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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)becker3316-12/+203
* 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
2017-07-18Improve version detection of release versions (#4816)Adam J. Stewart2-0/+3
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.
2017-07-18Open ended variants (#4746)becker331-1/+7
* Change directives to allow open-ended variants more easily * make None default to open-ended
2017-07-18Change path to CMakeLists.txt to be relative to root, not pwd (#4420)Adam J. Stewart9-23/+20
* 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
2017-07-18package: removed default no-op patch (#4103)Massimiliano Culpo1-4/+5
* package: removed default no-op patch fixes #4085 * do_patch: handles NoSuchMethodError nicely
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
2017-07-18pcma: new package (#4793)Audrey Thoma1-0/+43
2017-07-18New Package: tig (#4794)Adam Fidel1-0/+36
2017-07-17Package/minixyce (#4789)homerdin1-0/+78
* New Package: miniXyce * Removed Tag
2017-07-17partitionfidner: new package (#4791)Audrey Thoma1-0/+52
2017-07-17qhull: fix to work around a known issue of the library with intel compiler ↵Massimiliano Culpo2-0/+20
(#4648)
2017-07-17bsseeker2: new package (#4770)Audrey Thoma1-0/+49
2017-07-17codar-cheetah: Experimentation harness from the ECP CODAR project (#4658)Kshitij Mehta1-0/+45
* codar-cheetah: Experimentation harness from the ECP CODAR project * codar-cheetah: conforming to flake8