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2018-11-09Update Dyninst package file for TBB dependency (#9728)Jim Galarowicz5-7/+12
* Update Dyninst package file for TBB dependency Dyninst master and 10.0 release versions require the tbb package. This mod updates the tbb versions adding the one that dyninst uses and adds the required spack package changes to dyninst/package.py. * Put new version of tbb in proper location, per reviewer comment. * Only depend on tbb if building the development version. * Changes for the release of Dyninst 10.0.0
2018-11-09Introduce fftw-api virtual package for Intel-MKL and FFTW (#9618)Nichols A. Romero2-0/+4
* Introduce FFTW2 and FFT3 providers for Intel-MKL and FFTW Spack packages. * make fftw default package for fftw-api virtual package * virtual package test assertion now provides location of default virtual packages. * Change name of virtual package to fftw-api and used versioned interface.
2018-11-09utils: merge spack.environment into spack.util.environmentTodd Gamblin3-3/+3
- `spack.util.environment` is the new home for routines that modify environment variables. - This is to make room for `spack.environment` to contain new routines for dealing with spack environments
2018-11-08canu: use built-in makefile install (#9726)Justin Stanley1-11/+3
2018-11-08muparser: minor fixes to 2.2.5 and add 2.2.6 with CMake (#9724)Denis Davydov2-4/+27
* muparser: minor fixes to 2.2.5 and add 2.2.6 with CMake * dealii: make muparser optional
2018-11-08ncl: Add 6.5.0 (#9736)Michael Kuhn1-3/+4
2018-11-07r-delayedarray: new dep in latest vers (#9731)Levi Baber1-0/+1
2018-11-07Use the raw compiler path for the preprocessing pass in CLAW driver (#9748)Valentin Clement (バレンタイン クレメン)1-0/+3
2018-11-06New repo for advanced packaging tutorial (#9711)Peter Scheibel13-0/+947
* modified tutorial packages * update hint in hdf5 tutorial file (typo for suggested argument) * add repo.yaml to tutorial repository * update tutorial docs to refer user to tutorial package repository * flake edits * recommend site scope vs. defaults * you don't specify the repo's name when adding a repo, just the path
2018-11-06snpeff: add wrapper for SnpSift.jar (#9674)Levi Baber2-14/+21
2018-11-06Add OpenMPI 3.1.3 and a bug patch (#9680)sknigh2-0/+33
2018-11-05py-backports-functools-lru-cache: add to 'backports' namespace (#9720)Gregory Lee1-0/+2
2018-11-02new package: homer (starting at 4.9.1) (#9669)Justin Stanley1-0/+48
2018-11-02freetype: enable-freetype-config build option for 2.9.1 (#9653)Eric1-1/+4
This builds the 'freetype-config' binary which can be used to get configuration information about the freetype install, used by some dependents.
2018-11-02Add version 2.0.2 of BookLeaf_Cpp and version 3.0.2 of Typhon. (#9662)Tim Law2-0/+3
2018-11-01henson: new package (#9657)Dmitriy1-0/+38
* henson: new package * henson: change github path to henson-insitu * henson: make mpi-wrappers=off by default * henson: remove unsued variable and spaces to make linter happy * henson: rename version master to develop
2018-10-31xeus: new package (#9682)Thomas Stitt6-5/+113
* xeus: new package cppzmq: add version 4.3.0 zeromq: make libsodium optional, on by default * xeus: add patch so it builds, add new version nlohmann-json: add more versions cryptopp: add more versions * xeus: flake8 * xeus: fix license
2018-10-31ecp-proxy-apps: disable building CANDLE Benchmarks by default (#9691)Abhinav Bhatele1-2/+5
add as a variant
2018-10-31lbzip2: add new package (#9688)Federico Ficarelli1-0/+16
2018-10-31Provide a newer doxygen version. (#9681)Kelly (KT) Thompson2-0/+32
* Provide a newer doxygen version. + Also provide a patch that allows collaboration diagrams to work properly with C++ std::shared_ptr<T>. Ref: https://github.com/Sleepyowl/doxygen/commit/6c380ba91ae41c6d5c409a5163119318932ae2a3?diff=unified
2018-10-31Packmol: a new package. (#9687)健美猞猁1-0/+16
2018-10-31r-dismo: new package starting at 1.1-4 (#9675)Justin Stanley1-0/+21
2018-10-30Update openspeedshop and cbtf-krell module creation code (#9234)Jim Galarowicz7-112/+148
* Add the setting of CBTF_MPI_IMPLEMENTATION to the cbtf-krell and openspeeedshop package files, so that the mpi implementation can be found by the tool. This allows users to not have to set this manually if only one mpi implementation is specified in the build. * Update version ranges for dependencies of cbtf packages
2018-10-30Update dependencies for py-llvmlite (#9668)Ross Miller1-1/+1
Change dependency on llvm from >=6.0 to 6.0:6.99. Refs #9667
2018-10-30New package: RegCM, regional climate model. (#9655)Alberto Chiusole1-0/+73
2018-10-30GCC: ISL and mpfr upper bounds (#9513)Axel Huebl2-6/+14
* GCC: constrain version 6, 7, and 8 to build with ISL version at most 0.18 * GCC version 9 (not yet released) will be compatible with ISL version 0.20 so future GCC releases are constrained to build with ISL version at most 0.20 * ISL: Add v0.15, replace all md5 sums with sha256 sums for ISL versions * GCC versions before 6 were constrained to build with ISL 0.14 but have been confirmed to work with ISL 0.15 * GCC: Place an upper bound on GCC's mpfr dependency
2018-10-30vtk: remove redundant option setting (#9597)Ruben Di Battista1-7/+0
This eliminates duplicates for a couple options which are set multiple times.
2018-10-30caliper: specify path to libunwind (#9670)Abhinav Bhatele1-0/+2
2018-10-30warpx: Fixes for building on NERSC (#9671)Dave1-0/+6
2018-10-30Jthies/xsdk add phist (#8980)jthies2-3/+37
* packages/phist: add variant 'fortran' to enable/disable building the Fortran bindings * xsdk: add phist * packages/xsdk: add a comment reg. updating phist dependency * packages/phist: +fortran variant is only for versions 1.7: * packages/phist: update comments * xsdk: forgot to specify kernel library for phist (picked tpetra, assuming trilinos+tpetra will be installed) * packages/phist: add variant 'openmp' to allow disabling OpenMP * phist: fix compile error due to missing -lm * flake8: fix warnings * packages/phist: fix cmake flag: XSDK_ENABLE_Fortran (rather than XSDK_BUILD_Fortran) * packages/phist: allow disabling building the scamac matrix generator (which causes trouble on some systems) * packages/xsdk: disable scamac within phist because it caused problems for @balay and is not essential for now * packages/phist: actually disable scamac via cmake if ~scamac * phist: disable openmp from xsdk
2018-10-30packages/phist: new version 1.7.3 (#9672)jthies1-0/+1
2018-10-29R rjags - new version (#9568)Dan Han1-1/+3
* REMOVED: -callr: updated to newest version, added sha256, added listurl * r-rjags: updated * r-rjags: fix new version
2018-10-29hoomd-blue: fixing issue during build with newer cmakes (#9543)snehring1-1/+4
* Constrain to build with CMake <= 3.9.6 * Specify installation prefix to match install prefix format of other Spack python libraries
2018-10-29strumpack: update to version 3.1.1 (#9666)Satish Balay1-0/+1
2018-10-29slepc: update to version 3.10.1 (#9665)Satish Balay1-0/+1
2018-10-29add package Feature/sentieon (#9557)Miles Perry1-0/+39
* added package sentieon * change file location * updated spack header license and added license_vars * fixed flake8 error * fixed license header * fix license header * license * added import os.path * edits * flake8 edits
2018-10-29orca: new package starting at 4.0.1.2 (#9297)Justin Stanley1-0/+46
* orca: new package starting at 4.0.1.2 * orca: fix typo * orca: fix boilerplate * orca: reorder deps, add openmpi runtime dependency * orca: license update
2018-10-29Expand the libMesh dependency list (#9642)David Wells1-17/+182
This commit overhauls the libMesh package script in a number of ways: * We now inherit from AutotoolsPackage. * libMesh contains about a dozen third-party dependencies that can only be provided by the copy bundled with libMesh. This patch enumerates all such bundled dependencies and disables all of them by default. * libMesh supports compilation with external installations of boost, eigen, hdf5, slepc, and tbb; this patch adds all of them to package.py. * libMesh will look for a few system executables (xz, bzip, gdb) by default. This is now disabled. * libMesh will now used a copy of perl installed by spack instead of trying to find the system copy. * Compilation with non-system MPI installations requires an additional flag (--with-mpi=); this has been added.
2018-10-29diy: new package (#9628)Dmitriy1-0/+21
2018-10-29Updated octave and gnuplot versions (#9660)Denis Davydov2-0/+4
* octave: add 4.2.2, 4.4.0 and 4.4.1 * gnuplot: add 5.2.5
2018-10-26pyfypp: add setuptools build dependency (#9650)Denis Davydov1-0/+2
2018-10-26damaris: add support for VisIt and Catalyst (#9651)dorier1-5/+17
2018-10-26new package: phyluce (starting at 1.6.7) (#9633)Justin Stanley1-0/+44
2018-10-26VisIt: build vtk without mpi support (#9649)dorier1-1/+1
VisIt cannot use VTK built with mpi support (which was enabled by default starting in #9494)
2018-10-26valgrind: add 3.14.0 (#9648)Denis Davydov1-0/+1
2018-10-26new package: msmc (starting at 1.1.0) (#9654)Justin Stanley1-0/+34
2018-10-26kokkos: add pic option (#9643)Jonas Lippuner1-0/+8
Since kokkos only compiles a static library, the -fPIC compiler flag is required to link kokkos into a Fortran executable
2018-10-26fmt: add new versions and update constraints (#9634)Federico Ficarelli1-11/+26
Update versions and constraints on cmake and supported toolchains (as stated by the documentation).
2018-10-26cabana: added v0.1.0 (#9644)Christoph Junghans1-1/+2
2018-10-25Fix issue with miniconda attempting to install the incorrect version (#9589)Ross Miller2-8/+8
The install() function in the miniconda2 & 3 package.py files referenced self.url, which is hard-coded to 4.3.11. That's not necessary the version that the user requested, though. Changed the install() function to reference self.stage.archive_file. Also added a version string for 4.5.11.