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2019-11-03Update package saga gis (#13520)Jannek Squar1-10/+38
* Improvements of saga-gis package * Added explicit version ranges for old saga-gis version * Update var/spack/repos/builtin/packages/saga-gis/package.py Creative usage of redefinition of getter method Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/saga-gis/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/saga-gis/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-11-03constexpr_longdouble.patch should be applied to v6 too (#13548)Daryl W. Grunau1-1/+1
2019-11-02Add latest version of protobuf (#13551)Adam J. Stewart1-10/+11
2019-11-02Add QNNPACK package (#13549)Adam J. Stewart2-1/+85
2019-11-02chgcentre: a new package. (#13500)健美猞猁1-0/+20
* chgcentre: a new package. * flake8.
2019-11-01spack create: http -> https (#13547)Adam J. Stewart1-2/+2
2019-11-01Bugfix: respect order of mirrors in mirrors.yaml (#13544)Peter Scheibel1-1/+4
Commands like "spack mirror list" were displaying mirrors in a different order than what was listed in the corresponding mirrors.yaml file. This restores commands to iterate over mirrors in the order that they appear in the config file.
2019-11-01environments: make shell modifications partially unconditional (#13523)Greg Becker2-1/+37
* environments: make shell modifications partially unconditional * flake * missing module name * add regression test * flake
2019-11-01Add py-tables 3.6.1 (#13536)Adam J. Stewart1-1/+2
2019-11-01libxc: update URL / new API (#13471)Simon Pintarelli2-36/+3
- setup_environment -> setup_build_environment - remove patch
2019-11-01allow bootstrap buildcache install of patchelf (#13430)Marc Mengel2-3/+36
* allow bootstrap buildcache install of patchelf * file not path_name on one * style * add test for relocating patchelf * blank lines..
2019-11-01bugfix: spack.util.url.join() now handles absolute paths correctly (#13488)Omar Padron3-2/+379
* fix issue where spack.util.url.join() failed to correctly handle absolute path components * add url util tests
2019-11-01sbang: use utf-8 for encoding when patching (#13490)Gregory Lee1-4/+13
This fixes a UnicodeDecodeError in the sbang patching function.
2019-11-01Specs with quoted flags containing spaces are parsed correctly (#13521)Massimiliano Culpo2-1/+22
2019-11-01targets: print a warning message before downgrading (#13513)Massimiliano Culpo2-25/+57
* Make package preferences a soft failure for targets, instead of a hard failure. * Added unit tests for preferences expressed via packages.yaml
2019-10-31hypre: add version 2.18.2 (#13527)Satish Balay1-0/+1
2019-10-31dd Open MPI v. 4.0.2 (#13257)Daniel Topa1-1/+2
Verification builds on LANL Darwin x86_64, ARM, and, Power9: x86_64: OPTANE dantopa@cn733:pr-openmpi-4.0.2.spack $ spack arch linux-centos7-skylake_avx512 $ spack install openmpi @ 4.0.2 % gcc @ 4.8.5 ... ==> Installing openmpi ... ==> Successfully installed openmpi Fetch: 2m 15.65s. Build: 6m 13.17s. Total: 8m 28.82s. [+] /scratch/users/dantopa/new-spack/pr-openmpi-4.0.2.spack/opt/spack/linux-centos7-haswell/gcc-4.8.5/openmpi-4.0.2-jrypg7vfnk6nl5if2rnzt65wdrjelxsq NEHALEM $ spack arch linux-centos7-nehalem $ spack install openmpi @ 4.0.2 % gcc @ 4.8.5 ... ==> Installing openmpi ... ==> Successfully installed openmpi Fetch: 50.48s. Build: 9m 11.45s. Total: 10m 1.93s. [+] /scratch/users/dantopa/new-spack/pr-openmpi-4.0.2.spack/opt/spack/linux-centos7-nehalem/gcc-4.8.5/openmpi-4.0.2-4jz3bcwjci44taizt4jqzxqh4y75uswc ARM $ spack arch linux-rhel7-aarch64 $ spack install openmpi @ 4.0.2 % gcc @ 4.8.5 ... ==> Installing openmpi ... ==> Successfully installed openmpi Fetch: 1m 10.47s. Build: 11m 41.45s. Total: 12m 51.92s. [+] /scratch/users/dantopa/new-spack/pr-openmpi-4.0.2.spack/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/openmpi-4.0.2-ygr77roadqzdnsdgqz3uactjqnb5nayn POWER9 $ spack arch linux-rhel7-power9le $ spack install openmpi @ 4.0.2 % gcc @ 4.8.5 ==> Warning: Using GCC 4.8 to optimize for Power 8 might not work if you are not on Red Hat Enterprise Linux 7, where a custom backport of the feature has been done. Upstream support from GCC starts in version 4.9 ... ==> Installing openmpi ... ==> Successfully installed openmpi Fetch: 23.95s. Build: 9m 7.67s. Total: 9m 31.62s. [+] /scratch/users/dantopa/new-spack/pr-openmpi-4.0.2.spack/opt/spack/linux-rhel7-power8le/gcc-4.8.5/openmpi-4.0.2-cid4wfzr2iwgz6ybhkexludwu7koi266 $ spack find -ldf openmpi ==> 4 installed packages -- linux-centos7-haswell / gcc@4.8.5 ---------------------------- jrypg7v openmpi@4.0.2%gcc lliismp hwloc@1.11.11%gcc 7dqpxas libpciaccess@0.13.5%gcc viidrh5 libxml2@2.9.9%gcc yhvj3br numactl@2.0.12%gcc pkmj6e7 zlib@1.2.11%gcc -- linux-centos7-nehalem / gcc@4.8.5 ---------------------------- 4jz3bcw openmpi@4.0.2%gcc pcauu6w hwloc@1.11.11%gcc yiqf6bj libpciaccess@0.13.5%gcc wpfgqf2 libxml2@2.9.9%gcc fd2xpnm numactl@2.0.12%gcc xguzaxf zlib@1.2.11%gcc -- linux-rhel7-aarch64 / gcc@4.8.5 ------------------------------ ygr77ro openmpi@4.0.2%gcc omy3xi2 hwloc@1.11.11%gcc 6a4he35 libpciaccess@0.13.5%gcc txqo4cc libxml2@2.9.9%gcc m5neuus numactl@2.0.12%gcc 67s2oqn zlib@1.2.11%gcc -- linux-rhel7-power8le / gcc@4.8.5 ----------------------------- cid4wfz openmpi@4.0.2%gcc zcdnwb3 hwloc@1.11.11%gcc lencfon libpciaccess@0.13.5%gcc bve4jop libxml2@2.9.9%gcc kajzqwg numactl@2.0.12%gcc tjbynt2 zlib@1.2.11%gcc Thu Oct 17 19:02:50 MDT 2019 Signed-off-by: Daniel Topa <dantopa@lanl.gov>
2019-10-31Bugfix: BundlePackage staging/installation (#13524)Peter Scheibel1-0/+3
4af4487 added a mirror_id function to most FetchStrategy implementations that is used to calculate resource locations in mirrors. It left out BundleFetchStrategy which broke all packages making use of BundlePackage (e.g. xsdk). This adds a noop implementation of mirror_id to BundleFetchStrategy so that the download/installation of BundlePackages can proceed as normal.
2019-10-31Docs: unlock requirement versions (#13384)Adam J. Stewart1-3/+3
2019-10-31Travis CI: Test Python 3.8 (#13347)Adam J. Stewart4-15/+35
* Travis CI: Test Python 3.8 * Fix use of deprecated cgi.escape method * Fix version comparison * Fix flake8 F811 change in Python 3.8 * Make flake8 happy * Use Python 3.8 for all test categories
2019-10-31Bump up PGMath Library to latest version. More transparent name of the ↵Nichols A. Romero1-2/+3
branch, version name equals branch name. (#13511)
2019-10-31Add GRASS 7.8.0 (#13026)Adam J. Stewart1-49/+99
* Add GRASS 7.8.0 * Add new variants/dependencies * Remove unused dep * Filter entire libiconv line
2019-10-31kokkos: turn host_values into a property (#13518)Christoph Junghans1-3/+6
* kokkos: turn host_values into a property * Update package.py * Update package.py
2019-10-31ipopt: Add condition for 'aarch64' to Ipopt/config.guess (#13499)t-karatsu2-0/+13
2019-10-31MeshToolKit package (#12870)Julien Loiseau1-0/+93
* Adding flecsph package * Correcting header * Boost version update * Correcting Flake8 errors * Correcting headers * Develop preferred in FleCSI * Removing FleCSPH branch of FleCSI * MeshToolKit package * formatting * Formatting * Correcting MSTK package * Format * Update var/spack/repos/builtin/packages/mstk/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/mstk/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/mstk/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/mstk/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/mstk/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/mstk/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/mstk/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/mstk/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/mstk/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/mstk/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update package.py * Format * Format * Correcting package behavior * Correcting format * Corrections * Update var/spack/repos/builtin/packages/mstk/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Multiline
2019-10-31VTK-m: Add support for the 1.5 release (#13514)Robert Maynard1-5/+6
2019-10-31portage: fix lapacke linkage (#13517)Christoph Junghans1-1/+1
2019-10-30Documentation: Database.query methods share docstrings (#13515)Greg Becker1-41/+53
Currently, query arguments in the Spack core are documented on the Database._query method, where the functionality is defined. For users of the spack python command, this makes the python builtin method help less than ideally useful, as help(spack.store.db.query) and help(spack.store.db.query_local) do not show relevant information. This PR updates the doc attributes for the Database.query and Database.query_local arguments to mirror everything after the first line of the Database._query docstring.
2019-10-30cpu: fix clang flags for generic x86_64 (#13491)Greg Becker2-8/+16
* cpu: differentiate flags used for pristine LLVM vs. Apple's version
2019-10-30cuda: fix conflict statements for x86-64 targets (#13472)Massimiliano Culpo1-4/+6
* cuda: fix conflict statements for x86-64 targets fixes #13462 This build system mixin was not updated after the support for specific targets has been merged. * Updated the version range of cuda that conflicts with gcc@8: * Updated the version range of cuda that conflicts with gcc@8: for ppc64le * Relaxed conflicts for version > 10.1 * Updated versions in conflicts Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
2019-10-29fix openmpi wrappers with libfabric (#13439)Gregory Lee1-10/+16
* fix openmpi wrappers with libfabric * flake8 fix * flake8 fix * openmpi fix deprecated API * openmpi fix deprecated API
2019-10-29mumps: Fix compile commands. (#13497)t-karatsu1-3/+3
2019-10-29r-bio3d: new package at 2.3-4 (#13496)Justin S1-0/+19
2019-10-29r-fields: new package at 9.9 (#13495)Justin S1-0/+20
2019-10-29r-spam: new package at 2.3-0.2 (#13494)Justin S1-0/+19
2019-10-29r-dotcall64: new package at 1.0-0 (#13493)Justin S1-0/+19
* r-dotcall64: new package at 1.0-0 * r-dotcall64: break up long line
2019-10-29r-dada2: new package at 1.14 (#13492)Justin S1-0/+29
* r-dada2: new package at 1.14 * r-dada2: add gmake dependency * Update var/spack/repos/builtin/packages/r-dada2/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-10-29syaml_int type should use int.__repr__ rather than str.__repr__ (#13487)Peter Scheibel1-1/+1
2019-10-29mumps: Add '-DMAIN_COMP' when using Fujitsu compiler. (#13480)t-karatsu1-4/+6
2019-10-29new package: py-scs (#13477)Sinan1-0/+43
* new package: py-scs * rename * flake8 * Update var/spack/repos/builtin/packages/py-scs/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-10-29CP2K: drop json-fortran dependency and add support for the Nvidia V100 (#13468)Tiziano Müller1-7/+2
* cp2k: drop json-fortran dep since that's now handled in SIRIUS internally * cp2k: gained support for Nvidias V100
2019-10-29bugfix: make `spack -d test test_changed_files` work (#13229)Tamara Dahlgren1-1/+1
The `test_changed_files` in `test/cmd/flake8.py` was failing because it calls `ArgumentParser.parse_args()` without arguments. Normally that would just parse `sys.argv` but it seems to fail because of something in either `spack test` or `pytest`. Call it with an empty array so that it doesn't try to touch`sys.argv` at all. - [x] allow `-d` spack option for `test_changed_files`
2019-10-28Add SpFFT: sparse 3D FFT library (#13458)Simon Pintarelli1-0/+44
* Add SpFFT: sparse 3D FFT library SpFFT is required as a dependency for SIRIUS * cleanup * add missing dependency
2019-10-28new package: py-cvxpy (#13478)Sinan1-0/+28
* new package: py-cvxpy * improve dependency specs
2019-10-28new package: py-ecos (#13476)Sinan1-0/+21
* new package: py-ecos * flake8
2019-10-28new package: py-osqp (#13475)Sinan1-0/+22
2019-10-28Update URL parsing regexes and tests (#13411)Adam J. Stewart240-805/+773
* Update URL parsing regexes and tests * Get rid of no longer used README * Merge py-udunits and py-cf-units * netcdf -> netcdf-c * setup_environment -> setup_*_environment * Fix doc tests * Few last minute fixes * Simplify prefix removal copypasta
2019-10-28Update the module files for cbtf-krell and openspeedshop (#13400)Jim Galarowicz5-86/+97
* Update the module files for cbtf-krell and openspeedshop adding man paths and needed papi and libmonitor paths. * Update module files for new API. * Use the same python for both develop and release branches.
2019-10-28new Package/scs (#13454)Sinan2-0/+55
* new package: SCS * make flake8 happy * add missing patch, improve style * fix typo * Update var/spack/repos/builtin/packages/scs/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * move filefilter to edit phase
2019-10-28update conduit for 0.5.0 release (#13455)Cyrus Harrison2-25/+92
* add support for static (via ~shared) and use vtk-m 1.2 * updating vtkh package to output cmake configure file and pinning it to vtkm 1.2 * trying a different cmake for vtkh * removing problematic b * making conduit respect ~python * fixing ascent python logic * update ascent package * consistant cmake usage * conditionally add tbb in ascent if vtkh * applying becker fix * adding vtkh tag * fixing vtkh tagged version * updating ascent and conduit for static builds * enabling openmp * reverting files that should not have been changed * ascent updates * more robust handling of variants * fixing ascent package typo * ascent: add optional support for mfem * enable mfem conduit support for ascent * add optional adios dep to conduit * remove ver req from conduit * ascent: remove confusing comment * tweaks to conduit and ascent pkg recipes * fix typo in conduit package * pref conduit master * fixing mfem typo for ascent * reverting files * adding mirror for bzip * changing mfem to depend on conduit@master to get updated relay * restore use of conduit 0.3.1 or greater for mfem * set master as prefered conduit version * allow mfem to use conduit master * adding rover package and editing ascent * updating vtkm cmake dep * updates from axom * guard ascent python support on +shared * removing rover to simply ascent package * add fortran variant to conduit, to allow us to turn off conduit support even when a fortran compiler is specified * fix fortran compiler check so it can work on cray systems * working towards cuda fix for vtkm lagrange filter * update ascent package with more variants, and patch to avoid nvcc issue * hdf5 flags fix for BGQ * flake8 * extra guards for cuda patch * conduit and ascent fortran fix * fix patch for non cuda case * add test variant to conduit, tweak ascent pkg * change min ver of cmake used for ascent * h5z-zfp package: unset FC when ~fortran * conform to expected upstream solution * pinning vtkm * going back to vtkm master * add back vtk-m variant for shared libs * update ascent and vtkh packages * wire up option to run tests during install * add post install test * add testing to ascent * tweak for blueos xl * add ctest output on error for run_tests * enable ctest output on error for run_tests * add testing of the using-with-make example * update using-with-make examples * typo in ascent using-with-cmake test * fix ascent using test exe names * more fixes, less sleep * more fixes, less sleep ... * remove unwired up version * improvments suggested on review * adding new cmake * Update package.py * Update package.py * changes post cori os update * fix cray hack * Update package.py Fixing 'fix'. Inconsistent variable names in conduit package * type in spack recipes * add zfp support to conduit * fix indent error in conduit pkg * move to use build phases, add sphinx rtd as dep, fix ex names in tests * add conduit 0.5.0 release * flake8 * remove old cray hack * incorp feedback from review * fix to use proper build env sig
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