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2020-01-15Update RocksDB to current version (#14524)Olaf Mersmann1-1/+23
* rocksdb: Fix for rocksdb issue 5303 * rocksdb: Explicitly disable features * rocksdb: Add TBB variant. * rocksdb: New version 5.18.3 and 6.5.3
2020-01-15Add version constraint to graphviz patches (#14377)Glenn Johnson1-4/+9
* Add version contraint to graphviz patches This PR restricts the graphviz version that the patches for building with the Intel compiler apply to. The two patches that were needed for building graphviz-2.40.1 with the Intel compiler are not needed for graphviz-2.42.2. * Adjust the qt dependencies The qt5 patch is only needed for graphviz-2.40.1. However, that version will only compile with GCC-6 or greater.
2020-01-15perl: Add 5.30.1 (and 5.31.7) (#14509)Michael Kuhn1-1/+24
This also fixes actually building the development releases.
2020-01-15mariadb-c-client: Add 3.1.6 and 3.1.5 (#14510)Michael Kuhn1-0/+2
2020-01-15hpctoolkit: add version 2019.12.28 (#14519)Mark W. Krentel1-13/+18
Add version 2019.12.28 and update the prereqs for the latest master.
2020-01-15New package Jali - unstructured mesh infrastructure for multiphysics ↵Rao Garimella1-0/+56
applications (#14498) * add variant for enabling testing * add variant for enabling testing * enable tests and clean up other options * enable tests and clean up other options * add numbered versions * add numbered versions * updates to avoid enable_tests variant; correct versioning * updates to avoid enable_tests variant; correct versioning * fixes for style * appropriate partitioners are enabled if 'all' is specified - so no need to check in spec * revert accidental change to copyright * remove erroneously re-introduced line about tests * new spack recipe for build Jali - unstructured mesh infrastructure for multiphysics applications * remove the +parallel condition for mstk, update 1.1.1 sha256sum and whitespace cleanup * reformat description * cut down description
2020-01-15Adds MPI_THREAD_MULTIPLE support for OpenMPI to the variant with UCX fabrics ↵Robert Mijakovic2-1/+17
(#14194) * Fixes: 1. MPI_THREAD_MULTIPLE problem with OpenMPI and UCX. Changes: 1. OpenMPI provides two new depends_on options which result in UCX being compiled with multiple threads support. One implicit when OpenMPI 3.x is used, MPI_THREAD_MULTIPLE is enabled by default, and one explicit for OpenMPI <= 2.x, MPI_THREAD_MULTIPLE is disabled by default. 2. Extends UCX package to allow "Enable thread support in UCP and UCT" option. 3. Adds sha256 sums of UCX releases 1.6.1 and 1.2.0. More details: Fixes the issue with OpenMPI where programs which use MPI_THREAD_MULTIPLE will fail to execute because UCP worker didn't support it. During the OpenMPI package installation it's the +thread_multiple spec was not propagated to UCX nor UCX handled it at all. Now, the OpenMPI package is capable of handling +thread_multiple spec when UCX is request and the UCX package correctly handles +thread_multiple and compiles with the --enable-mt option. Error message during runtime: pml_ucx.c:226 Error: UCP worker does not support MPI_THREAD_MULTIPLE * Adapts check of specs to read better and is the suggested form in the docs. * Explicitly disables multithreading of UCX if +thread_multiple option is not used.
2020-01-15Rework texlive package to install from source (#14332)Glenn Johnson1-19/+153
* Rework texlive package to install from source This PR reworks the texlive package so that it installs from versioned source distibution files. This is preferred over installing the binary package for several reasons. For the binary installation: 1. Each component is downloaded, so can not use a spack mirror. 2. Changes in components over time are not reflected in spack hash. 3. Some of the binaries do not run due to glibc issues, depending on OS. This PR keeps the binary installation as an option but it should be considered deprecated, and probably rewmoved at some point. This PR depends on zziplib from PR #14318. * Fix flake8 issues
2020-01-15Convert encoding of script in interproscan (#14356)Glenn Johnson2-0/+13
One of the perl scripts was encoded with ISO-8859-1, which caused the sbang replacement process to fail when spack uses python3. This PR converts the ps_scan script to UTF-8 encoding.
2020-01-15Change encoding for scripts in repeatmasker (#14358)Glenn Johnson2-0/+200
This PR converts ISO-8859 encoding to UTF-8 encoding for three scripts in repeatmasker. - the main RepeatMasker script - SimpleBatcher.pm - wublastToCrossmatch.pl The ISO-8859 encoding prevented the sbang replacement of long paths when spack uses python3.
2020-01-15python: Add 3.7.6 and 3.7.5 (#14497)Michael Kuhn1-1/+3
2020-01-14Update the icu4c package (#14450)Glenn Johnson1-5/+14
* Update the icu4c package This PR makes several changes to the icu4c package 1. add updated version to 65.1 2. modify the default url as project has moved to github 3. set UTF-8 locale to support building from source files in UTF-8 format Note that the older versions are not available on github so explicit urls were used. This PR will close #14399. * Consolidate the urls Consolidate the URLs in the `version` directives by using an if test in `url_for_version`. * Put version and sha256 on same line * Put top level url back
2020-01-14Update and fix bcftools package (#14505)Glenn Johnson6-1/+372
* Update and fix bcftools package This PR updates bcftools to 1.10.2 and is dependent on PR #14504. This PR also fixes builds of other versions. Versions 1.2-1.4 did not use autotools so when the packaeg was converted to use autotools with version 1.6 those older versions could no longer build. Also, those versions needed to be patched to use an external htsllib. The method of finding the external htslib is also different for those older versions. In addition, this PR adds two variants to bcftools: - libgsl - perl-filters Finally, dependencies for perl and python are added, and an unused dependency for libzip was removed. * Do not use '@' in variant description The '@' character in a variant description will cause a problem with `spack info`. ``` ==> Error: Incomplete color format: '@' in expressions, for @1.8: ``` * Fix error with python2 processing this package
2020-01-14Update armadillo (#14499)Erik Schnetter1-0/+1
2020-01-14Update HDF5 to 1.10.6 (#14500)Erik Schnetter1-0/+1
2020-01-14h5cpp: New package (#14501)Erik Schnetter1-0/+28
2020-01-14trnascan-se: add and configure infernal dependency (#14502)Justin S1-0/+7
* trnascan-se: add and configure infernal dep * trnascan-se: use patch() for infernal config
2020-01-14mpich: Correct package name in output (#14503)Erik Schnetter1-1/+1
2020-01-14Update htslib and add libcurl variant (#14504)Glenn Johnson1-2/+19
* Update htslib and add libcurl variant This PR updates htslib to version 1.10.2 and adds a libcurl variant. The libcurl variant defaults to True because, while it is optional, it is highly recommended by the project developers. Other things done: - be consistent with quotes * Change version in variant description Apparently, `spack info` does not like the `@` character in a variant description. ``` ==> Error: Incomplete color format: '@' in @1.3:. ```
2020-01-14py-yajl: new package at 0.3.5 (#14278)Justin S1-0/+17
* py-yajl: new package at 0.3.5 * py-yajl: use PyPI mirror * py-yajl: use short PyPI url * remove py-ujson package * py-yajl: remove unused imports
2020-01-14gapfiller: traverse subdirectories in patch (#14375)Justin S1-1/+1
* gapfiller: traverse subdirectories in patch * gapfiller: revert glob function change * gapfiller: use more precise glob
2020-01-14new package: variorum (#13624)Stephanie Brink1-0/+80
2020-01-14Update MSTK to 3.3.1 (#14494)Rao Garimella1-1/+2
2020-01-14add new package : rocketmq (#14442)darmac1-0/+29
* add new package : rocketmq * remove url_for_version()
2020-01-14add new package : py-ansible (#14436)darmac1-0/+31
* add new package : py-ansible * update license info * update py-ansible depends
2020-01-14codar-cheetah: Added version 0.5 (#14487)Kshitij Mehta1-8/+6
* codar-cheetah: Added version 0.5 * codar-cheetah: Dropped v0.1 as it was not built as a Python package.
2020-01-14Sometimes debugging symbols are helpful (#14452)Rob Latham1-0/+6
2020-01-14Flang OpenMP target support for NVidia GPUs. (#14486)Nichols A. Romero1-0/+16
* Flang OpenMP target support for NVidia GPUs. * explictly disable gpu option with else clause.
2020-01-14upcxx depends on python 2 >= 2.7.5 (#14462)eugeneswalker1-0/+2
2020-01-13libcircle: add develop version from git master branch (#14420)Elsa Gonsiorowski, PhD1-2/+11
* libcircle: add develop version from git master branch * Update var/spack/repos/builtin/packages/libcircle/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * libcircle: flake8 fix i think * libcircle: naming things * libcircle: :sheep: my sacrifice to the flake8 gods Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-01-13verrou: Add support for verrou v2.2.0 (#14480)Hadrien G1-1/+8
* Add support for verrou v2.2.0 * Add myself as a maintainer
2020-01-13r-mass: Add version '7.3-51.5' and fix checksum. (#14439)t-karatsu1-1/+2
2020-01-13add new package : gpdb (#14440)darmac1-0/+41
* add new package : gpdb * update docstring and license info
2020-01-13add new package : hive (#14443)darmac1-0/+27
2020-01-13add new package : drill (#14444)darmac1-0/+28
2020-01-13Flume (#14445)darmac1-0/+33
* add new package : flume * add new package : flume
2020-01-13add new package : flink (#14446)darmac1-0/+31
2020-01-13added intel parallel 2020.0 and components (#14451)Gregory Lee6-0/+11
2020-01-13Support for more libfabric providers (#14453)Rob Latham1-1/+3
Add support for (just about) every provider libfabric knows about
2020-01-13new package: librsb (#14455)MIchele Martone1-0/+31
* new package: librsb * flake8, be good * no hardocded FC=gfortran
2020-01-13add new package : keepalived (#14463)darmac1-0/+28
2020-01-13Remove overlapping depends_on statement for py-basemap (#14475)Glenn Johnson1-2/+1
This PR resolves an overlapping dependency specification for py-basemap.
2020-01-13Add version 3.3.0 to MSTK spackage (#14476)Rao Garimella1-1/+2
2020-01-13python: Fix post-install script without C++ compiler (#14481)Michael Kuhn1-1/+2
2020-01-13Add Python 3.8.1 (#14484)Adam J. Stewart1-0/+1
2020-01-13Add GDAL 3.0.3 and 2.4.4 (#14485)Adam J. Stewart1-1/+3
2020-01-13openPMD-api: Depends on ADIOS 2.5.0 (#14489)Axel Huebl1-3/+3
Only ADIOS2 versions we support.
2020-01-13New package: qemu (#14184)Jonathon Anderson1-0/+105
2020-01-13Add Go version 1.13.6 and 1.12.15 (#14482)Paul1-0/+2
2020-01-13SIRIUS, SpFFT: updated package recipes and versions (#14469)Simon Pintarelli2-3/+11
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