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2018-01-06Updating OpenFAST to use explicit lapack and blas libraries from Spack. (#6824)Jon Rood1-1/+8
* Updating OpenFAST to use explicit lapack and blas libraries from Spack. * Simplifying openfast blas lib logic and fixes flake8 errors. * Changing order of blas and lapack libs in openfast package.
2018-01-05sailfish: Create new package (#6827)Eric1-0/+37
* sailfish: Create new package * sailfish: fix tbb dependency * sailfish: fix dependency type
2018-01-05py-pybedtools: Create new package (#6487)Eric1-0/+42
* py-pybedtools: Create new package * py-pybedtools: add py-six requirement * py-pybedtools: remove py-cython dependency for release version * py-pybedtools: include minimum version of py-pysam
2018-01-05Fixes the bug in spack configure spotted in #6833 (#6837)Massimiliano Culpo1-1/+1
2018-01-05Fix spack configure output (#6835)Adam J. Stewart1-1/+1
2018-01-05Add a package: ctffind. (#6836)健美猫1-0/+37
* Add a package: ctffind. * Add a package: ctffind.
2018-01-05Provide build_type variant for Metis. (#6808)Kelly (KT) Thompson1-11/+22
* Provide build_type variant for Metis. + Ideally, we would make Metis a CMakePackage, but `metis@:5` doesn't use CMake. + For now, provide a `build_type=` variant similar what is found in CMakePackage. + There is a potential for duplicate specification of `CMAKE_BUILD_TYPE` if both variants `+debug` and `build_type=` are specified. I am looking for advice on how this can be resolved. * Update metis recipe in response to flake8 and user comments. + Wrap comment lines that used more than 80 columns. + Change `+debug` variant to avoid potential for multiple `-DCMAKE_BUID_TYPE=` arguments provided to cmake. Specifying this variant no longer appends this configure option. However, if `+debug` is specified, require `build_type=Debug` to maintain expected behavior. * For metis, remove +debug variant; use build_type= instead. + Update recipe for metis@4 to extract `build_type=` values and set `OPTFLAGS` accordingly. + For metis@5:, the behavior from the previously supported variant `+debug` can be obtained with the options `+gdb build_type=Debug` * Conflicts added for metis@4 when build_type != Release|Debug. * Use spack function conflicts instead of 'raise InstallError'.
2018-01-05Fix pymongo package (#6832)David Hows1-2/+3
And update to 3.6
2018-01-04Create a symbolic link to the MotionCor2_x.x.x executable. (#6826)健美猫1-0/+2
* Create a symbolic link for MotionCor2. * Create a symbolic link for MotionCor2. * Create a symbolic link for MotionCor2. * Create a symbolic link for MotionCor2.
2018-01-04Revert "openssl: Add perl dependency" (#6831)Adam J. Stewart1-1/+5
* Revert "Added i3 and its dependencies. (#6805)" This reverts commit a00a09a234886d3bb4e53f873579a56aca11d3ba. * Revert "Adding NEURON simulator package (#5097)" This reverts commit d24782c86d84d51ac3ef7404c9e4a4eb6b9eab7e. * Revert "openssl: Add perl dependency (#5188)" This reverts commit 395ee97f3b1cdd96ae00bdae6d27d3145c50fc5e.
2018-01-04Added i3 and its dependencies. (#6805)stefanosoffia5-0/+233
2018-01-04Adding NEURON simulator package (#5097)Pramod S Kumbhar1-0/+224
* Adding NEURON package widely used in computational neuroscience community * flake8 fixes * Add rx3d variant * Addressed review comments from Adam * Addressed 2nd review comments * Added check for +mpi on bg-q * Filter spack compiler wrappers in NEURON scripts Add gcc march=native flag to make front-end build robust * Make develop as preferred version due to bug in long filename handlings in <= v7.4 * Avoid use of gcc in cross compiling environment Use arch specific options on cray and bg-q arch * Simplify cross compiling build: - v7.5 added and no longer need develop as preferred version - legacy cray related options removed - cross compiling args reduced - python arguments reduced as neuron finds proper libraries * Simplify bg-q configurations * Cleanup and unify arch options * Make sure to add commonly available packages as dependency * Arch path added to dependent_environment as nrniv needed at runtime * Support for Power 8 architecture * Fix python3 on OS X * flake8 fix * remove unnecessary conflcist directives
2018-01-04openssl: Add perl dependency (#5188)Michael Kuhn1-5/+1
perl is required for the configure script.
2018-01-04Protobuf intel patch (#5233)Brian Van Essen2-0/+27
* Added a package for the MDAnalysis toolkit. * Added a patch file to get rid of compiler warnings with intel compiler and inlining. Added checksum values for other versions of protobuf. * Added dependency on Intel compiler for intel patch
2018-01-04Fix build of paraview (#5802)Simone Bnà1-1/+14
* added variant examples to paraview package.py * qt: added libxt dependency * add variant to use external hdf5, this is needed when compiling with gcc@4.8.5 * paraview: added python dependecies to PYTHONPATH
2018-01-04make nghttp2 optional for curl, as it does not build for older compilers. ↵Todd Gamblin1-4/+7
(#5977)
2018-01-04Adding Nek5000 to Spack (#6153)Thilina Rathnayake2-0/+154
* Start adding Nek5000 package * Add tools to install: genmap, prenek, postnek * Address comments by @davydden * Use install_tree (thanks @junghans) and polish * Update url * Fix flake formatting errors * Change F77 and CC compilers Apparently spack compilers can't be called outside spack and we have an underscore test in our Nek5000/core/makenek.inc file which calls F77 compiler. * Add support for visit and profiling options * Fix a typo * Fix a typo * Remove the C check * Add visit variant * Update the install of int_tp tool * Let MAXNEL to be set during installation
2018-01-04r-rgraphviz: Create new package. (#6316)lingnanyuan1-0/+38
2018-01-04Set SMPI library path in dependent packages (#6548)serbanmaerean1-0/+2
* Added magma package * Incorporated Serban's change * Remove deleted files * argparse.py * Sync forked Spack repo in github * Add spectrum-mpi lib path to LD_LIBRAY_PATH in spack_env. As a result of supporting alternate installation directories, spectrum-mpi does not use rpath anymore, so we need to set LD_LIBRARY_PATH in spack_env to allow MPI programs to run during dependent package configuration. * Fix flake8 error (blank line at EOF)
2018-01-04RNA-SeQC: Create new package (#6555)Eric2-0/+66
* RNA-SeQC: Create new package * RNA-SeQC: Fix flake8 error * RNA-SeQC: Fix Travis error
2018-01-04r-rgeos: Create new package. (#6592)lingnanyuan1-0/+42
2018-01-04qt: add 5.10.0, fix macOS build, clean-up comments/TODOs (#6766)Denis Davydov2-7/+57
* qt: add 5.10.0, fix macOS build, clean-up comments/TODOs * qt: fix pkgconfig files * qt: restore-pc-files.patch * add version constraint to the patch * qt: adjust url_for_version for 5.10.0
2018-01-04xios: I/O management for climate models (#6796)Milton Woods4-0/+289
* xios: XML-IO-SERVER library for IO management of climate models * xios: install to prefix directory * xios: add a test case * xios: define versions to use cache and mirror directories * xios: use proper svn URL for version 910 * xios: package url must be defined, otherwise uninstall fails * xios: add trunk version to allow building latest revision * xios: enable parallel build * xios: allow installation with mpif90 compiler wrappers * xios: use mpi variants of dependencies * xios: allow user to specify MPI launcher via MPIRUN environment variable * xios: prefer spack versions of blitz and boost (needed for gcc@7) * xios: enable builds with clang+gfortran on OSX * xios: use numeric versions for releases, @develop for trunk * xios: different patches required for @1.0 and @develop * xios: patch function for clang works across revisions * xios: link blitz library * xios: workaround bug 17782 in llvm * xios: whitespace adjustments for flake8 * xios: avoid bare except clause * xios: netcdf-fortran inherits ^netcdf+mpi from xios dependencies
2018-01-04py-umi-tools: Create new package (#6823)Eric1-0/+45
* py-umi-tools: Create new package * py-umi-tools: fix dependencies
2018-01-03Update grackle (#6822)Loikki1-2/+3
2018-01-03package openfoam-com: add version 1712 and update patches (#6820)Mark Olesen12-906/+956
* combine all patches for 1612 into a single file, with additional comments to explain the rational. * Add kahip decomposition variant. * Add support for ARM64 architecture. * filter instead of patching etc/config.*/settings. This eliminates patch files for 1706, perhaps for the future as well. * URLs at or before version 1612 have a different structure, so provide a url_for_version implementation to handle this
2018-01-03package/r-rjags: create new package (#6804)Sinan1-0/+46
* package/r-rjags: create new package * fix typo fix typo * package/r-rjags small fix to pass flake8 tests * package/r-rjags: more fixes to satisfy flake8 tests
2018-01-03fltk depends on libx11. (#6816)健美猫1-0/+2
2018-01-03Add a new version and runtime dependency for MotionCor2. (#6817)健美猫1-0/+3
* Update motioncor2 to 1.0.4 and add libtiff dependency. * Add comments for libtiff dependency in MotionCor2.
2018-01-03Add libtiff@3. (#6818)健美猫1-0/+1
2018-01-03suite-sparse: support 64bit BLAS (#6767)Denis Davydov1-0/+6
* suite-sparse: support 64bit BLAS * use double quotes instead of escaped quotes
2018-01-03Flex v2.6.4 conflicts with gcc@7.2.0 (#6819)stefanosoffia1-0/+4
2018-01-02singularity - added master branch (#6631)Douglas Duckworth1-0/+1
* singularity - added master branch as this has latest fixes - 2.4 does not compile on centos 6 without use of this branch * renamed to develop * added master branch properly
2018-01-02New Package: py-adios (#5686)Axel Huebl1-0/+78
The ADIOS1 numpy bindings depend on an installed, fully loaded ADIOS C library + its config tools to build properly.
2018-01-02Intel mkl dnn (#6268)Brian Van Essen1-0/+39
* Added a package for the MDAnalysis toolkit. * Added a package for the Intel MKL-DNN project. * Fixed flake8 errors. * Fixed Flake8
2018-01-02Fix HTML detection (#6394)Michael Kuhn1-1/+2
Some servers report a content-type header instead of Content-Type.
2018-01-02rsem: update version 1.3.0 md5sum (#6650)Eric1-1/+1
2018-01-02atom-dft: new package plus dependencies (#6653)Michael Kuron3-0/+156
* atom-dft: new package plus dependencies * Indentation fix * Use the compiler wrappers * Pass variables instead of using FileFilter
2018-01-02Install all the cli tools from all the sub-directories (#6705)Jimmy Tang1-1/+6
* Install all the cli tools from all the sub-directories * Satisfy pep8
2018-01-02py-lrudict: a LRU-based cache dictionary (#6734)Feiyi Wang1-0/+38
* add py-lrudict * style fix * style fix: add blank lines
2018-01-02py-scandir: a better directory iterator, backport to 2.7 (#6739)Feiyi Wang1-0/+37
2018-01-02gatk: boilerplate cleanup (#6744)Levi Baber1-15/+0
2018-01-02add OctavePackage (#6746)Denis Davydov9-49/+88
* add OctavePackage 1. remove import CudaPackage which is not needed anymore 2. mention CudaPackage and OctavePackage in packaging guide 3. adjust OctavePackageTemplate 4. add clue file for Octave build 5. sanity check on self.prefix * use setup_environment
2018-01-02py-xattr: a python interface to access extended file attribute (#6747)Feiyi Wang1-0/+38
* py-xattr: a python interface to access extended file attribute * py-xattr: style fix
2018-01-02Lbann update (#6751)Brian Van Essen1-2/+59
* Added a package for the MDAnalysis toolkit. * Updated the LBANN recipe to use the revised cmake environment being rolled out. * Flake8 errors
2018-01-02likwid: add stable 4.3.0 (#6761)Denis Davydov1-3/+2
2018-01-02mesa: disable binutils on macOS (#6763)Denis Davydov1-2/+2
2018-01-02jags: lapack fix (#6764)Levi Baber1-2/+4
* jags: fixing openblas thows a lapack error when compiling. atlas works. other lapack providers may work. also adding tags * changing blas/lapack reference * removing openblas conflict * jags: whitespace cleanup for flake8
2018-01-02Esmf fixes for Cray, OSX and mpich (#6768)Milton Woods2-3/+31
* esmf: put .mod files in the spack compiler search path * esmf: allow building with Cray mpi * esmf: create run-path dependent libraries on osx * esmf: link fortran interface libraries when building with mpich
2018-01-02Adding option to build Nalu with Hypre support. (#6782)Jon Rood1-1/+10
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