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2017-07-22Make testing spack commands simpler (#4868)Todd Gamblin3-10/+3
Adds SpackCommand class allowing Spack commands to be easily in Python Example usage: from spack.main import SpackCommand info = SpackCommand('info') out, err = info('mpich') print(info.returncode) This allows easier testing of Spack commands. Also: * Simplify command tests * Simplify mocking in command tests. * Simplify module command test * Simplify python command test * Simplify uninstall command test * Simplify url command test * SpackCommand uses more compatible output redirection
2017-07-21Savanna (#4856)Kshitij Mehta1-2/+3
Installing the stable version 0.5 through the checksummed tar.gz does not fetch the git submodule in the package. The submodule appears as an empty directory. Thus, clone the commit tagged as v0.5 using git to get around this issue * savanna: modified adios dependency spec * Replaced adios+staging with adios+flexpath+dataspaces * savanna: Enabling fortran support in adios by default * savanna: reverting to variant 'staging' for enabling all staging transports
2017-07-21sparta: new package (#4867)Audrey Thoma1-0/+46
* sparta: new package * fixing homepage
2017-07-21new package: miniGMG (#4849)jiseung1-0/+67
* new package: miniGMG * changed based on comments * removed cuda version
2017-07-21revbayes: trying this again (#4861)Audrey Thoma1-0/+62
2017-07-21sortmerna: new package (#4866)Audrey Thoma1-0/+44
2017-07-21added new pruners-ninja version (#4859)Gregory Lee1-0/+1
2017-07-21lmdb: Update to 0.9.21 (#4830)Michael Kuhn1-32/+30
Convert to MakefilePackage and add pkg-config file.
2017-07-21singularity: new package (#4852)Audrey Thoma1-0/+40
2017-07-21smalt: new package (#4853)Audrey Thoma1-0/+34
2017-07-21seqprep: new package (#4850)Audrey Thoma1-0/+39
2017-07-21sickle: new package (#4851)Audrey Thoma1-0/+43
2017-07-21New Package: C-Ares (#4840)Axel Huebl1-0/+41
Adds the c-ares library, a C library for asynchronous DNS requests. Required for the google gRPC library.
2017-07-21salmon: new package (#4833)Audrey Thoma1-0/+41
2017-07-21satsuma2: new package (#4838)Audrey Thoma1-0/+41
2017-07-20py-cdat-lite: ensure that RPATH includes netcdf (#4521)Milton Woods1-0/+11
2017-07-20add mesa +swrender variants (gallium software/off-screen rendering) (#4602)Mark Olesen1-13/+64
- +swrender variant lets you compile an off-screen only version for software rendering on clusters. - +swrender+llvm for using llvm for the software pipe - added newer versions (17.1 and 13.0) and corrected the url location to use the canonical location.
2017-07-20GTKorvo (#4657)Kshitij Mehta6-0/+266
* gtkorvo-atl: atl library from gtkorvo * gtkorvo-dill: dill library from gtkorvo * gtkorvo-cercs-env: cercs_env library from gtkorvo * gtkorvo-enet: Enet networking library from gtkorvo * libffs: FFS middleware communication library from GTKorvo * libevpath: EVPath high performance communication library from GTKorvo * gtkorvo-cercs-env: Added homepage and removed function configure_args * gtkorvo-cercs-env: Re-add of accidental removal of cmake_args function in previous commit * gtkorvo-enet: Removed configure_args since unused
2017-07-20New Package: SNbone. (#4754)pkondamudi1-0/+64
* removed the tags as per comment in PR# 4749 * addressed above comments * changed fortran compiler. * added proxy application tags. * added tags by removing them from description. * addressed comments * used join_path instead of path concat. * addressed comments * removed string formatting for LDFLAGS.
2017-07-20Spack updates to three Krell packages (#4765)Jim Galarowicz5-558/+242
* 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.
2017-07-20kentutils: new pacakge (#4831)Audrey Thoma1-0/+52
2017-07-20new package:SNAP (#4826)jiseung1-0/+62
2017-07-19Allow packages to control handling of compiler flags (#4421)becker3310-12/+34
* Initial work on flag trapping using functions called <flag>_handler and default_flag_handler * Update packages so they do not obliterate flags * Added append to EnvironmentModifications class * changed EnvironmentModifications to have append_flags method * changed flag_val to be a tuple * Increased test coverage * added documentation of flag handling
2017-07-19Add info for zsh@5.3.1 (#4827)George Hartzell1-0/+1
2017-07-19Add MPI support and tags to embs package (#4824)pkondamudi1-1/+24
2017-07-19Add tags to nekbone package (#4825)pkondamudi1-0/+3
2017-07-19new package: cns-nospec (#4806)jiseung1-0/+67
* new package: cns-nospec * made changes as suggested and added proxy-app tag * updated edit() * adjusted logic for '+debug'
2017-07-19new package: amr-exp-parabolic (#4821)jiseung1-0/+78
* new package: amr-exp-parabolic * removed boilerplate and added tag
2017-07-19Package/xsbench (#4822)pkondamudi1-4/+10
* removed the tags as per comment in PR# 4749 * addressed above comments * changed fortran compiler. * added proxy application tags. * added tags by removing them from description. * addressed comments * used join_path instead of path concat. * added tags and other minor changes. * removed tags from description.
2017-07-19new package PENNANT added (#4708)jiseung1-0/+99
* new package PENNANT * made adjustments based on comments * edited logic for mpi variant * replaced with 'else' * prefix.bin instead of 'bin'
2017-07-19 Added Proxy App CoSP2 (#4726)Akhil Reddy Patlolla1-0/+74
* Added Proxy App CoSP2 * Updated the PATH * Updated MPI Fix * Fixed Issues * Fixed Issues with compiler and Flake8 * Enhanced block of code. * Intended
2017-07-19Added Proxy App CoHMM (#4727)Akhil Reddy Patlolla1-0/+61
* Added Proxy App CoSP2 * Added Proxy App CoHMM * Updated PATH cohmm * Chages Fixing Minor issues * Minor Fix git add cohmm/package.py * Updated * Resolved TAG Conflict * Updated based on the codecov failure
2017-07-19new package: CLAMR (#4728)jiseung1-0/+91
* new package: CLAMR * changed from bool variants to single value variants and corresponding logic in build_type and cmake_args * lowercase variant values * updated conditionals for variants * adjusted url and docstring
2017-07-19New Package: SimpleMOC (#4742)pkondamudi1-0/+68
* New Package SimpleMOC * addressed comments * removed tags as per PR# 4749 * flake8 fix. * travis fix. * added proxy app tags to description. * added mpi and openmpi depedency. * removed openmpi depdedency. * addressed comments. * adding openmp flag conditionally. * flake 8 fix for tabs.
2017-07-18codar-cheetah: URL fix (#4815)Kshitij Mehta1-1/+1
2017-07-18new package: SMC (#4817)jiseung1-0/+80
* new package: SMC * removed template and added proxy-app tag * added comp variant in edit() * edited comp variant in edit()
2017-07-18Misc python updates (#4807)Gregory Lee2-3/+4
* updated py-pylint version * setuptools required at runtime for pkg_resources * fixed url for updated pylint
2017-07-18Always install xproto in serial (#4809)Adam J. Stewart1-0/+5
2017-07-18poamsa: new package (#4808)Audrey Thoma1-0/+50
* poamsa: new package * fixed version specs
2017-07-18new package to be added: NuT (#4760)jiseung1-0/+62
* new package to be added: NuT * removed cmake_args() and made other changes as suggested * Added setup_environment() * PEP8 compliant * edited version name, build_targets, and files/directories to install * corrected executable directory * compiler dependencies based on version
2017-07-18price: new package (#4810)Audrey Thoma1-0/+40
2017-07-18New package busco (#4678)Audrey Thoma1-0/+59
* busco: new package * busco: fixing fussy paths * removing paths, probably was a problem with our module setup * fixed dep type
2017-07-18Adding a bit more Mellanox MXM capability to OpenMPI. (#4762)Jon Rood1-0/+23
2017-07-18raxml: new package (#4777)Audrey Thoma1-0/+107
* raxml: new package * changed compiler variable * removing if statement regarding intel compiler
2017-07-18Package/minimd (#4788)homerdin1-0/+74
* New Package: miniMD * Minor Changes * Corrected Dependency * Renamed Executable * Change to use build directory directly
2017-07-18New Package: OpenMC (#4790)pkondamudi1-0/+89
* New Package: OpenMC * comments addressed. * comments addressed. * changed 'os.makedirs' to 'mkdirp' * flake 8 fix.
2017-07-18Change path to CMakeLists.txt to be relative to root, not pwd (#4420)Adam J. Stewart8-19/+11
* Change path to CMakeLists.txt to be relative to root, not pwd * Changes requested during code review * Revert back to old naming of root_cmakelists_dir * Make relative directory more clear in docs * Revert change causing build_type AttributeError * Fix forgotten abs_path var * Update CLHEP with new relative path * Update more packages with new root_cmakelists_dir syntax
2017-07-18Repalce ftp:// with http:// for gdbm, mesa-glu and udunits2. (#4798)健美猫3-3/+3
2017-07-18somatic-sniper depends_in('curses') (#4796)George Hartzell1-0/+2
somatic-sniper installs its own copy of samtools, which needs curses. I'm not sure why I didn't stumble on this in my dev environment, but I just stumbled over it in a standalone build.
2017-07-18Add version 3.4.1 for r. (#4799)健美猫1-0/+1
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