summaryrefslogtreecommitdiff
path: root/var
AgeCommit message (Collapse)AuthorFilesLines
2018-04-11add package py-gdbgui (#7715)healther1-0/+43
* add package py-gdbgui Change-Id: I553e1e4c4f6385348190817199e05b25522b57b4 * fix alignment * add setuptool runtimedependency * add gdb run dependency
2018-04-11Add package py-slurm-pipeline (#7681)healther1-0/+41
* add package py-slurm-pipeline Change-Id: Iade405a7e96f04e476cea76e460cac2ebdf21f95 * add missing py-six dependency Change-Id: I382fa4139880c1a61af3f314c74ed6e7c2e88c5b * Update package.py * Update package.py * Update package.py * fix flake8
2018-04-11Add ANTs package (#7717)Simon Flood1-0/+48
* Add ants package Add a package for ANTs (version 2.2.0) * Update package.py * Update package.py * Update package.py * Update package.py * Update package.py
2018-04-11add package py-python-socketio (#7721)healther1-0/+43
* add package py-python-socketio * fix indention * add description to eventlet variant * fix dependencies Change-Id: I425ae165dfcce30df6cbbd671cd6ef1bef5078dc * Update package.py * Update package.py * Update package.py * Update package.py
2018-04-10py-cnvkit: add new package (#7688)peetsv1-0/+46
* py-cnvkit: add new package * updating dependencies * correcting flake8 error * adding py-setuptools dependency
2018-04-10add package py-gevent (#7712)healther1-0/+40
* add package py-gevent Change-Id: I49722e02a961f20b9177ae8575b78b42bf6c01c9 * fix alignment * add cffi dependency
2018-04-10add package py-eventlet (#7722)healther1-0/+37
2018-04-10add package py-greenlet (#7720)healther1-0/+33
* add package py-greenlet * remove optional setuptools dependency
2018-04-10add package py-python-engineio (#7723)healther1-0/+39
* add package py-python-engineio * flake8 fix
2018-04-10lammps: add v20180316 (#7725)Christoph Junghans2-2/+5
* lammps: add v20180316 * add latte@1.1.1 and make lammps use it
2018-04-10hwloc: add v 2.0.1 (#7724)Daniel Topa1-1/+2
Signed-off-by: Dan Topa <dantopa@lanl.gov>
2018-04-10go: Update to 1.10.1 (#7708)Michael Kuhn2-11/+15
Also update go-bootstrap to the 20171003 snapshot.
2018-04-10add package py-pygdbmi (#7711)healther1-0/+36
* add package py-pygdbmi Change-Id: I9850ccecebb1d46e983cda39c371caab23ad61e9 * add runtime setuptools dependency (from distutils import) * remove unnecessary run dependency
2018-04-10Added C-Lime Package (#7707)thecorkscrew1-0/+37
* Added C-Lime Package * Small fix
2018-04-10add py-cython@0.28.1 (#7709)healther1-1/+1
Change-Id: I7e3931f8224a367ce1657256b3100139abcc4f86
2018-04-10add py-flask@0.12.2 (#7710)healther1-0/+1
Change-Id: I51887f661e6dd896a9f740b51f4e81bdf532f9b4
2018-04-10add package py-flask-compress (#7713)healther1-0/+38
* add package py-flaks-compress Change-Id: Ia67f292364f339907c7c0a5bd707a7a1e69877be * fix alignment * linebreak to make flake8 happy
2018-04-10add package py-flask-socketio (#7714)healther1-0/+44
* add package py-flask-socketio Change-Id: Ib9bb41b9c3de06f07ffb47449edf02476827b610 * fix alignment * add missing werkzeug dependency
2018-04-10Perl file copy recursive 0.40 (#7718)peetsv1-0/+1
* perl-file-copy-recursive: add newer version v0.40
2018-04-10Add latest versions of libxcb and xcb-proto (#7650)Adam J. Stewart2-5/+17
2018-04-10Fix GCC 6/7 build on APFS (#7696)Adam J. Stewart1-8/+7
2018-04-10fermi: Create new package. (#7702)lingnanyuan1-0/+42
* fermi: Create new package. * fermi: Add missing dependency. * fermi: Change dependency type of perl to run.
2018-04-09wgsim: Create new package. (#7674)lingnanyuan1-0/+47
* wgsim: Create new package. * fix flake8 error. * wgsim: change cc compiler to spack_cc. * add missing dependency.
2018-04-08new package "DSRC" (bioinformatics) (#7680)Sinan1-0/+45
* new package "DSRC" (bioinformatics) * remove uncommented line * get rid of unnecessary import * convert to MakefilePackage class * get rid of make() in install phase, remove spaces * make flake8 happy!
2018-04-07Add Package: nlohmann_json (#7690)Axel Huebl2-1/+61
Adds a spack package for the JSON C++ library https://github.com/nlohmann/json
2018-04-07Catch2: make install (#7668)Axel Huebl1-1/+18
Add a proper install variant for Catch(2). This allows to use Catch2 downstram with `pkg-config` and CMake's `find_package` commands via standard environment hints.
2018-04-06py-pyfaidx: adding new package (#7684)peetsv1-0/+37
* py-pyfaidx: adding new package * updating the url
2018-04-06Darshan 3.1.6 (#7686)carns2-0/+4
* update darshan-util to 3.1.6, add bzip2 option * add darshan-runtime 3.1.6
2018-04-06Fix build of xerces-c (#7611)Eric Müller1-0/+5
The build requires libiconv (but it doesn't find it when not providing LDFLAGS).
2018-04-06Package 'serf': link to the spack provided zlib installation. (#7667)Sergey Kosukhin1-0/+13
2018-04-06hapdip: Create new package and its dependency k8. (#7685)lingnanyuan2-0/+85
* k8: Create new package. * hapdip: Create new package. * Change description.
2018-04-05readfq: Create new package. (#7673)lingnanyuan1-0/+38
* readfq: Create new package. * fix flake8 error
2018-04-05Don't prepend Tcl/Python to PATH if in system directory (#7677)Adam J. Stewart2-2/+9
2018-04-05add package py-discover (#7671)healther1-0/+34
Change-Id: I67b9e4eb4dfd3a962b7fe8840f5eb012fcd009cc
2018-04-04rsync: adding version 3.1.3 (#7669)peetsv1-0/+1
2018-04-04octopus: add 7.3 (#7666)Denis Davydov1-5/+6
2018-04-04mvapich2: added version 2.3rc1 + variant to use alloca if available (#7595)Massimiliano Culpo2-35/+16
* mvapich2: added version 2.3rc1 + variant to use alloca if available * mvapich2: removed version 1.9 + cleaned recipe
2018-04-03soapdenovo-trans: Create new package. (#7649)lingnanyuan1-0/+52
* soapdenovo-trans: Create new package. * change header * soapdenovo-trans: change package type to makefile. * soapdenovo-trans: fix flake8 error.
2018-04-03fix dealii dependencies for Clang 9.1.0 C++17 (#7644)Denis Davydov5-4/+88
* fix boost and muparser for Clang 9.1.0 with C++17 * muparser: add C++11 flags * dealii: temporary disable python by default * dealii: make CMake find right python
2018-04-02lsof: create new package (#7660)Matthias Diener1-0/+47
2018-04-02Open MPI: add 3.0.1 (#7661)Howard Pritchard1-1/+2
Open MPI 3.0.1 bug fix release is out the door! Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2018-04-02Current versions of kokkos conflict with hwloc 2.x (#7654)Robert Pavel1-1/+2
* Current versions of kokkos conflict with hwloc 2.x Current versions of kokkos cannot build with hwloc v2.x due to changes in the associated structs. Requiring v1.11.9 for the time being until it becomes clear what the kokkos model will be * Explicitly commenting fix for posterity Explicitly commented version number of hwloc dependency for kokkos for posterity purposes and to pass code coverage for speedy merging * Generalized Kokkos's Hwloc Dependency Generalized dependency to v1.x of hwloc * Fixed Flake8 issue Fixed comment to conform to flake8 * Fixed ordering for Version Requirements Fixed ordering to indicate <= 1.11.9, not >1 * Generalized kokkos dependency
2018-04-02r-flexclust: new package (#7656)Yifan Zhu1-0/+44
2018-04-02r-gss: new package (#7655)Yifan Zhu1-0/+36
2018-03-31Features/pindel (#7619)David Orman1-0/+74
* added htslib 1.7 and checksum * pindel: added new package pindel * pindel: added package pindel * removed py-pybind11 edit * made flake8 happy * fixed additional flake8 errors * added comments about Makefile2 and removed FIXME template section * spelling
2018-03-31Features/py breakseq2 (#7642)David Orman1-0/+41
* added htslib 1.7 and checksum * py-breakseq2: new package!!!! * py-breakseq2: fixed whitespace * py-breakseq2: added additional dependencies * py-breakseq2: fixed build/run depends * py-breakseq2: added additonal dependencies
2018-03-31Fix build of boost@:1.58.999 +python (and +mpi) (#7630)healther1-2/+11
* explicitly specify user-config.jam as it isn't found via the environment variable on older boost versions (cf. what debian/rules does) => fixes +mpi build * fix "error: Ambiguous key" error on :1.58.999 boost (cf. https://github.com/boostorg/boost/blob/boost-1.59.0/bootstrap.sh#L357)
2018-03-31CEED 1.0 (#7423)Aaron Fisher19-212/+1099
* ceed bundle package including OCCA, MAGMA, Nek5000, mfem, and PETSc Very preliminary, a lot of ad hoc decisions, fragile, missing functionality All packages do build on my MacOS laptop with Cuda Funded-by: ECP Project: CEED Time: 4 hours Reported-by: Tzanio Kolev <kolev1@llnl.gov> * Some adjustments in a few CEED-related packages. This is still very preliminary, but with these changes I'm able to build from scratch on a Mac laptop and a Linux desktop (RHEL7). Note that there doesn't seem to be a good way to support CUDA in Spack, so you'll have to install that manually yourself. You will also need a Fortran compiler, in particular on a Mac where you also have to make sure that it is being picked up in ~/.spack/darwin/compilers.yaml. * ceed bundle package including OCCA, MAGMA, Nek5000, mfem, and PETSc Very preliminary, a lot of ad hoc decisions, fragile, missing functionality All packages do build on my MacOS laptop with Cuda Funded-by: ECP Project: CEED Time: 4 hours Reported-by: Tzanio Kolev <kolev1@llnl.gov> * Reverting Mac-related CUDA checks in the OCCA and MAGMA packages. A much better solution is to install CUDA manually and add it to ~/.spack/darwin/packages.yaml: packages: cuda: paths: cuda@8.0.54: /usr/local/cuda * Fix flake8 warnings Funded-by: CEED Project: CEED/Spack * remove unneeded commented out code Funded-by: CEED Project: CEED/Spack * Don't have PETSc use MUMPS to speedup install time, try parallel installs for Magma Funded-by: CEED Project: CEED/Spack * Added libceed package and made changes to get the ceed metapackage up and running. * Get the ceed package up and running and added installing the .h file in the libceed package. * All packages are now pointed at specific versions (either tagged or git hashed. * Changed some of the specific versions in the CEED metapackage. * Some version updates. * Applied Cameron Smith's patch for the latest pumi. * Merge * Nek5000: Use tarball instead of git tag * Major update of the mfem package - needs more testing. Add a testing shell script for mfem, test_builds.sh, in the mfem directory. It builds a number of mfem configurations to ensure they all work. Add 'suite-sparse' variant to petsc. Add 'develop' version of libceed. Add 'metis' variant of laghos. Update the dependencies of ceed. * Changes in petsc's handling of zlib to make the latest build work on Mac. * [MFEM] When using '+libunwind', mfem needs '-ldl'. * [OCCA] Remove debug print statements. * [PETSc] Replace the check ('zlib' in spec) with ('+zlib' in spec) - the latter checks if 'zlib' variant of petsc is enabled which is incorrect; the former checks if petsc is configured to depend on 'zlib'. * [MFEM] Add conduit variant. * [libCEED] Enable testing using 'make prove'. * [MFEM] Tweak test_builds.sh - all builds pass on fedora 27. * Add a post install test * Add a post installation check for NekCEM * pumi: bump git hash, remove unused patch * Fixed testing of Laghos package * Adding variants in CEED package * Empty file for URL didn't work on LLNL/LC. Replacing with bundle-package.txt -> README.md. * [MFEM] If the spec defines the 'cxxflags' compiler flags, use that value to set the CXXFLAGS value in the mfem build system. * Disabling HDF5 by default. You can still build it with "spack install ceed+hdf5". * libceed: fix use of prefix versus DESTDIR * Added cuda variant for libCEED (off by default) * [libCEED] When building v0.1, fix ceed.pc before installing it. * [CEED] Add variants for OCCA and PUMI. Replace the hdf5 variant with a variant called quickbuild that disables variants in packages to speedup the build - currently hdf5, boost, and superlu-dist in PETSc. * [libCEED] Remove unused 'import os'. * [MAGMA] Add version 2.3.0. * [OCCA] Major update of occa/package.py. * [libCEED] Several improvements. * [CEED] Use fixed versions for occa and libceed. * [OCCA] Fix a bug in CUDA setup. * NekCEM doesn't need depends_on('python') * [OCCA,libCEED,MFEM,CEED] Update occa and libceed versions plus a few tweaks in occa and mfem. * Switching to gslib-1.0.2 to fix summitdev bug. * [Nek5000] Use the Fortran 77 compiler instead of the 'fc' compiler. Propagate any 'fflags' and 'cflags' specifications to the Nek tools. * [MFEM] Tweak for 'ppc64le'. * attempt to override fips compatibility error for md5 * Compiler option changes in libCEED to fix summitdev build. * Disable the nekcem install test until it can be fixed. * [NekCEM] Major update of the package to fix various issues. * [NekCEM] Fix formatting * zoltan: remove non-portable -g0 flag the pgi compiler does not accept it * pumi: specify dependency on cmake > 3 * [Nek5000] Add dependency on libx11 when needed. Various hacks to support IBM XL compilers. * [NekCEM] Link with the pthreads library - it is required. * [MAGMA] Add a patch for magma v2.3.0 when building with gcc <= 4.8. Add dependency on BLAS. * [CEED] Update to magma 2.3.0. When building with gcc < 4.9 constrain the used suite-sparse version to <= 5.1.0 - starting with v5.2.0, suite-sparse requires gcc >= 4.9. * Small updates * [libceed, gslib] Fix style * [Nek5000] Need 'libxt' as a dependency as well. * [MUMPS] Temporary workaround for ray. * Updating occa and libceed to laters pre-1.0.0 and pre-0.2 hashes * petsc: add pkg-config patch for variable quoting Variable definitions in pkg-config are processed more like make than a shell, so don't need quoting. Older versions of pkg-config (<= 0.28) did not remove the quotes when printing the value. Freedesktop #67904 (https://bugs.freedesktop.org/show_bug.cgi?id=67904) Reported-by: Tzanio Kolev <kolev1@llnl.gov> * petsc: add 3.8.4 and myself as co-maintainer * Updating libceed to latest pre-0.2 hash. * [PETSc] Add the 'headers' and 'libs' properties. * [MFEM] Explicitly add rpaths to link flags for external packages. This is necessary when MFEM's exported options (in config.mk) are used outside of Spack for linking against MFEM. * Unset MFEM_DIR before building MFEM * [PETSc] As observed by @jedbrown, there is no need to define the 'libs' property explicitly - the default handler works fine too. * Build MAGMA shared by default, install a few additional headers * Forgot a self * Switching to OCCA tag v1.0.0-alpha.4. Adding urls for OCCA and libCEED ('spack uninstall' complains otherwise). * Removed FIXMEs for OCCA tag * [occa] Cleaned up tagged versions * [libceed] Updated occa to v1.0.0-alpha.5 * [ceed] Updated occa to v1.0.0-alpha.5 * [libCEED] Always define the 'NDEBUG' makefile option based on the 'debug' variant setting - this should always work regardless of the default setting inside the libceed makefile. * [MUMPS] Revert a temporary workaround. * [CEED, libCEED] Minor tweaks. * libCEED v0.2 release * [CEED] Use version 0.2 of libCEED. * [HPGMG] Remove duplicate version. * [CEED] Update the hpgmg version * hpgmg: use tarball for 0.3 The Git repository contains somewhat heavy documentation so the tarballs are much faster. * hpgmg: +fe was default for the 0.3 release * hpgmg: explicitly name build directory to avoid use of ambient PETSC_ARCH * [HPGMG] Fix flake8 formatting * libceed@0.2: work around occaFree issue
2018-03-30Merge pull request #7532 from spack/v-dobrev/mumps-impovementsVeselin Dobrev1-41/+90
[MUMPS] Various improvements in the package
2018-03-30Features/mindthegap (#7648)David Orman1-0/+41
* added htslib 1.7 and checksum * mindthegap: New package
generated by cgit v1.2.3-60-g2f50 (git 2.42.0) at 2024-07-15 07:01:46 +0000