Commit graph

5596 commits

Author SHA1 Message Date
Douglas Duckworth
0f114d9718 Relion 2.1 - Using CudaPackage class (#6707) 2018-03-07 07:45:48 +01:00
Christoph Junghans
95b2738549 lammps: add version 20180222 (#7408) 2018-03-07 06:32:06 +01:00
Christoph Junghans
360feb4193
minighost: rework link logic (#7402) 2018-03-06 15:51:12 -07:00
Mike Pozulp
b0795d84c7 adds patches required to build hdf5 1.8.10 (#7386)
For hdf5 `1.8.10` and some compilers, the hdf5 build system adds the
'-ansi' flag. hdf5 1.8.10 is not actually ansi compliant so this
adds a patch to modify the places where it violates ansi
compatibility (which ends up being a few comments).
2018-03-06 12:49:36 -08:00
Eric
ea7879bce5 bowtie2: Add version 2.3.4.1 (#7252) 2018-03-06 18:48:48 +01:00
Geoffrey Oxberry
5ed6e6f184 pnmpi@1.7: new package (#7051)
Add PnMPI, a dynamic MPI tool infrastructure that builds on top of the
PMPI interface.
2018-03-06 18:48:28 +01:00
健美猫
c0f6cb5393 Add the libssh2 variant for curl. (#6980) 2018-03-06 18:41:22 +01:00
Eric
2be8712406 perl-net-scp-expect: Create new package (#7028) 2018-03-06 18:39:13 +01:00
Christoph Junghans
274036bfed gromacs: add v2018 (#7050) 2018-03-06 18:37:45 +01:00
Simon Flood
fa5911af83 Update package.py (#7327)
Add versions released after 3.5.0 (3.4.3, 3.5.1, and 3.6.x)
2018-03-06 18:28:02 +01:00
peetsv
d649fda48a py-crossmap: adding new package (#7108) 2018-03-06 18:27:03 +01:00
Sergey Kosukhin
8d6738a3e6 Setup dependent environment for pkgconf. (#7102) 2018-03-06 18:25:00 +01:00
Elizabeth Fischer
02bed55007 py-rasterio: Added with dependencies. (#7156) 2018-03-06 18:21:34 +01:00
Geoffrey Oxberry
45e78a42cf sosflow: add missing dependencies (#7182)
SOSflow depends on MPI and pkg-config, but neither of these
dependencies are currently in the spack package, so this commit adds
them.
2018-03-06 18:17:49 +01:00
Paschalis Korosoglou
ceb8963362 Add cmor version 3.3.0 (#7197) 2018-03-06 18:16:52 +01:00
Eric
d77a2eecbe perl-graph-readwrite: Create new package (#7284) 2018-03-06 18:12:06 +01:00
mcneish1
642484caeb Add sqlite 3.22.0 (#7335) 2018-03-06 18:09:09 +01:00
healther
b106c86fa3 Fix apr pick up of log4cxx (#7347) 2018-03-06 18:08:51 +01:00
Michael Kuhn
17772fcd43 likwid: Fix build (#7244)
likwid uses the current directory when building the paths to its
internal libraries. Spack overwrites PWD, causing likwid to not find
hwloc.h.
2018-03-06 18:07:37 +01:00
Veselin Dobrev
65a1655022 mumps: add the libs property (#7264) 2018-03-06 18:05:58 +01:00
Ricardo Silva
4a54178ff8 Make neuron package more generic (#7393)
Make neuron package more generic

* find the bin directory dynamically for use in run_env and spack_env
* replace filter_compilers after install with filter_compiler_wrappers
* update checksum for _current_ 7.5 version
* make +python conflict with ~shared
* prepend the architecture specific lib directory to the LD_LIBRARY_PATH

Signed-off-by: Ricardo Silva <ricardo.silva@epfl.ch>
2018-03-06 16:31:28 +01:00
Matthias Diener
8f350d0002 Colordiff: new package (#7070) 2018-03-06 13:14:29 +01:00
Eric
bcae9c3506 py-bitstring: Create new package (#7190) 2018-03-06 13:04:16 +01:00
Veselin Dobrev
7482cf1d9f suite-sparse: add a package-specific 'libs' property (#7269) 2018-03-06 10:09:20 +01:00
Yifan Zhu
9c828f3068 trnascan-se: new package (#7351) 2018-03-06 09:58:05 +01:00
Axel Huebl
c7a8c4a44c libSplash 1.7.0: Root Fix (#7368)
Fix installs as "root" user for the last libSplash release.
Missing quoting of string compares resulted in a CMake error
when run as root (e.g. in a Docker build).
2018-03-06 09:38:40 +01:00
lingnanyuan
7aff7cbaec snpEff: Create new package. (#7382) 2018-03-06 09:34:22 +01:00
Eric Müller
2f06292abc mosh build depends on pkg-config (#7365) 2018-03-06 09:34:00 +01:00
Eric
c2d1344c51 perl-file-slurper: Create new package (#7378) 2018-03-06 09:28:37 +01:00
Christoph Junghans
ca367b4de3 exasp2: add v1.0 (#7398) 2018-03-06 09:01:53 +01:00
Yifan Zhu
d90b03db09 braker: added list_url (#7058) 2018-03-06 08:51:43 +01:00
Yifan Zhu
4a7e88cc71 r-sf: new package (#6547)
* r-sf: new package

* r-sf: added version requirements for dependencies
2018-03-05 23:45:19 -06:00
Christoph Junghans
96f9576426
minighost: another Ubuntu fix (#7359) 2018-03-05 17:39:21 -07:00
Christoph Junghans
94c8299a1e
minismac2d: fix build with external Debian MPI (#7318) 2018-03-05 16:07:41 -07:00
Eric
35115127bc perl-extutils-depends: Create new package (#7376) 2018-03-05 21:32:22 +01:00
Federico Ficarelli
fa442ed61a rapidjson: new package (#7391) 2018-03-05 21:10:02 +01:00
Mario Melara
ccb24b1438 Fix pkgconf on Crays (#7171)
This updates Cray.setup_platform_environment to use cray-specific
pkgconfig paths so that all providers of 'pkgconfig' have access
to them (previously the 'pkg-config' provider had this but the
'pkgconf' provider did not).
2018-03-05 12:08:11 -08:00
Adam J. Stewart
89a591eb3b Fix version-specific URLs for Python packages (#7394) 2018-03-05 12:00:49 -08:00
Veselin Dobrev
e4597f09be openmpi: add package-specific 'headers' property (#7267)
* [OpenMPI] Add the 'headers' property. This removes some redundant
headers from sub-directories, returned by the default '.headers'
handler.

* [OpenMPI] In the .headers property, add a fallback to search all of
prefix for the mpi.h header. Recommended by @junghans to support some
external configurations, see #7268.
2018-03-05 12:53:36 -07:00
Federico Ficarelli
3cf2cda4ec tclap: new package (#7390) 2018-03-05 14:53:42 +01:00
Eric
ca336b60fa bracken: Create new package (#7375) 2018-03-05 14:16:27 +01:00
Mike Pozulp
90c8243113 add -ldl to silo ldflags when building with static hdf5 in order to fix #7384 (#7385) 2018-03-05 13:28:37 +01:00
Cyrus Harrison
d59ee8d07d update for conduit 0.3.1 release (#7344) 2018-03-05 11:04:21 +01:00
Eric Müller
1a77884c07 fix ruby build on gcc >= 7 (#7387)
* pkgconfig fixes a "libffi.a requires -fPIC" build error
* the patches solve the mentioned problem on GCC 7.x
2018-03-05 10:01:23 +01:00
Axel Huebl
189d9ec138 Rsync package: Fix Src Link (#7367)
Fix the source link to rsync downloads.

The old link only contained the latest release, the new link
contains all.
2018-03-01 22:42:26 -08:00
junkudo
6213463aeb new package: hiop (#7039) 2018-03-01 15:26:28 -08:00
Eric
86afd0e851 new package: perl-parallel-forkmanager (#7049) 2018-03-01 12:37:16 -08:00
healther
1ac0bce3e9 help gdb pick up python3 (#7104)
* Update gdb to autotools package
* Help gdb find python libraries for python 3
2018-02-28 23:13:06 -08:00
Omri Mor
b4b01b82ac mpich@develop: needs git submodules (#7357) 2018-02-28 19:48:57 -06:00
Eric
da2d6cccd6 new package: py-goatools (#7328) 2018-02-28 17:41:22 -08:00
Denis Davydov
98949bd79b change recurse into recursive in a few places (#7342) 2018-02-28 20:15:26 +01:00
Christoph Junghans
3089207ced minighost: fix build on Ubuntu (#7354)
* minighost: fix build on Ubuntu

* minighost: append -lgfortran only for gcc
2018-02-28 09:37:01 -08:00
Christoph Junghans
6c2fe27f41
examinimd: fix a typo (#7352) 2018-02-28 10:02:33 -07:00
healther
f302d64235 add package verilator (#7332)
* add verilator package

* try to add environment variable and include folder

* manually install existing scripts and patch out spack's CXX wrapper

* added some comments

* make flake8 happy
2018-02-27 23:46:02 -08:00
Mark C. Miller
0e326c9687 updating zfp version (#7304) 2018-02-27 21:49:04 +01:00
Robert Pavel
5689fd304c Added initial Spackage for examinimd (#7350) 2018-02-27 11:42:35 -07:00
Christoph Junghans
2244e43e2b minighost package: fixed a typo (#7349) 2018-02-27 10:23:33 -08:00
Geoffrey Oxberry
ae1759eb16 aspcud@1.9.4: new package (#7094) 2018-02-27 13:16:40 +01:00
Axel Huebl
0c85aa09af MPark.Variant (#7251)
Adds Michael Park's C++11 `std::variant` (a C++17 stdlib feature).
2018-02-27 13:15:59 +01:00
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
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
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