997
Update GATK versions. (#19521) 2020-10-26 13:32:35 -05:00
takanori-ihara
b9d3d668d9
fujitsu-ssl2: update package.py (#19519) 2020-10-26 13:31:45 -05:00
Geoffrey Gunter
7ce4518cc0
abseil-cpp: add versions 20200923.{1,2} (#19517) 2020-10-26 13:29:16 -05:00
Jen Herting
7649c652c0
New package: py-visdom (#19479)
* [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
2020-10-26 13:24:30 -05:00
David Beckingsale
7ca1f6c5d5
Add BLT package (#19410)
* 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>
2020-10-26 12:15:55 -05:00
Tiziano Müller
f921bcbe0b
cp2k, libxc, libint: fix builds with %intel, resp. intel-parallel-studio+mkl (#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
2020-10-26 16:32:15 +01:00
Sinan
2e3355d2f9
package/pmdk add variants, version 1.9 (#19512)
* 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>
2020-10-25 20:39:44 -05:00
jthies
182ca4cb68
phist: two new versions and disable ccache because we don't have a 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>
2020-10-25 16:35:43 -05:00
Massimiliano Culpo
6752a39629
py-coverage: added v5.3 (#19509) 2020-10-24 22:29:48 +02:00
Marty Kandes
4cf85ed5f7
Fix GROMACS to require FFTW when using cuda (#19505)
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.
2020-10-23 18:58:13 -05:00
iarspider
978d8ad0af
New package: py-rise (#19496)
* 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>
2020-10-23 14:59:52 -05:00
Tiziano Müller
bbc048e615
let intel-parallel-studio provide fftw-api for +mkl (#19497) 2020-10-23 11:02:56 -05:00
Scott McMillan
ccc331af26
CMake fix: narrow versions that the PGI patch is applied to (#19495)
Co-authored-by: Scott McMillan <smcmillan@nvidia.com>
2020-10-23 11:00:16 -05:00
iarspider
1d56ad0cdb
New package: py-gsi (#19494)
* New package: py-gsi

* Add dependency on py-setuptools
2020-10-23 10:59:31 -05:00
lorddavidiii
4d414e58b9
Update asciidoc-py3 and fix build problem (#19491)
* asciidoc-py3: add new version 9.0.3

* asciidoc-py3: fix build

- add libxml2 and libxslt as dependency
2020-10-23 10:47:38 -05:00
daichi-nishi
270c647e71
modified:var/spack/repos/builtin/packages/ppopen-appl-fem/package.py (#19489) 2020-10-23 10:46:57 -05:00
daichi-nishi
5e3e3672f6
modified:var/spack/repos/builtin/packages/ppopen-appl-fdm/package.py (#19488) 2020-10-23 10:46:30 -05:00
Tiziano Müller
33989341bd
gaussian-src: initial commit, gaussian-view: update to 6.1.1 (#17711)
* 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
2020-10-23 10:43:34 -05:00
Michael Kuhn
dcf8cf317b
gcc: Fix zstd patch version range (#19490)
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.
2020-10-23 07:37:15 -05:00
darmac
4d4f7393a3
Add new package: acpica-tools (#18739)
* Add new package: acpica-tools

* refine build dependencies
2020-10-23 10:17:46 +02:00
Thomas Green
fe04f06896
gcc: fix build of gcc@master by limiting the version range of a patch (#19482)
Co-authored-by: Thomas Green <ca-tgreen@gw4a64fxlogin00.head.gw4.metoffice.gov.uk>
2020-10-23 09:32:05 +02:00