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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>
2019-08-12openblas@0.3.7: New version (#12391)Janne Blomqvist1-0/+1
This adds OpenBLAS 0.3.7 (released 2019-08-11).
2019-08-12Apply xl patch for cce@9: to fix cmake. (#12392)Kelly (KT) Thompson1-0/+1
2019-08-12packages/skopeo (#12348)Daryl W. Grunau1-0/+43
* bump eospac version * Revert "bump eospac version" This reverts commit 835b1f822d8c083f6ab9eb17222c00409e8eb3da. * new package: skopeo * address flake8 issues * address adamjstewart's comments * use the Executable class and undocumented 'str' feature for output * Package -> MakefilePackage * add missing build phase * patch -> edit phase
2019-08-11Update SWIG versions and add Fortran fork (#12185)Seth R. Johnson1-1/+17
* Add git repositories for SWIG and SWIG-Fortran * Fix typo in documentation * Move 'master' to top of SWIG version list
2019-08-11Fix py-matplotlib build with Intel compiler (#12144)Glenn Johnson1-5/+0
Not sure what happened between #5321 and now but the CC=CXX fix now prevents py-matplotlib from building with the Intel compiler. I verified with versions of py-matplotlib from 2.0.2 to 3.0.2 and intel-17.0.4 and 19.0.4 that py-matplotlib successfully builds with the Intel compiler without that code.
2019-08-11Use correct GCC installation when installing clang with GCC (#12381)Seth R. Johnson1-0/+4
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