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2019-02-06genemark et package: add version 4.38 (#10519)Levi Baber1-1/+9
Also add heu_dir to bin/
2019-02-06Paraview package: update PYTHONPATH for dependents (#10501)Jon Rood1-2/+7
Add vtkmodules directory to PYTHONPATH in Paraview for Trilinos
2019-02-06Add Python 3.7.2 updated (#10531)Daniel Topa1-1/+6
Also add versions 3.7.1, 3.6.8, 3.6.7, 3.6.6. Does NOT alter preferred version (2.7.15). Supplants PR 10491 "Add Python 3.7.2" (https://github.com/spack/spack/pull/10491). Verification builds on LANL Darwin: **Intel Xeon** [+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/general/opt/spack/linux-centos7-x86_64/gcc-4.8.5/python-3.7.2-d3p7vg6w2r563cpmwsmbgjbsiqc4j4fq [+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/general/opt/spack/linux-centos7-x86_64/gcc-4.8.5/python-3.7.1-ibom6qj2z64egyaqz5htkwp5tr362il6 [+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/general/opt/spack/linux-centos7-x86_64/gcc-4.8.5/python-3.6.8-rkifc3c7mjgdglw27upiap767ut4wpkz [+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/general/opt/spack/linux-centos7-x86_64/gcc-4.8.5/python-3.6.7-meuesn43twttt756exyzqgdhohjgipjq [+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/general/opt/spack/linux-centos7-x86_64/gcc-4.8.5/python-3.6.6-qwnwme7otyuoqqudcglfmfy75t5npywl **Arm** [+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/arm/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/python-3.7.2-qj27kzs4ttdqudm3hsi3pt57kv7lshco [+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/arm/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/python-3.7.1-io5eneirgvpegy3tosvp6wq5ndf7yjis [+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/arm/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/python-3.6.8-ej3vnvta2hbtrh7p5hokfqkuewxeqgsa [+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/arm/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/python-3.6.7-l3qnue72ewppn2wxza3w6l62l7ijlque [+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/arm/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/python-3.6.6-b55pdoqsr5bie4k5djd4vokm3nywhm45 **Power9** [+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/power9/opt/spack/linux-rhel7-ppc64le/gcc-4.8.5/python-3.7.2-cicayvl7ki4tswoqlljsmcetwqcnoh3x [+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/power9/opt/spack/linux-rhel7-ppc64le/gcc-4.8.5/python-3.7.1-7vej3zvnvyj2jvz5lnxhnts3ok2fcxbp [+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/power9/opt/spack/linux-rhel7-ppc64le/gcc-4.8.5/python-3.6.8-xijljmdanyrybcx2rv65qshycmbrfv6c [+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/power9/opt/spack/linux-rhel7-ppc64le/gcc-4.8.5/python-3.6.7-vqdhzg7c3xxxregqmzxsqqfzxt2hajvq [+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/power9/opt/spack/linux-rhel7-ppc64le/gcc-4.8.5/python-3.6.6-jf4bnsdwk3qjhtmvjjhblnrcz5dztfdq 2019-02-05 Signed-off-by: Daniel Topa <dantopa@lanl.gov> Signed-off-by: Daniel Topa <dantopa@lanl.gov>
2019-02-06CUDA compiler conflicts for Linux (#10460)Nichols A. Romero1-14/+69
* CUDA compiler conflicts for Linux. * Add Volta and Turing GPUs. * Add mandatory conflict for Volta and Turing GPUs. * Revert "CUDA compiler conflicts for Linux." This reverts commit 7d4ff654ac53aad272c59e9f7f8bb3fbb32bcec4. * Compiler conflicts introduced from previous commit into CUDA packaged moved and integrated into CUDA build system. * More conversative with compiler conflicts for cuda 10.0.130, since I don't know what will happen with future cuda 10.x releases. * Correct off-by-one errors in clang conflicts for x86_64 Linux. * No restrictions on Apple Clang compiler until we are able to distinguish Xcode clang from github clang more easily. Note to fix this in the future. * Change comment to clarify that github clang refers to LLVM clang. * Fix and simplify index range. * Fix overlapping conflicts for CUDA 10.0.130 * Removed extra ^cuda from conflict.
2019-02-06Update CLAW package with version 1.2.1 (#10528)Valentin Clement (バレンタイン クレメン)1-0/+1
2019-02-06perl-yaml: new package (#10514)Levi Baber1-0/+17
2019-02-06wordnet: new package (#10526)simo-tuomisto1-0/+33
2019-02-06xsdk: enable slepc in deal.ii (used to be a concretization error) (#10218)Denis Davydov1-2/+2
2019-02-05New package: PMDK (#10453)Phil Carns2-0/+75
2019-02-05r-wgcna: new package at 1.64-1 (#10392)Justin Stanley1-0/+31
2019-02-05MPark: Variant v1.4.0 (#10512)Axel Huebl1-1/+2
Add the latest release of Michael Park's C++ Variant lib.
2019-02-04mercury package: add 'udreg' variant (#10415)Phil Carns1-0/+10
Faster and/or more robust in some cases on Cray platforms
2019-02-04New package: perl-hash-merge (#10506)Levi Baber1-0/+18
2019-02-04New package: perl-clone-choose (#10507)Levi Baber1-0/+16
2019-02-04votca*: add v1.5 (#10495)Christoph Junghans4-10/+15
* votca-tools: add v1.5 * votca-csg: add v1.5 * votca-xtp: add v1.5 * votca-ctp: add v1.5
2019-02-04augustus: fix bam2wig auxprog build (#10362)Justin Stanley1-5/+35
* augustus: fix bam2wig auxprog build * augustus: few more changes to make new versions work
2019-02-04tar: add version 1.31 (#10485)Matthias Diener1-0/+1
2019-02-04Catch2: v2.6.0 (#10490)Axel Huebl1-0/+1
Add the latest Catch2 release.
2019-02-01New package: py-alembic (#10436)wspear1-0/+17
2019-02-01New package: py-prometheus-client (#10440)wspear1-0/+17
2019-02-01plumed package: add versions 2.4.4 and 2.5.0 (#10496)Nicholas Labello1-1/+3
2019-02-01dyninst: add patch to work with new boost (#10454)Mark W. Krentel2-0/+35
Add tribool.patch to add explicit casts from tribool to bool in two places. Boost, starting with version 1.69, turned on explicit conversions for tribool, which breaks the build for dyninst. This is merged into the current dyninst develop and is expected to be part of the next release, so the version range uses the current release as an upper bound.
2019-02-01New package: py-async-generator (#10439)wspear1-0/+18
2019-01-31gatk package: new versions, updated helper script (#10459)zschulte1-44/+76
Closes #10168 * Add versions 4.1.0.0 and 4.0.12.0 * Replace md5 checksums with sha256 * Logic to generate a helper script for versions earlier than 4 was not running. This corrects the branch which controls whether this script is generated. * Constrain Java dependency to version 8 (GATK does not work with Java 11) * Avoid adding scripts that have dependencies not handled by Spack such as gcloud and google-chrome. These scripts are good candidates for later extensions.
2019-01-31py-pybigwig: fix build with python3, add numpy variant (#10444)Ricardo Silva2-2/+23
* added patch to correctly pick up non-system curl when building with Python 3 * added numpy variant * add version 0.3.12 * update checksums to sha256
2019-01-31New package: openjdk (#9861)snehring1-0/+98
Closes #2622 This retrieves and installs the binary of Oracle's OpenJDK (an open-source JDK implementation). The logic is largely based on the Spack JDK package (Oracle's closed-source JDK implementation). For now this is only supports Linux. If the download could be customized based on OS (for the same version), binaries are also available for MacOS and Windows.
2019-01-30git-lfs: add version 2.6.1, update build system (#10405)Matthias Diener1-13/+6
Build system was changed to use a Makefile. Therefore older versions (which don't support this) are removed. The new build system also supports testing by default.
2019-01-30fftw: fix include error for 2.x versions (#10039)Tom Payerle1-6/+15
Fixes #7372 Added patch method which renames config.h in the fftw subdir of the source tree. fftw 2.1.5 appears to ship with a copy of this file with all defines commented out. This gets read by the #include directives instead of the version in the build directory with the correct defines. As a result, many C preprocessor macros left undefined, including F77_FUNC_ which causes the bulk of fttwf77.c to be skipped due to an #ifdef, so fftw_reverse_int_array et al not included in library. Fixes #7372 Also fixed some inconsistencies with the handling of quad and long_double in specs between the configure method and the build, check, and install methods.
2019-01-30HDF5: Add develop Version (#10382)Axel Huebl1-0/+13
2019-01-30Mercury package: update libfabric dependency on Cray (#10408)Phil Carns1-1/+0
The Mercury package previously depended on libfabric@develop on Cray platforms in order to pick up a fix for the GNI provider that was only available in git. This is no longer needed now that the libfabric package is at 1.7.0.
2019-01-30r-pkgmaker: add 0.27, new dependencies (#10419)Justin Stanley1-0/+14
2019-01-30gobject-introspection: add 1.56.1 and fix download (#10462)Michael Kuhn1-0/+5
Define url_for_version, since Spack's default substitution is not sufficient
2019-01-30go: fix directory structure issue for 1.11.5 (#10484)Matthias Diener1-2/+9
2019-01-30cmake: Fix linker errors on Darwin when using external dependencies (#10467)Chuck Atkins2-0/+33
Adds upstream patch for a missing framework. This is anticipated to be fixed by CMake 3.13.4 so is only applied up to version 3.13.3
2019-01-30libsodium: Updates source URL. (#10483)Matt Belhorn1-1/+1
The source URL for versions 1.0.15 and older is updated to reflect where those archives are now hosted by the upstream libsodium developers.
2019-01-30ninja: Add kitware version with fortran capability (#10470)Jon Rood1-1/+3
2019-01-30New package: SLATE (#10434)G-Ragghianti1-0/+63
2019-01-30jemalloc: Add variant to prepend public api with "je_" prefix (#10356)Jason Lee1-0/+3
2019-01-30redundans: add 0.14a (#10006)Justin Stanley1-10/+15
Also update install to use globbing
2019-01-30New package: simgrid (#10076)Samuel Thibault1-0/+76
2019-01-30zoltan: detect metis int64 variant (#10051)Cameron Smith1-0/+4
Configure zoltan depending on metis int64 support
2019-01-30Package py-keras: add new versions and dependencies (#10353)dorier3-7/+70
Add new versions for py-keras. Versions of py-keras at or after 2.2.0 require keras-processing and keras-applications packages. Add these packages to Spack and add dependencies to the py-keras package.
2019-01-30cudnn package: add version 7.2 (#10481)Jimmy Tang1-0/+2
2019-01-30Update opa-psm2 package (#10344)sknigh1-8/+14
* Add version 11.2.68 * Add variant to disable AVX2 for older hardware * Change the makefile so libraries and includes are not placed under $PREFIX/usr * Updated URL and homepage
2019-01-30r-preprocesscore: add version 1.44.0 (#10389)Justin Stanley1-0/+1
2019-01-30r-impute: add version 1.56.0 (#10390)Justin Stanley1-0/+1
2019-01-30codes package: add version 1.1.0 (#10414)Abhinav Bhatele1-0/+1
2019-01-30r-runit: new package at 0.4.32 (#10416)Justin Stanley1-0/+19
2019-01-30r-bibtex: new package at 0.4.2 (#10417)Justin Stanley1-0/+22
2019-01-30r-rngtools: add 1.3.1 (#10418)Justin Stanley1-0/+1
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