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2018-06-26Add version 3.904 of verilator (#8577)Andreas Baumbach1-3/+4
* Add specific version to package verilator Change-Id: If7645410ec192f92a5eed83ee9b317b569576b4a * fix dependency types Change-Id: Ib36c72257c1fa6678c8553225ca21a010d7ae6d1
2018-06-26Add py-imageio for python3 (#8553)Sajid Ali1-0/+46
* new file: var/spack/repos/builtin/packages/py-imageio/package.py * modified: var/spack/repos/builtin/packages/py-imageio/package.py * Update package.py
2018-06-26Docker dedupe (#8441)Omar Padron22-768/+125
* Add Dockerfile for Scientific Linux 7 (RHEL7 recompile) * revert version change * remove duplicate docker-related files
2018-06-26bugfix: fix macos incompatibility in lock test (#8573)Todd Gamblin3-16/+29
- Spack was assuming that a group with gid == current uid would always exist. - This was breaking the travis build for macos. - also fix issue with the DB tarball test finding coverage filesx
2018-06-26Add Dockerfile for Scientific Linux 7 (RHEL7 recompile) (#8422)Patrick Gartung5-0/+253
* Add Dockerfile for Scientific Linux 7 (RHEL7 recompile)
2018-06-25refactor: move pytest.ini and top-level conftest.py to lib/spack/spack/testTodd Gamblin4-54/+28
- removes two files from root of repository - `spack test` still works fine to run tests
2018-06-25HiC-pro depends on python+ucs4. (#8564)健美猞猁1-1/+1
2018-06-25A new perl package: perl-io-compress. (#8566)健美猞猁3-0/+112
* A new package: perl-compress-raw-zlib. * A new package: perl-compress-raw-bzip2. * A new perl package: perl-io-compress. * flake8. * Add zlib and bzip2 dependency.
2018-06-25refactor: move issue_template.md to .github directoryTodd Gamblin1-0/+0
2018-06-24coreutils: add version 8.29Todd Gamblin1-0/+1
2018-06-24refactor: move templates from root to share/spackTodd Gamblin12-16/+17
- This complies with the unix directory hierarchy standard (which Spack attempts to follow) - Also unclutters the repo root directory.
2018-06-24sowing: update to version used by current petsc -i.e 1.1.25-p1 (#8561)Satish Balay1-0/+1
2018-06-24tests: test file/line attribution in config errorsTodd Gamblin3-30/+140
2018-06-24tests: add a test for `spack debug` commandTodd Gamblin3-2/+66
2018-06-24tests: test html output for `spack list`Todd Gamblin1-62/+37
- make list test use SpackCommand - convert to pytest - add a test for HTML output
2018-06-24Add `spack -H` shortcut for `spack help --all`Todd Gamblin1-18/+17
- I keep typing this based on `spack test -h` and `spack test -H` - This finally makes my fingers happy
2018-06-24Balay/petsc remove boost dependency (#8508)Satish Balay4-13/+16
* petsc: remove dependency on boost - its required only as a dependency on trilinos Also set COPTFLAGS='' etc - this way CFLAGS is the primary way optimization flags are set by spack * petsc: update pkgs with petsc~boost dependency * fix flake8 * boost is optional for trilinos - so adjust petsc dependency on boost [via trilinos] accordingly * do not add boost dependency on petsc [due to trilinos requirement]. Trilinos adds this dependency anyway.
2018-06-24xsdk: update xsdk@develop to use plasma@develop (#8555)Satish Balay2-7/+15
plasma@develop has another flag 'DHAVE_MKL' that needs to be disabled [for non-mkl build] add dependency on gcc-6.0 add in new dependency on readline plasma: requires both LIBS in make.inc and command line? If cmd line is missing -some internal values from plasma makefile gets used - causing link errors [on Mac] tools/lua-5.3.4/src/Makefile: $(MAKE) $(ALL) SYSCFLAGS="-DLUA_USE_LINUX" SYSLIBS="-Wl,-E -lreadline" if make.inc is missing - I get: /usr/bin/ld: cannot find -lmkl_intel_lp64 /usr/bin/ld: cannot find -lmkl_sequential /usr/bin/ld: cannot find -lmkl_core collect2: error: ld returned 1 exit status Also add a new dependency -ldl
2018-06-23Fix m4 on OS X highsierra (#8559)George Hartzell2-0/+18
m4 exited immediately (causing the nettle build to fail). ``` (alice)[11:09:46]spack>>/Users/hartzell/tmp/spack-mac/spack/opt/spack/darwin-highsierra-x86_64/clang-9.1.0-apple/m4-1.4.18-caxsf7l5yd7qbq2bown6bzi5el3ltfwf/bin/m4 Abort trap: 6 (alice)[11:10:18]spack>>fg ``` Tracked down a fix via the Homebrew recipe. I'll send a note to the `bug-m4@gnu.org` list to ensure that upstream knows about it.
2018-06-23Fix gcc@5.5.0 on OS X 10.13.5 (#8540)George Hartzell2-1/+132
* Fix gcc@5.5.0 on OS X 10.13.5 gcc@5.5.0 failed to build on my OS X 10.13.5 box. I found/modified a patch in the MacPorts world that traced back to Homebrewy, https://trac.macports.org/ticket/56502#no1 The issue has also been reported to gcc, https://gcc.gnu.org/bugzilla/show_bug.cgi?id=83531 I eventually discovered a nearly identical version of the patch at Homebrew. https://github.com/Homebrew/formula-patches/blob/master/gcc%405/10.13_headers.patch gcc builds with this and I can compile many things, but e.g. curl and cmake both fail. As @davydden and others observed in #1847, it seems to be an apple thing. * Fix mistaken change to patch when clause (added :) I mistakenly deleted a colon from the 'darwin/gcc-7.1.0-headerpad.patch'.
2018-06-23kokkos: add support for version 2.7.00 of kokkos (#8521)Geoff Womeldorff1-1/+2
2018-06-23omega-h: fix -std=c++11 build error (#8543)Satish Balay1-0/+6
cd /tmp/balay/spack-stage/spack-stage-joxtpr/omega_h-9.13.4/spack-build/src && /home/balay/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.1.0-7ws4tgx4z3o ru5g5skjrxs5sobpeiyef/bin/mpic++ -Domega_h_EXPORTS -I/home/balay/spack/var/spack/stage/omega-h-9.13.4-th4b67fz5es6cbgcar742jxamjt3tqjb/omega_h-9.13.4/src -I/tmp/bala y/spack-stage/spack-stage-joxtpr/omega_h-9.13.4/spack-build/src -I/home/balay/spack/var/spack/stage/omega-h-9.13.4-th4b67fz5es6cbgcar742jxamjt3tqjb/omega_h-9.13.4/tpl -I/home/balay/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb/include -O2 -g -DNDEBUG -fPIC -o CMakeFiles/omega_h.di r/Omega_h_map.cpp.o -c /home/balay/spack/var/spack/stage/omega-h-9.13.4-th4b67fz5es6cbgcar742jxamjt3tqjb/omega_h-9.13.4/src/Omega_h_map.cpp In file included from /usr/include/c++/5/chrono:35:0, from /home/balay/spack/var/spack/stage/omega-h-9.13.4-th4b67fz5es6cbgcar742jxamjt3tqjb/omega_h-9.13.4/src/Omega_h_timer.hpp:4, from /home/balay/spack/var/spack/stage/omega-h-9.13.4-th4b67fz5es6cbgcar742jxamjt3tqjb/omega_h-9.13.4/src/Omega_h_timer.cpp:1: /usr/include/c++/5/bits/c++0x_warning.h:32:2: error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support must be enabled with the -std=c++11 or -std=gnu++11 compiler options. #error This file requires compiler and library support \ ^
2018-06-22Fix version detection for gcc@8 (#8511)Michael Kuhn1-2/+2
2018-06-22Package/grass (#8505)Tom Merrick1-0/+202
* Add the grass74 GIS system. * Correct flake8 errors * Made requested changes * added correct types to python
2018-06-22Updating py-pillow with change in checksum for version 5.1.0. (#8547)Jon Rood1-1/+1
2018-06-22New package ncbi-magicblast (#8517)Yifan Zhu1-0/+41
* ncbi-magicblast: new package * updated package.py * updated ncbi-magicblast
2018-06-22silo: Make silo use AutotoolsPackage (#8551)Nick Forrington1-13/+9
To benefit from updates to config.guess for newer architectures. More info: https://github.com/spack/spack/issues/2063
2018-06-22added ReMPI version 1.1.0 (#8548)Gregory Lee1-0/+1
2018-06-22Added minuit package (#8536)Paul Chelarescu4-0/+203
* Added minuit package * Removed default method and template * Different URLs for old versions * Patches for versions down to 1.5.0 * Reverted ROOT package changes * Removed print statement * Added checksums for older versions * Consistent version names
2018-06-22Fixed linking of R with MKL + configure issue in a dep (pixman) (#8449)Massimiliano Culpo2-1/+20
2018-06-22elpa: add 2018.05.001.rc1 and 2017.11.001 (#8512)Denis Davydov1-1/+3
* elpa: add 2018.05.001.rc1 and 2017.11.001 * elpa: shift preferred
2018-06-21new packages: workrave and its dependencies (#7753)Mike Pozulp11-0/+463
2018-06-21Add tags for ECP applications that are in Spack.Todd Gamblin9-1/+17
- All now have both 'ecp' and 'ecp-apps' tags. - ECP ST projects will eventually also have ecp and ecp-software tags.
2018-06-21Correcting position independent code setting for boxlib and amrex. (#8537)Jon Rood2-2/+2
2018-06-21use new valgrind repo (#8538)Cyrus Harrison1-1/+1
2018-06-21cmake: update package (#8539)Matthias Diener1-0/+1
2018-06-21openmpi: add latest release 3.0.2 (#8452)Daniel Topa1-0/+1
* Add latest release 3.0.2 https://www.open-mpi.org/software/ompi/v3.0/:x Signed-off-by: Daniel Topa <dantopa@lanl.gov> * Add in library version in comment
2018-06-21dealii: add msg= to conflicts statements (#8509)Denis Davydov1-15/+30
2018-06-20poppler needs it test repo URL updated (#8519)Peter Doak1-1/+1
2018-06-20pytest: add _pytest/_version.py and LICENSETodd Gamblin4-1/+49
- pytest was not reporing the correct version from pytest.__version__. It reported 'unknown' - this fixes issues on some systems where system-installed pytest plugins would try to use the version and convert it to an int
2018-06-20externals: move spack.util.ordereddict to external/ordereddict_backportTodd Gamblin5-8/+5
2018-06-20New package xxhash. (#8530)Chris Green1-0/+49
* New package xxhash. * Change requested by @adamjstewart.
2018-06-20Add kealib 1.4.8 (#8522)Adam J. Stewart1-0/+1
2018-06-20openPMD-api: update dependencies (#8528)Axel Huebl1-2/+7
update the dependencies of openPMD-api
2018-06-20glib: Update to 2.56.1 (#8523)Michael Kuhn1-0/+1
2018-06-20mitofates: needs perl at runtime (#8526)Levi Baber1-0/+1
2018-06-20Bump ZeroMQ from v4.2.2 to v4.2.5 (#8514)Chuck Atkins1-2/+5
This addresses some build issues with GCC 8 and the addition of the -Werror=stringop-truncation warning.
2018-06-19added albacore version 2.3.1 (#8513)Douglas Duckworth1-1/+2
2018-06-18Allow docs to be built with Sphinx 1.7.1+ (#8500)Adam J. Stewart1-1/+7
* Allow docs to be built with Sphinx 1.7.1+ * Allow docs to be built with Sphinx 2.0+
2018-06-18Percept requires googletest to be a static library. (#8506)Jon Rood1-1/+1
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