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2017-06-28New package allpaths-lg (#4632)Audrey Thoma1-0/+45
* allpathslg: adding package. compiler specs iffy, will fix * allpaths-lg: adding new package * allpaths-lg: fixing conflicts
2017-06-28Requested changes related to mumps compilation (#4614)Darach Golden3-3/+10
* * add mpii* wrappers for use with intel compilers * in mumps package, scotch is compiled without metis option when ptscotch variant is selected. This removes confusion over which metis.h to use * for intel mkl, add SPACK_COMPILER_EXTRA_RPATHS ending in 'intel64' * scotch lib requires libz when compression is turned on. This caused a link issue on some Ubuntu distributions (not redhat). Change Scotch package to add -lz when needed * * intel-mkl append to SPACK_COMPILER_EXTRA_RPATHS rather than setting * use more concise method to obtain libz libraries for scotch * remove changes to intel mpi * remove commented out depends_on * fix flake8 errors
2017-06-28new package for KaHIP (#4613)Mark Olesen1-0/+80
2017-06-28Update intel-parallel-studio and intel packages (#4628)Kyle Fernandes, né Jacobs2-8/+8
2017-06-28Add package for primer3 (#4615)George Hartzell1-0/+46
* Add package for primer3 Built and mildly tested on CentOS 7. * Convert to MakefilePackage I always forget about this... * Set build_directory the easy way Life's not always complicated. Don't go out of my way to make it so.... * Fix Flake8 issue
2017-06-28Add package for muscle (#4616)George Hartzell1-0/+40
* Add package for muscle Minimally tested on CentOS7. * Convert to MakefilePackage Do it the easy way...
2017-06-28beast2: adding new package beast2 (#4617)Audrey Thoma1-0/+51
2017-06-28Add package for ngmlr (#4618)George Hartzell1-0/+36
Minimally tested on CentOS 7.
2017-06-28angsd: adding package angsd (#4620)Audrey Thoma1-0/+50
2017-06-28pegtl: version bump (#4621)Christoph Junghans1-6/+12
* pegtl: version bump * pegtl: added 2.1.4 * pegtl: reorder versions * pegtl: fix flake8
2017-06-28vpic: new package (#4624)Christoph Junghans1-0/+58
2017-06-27Added STAR-Fusion (#4380)Douglas Duckworth4-0/+176
* added perl-star-fusion and perl-intervaltree * added perl-star-fusion and all dependencies * changes * made changes as requested to perl-star-fusion dependencies * changed perl-intervaltree dependency * changes to star fusion * now using perl properly
2017-06-27Fix xl/trilinos (#4607)serbanmaerean2-0/+14
* Added magma package * Incorporated Serban's change * fix-xl/trilinos: add -qfixed to Fortran flags in seacas package * fix-xl/trilinos: fixed spack flake8 errors
2017-06-27BUG: inconsistent -fPIC causes adios/mxml linkage problem (fix #4605) (#4606)Mark Olesen1-2/+6
- Thanks to pointer from @adamjstewart - can avoid this either by avoiding an external mxml dependency, or by making certain that they both use consistent code generation. The adios package uses '-fPIC' for python linkage and this seems to require the same for mxml too. If the adios-internal version of mxml is used, it has the same flags for both.
2017-06-26added py-multiqc and dependencies (#4381)Douglas Duckworth4-0/+160
* added py-multiqc and dependencies * added requested changes per #4381 * added colormath dependency per https://github.com/jsvine/spectra/blob/master/requirements.txt * py-multiqc changes * py-multiqc does not need colormath - spectra does
2017-06-26update for clhep (#4588)Lynn Garren1-17/+26
* adding clhep 2.3.4.4, etc and modernizing package.py * add remaining 2.3.x.y clhep releases * setting list_depth to 1 is sufficient * remove whitespace
2017-06-26Cleanup some depends_on flex for scotch and things depending on scotch ↵Mark Olesen5-6/+6
(#4600) (#4601) - The buggy flex-2.6.2 was blacklisted in the corresponding flex package, but now also removed the md5sum to avoid suggesting that this version should be revived. The 2.6.3 has similar problems (at least for scotch), but 2.6.4 seems to work. - Rejig flex restriction for scotch to exclude 2.6.2-2.6.3 only. Since flex-2.6.4 appears to be okay again, we can remove the flex version restriction that trickled through into the openfoam packages as a consequent of an spack spec bug. - Make flex a build dependency for the openfoam packages (seems to have been an earlier oversight).
2017-06-25Update libbson and libmongoc to 1.6.3 (#4599)Michael Kuhn2-2/+4
2017-06-24Allow arbitrary Prefix attributes (#4591)Adam J. Stewart6-17/+17
* Allow arbitrary Prefix attributes * Test attribute type as well * Flake8 fixes * Remove __new__ method * Fewer uses of join_path in the docs
2017-06-24Make LICENSE recognizable by GitHub. (#4598)Todd Gamblin1617-1657/+1654
2017-06-24votca-xtp: new package (#4597)Christoph Junghans1-0/+55
2017-06-24Add cgm to moab, for resolving conflicts installing MeshKit on a brand new ↵Rajeev Jain1-1/+1
machine. (#4596) Use spack install meshkit ^cgm+oce, for geometry engine support, by default cgm is facet-based
2017-06-23relax qt dependency for paraview (#4592)Mark Olesen1-3/+2
- previously restricted everything to QT-4, but now only have that restriction for older paraview versions.
2017-06-23update for new version: qt-5.9.0 (#4590)Mark Olesen1-1/+7
2017-06-23cp2k: added missing macros to the makefile (#88) (#4589)Massimiliano Culpo1-0/+2
2017-06-23Minor fixes to CNTK package (#4429)Jimmy Tang2-17/+6
* Remove unneeded patch lines which fail for the most recent CNTK version on the head of the git repo * Really check for NVML/GDK * Fix some violations
2017-06-23Gtkplus icons (#4511)Milton Woods5-0/+60
* gtkplus: set XDG_DATA_DIRS * shared-mime-info: database of common MIME types * gtkplus: needs shared-mime-info for correct handling of stock icons * shared-mime-info: builds with newer intltool than provided by some platforms * atk: set XDG_DATA_DIRS at run-time * gdk-pixbuf: set XDG_DATA_DIRS at run-time * gtkplus: set XDG_DATA_DIRS at run-time * pango: set XDG_DATA_DIRS at run-time * shared-mime-info: set XDG_DATA_DIRS at run-time
2017-06-23caliper: Update caliper package (#4532)David Böhme1-12/+48
* caliper: Update caliper package * caliper: Explicitly enable/disable cmake options for all variants * caliper: Fix flake8 warnings * caliper: Modify defaults for Mac * caliper: Fix some more flake8 warnings
2017-06-23Moab 5.0 and meshkit 1.5 (#4557)iulian7874-41/+295
* enable some of the tools do not make zoltan default * modify moab package add shared, debug options to cgm, too build some tools by default (mbsize, mbconvert) add hdf5, netcdf dependency add pnetcdf variant (dependency), metis, parmetis, zoltan add shared, debug, fortran options to moab * few kinks for moab zoltan should be built without fortran api, otherwise moab complains (need to fix) also, notice that when built with cgm, shared can't find cgm libraries for the new tools/geometry execs install in serial for the time being (because of example makefile duplicate?) for example, these builds are successful: spack install moab+mpi+hdf5+zoltan ^mpich@3.2 spack install moab+mpi+hdf5+shared ^mpich@3.2 * force hdf5+mpi if both are specified also, something like this works: spack install moab+mpi+hdf5+cgm ^mpich@3.2 ^cgm+oce+mpi ^oce@0.17.2 use mpich32, and cgm built with oce 0.17.2 * forgot about irel, fbigeom, mbcoupler * add meshkit package simple build so far, moab and cgm deps only also, an example of complex build for cgm spack install moab+mpi+hdf5+cgm+irel+fbigeom ^mpich@3.2 ^cgm+oce+mpi ^oce@0.17.2 * for meshkit, moab needs to have irel, fbigeom * forgot to self.spec after building moab with cgm with oce 0.17.2, we can build meshkit with something like this spack install meshkit ^moab/tsb75zk cgm depencency is found out from moab moab has to be built with irel and fbigeom * add netgen package and review do not support yet older versions of meshkit (which depend on lasso, etc) add netgen package; tested with meshkit (netgen has to be built without occ, for meshkit) We are not enforcing that yet, we may have to test * use conflicts where needed, suggested by review remove release candidates * flake8 alignment errors * flake8 * reviews flake8 alignment explicit options, even for default variants variant for netgen should be "gui", with the default ~gui (False) FIXME: with-occ does not work right for netgen ; maybe it should be disabled? also, with +gui, it should depend on a lot more, like tk, tcl? * flake8 issues whitespaces and a comment in netgen * add more explicit options --without-mpi needs fixing for cgm, moab and meshkit add variable url for netgen (although we don''t know if other versions will appear) * flake8, trailing whitespace
2017-06-23ninja-fortran: a Fortran-capable fork of ninja build tool (#4539)Andrey Prokopenko2-6/+54
* ninja-fortran: a Fortran-capable fork of ninja build tool * Use url_for_version for clarity * Clean ninja-fortran * Cleanup in the original ninja package
2017-06-23Remove test dependencies from Python packages (#4572)Adam J. Stewart6-12/+20
* Remove test dependencies from Python packages * Make test deptype more clear for a couple more packages
2017-06-23suite-sparse: add openmp variant (#4563)Geoffrey Oxberry1-38/+37
Fixes #4549.
2017-06-23BUG: flex+lex fails with lib64/ installation (issue #4583) (#4584)Mark Olesen1-7/+12
- new version 2.6.4 as well
2017-06-22New package augustus (#4586)Audrey Thoma1-0/+70
* augustus: adding augustus * augustus: fixing flake8 things * augustus: simplifying verbose
2017-06-22Add latest version of libtiff (#4574)Adam J. Stewart1-1/+2
2017-06-22Add latest version of libmng (#4575)Adam J. Stewart1-2/+8
2017-06-22created py-tomopy package and fixed its dependencies (#4576)Stas Sergienko14-15/+140
* added py-tomopy package * fixed dependencies and added import_modules * edited deps for tomopy with import_modules and added py-olefile pkg * changed module name * changed dependency to python because it will not build with setuptools * fixed dependency list for py-tomopy and py-dxchange * added py-nose dependency * fixed tests * commented out dependency py-counter * fixed dependency py-pybtex-docutils * removed nose as a dependency * fixed flake8 errors * fixed import_modules * fixed import_modules indent * fixed various issues in tomopy and deps files
2017-06-22New package albert (#4568)Audrey Thoma1-0/+41
* albert: adding new package albert * albert: fixing dependency type and build process
2017-06-22gmap-gsnap: adding gmap-gsnap package (#4570)Audrey Thoma1-0/+36
2017-06-22Update for paraview 5.4.0 (#4582)Mark Olesen1-0/+8
- paraview 5.2.1 -> 5.4.0 supports both Qt4 and Qt5, but the assumed default version changes between versions. So explicitly define which QT major version is being used.
2017-06-21mumps: fixed compilation issues due to scotch not found at link time (#4567)Massimiliano Culpo4-7/+38
2017-06-21refactor openfoam packages (#3669)Mark Olesen14-756/+1315
* Several improvements for the openfoam packages -- Refactor openfoam packages by adding an OpenfoamArch class Use separate configure, build, install phases. Provide FOAM_PROJECT_DIR dependent env for openfoam packages - easier way to locate Eliminate intermediate installation directories - unneeded clutter. - makes it less than easy to find the etc/bashrc file Add versioning for all openfoam patches - no certainty which parts (if any) will be needed in future versions, especially if we strive to ensure that the upstream version builds well with spack to begin with. Support build of develop branches - helps track build regressions for future openfoam releases STYLE: use common/ and assets/ to provide additional (build) resources ... * - adjust OpenFOAM provider Move openfoam-com up front since this is the one being used as a base for the others
2017-06-21Andi and libdivsufsort (#4559)Audrey Thoma2-0/+77
* andi: adding andi and libdivsufsort * andi: adding andi and dependency libdivsufsort * andi: adding andi and dependency libdivsufsort * andi: fixing autotool dependency types * andi: fixed whitespace to make flake8 compliant
2017-06-21Modified ipopt package to support build on ppc64le (#4561)Jonathan Wong2-0/+28
Added line in package.py to patch using ipopt_ppc_build.patch. The patch simply adds support in config.guess and Ipopt/config.guess to build ipopt on ppc64le.
2017-06-21adding H5Z-ZFP; updating zfp to use choice variant for bit stream word size ↵Mark C. Miller2-8/+77
(#4466) * adding H5Z-ZFP; updating zfp to use choice variant for bit stream word size * fixing homepage url * removed fortran error message...just build fortran if can, otherwise ignore
2017-06-21Fix for SAMRAI build debug spec bug (#4564) (#4565)Jim Eliot1-1/+1
2017-06-20FFTW: remove search for IBM XL threaded compiler when compiler is not gcc ↵serbanmaerean2-0/+122
(#4187) * Added magma package * Incorporated Serban's change * fftw: patch configuration file to remove search for xlc_r compiler when compiler not gcc FFTW assumes there are only 2 compilers: gcc and IBM XL. When building threaded fftw, the configuration file is looking for the threaded IBM XL's xlc_r compiler when the compiler is not gcc. The PGI compiler is not gcc.
2017-06-20Add abyss package (#4555)Audrey Thoma1-0/+54
* abyss * abyss: deleting attemped test from script * abyss: adding new package abyss * abyss: partially fixing mpi dependency issue * abyss: added mpi provider conflicts
2017-06-20Features/votca (#4556)Christoph Junghans3-2/+109
* votca-csg: needs non-mpi version of gromacs * votca-csg: fixed deps * votca-moo: new package * votca-ctp: new package * votca-ctp: make flake8 happy
2017-06-20fontconfig should depend on gperf (#4551)George Hartzell1-0/+1
* Include depends_on for gperf Sometime around 2.12.2 fontconfig acquired a build-time dependency on `gperf` (this commit, I think: 59fd9960bbb58fd6257adb13ec0f918882149332). This adds the dependency. `gperf` is called in the `src/Makefile`, see line 907 of `src/Makefile.in`. * Only depend_on gperf if @2.12.2: The gperf dependency *seems* to only be required when @2.12.2:. Earlier releases do not check the arg type of the gperf lookup function (which requires gperf) and are able to use pre-generated files so gperf is not required at build time.
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