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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
2018-06-18samrai: update package for 3.12.0 and fix compilation bugs for earlier ↵twang151-10/+16
versions (#8501) * SAMRAI: remove dependency on boost for samrai 3.12.0 or later versions, but keep the older versions ccontinuing working with boost 1.64.0 or earlier. Also, the older versions cannot compile with boost 1.65.0 or above. (#8491) * SAMRAI: fix typos of comments and remove obsolete code.
2018-06-18Albany: Add Albany package. (#8332)Glen Hansen1-0/+121
* Add package.py to support the Albany GitHub project builds.
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