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2019-08-20mvapich2 depends on slurm when built with process_managers=slurm (#12489)Jeffrey Salmond1-1/+3
2019-08-20prefix -> self.prefix (#12487)Daryl W. Grunau1-1/+1
2019-08-20UnifyFS: new package - rename from UnifyCR (#12439)Cameron Stanavige1-10/+10
UnifyCR has been renamed to UnifyFS. Renaming the Spack package is the last step in this process. This renames the package and changes any UnifyCRs to UnifyFS within the package.
2019-08-20kim-api: added version 2.1.3 (#12457)Ryan S. Elliott1-1/+2
2019-08-20Add Kokkos 2.9.0 (#12466)Teodor Nikolov1-0/+1
2019-08-20r: added version 3.6.1. (#12470)健美猞猁1-0/+1
2019-08-16py-pyfaidx: tweak dependencies; fixes #12445 (#12446)Pariksheet Nanda1-1/+4
* py-pyfaidx: tweak dependencies; fixes #12445 * py-pyfaidx: add suggestions for #12446
2019-08-16Solve compilation error on summit. (#12305)Dan Lipsa2-0/+19
* This constexpr does not compile on summit. I tried gcc6.4 and gcc7.4 * Add link the the llvm bug report.
2019-08-16preCICE: Fix Eigen include directory (#12441)Frédéric Simonis1-1/+2
2019-08-15new package: laszip (#12432)Sinan1-0/+15
2019-08-15camx: add version 6.50 (#12437)Pariksheet Nanda1-0/+129
* camx: add version 6.50 * camx: remove unpredictable download URL * camx: install manual and data files
2019-08-15Overhaul PyTorch package (#12420)Adam J. Stewart1-30/+155
* Overhaul PyTorch package * Flake8 * Distributed requires MPI, NCCL not specified correctly * Binary was being specified incorrectly * Run tests at install time * Disable GLOO in addition to GLOO_IBVERBS
2019-08-15hpctoolkit: add version 2019.08.14 (#12435)Mark W. Krentel1-1/+3
Add version 2019.08.14 and rename 'develop' to 'master' to match the git branch name (now that master is also a special name).
2019-08-15go: Add 1.12.8 and 1.11.13 (#12433)Michael Kuhn1-0/+2
Both address security issues: https://groups.google.com/forum/#!topic/golang-nuts/fCQWxqxP8aA
2019-08-15Update VisIt to version 3.0.1 and fix on mac (#12396)Seth R. Johnson6-39/+135
* Add option to disable QTDesigner plugin for qwt Qt designer shouldn't be necessary to build downstream GUI code. Currently `qwt^qt~tools` fails to build: (darwin clang@10.0.1) ``` compiling qwt_designer_plugin.cpp compiling qwt_designer_plotdialog.cpp moc qwt_designer_plugin.h moc qwt_designer_plotdialog.h rcc qwt_designer_plugin.qrc qwt_designer_plugin.h:23: Error: Undefined interface make[1]: *** [moc/moc_qwt_designer_plugin.cpp] Error 1 make[1]: *** Waiting for unfinished jobs.... qwt_designer_plugin.cpp:17:10: fatal error: 'QDesignerFormEditorInterface' file not found ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1 error generated. make[1]: *** [obj/qwt_designer_plugin.o] Error 1 make: *** [sub-designer-make_default-ordered] Error 2 ``` * Update VTK for newer VisIt and compiler versions Several changes/enhancements to VTK package --- Add version 8.1.0 (default version for VisIt 3.x) --- Tweak VTK options for version 8 and VisIt: - only add mpi4py version option when mpi4py is enabled - Require object factory for downstream packages - Remove OpenGL preference for VTK 8 --- Combine +python3 into +python The spec for using python3 should just be `+python^python@3:`. --- Remove unused VTK cmake argument on newer version --- Patch for Python 3 fails on VTK 6.1 (needed for VisIt 2.x): ``` ==> Patch /rnsdhpc/code/spack/var/spack/repos/builtin/packages/vtk/python3.7-const-char.patch failed. ==> Error: ProcessError: Command exited with status 1: '/usr/bin/patch' '-s' '-p' '1' '-i' '/rnsdhpc/code/spack/var/spack/repos/builtin/packages/vtk/python3.7-const-char.patch' '-d' '.' ``` and as it happens, VisIt 2.13 is incompatible with Python 3 anyway. --- Fix compiler error: As spack's configuration warning says, double-quotes can cause trouble: ``` ==> [2019-07-29-11:47:55.269653] Warning: Quotes in command arguments can confuse scripts like configure. The following arguments may cause problems when executed: -DVTK_REQUIRED_OBJCXX_FLAGS="" Quotes aren't needed because spack doesn't use a shell. Consider removing them ``` They were being added to the compile line, causing clang to think it was asked to compile an empty file: ``` cd /private/var/folders/fy/x2xtwh1n7fn0_0q2kk29xkv9vvmbqb/T/s3j/spack-stage/spack-stage-3nk9bwe_/spack-build/Rendering/OpenGL && /rnsdhpc/code/spack/lib/spack/env/clang/clang++ -DVTK_IN_VTK -DvtkRenderingOpenGL_EXPORTS -F/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks -DGLX_GLXEXT_LEGACY -O2 -g -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -fPIC -fvisibility=hidden -fvisibility-inlines-hidden "" -o CMakeFiles/vtkRenderingOpenGL.dir/vtkCocoaGLView.mm.o -c /rnsdhpc/code/spack/var/spack/stage/vtk-6.1.0-b2mj276iz77fadisv2me365qe27t3gxt/spack-src/Rendering/OpenGL/vtkCocoaGLView.mm clang: error: no input files make[2]: *** [Rendering/OpenGL/CMakeFiles/vtkRenderingOpenGL.dir/vtkCocoaGLView.mm.o] Error 1 ``` * Modernize/PEP-8 visit package statements * Add new VisIt version and patches for building on Mac - VisIt's cmake assumes a 'vtk(tiff|jpeg|png)' *library* target exported by VTK, but VTK 8.1.x on my configuration seems to have these as header-only targets with library dependencies. - Explicitly add QT path to visit configure: Without this, somehow `${VISIT_QT_DIR}` was being set to empty, so that the build failed with `missing /bin/moc`. - VisIt assumes that if it isn't being built statically, QWT has been built as a mac Framework. QWT actually is built as a framework based on whether QT itself is. Error message: ``` -- Looking for QWT CMake Error at CMake/SetUpThirdParty.cmake:131 (MESSAGE): Include Directory for QWT (/rnsdhpc/code/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/qwt-6.1.3-bmfxirweplzhjoiil4rw632evkyteuwk/lib/qwt.framework/Versions/Current/Headers) does not exist. Call Stack (most recent call first): CMake/FindQwt.cmake:57 (SET_UP_THIRD_PARTY) CMakeLists.txt:1251 (INCLUDE) ```
2019-08-15ADIOS 2.4.0: Add new Deps (#12414)Axel Huebl1-9/+40
* ADIOS 2.4.0: Add new Deps Version 2.4.0 of ADIOS2 added new dependencies that are not yet listed as `depends_on` and/or disabled otherwise. Add them now to avoid picking them up from system paths, e.g. `libpng`. * ADIOS2: Variant Defaults Change * Python: False by default * ADIOS1: only used prior to 2.3.0
2019-08-14Update icu4c to version 64.1 (#12429)Seth R. Johnson1-0/+1
Version 60.1 fails to build on linux with clang@7.0.1 and clang@8.0.0: ``` digitlst.cpp:508:9: error: use of undeclared identifier 'freelocale' freelocale(gCLocale); ^ clang++ ... coll.cpp digitlst.cpp:520:26: error: use of undeclared identifier 'LC_ALL_MASK' gCLocale = newlocale(LC_ALL_MASK, "C", (locale_t)0); ^ clang++ ... sortkey.cpp clang++ ... bocsu.cpp clang++ ... ucoleitr.cpp clang++ ... ucol.cpp clang++ ... ucol_res.cpp 2 errors generated. clang++ ... ucol_sit.cpp clang++ ... collation.cpp *** Failed compilation command follows: ---------------------------------------------------------- /projects/spack/lib/spack/env/clang/clang++ -D_REENTRANT -DU_HAVE_ELF_H=1 -DU_HAVE_ATOMIC=1 -DU_HAVE_STRTOD_L=1 -DU_HAVE_XLOCALE_H=1 -I. -I../common -DU_ATTRIBUTE_DEPRECATED= -DU_I18N_IMPLEMENTATION -std=c++11 -W -Wall -pedantic -Wpointer-arith -Wwrite-strings -Wno-long-long -c -DPIC -fPIC -o digitlst.o digitlst.cpp --- ( rebuild with "make VERBOSE=1 all" to show all parameters ) -------- make[1]: *** [digitlst.o] Error 1 make[1]: *** Waiting for unfinished jobs.... clang++ ... collationsettings.cpp make[1]: Leaving directory `/build/s3j-spack/spack-stage/spack-stage-k9ba3gqo/spack-src/source/i18n' make: *** [all-recursive] Error 2 ```
2019-08-14Update BOLT package (#12423)Shintaro Iwasaki1-1/+7
* bolt: add new versions * bolt: add argobots dependency From this version, BOLT uses an external Argobots, not a builtin one.
2019-08-14Fix skopeo dependencies (#12425)Daryl W. Grunau1-0/+2
2019-08-14Fix charliecloud dependencies (#12427)Daryl W. Grunau1-0/+2
2019-08-14UnifyCR: update dependencies and build options (#12216)Cameron Stanavige1-6/+36
* UnifyCR: update dependencies and build options This adds some specifics about dependencies and conflicts and adds additional build options and variants. UnifyCR now also has limited fortran support. * Remove debug statements condition on Spack debug Change debug print statements to now be turned on when the -g cflag is found in the flags the user sets.
2019-08-14Package umoci dependency (#12422)Daryl W. Grunau1-0/+1
* bump eospac version * Revert "bump eospac version" This reverts commit 835b1f822d8c083f6ab9eb17222c00409e8eb3da. * umoci depends on go-md2man
2019-08-14lammps: add version 20190807 (#12424)Christoph Junghans1-0/+1
2019-08-14New package: device-mapper (#12406)Daryl W. Grunau1-0/+47
* bump eospac version * Revert "bump eospac version" This reverts commit 835b1f822d8c083f6ab9eb17222c00409e8eb3da. * new package: device-mapper * address comments by @hartzell * extraneous whitespace * capitalization * device-mapper -> lvm2 * unprovide device-mapper * address comments by @adamjstewart * address comments by @adamjstewart
2019-08-14r-rmutil: new package at 1.1.3 (#12417)Justin S1-0/+19
* r-rmutil: new package at 1.1.3 * r-rmutil: use cloud.r-project.org
2019-08-14New package: go-md2man (#12397)Daryl W. Grunau1-0/+45
* bump eospac version * Revert "bump eospac version" This reverts commit 835b1f822d8c083f6ab9eb17222c00409e8eb3da. * new package: go-md2man * address comments by @adamjstewart
2019-08-14NCCL: fix build on older Linux systems (#12415)Adam J. Stewart2-1/+19
2019-08-14masurca: build on arm. (#12416)Toyohisa Kameyama2-0/+55
* remove -minline-all-stringops when target is arm. * change int3 to raise(SIGTRAP) when target is arm.
2019-08-14add new package: py-python-magic (#12409)Sinan1-0/+18
* add new package: py-python-magic * tidy up * Update var/spack/repos/builtin/packages/py-python-magic/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-08-13zstd: fix build linking error (#12413)Adam J. Stewart1-3/+7
2019-08-13starce: new version and build on ARM. (#12401)Toyohisa Kameyama1-1/+11
1. souce URL change to github. 2. Add version 5.1 and 5.2 3. enable build on ARM.
2019-08-13add charliecloud master branch; add dependencies (#12327)Jordan Ogas1-0/+13
* add master and dependencies * remove gcc and make * add variants, make doc and ch-grow dependencies optional * capitalize description sentence * move dependencies and variants below version block * fix typos
2019-08-13packages/umoci (#12346)Daryl W. Grunau1-0/+39
* bump eospac version * Revert "bump eospac version" This reverts commit 835b1f822d8c083f6ab9eb17222c00409e8eb3da. * new package: umoci * Package -> MakefilePackage * add missing build phase * relax expand=False requirement
2019-08-13add new versions (#12393)Sinan1-0/+2
2019-08-13add new version (#12394)Sinan1-0/+1
2019-08-13add new version (#12395)Sinan1-0/+1
2019-08-13subread: build on ARM. (#12400)Toyohisa Kameyama1-0/+14
2019-08-13package/gromacs: simd optimizations autodetection for more versions (#12402)Ricardo Silva3-2/+14
* gromacs: fix simd detection for pre 2018 versions * pre 2018 the cmake file was named differently * fixed up post 2018 patch file which was non pretty * Trim patch
2019-08-13Add version 2.4.0 for cantera. (#12405)健美猞猁1-0/+1
2019-08-13patch opa-psm2 to build with spack wrappers (#12407)Gregory Lee2-1/+54
2019-08-13Fix package gpgme dependency (#12410)Daryl W. Grunau1-0/+1
* bump eospac version * Revert "bump eospac version" This reverts commit 835b1f822d8c083f6ab9eb17222c00409e8eb3da. * build depends on gnupg which provides gpgsm binary
2019-08-13gcc: Add 9.2.0 (#12411)Michael Kuhn1-0/+1
2019-08-13CP2K/SIRIUS: add support for building with CUDA, fix CP2K build with MKL ↵Tiziano Müller3-16/+169
(#11418) * cp2k/sirius: add CUDA support * cp2k: fix building with MKL * sirius: make sure to link against Spacks blas/lapack/scalapack
2019-08-13new package: asagi: create package.py (#11931)brietzke1-0/+73
* Create package.py * applied reviewer suggestions * Update package.py * remove CamelCase from variant names * add comment on why fetching package via git * found typo in variant to cmake-argumentlist translation * rename variants to ~nonuma ~nompi to be in sync with cmake-args, refine mpi@3-dependency definition * Revert "rename variants to ~nonuma ~nompi to be in sync with cmake-args, refine mpi@3-dependency definition" This reverts commit 58e8cf7d93c5665f0b4b50228946857734716cef. * remove version-preference
2019-08-12Package/grass: fix iconv linking issue (#12165)Sinan1-0/+9
* fix iconv linking issue, package_grass fix linking iconv, add more comments
2019-08-12singularity: update version to 3.3.0 (#12295)Owen Solberg1-2/+8
* add checksum for singularity release 3.3.0 * update singularity doc URL URL at the lbl.gov domain has message saying: "This website is going away soon! Update your bookmarks!" * add note about build log file for post-install step * provide links to both 2.x and 3.x security docs * remove whitespace. Passing flake8 confirmed locally this time :) * add TODO comment for fakeroot support
2019-08-12New package: TexStudio (#12301)Jean-Paul Pelteret3-3/+86
* Poppler library: Add new versions * Poppler library: Allow building with QT4 * Poppler library: Install header files * Add patch to Poppler package * Add new package: TexStudio
2019-08-12blaze: converted to CMakePackage (#12357)Russell J. Hewett1-4/+4
The previous version does not properly install the required cmake configuration files for blaze-lib, so find_package does not work correctly. This patch converts the blaze-lib package to use CMakePackage, adds the required cmake dependency, and removes the install() member function, which is not working correctly and is no longer needed.
2019-08-12gtksourceview: new package (#12387)Geoffrey Oxberry1-0/+49
2019-08-12openblas: fix target detection for cross-compiling (#12390)Janne Blomqvist1-1/+1
In a review of a previous pull request ( https://github.com/spack/spack/pull/10713 ) it was mentioned that the proper way to figure out the target architecture is via spec.architecture.target. This patch fixes this for the openblas package. Signed-off-by: Janne Blomqvist <janne.blomqvist@aalto.fi>
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