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2018-10-02MACSio: update package (#9412)Abhinav Bhatele1-1/+3
2018-10-02Intel parallel studio 2019 cluster edition (#9295)David Orman1-0/+2
* untracking file * intel-parallel-studio: added 2019 cluster edition and checksum
2018-10-02new package: TraceR (#9298)Abhinav Bhatele1-0/+58
2018-10-02raxml: build all matching variants (#9377)Justin Stanley1-13/+15
2018-10-01ytopt: new package (#9403)Prasanna Balaprakash1-0/+42
2018-10-01kokkos: bugfix for case wherein kokkos backends enabled in spack but not ↵Geoff Womeldorff1-3/+3
parsed correctly (#9396)
2018-10-01nvptx-tools: add new package (#9378)Matthias Diener1-0/+50
* nvptx-tools: add new package * Update package.py * Update package.py
2018-10-01patching p4est to select the proper openmp lib (#9381)Ricardo Silva1-1/+26
* patching p4est to select the proper openmp lib * For when compiler.openmp_flag isn't supported * authored by @nrichart, I only tested it * Adding openmp variant Signed-off-by: Ricardo Silva <ricardo.silva@epfl.ch>
2018-10-01kokkos: add serial backend explicitly. add kokkos options and kokkos cuda ↵Geoff Womeldorff1-3/+95
options. (#9276)
2018-10-01redundans: add py-numpy dep, snap-berkeley version constraint (#9354)Justin Stanley1-1/+2
2018-09-30Laghos: add version 1.1 (#9389)Abhinav Bhatele1-2/+4
2018-09-28lighttpd: install to bin vs sbin (#9337)Justin Stanley1-0/+3
2018-09-28gsnap: add 2018-07-04 (#9356)Justin Stanley1-0/+1
2018-09-28py-flake8-polyfill: removing unnecessary build_args (#9284)Levi Baber1-6/+0
2018-09-28libsigcpp: add a real homepage (#9282)Levi Baber1-1/+1
2018-09-28Gapfiller 1.10 f01 (#9163)Aronnax, Miles V. [ISU/LAS]1-4/+16
* GapFiller.pl fixes: line endings, env perl, convert to Getopt::Std, requires perl with threads. * GapFiller.pl fixed source path, install location. * Fixed missing space.
2018-09-28perl-dbd-sqlite: new package starting at 1.56 (#9338)Justin Stanley1-0/+39
2018-09-28r-biocparallel: new link dependency added in last version (#9274)Levi Baber1-0/+1
2018-09-28r-misc3d: add a real homepage (#9283)Levi Baber1-1/+1
2018-09-28perl-cgi: new package starting at 4.37 (#9339)Justin Stanley1-0/+42
2018-09-28r-rots: fix package type (#9344)Justin Stanley1-1/+1
2018-09-28Add PETSc 3.10.1 to PETSc's spackage file (#9382)Serban Maerean2-0/+20
* Add version 3.10.1 to the PETSc spackage file. * Makefile changes required for building PETSc native tests with the XL compiler.
2018-09-28gmap-gsnap: set default value for simd variant (#9366)snehring1-1/+5
Also add zlib/bzip2 dependencies.
2018-09-28libpfm4: add version and compiler flags (#9291)Mark W. Krentel1-0/+19
Set default optimization level (-O2) if not specified in cflags.
2018-09-28mpich: fix 3.2 patch (#9330)Denis Davydov1-1/+1
patch does not apply to 3.2.1 (released in late 2017). Given that it fixes the issue discussed in May 2016, most likely it shall apply only to 3.2
2018-09-27Module path parsing: CRAY_LD_LIBRARY_PATH and PACKAGE_DIR (#9374)Peter Scheibel2-3/+24
Fix two bugs with module file parsing: * Detection of the CRAY_LD_LIBRARY_PATH variable was broken by #9100. This fixes it and adds a test for it. * For module names like "foo-bar/1.0", the associated PACKAGE_DIR environment variable name would be "FOO_BAR_DIR", but Spack was not parsing the components and not converting "-" to "_"
2018-09-27Bazel: update env handling, add versions (#9369)Eric Müller4-3/+170
Building bazel yielded errors since commit cd9691d. The first commit fixes the build for older bazel versions, the second commit adds new versions and ports the patches to these versions.
2018-09-27Set libs property for tcl and tk (#9372)sknigh2-0/+9
2018-09-27Added legacylaunchers variant to openmpi (#9336)sknigh1-1/+7
Lots of programs still have mpiexec/mpirun baked in.
2018-09-27yaml-cpp: conflict with gcc 4.7 instead of 4.8 (#9371)sknigh1-1/+1
4.8 has c++11 support, and RHEL/Centos 7 still use 4.8.5
2018-09-27Added slurm 17.11 and 18.08 (#9345)sknigh1-0/+2
2018-09-27Added Cuda 10 (#9310)sknigh1-0/+2
2018-09-27ember: put all READMEs into docs and add executables in bin (#9362)Abhinav Bhatele1-9/+13
2018-09-26py-pybind11: add version 2.2.4 (#9355)dorier1-0/+1
2018-09-26arpack-ng: add version 3.6.3 (#9331)Denis Davydov1-0/+1
2018-09-26new package: r-processx (#9342)Justin Stanley1-0/+45
2018-09-26new package: r-ps (#9341)Justin Stanley1-0/+36
2018-09-26paml: remove old version, added 4.9h (#9360)Justin Stanley1-2/+2
2018-09-26new package versions: ucx, libhio, and hwloc (#9365)Daniel Topa1-3/+3
2018-09-26miniVite: new package (#9348)Abhinav Bhatele1-0/+65
2018-09-26fix build errors, make mpi variant default and add openmp variant (#9364)Abhinav Bhatele1-2/+6
2018-09-26new package: TALASS (#9326)Peer-Timo Bremer1-0/+77
2018-09-26update URLs for Laghos and MACSio (#9351)Abhinav Bhatele2-2/+2
2018-09-26VTK package: don't require "+llvm" for mesa dependency (#9256)dorier1-2/+3
2018-09-26gmap-gsnap: Add variant for different cpu support. (#8087)lingnanyuan1-0/+30
* gmap-gsnap: Add variant for different cpu support. * gmap-gsnap: fix flake8 error. * gmap-gsnap: remove sys import. * Change variant type to multi-valued. * remove if-statement. * gmap-gsnap: Build in seperate directories. * gmap-gsnap: remove make distclean. * gmap-gsnap: rewrite the recipe.
2018-09-25Increase and customize lock timeouts (#9219)Peter Scheibel7-89/+217
Fixes #9166 This is intended to reduce errors related to lock timeouts by making the following changes: * Improves error reporting when acquiring a lock fails (addressing #9166) - there is no longer an attempt to release the lock if an acquire fails * By default locks taken on individual packages no longer have a timeout. This allows multiple spack instances to install overlapping dependency DAGs. For debugging purposes, a timeout can be added by setting 'package_lock_timeout' in config.yaml * Reduces the polling frequency when trying to acquire a lock, to reduce impact in the case where NFS is overtaxed. A simple adaptive strategy is implemented, which starts with a polling interval of .1 seconds and quickly increases to .5 seconds (originally it would poll up to 10^5 times per second). A test is added to check the polling interval generation logic. * The timeout for Spack's whole-database lock (e.g. for managing information about installed packages) is increased from 60s to 120s * Users can configure the whole-database lock timeout using the 'db_lock_timout' setting in config.yaml Generally, Spack locks (those created using spack.llnl.util.lock.Lock) now have no timeout by default This does not address implementations of NFS that do not support file locking, or detect cases where services that may be required (nfslock/statd) aren't running. Users may want to be able to more-aggressively release locks when they know they are the only one using their Spack instance, and they encounter lock errors after a crash (e.g. a remote terminal disconnect mentioned in #8915).
2018-09-25qt: fix dbus builds (#9315)Justin Stanley1-1/+0
2018-09-24petsc: add new versions 3.9.4 and 3.10.0 (#9319)Satish Balay2-0/+7
* petsc: add new versions 3.9.4 and 3.10.0 * petsc:update superlu_dist dependency for version 3.10 [might have to change this later for xsdk] * slepc: add in new releases 3.9.2 and 3.10.0
2018-09-24superlu_dist: (master) has cxx11 sources - so update make.inc to list cxx11 ↵Satish Balay1-0/+5
compilers (#9316)
2018-09-24lighttpd: new package starting at 1.4.50 (#9325)Justin Stanley1-0/+36