Commit graph

6820 commits

Author SHA1 Message Date
EmreAtes
038efc623d New package: qbox (#4711)
* New package: qbox

* API changes

* Use install instead of shutil for comd

* Use any BLAS library

* Fix typo

* Python2 fix

* python2 + fix backslashes

* Modified to respond to ld_flags correctly

* Modified to use ld_flags

* Add ld_flags support
2017-08-10 20:12:08 -05:00
Akhil Reddy Patlolla
e3a4631037 Add AMG2013 package (#4836)
*  Updated Changes

*  Updated AMG with required MPI

*  Updated AMG with Version ' changes'

*  Fixed Issues with flag's and variant checks

*  Updated with MPI Alone and Changes - NO Serial Variant

*  Updated with MPI Alone and Changes - NO Serial Variant

* Fixed Flake 8 line length error

*  Updated Spack Issues
2017-08-10 20:09:59 -05:00
Akhil Reddy Patlolla
e4c22efc85 Variants Serial MPI openmp (#4897)
*  Variants Serial MPI openmp

*  Fixed Flake8 Issue  and remove Patch File

*  Fixed issues with openmp Flag

*  Edited Required Changes

* Fixed issues with flake8 and Added Conditional GCC Flags

* Fixed Flake 8 Issue

*  Fixed flag's issue with non GCC Compiler

*  Fixed condition and spacing issues
2017-08-10 20:08:56 -05:00
Audrey Thoma
2f29e9c18e braker & genemark-et: new packages (#5058)
* braker & genemark-et: new packages

* fixing install
2017-08-10 20:04:37 -05:00
Audrey Thoma
637f72a8fe fimpute: new package (#5060) 2017-08-10 20:04:10 -05:00
Audrey Thoma
967370aa0b impute2: new package (#5062) 2017-08-10 20:03:52 -05:00
Audrey Thoma
518993431d mothur: new package (#5055)
* mothur: new package

* fixing mpi things
2017-08-10 18:09:40 -05:00
Jim Galarowicz
df3bc3906d Update Krell products: Add new OpenSpeedShop gui package based on qt4/qt5 gui toolkit. (#5056)
* Update the krell institute products to use the latest features of spack for building on cluster platforms.

* Address travis error messages and resubmit the pull request.

* Update the contents of openspeedshop package.py so it passes the flake8 tests.

* Fix flake8 error-whitespack issue in mrnet package.py file.

* Add updates based on spack reviewer feedback.

* More fixes based on comments from reviewers.  Switch using extend to using append, remove additional setting of PATH and LD_LIBRARY_PATH that should not be required due to RPATH.

* More review related changes.  Update MPIOption.append lines and take out xercesc references.

* Create a base options function for common openspeedshop base cmake options to reduce redundencies.

* Add libxml2+python depends on to get around issues with the libxml2 package file.

* Using boost over 1.60.0 causes compile errors.  This is a known boost bug. Also, dyninst-9.2.0 is set to be the vesrion of dyninst to use with OSS, as of now. The newer version fails to build.

* Fix bad syntax in specifying the boost version range.

* Update the version numbers for the krell institute components and tools: cbtf and openspeedshop.

* Do not build glib for qt3, it is not needed and causes build problems at this time anyway.

* A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set.

* Update the fix for qt3 build by setting LD_LIBRARY_PATH instead of checking for whether it is set or not per Adams comment that spack clears LD_LIBRARY_PATH.

* A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set.

* Trim comments to fit more concisely.

* Fix tabs versus spaces and swap if and else clause check from a negative to a positive check.

* Add new OpenSpeedShop gui package based on qt4/qt5 gui toolkit.

* Fix flake8 errors.

* Fix flake8 errors.
2017-08-10 18:08:32 -05:00
Audrey Thoma
81a1d7b72b gblocks: new package (#5061) 2017-08-10 17:56:20 -05:00
Audrey Thoma
ee66c3a7aa kallisto: new package (#5063) 2017-08-10 17:54:29 -05:00
Audrey Thoma
e99834df6a fastphase: new package (#5059) 2017-08-10 17:51:46 -05:00
Michael Kuhn
887e4724c2 go: Fix cgo (#5052) 2017-08-10 09:42:02 -07:00
George Hartzell
c6cd447a8a Add version 2.19.1.403 to bcl2fastq2 package (#5047)
* Update bcl2fastq2 with info for 2.19.1.403

Heads up, the download location changed (domain name AND protocol).

* Flake8 fix

What's one space between friends?
2017-08-09 22:17:34 -05:00
Audrey Thoma
5bb86ce964 soapindel: new package (#5048)
* soapindel: new package

* fixed versioning
2017-08-09 21:39:06 -05:00
Jon Rood
58cdd46ebd Adding lower bound to pnetcdf conflict in Trilinos (#5039)
* Adding lower bound to pnetcdf conflict in Trilinos to allow for use of develop and master branch.

* Using even lower bound for pnetcdf conflict in Trilinos.
2017-08-09 18:50:28 -05:00
Audrey Thoma
869d40648f soap2: new package (#5045) 2017-08-09 18:50:11 -05:00
Audrey Thoma
3edf36b0a4 haploview: new package (#5036) 2017-08-09 17:03:14 -05:00
Audrey Thoma
7ca5e4f734 soapsnp: new package (#5046) 2017-08-09 17:00:59 -05:00
Brian Van Essen
28b0421eb1 Opencv fix (#5040)
* Added a package for the MDAnalysis toolkit.

* Changed cmake_options to args to be consistent with the rest of the
file and fix a cmake error about undefined errors.  Additionally,
added guards for both png and zlib to not include their cmake options
when those variants are not specified.
2017-08-09 15:40:10 -05:00
Audrey Thoma
0137f17306 shapeit: new package (#5042)
* shapeit: new package

* fixing versioning
2017-08-09 15:39:37 -05:00
Audrey Thoma
1f578c5777 pipits: new package (#5041)
* pipits: new package and dependencies

* fixing rdp-classifier java dep

* adding resources to pipits and fixing deps for py-biom-format
2017-08-09 15:04:21 -05:00
becker33
79f9548a9a bugfix for module_cmd (#5038)
* bugfix for modulecmd when bash is symlinked to sh

* update test to make sure module_cmd can interpret sh
2017-08-09 12:14:35 -07:00
Massimiliano Culpo
faeb1b77b2 Merged 'purge' command with 'clean' and deleted 'purge' (#4970)
* Merged 'purge' command with 'clean'. Deleted 'purge'. fixes #2942

'spack purge' has been merged with 'spack clean'. Documentation has been
updated accordingly. The 'clean' and 'purge' behavior are not mutually
exclusive, and they log brief information to tty while they go.

* Fixed a wrong reference to spack clean in the docs

* Added tests for 'spack clean'. Updated bash completion.
2017-08-09 10:02:38 -07:00
pkondamudi
9e8cce41e3 OpenMC parallel build fix. (#5037) 2017-08-09 11:11:09 -05:00
Denis Davydov
db4776fcd5 alglib: add new package (#5035) 2017-08-09 09:10:25 -07:00
Sergey Kosukhin
e463461ed1 Bugfixes for compiler detection on the Cray platform. (#3075)
* Typo fixes in docstrings.

* Let OS classes know if the paths they get were explicitly specified by user.

* Fixed regexp for cray compiler version matching.

* Replaced LinuxDistro with CrayFrontend for the Cray platform's frontend.
2017-08-09 09:00:34 -07:00
Massimiliano Culpo
d6fc2363af slurm: added initial recipe (#4802)
* slurm: added initial recipe

* Modified variants following Adam comment.

The MV variant 'features' has been turned into a set of BV variants. The
dependency on 'readline' has been made optional.
2017-08-09 08:13:33 -05:00
Brian Homerding
a33f52cfb0 Fixed minor issues from Cmake conversion (#5024) 2017-08-08 23:47:34 -05:00
jiseung
a66fb012da Packages/cns nospec (#5023)
* new package: cns-nospec

* made changes as suggested and added proxy-app tag

* updated edit()

* adjusted logic for '+debug'

* install readme and license

* install readme and license

* install readme and license; fix mpi version build issues

* fix build issues for ~mpi

* pep8 compliant
2017-08-08 20:25:00 -05:00
Audrey Thoma
3506f2674c xplor-nih: new package (#5030) 2017-08-08 20:24:42 -05:00
Axel Huebl
dfb34da689 Adios2: ZeroMQ (#5031)
During my last rebase the zeromq core dependency got missing.
Currently it's needed for all dataman WAN transports.
2017-08-08 20:24:27 -05:00
Audrey Thoma
1a3021d22c rtax: new package (#5025)
* rtax: new package

* fixing usearch version flexibility
2017-08-08 16:29:20 -07:00
jiseung
f6a9c7d79c Packages/amr exp parabolic (#5027)
* new package: amr-exp-parabolic

* removed boilerplate and added tag

* install license and readme

* fix mpi build issues

* change access to include/lib directories and pep8 compliant now
2017-08-08 17:25:27 -05:00
Audrey Thoma
7f4d94667c vmatch: new package (#5028)
* vmatch: new package

* adding url_for_version
2017-08-08 17:24:56 -05:00
Audrey Thoma
6323234135 astral: new package (#5022)
* astral: new package

* simplifying join_path

* adding build phase and changing jdk to java

* forgot to change jdk to java....
2017-08-08 16:35:19 -05:00
Audrey Thoma
f82fb75aae varscan: new package (#5026)
* varscan: new package

* changing jdk to java
2017-08-08 15:54:29 -05:00
Adam J. Stewart
97958d8347 Add latest version of Ninja (#4987)
* Add latest version of Ninja

* Re-add symlinks, add latest version of ninja-fortran
2017-08-08 11:33:24 -07:00
Jim Galarowicz
48f0e9592e Krell spack updates: Add Argo Navis/Krell new gui support library (#4964)
* Update the krell institute products to use the latest features of spack for building on cluster platforms.

* Address travis error messages and resubmit the pull request.

* Update the contents of openspeedshop package.py so it passes the flake8 tests.

* Fix flake8 error-whitespack issue in mrnet package.py file.

* Add updates based on spack reviewer feedback.

* More fixes based on comments from reviewers.  Switch using extend to using append, remove additional setting of PATH and LD_LIBRARY_PATH that should not be required due to RPATH.

* More review related changes.  Update MPIOption.append lines and take out xercesc references.

* Create a base options function for common openspeedshop base cmake options to reduce redundencies.

* Add libxml2+python depends on to get around issues with the libxml2 package file.

* Using boost over 1.60.0 causes compile errors.  This is a known boost bug. Also, dyninst-9.2.0 is set to be the vesrion of dyninst to use with OSS, as of now. The newer version fails to build.

* Fix bad syntax in specifying the boost version range.

* Update the version numbers for the krell institute components and tools: cbtf and openspeedshop.

* Do not build glib for qt3, it is not needed and causes build problems at this time anyway.

* A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set.

* Update the fix for qt3 build by setting LD_LIBRARY_PATH instead of checking for whether it is set or not per Adams comment that spack clears LD_LIBRARY_PATH.

* A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set.

* Trim comments to fit more concisely.

* Fix tabs versus spaces and swap if and else clause check from a negative to a positive check.

* Fix issues with the cbtf-argonavis build, update to use dyninst-9.3.2, fixes to openspeedshop package build.

* Fix issues with the cbtf-argonavis package.py files related to comments.

* Add changes for changing the krell packages from Package to CMakePackage.

* Add better changes for changing the krell packages from Package to CMakePackage.

* Add more modifications for changing the krell packages from Package to CMakePackage.

* Add additional modifications for changing the krell packages from Package to CMakePackage and fixing Travis erros

* Fix new travis errors.

* Fix new travis errors.

* Add more changes for PR 4765.

* Add more refinements to the conversion from Package to CMakePackage.

* Fix new travis errors.

* Add dependencies for MPI to be passed to cbtf-krell, so it can build the MPI collectors requested by the builder of openspeedshop.

* Remove extra unnecessary routine to adjust build arguments. Fix if-else clause issue.

* Fix more flake issues caused by last changes.

* Fix a bug where openspeedshop will not build when no mpi variants are specified.  Also switch to a multiple level variant for building the gui(s).  Use none, qt3, and qt4 as the variants with qt3 being the default.

* Add fix for spack issue #4843, where LTDL include files were not found.

* Add the build_type variant back into the openspeedshop package file.

* Add new package for the Argo Navis/Krell new graphical user support library: QtGraph.

* Revert "Add new package for the Argo Navis/Krell new graphical user support library: QtGraph."

This reverts commit f8883de446c404e46d4c33fe497ae1e9ab2f04a6.

* Add new package for the Argo Navis/Krell new graphical user support library: qtgraph.

* Fix flake8 errors.

* Fix flake8 errors.

* Fix flake8 errors.

* Fix flake8 errors.

* Fix flake8 errors.

* Add changes to support QMakePackage class instead of Package class for qtgraph.

* Update change for suggested reviewer improvements.

* Fix flake8 errors.

* Fix flake8 errors.
2017-08-08 10:23:04 -05:00
jiseung
6196b7f9dd New package: VPFFT (#4995)
* new package: VPFFT

* install readme and license

* misc

* changed version name to 'develop'

* removed the misplaced package file

* updated eigen path, fixed docstring, and updated 'docs' installation method

* pep8 compliant, changed installation of docs
2017-08-08 10:20:40 -05:00
Axel Huebl
6e721bab6a IceT: Ill-Place CMake Modules (#5014)
IceT places its CMake module in the wrong directory,
which is not included in the default CMake search paths.

This fixes it for *directly* depending packages without the
need to add
```yaml
    icet:
      environment:
        prepend_path:
          CMAKE_PREFIX_PATH: '${PREFIX}/lib'
```

to the `modules.yaml` as a workaround.
2017-08-08 09:14:40 -05:00
Pramod S Kumbhar
f74eaa874a Add new version of dyninst package (#5017) 2017-08-08 12:08:51 +02:00
Adam J. Stewart
2853a28b2a Add latest version of gmake (#5013) 2017-08-07 18:45:07 -05:00
zenln
33cb093870 Add a new package for molcas (#5008)
* Molcas 8.2: Adding molcas spec file

* Molcas 8.2: Putting in patch file for molcas driver not to be installed in spack stage directory

* Molcas making changes

* Making changes in ordering
2017-08-07 17:41:51 -05:00
Axel Huebl
323d2d9aed CMake: 3.9.0 (#5009)
Add new versions:

- 3.8.2
- 3.9.0
2017-08-07 17:41:34 -05:00
Pramod S Kumbhar
a0d3a35afc Fix typo : spec to self.spec (#5011) 2017-08-07 17:35:03 -05:00
Pramod S Kumbhar
a5b76d24cf Update openspeedshop and cbtf-krell to use latest binutils version (fix #4992) (#4997) 2017-08-07 17:03:51 -05:00
Pramod S Kumbhar
f4dd905447 Fix build error with mpiP: (#5006)
change dependency types to default (build/link)
    and provide mpi compiler as cc (fix #5005)
2017-08-07 16:38:53 -05:00
Audrey Thoma
825c3c68a3 transabyss: new package (#4892)
* transabyss: new package and dependencies

* fixed build deps in igraph and version conflict spec in abyss

* fixed versioning stuff and package structure

*  fixed dep type

* fixing dep type for real this time
2017-08-07 15:42:49 -05:00
Pramod S Kumbhar
82463f1fd6 Fix Scalasca build error: (#5004)
Build system "usually" autodetects mpi library but this is
    not the case on many platforms. Provide mpi library name/version
    as part for configure args.
2017-08-07 14:56:47 -05:00
Kshitij Mehta
f2871c7529 savanna depends on adios+sz (#4954)
* savanna: explicitly adding variant sz to adios since it is no longer enabled by default in adios

* savanna: removing +sz from adios as sz is now enabled in adios by default

* savanna: explicitly specifying adios variants required by savanna
2017-08-07 14:37:26 -05:00