Commit graph

8687 commits

Author SHA1 Message Date
Christoph Junghans
cba5457d62 minighost: fix mpi build (#7310) 2018-02-27 13:02:47 +01:00
Christoph Junghans
f04837b03e snbone: fix build gcc-4.8 (#7317) 2018-02-27 13:02:04 +01:00
Denis Davydov
03cf03e581 spglib: add new package (#7321) 2018-02-27 13:00:07 +01:00
Omar Padron
3a9cd2614e Docker-Based Developer Resource (#5871)
* add docker-based development resources

* incorporate feedback from @ax3l

* fix docs/improve ssh handling

* experiment with custom prompt

* add arch/fix missing core_compilers key

* add centos/minor tweaks

* make prompt experiment optional

* workaround problem with latest fedora docker image

* add docker documentation page to index toc

* try another documentation fix

* switch arch linux base to base/archlinux

* update the git urls in the Dockerfiles

* add opensuse

* switch CUSTOM_PROMPT variable to simply "PROMPT"
2018-02-27 00:36:14 -08:00
Axel Huebl
072e78dd52 cpu_features (#7302)
Adds Google's new cpu_features library.

Install was added recently, so don't take the `0.1.0` release but
the current `master` until a new version is published.
2018-02-26 20:47:22 +01:00
healther
3683ab87b5 llvm package: update python dependency (#7100)
llvm versions >= 5 can use python 3.x
2018-02-26 10:33:40 -08:00
Christoph Junghans
5b3e149f08
branson: needs mpi-2 (#7319) 2018-02-26 06:35:47 -07:00
Christoph Junghans
4b63ecd075
ebms: needs mpi-2 (#7320) 2018-02-26 06:35:34 -07:00
Christoph Junghans
dbcf243d37
hpgmg: more sane defaults for a proxy (#7330) 2018-02-26 06:35:17 -07:00
Mike Pozulp
8157f978b0 llvm and llvm-lld package updates (#7313)
* Combined llvm and llvm-lld: removed the separate llvm-lld package
  and added llvm-lld as an optional add on to the llvm package (the
  way several other llvm tools are maintained e.g. lldb)
* Added more lld hashes to llvm package
* The 'CppBackend' target doesn't exist for version 3.9.0 or later
  so exclude it for later versions
* Was incorrectly specifying 'sparc' as a target for the 'sparc'
  architecture - needed to specify 'Sparc'
* Fix issue #7248 building llvm: don't make the LLVMDemangle target
  for llvm < 4.0.0
2018-02-23 19:50:23 -08:00
Massimiliano Culpo
990f178341
accfft: added new package (#7213) 2018-02-23 23:29:12 +01:00
Massimiliano Culpo
9c7d4e34f7 Pin Sphinx version to v1.7.0 (#7337)
Later versions of Sphinx fail due to possible clashes with our custom
argparse.
2018-02-23 12:09:01 -08:00
scheibelp
4a807fca08
Make fix_darwin_install_name python3-compatible (#7329)
This updates the fix_darwin_install_name function to use the Spack
Executable object to run install_name_tool, which ensures that
process output is formatted as a 'str' for python2 and python3.
Originally fix_darwin_install_name was invoking subprocess.Popen
directly.
2018-02-23 10:24:59 -08:00
Nichols A. Romero
7db35ff05c QMCPACK - General Improvements (#6958)
* No longer need to patch CMake. Using CMAKE_CXX_FLAGS to include BLAS/LAPACK/MKL header files properly.

* Backport two patches to QMCPACK versions prior to 3.3.0:   https://github.com/QMCPACK/qmcpack/pull/621, https://github.com/QMCPACK/qmcpack/pull/623

* Insufficient to include lapack_dir in CMAKE_CXX_FLAGS, CMAKE_C_FLAGS is also needed.

* Make patched Espresso a default variant instead of a hard dependency. This is easier on computer architectures where Espresso is hard to build.

* Fix patching with QE variant. Now using correct form of patch command.

* Add QMCPACK v3.4.0

* Backport patch to QMCPACK versions prior to 3.3.0: https://github.com/QMCPACK/qmcpack/pull/643
2018-02-23 09:52:46 -08:00
healther
c2a4751237 fix url finding of lru-cache (#7118)
Change-Id: I65a93e3d5d1ea52a0be56bbc664c6b5d405e2bf4
2018-02-23 07:41:14 -06:00
Francesco Di Natale
0d0de09121 maestrowf: new package (#7300)
* Add Maestro Workflow Conductor to Spack

* Removal of a trailing whitespace character.
2018-02-22 16:01:18 -08:00
Jon Rood
d7b826a0aa nalu package: update dependency (#7245)
Yaml-cpp hasn't tagged a release in over 2 years, yet they have fixed
many things and now have the ability to use find_package in CMake.
Since we use this feature in Nalu, we require the latest yaml-cpp
until they tag a new release. I have also deprecated the now
unnecessary ENABLE_INSTALL flag.
2018-02-22 14:14:39 -08:00
Christoph Junghans
c4fcc245e2 remove dead Exact proxies (no fetch possible) (#7312) 2018-02-22 10:27:27 -08:00
Brian Van Essen
2dd93ed5fa ECP-CANDLE benchmark script (#7271)
* Added a package for the MDAnalysis toolkit.

* Added a variant to the candle benchmark to make MPI support optional.

* Added py-requests package.
2018-02-22 09:54:46 -08:00
Brian Van Essen
8bd7712da3 Added virtualenvwrapper python package (#7270)
* Added a package for the MDAnalysis toolkit.

* Adding a package for the Python virtualenvwrapper pacakge.  Included
dependent virtualenv-clone and stevedore packages. Updated py-pbr with
a new version to support this.

* Added extra necessary dependencies and fixed the file download paths.
2018-02-22 09:47:05 -08:00
Brian Van Essen
22d9a7e0ea Fixed Theano GPU support (#7325)
* Added a package for the MDAnalysis toolkit.

* Added a new package for pygpu, which is the python front end of the
libgpuarray.  Additionally changed the dependency for theano so that
it properly picks up the pygpu library.

* Added the libcheck package.  Fixed flake8 errors in py-pygpu recipe
and removed spurious dependency on cudnn for libgpuarray.
2018-02-22 09:45:37 -08:00
Christoph Junghans
1401d8a308
bml: enable MPI by default (#7324) 2018-02-22 09:04:49 -07:00
Christoph Junghans
c62f1d4722
bml: add version 1.2.3 (#7308) 2018-02-22 06:08:54 -07:00
Massimiliano Culpo
72c270419f
yambo: added new package (#7301) 2018-02-22 12:11:51 +01:00
Christoph Junghans
dba0c9ab6b
cohmm: use more sane defaults (#7296) 2018-02-21 15:03:53 -07:00
Denis Davydov
82aa76a867 mkl: fix order of libs (#7280) 2018-02-21 19:14:34 +01:00
Christoph Junghans
41aada9821 clamr: needs cmake-3.1 (#7297)
Found in proxyapps/proxy-ci#2
2018-02-21 09:11:50 -08:00
Christoph Junghans
17b7f05975 nut: needs cmake-3.0 (#7298)
Found in proxyapps/proxy-ci#2
2018-02-21 09:10:14 -08:00
Massimiliano Culpo
9ab80cc268
cbench set its environment using setup_environment (#7236)
The edit phase of cbench was used to set environment variables. Though
this works, the variables set this way are not dumped to build.env.
This commit fixes the issue by setting those variables in the
`setup_environment` function.
2018-02-21 06:42:51 +01:00
peetsv
3d68b7510b py-pyvcf: versions 0.6.7 and 0.6.8 (#6743)
* py-pyvcf: versions 0.6.0 and 0.6.7

* adding dependencies

* Changing location of source tarball

* updating url to eliminate embedded checksum
2018-02-20 17:14:06 -06:00
Yifan Zhu
0166d09ee2 new package: Soapdenovo2 (#7047) 2018-02-20 10:33:41 -08:00
Eric
c3e8df6c93 perl-text-csv: Create new package (#7258) 2018-02-19 22:13:50 -08:00
Mark C. Miller
2bab19d121 hdf5: fixing ~/+ fortran builds; updated to version 0.8.0 (#7260) 2018-02-19 22:13:13 -08:00
Veselin Dobrev
95fe8f7e07 sundials: add the 'headers' and 'libs' properties (#7282)
* [SUNDIALS] Add the 'headers' and 'libs' properties, plus a couple of
small tweaks.

* [SUNDIALS] Revert incorrectly changed conflicts() directive. Fix style.
2018-02-19 22:11:04 -08:00
snehring
e179883a5b updating package: gmap-gsnap (#7285)
* updating package: gmap-gsnap

* fixing version order
2018-02-19 22:09:05 -08:00
Levi Baber
12a670a556 Augustus update hash (#7286)
* augustus: 3.3 package hash changed

* augustus: bamtools libraries now seem to be in lib64
2018-02-19 22:06:40 -08:00
Eric
d9bec1a1f7 py-quast: Create new package (#7254) 2018-02-18 14:33:59 +01:00
Veselin Dobrev
dbf849240e netlib-scalapack: add the libs property (#7265) 2018-02-18 10:19:03 +01:00
Christoph Junghans
d849740b8b
Silo: depend on Non-mpi hdf5 (#7275)
See #7255 for discussion
2018-02-17 19:37:06 -07:00
Sinan
151f305ddc add new version (10.2) (#7272) 2018-02-17 07:27:26 +01:00
Sergey Kosukhin
819ceb4f6d Package 'cdo': new versions. (#7250) 2018-02-16 13:39:56 +01:00
Pramod S Kumbhar
8ae50ae8bb Use abspath to avoid permission errors(#7241)
Fixes #5189

When working with non-normalized paths containing ".." on some
file systems, Spack was found to encounter a permission error when
writing to the path. This normalizes a path written by the
intel-parallel-studio package and also normalizes all paths
written by the license install hook (for all packages) to avoid
this issue for intel-parallel-studio.
2018-02-15 17:26:37 -08:00
Eric
557e6ba2f9 new package: igvtools (#6974) 2018-02-15 16:27:46 -08:00
Eric
11e064d7d1 new package: pilon (#7033) 2018-02-15 16:23:59 -08:00
Geoffrey Oxberry
1810fac25f mfem: have hypre link line also link lapack+blas (#7165)
Spack's hypre package depends on LAPACK and BLAS, so linking to hypre
requires linking to the LAPACK and BLAS libraries used to build hypre.
2018-02-15 14:59:07 +01:00
Howard Pritchard
87043679ae pmix: add 2.1.0 and more (#7191)
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2018-02-14 16:26:49 -08:00
Axel Huebl
001106884b ADIOS 2.1.0 (#7240)
Adds the first stable API release of ADIOS2, v.2.1.0.

Also adds a missing `pybind11` CMake flag for proper Python
selection (needed in both the new and previous version).
2018-02-14 13:54:13 -08:00
Geoffrey Oxberry
277ab2d355 libtool: symlink correctly on darwin (#7179)
To accommodate build systems on Darwin which look for glibtool/ize,
#7060 attempted to provide glibtool/ize symlinks for libtool/ize
but accidentally created the same symlink twice. #7073 reverted this
and replaced libtool/ize with glibtool/ize on Darwin. This led to
#7163 since AutotoolsPackages depend on the presence of the 'libtool'
binary, so this returns to the approach of #7160 but makes the
correct symlinks.
2018-02-14 13:52:44 -08:00
Geoffrey Oxberry
a7b8d26fa7 xbraid: add libs method (#7233)
XBraid installs `libbraid.a`, but the default `libs` method
implementation will search for `libxbraid`, which does not exist. This
commit fixes the behavior of the `libs` method for the `xbraid`
package by overriding package's `libs` method.
2018-02-14 10:40:56 +01:00
Yifan Zhu
f36e83fa5f r-seqlogo: new package (#7229) 2018-02-14 09:42:40 +01:00