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* wgsim: Create new package.
* fix flake8 error.
* wgsim: change cc compiler to spack_cc.
* add missing dependency.
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* 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!
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Adds a spack package for the JSON C++ library
https://github.com/nlohmann/json
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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.
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* py-pyfaidx: adding new package
* updating the url
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* update darshan-util to 3.1.6, add bzip2 option
* add darshan-runtime 3.1.6
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The build requires libiconv (but it doesn't find it when not providing
LDFLAGS).
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* k8: Create new package.
* hapdip: Create new package.
* Change description.
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* readfq: Create new package.
* fix flake8 error
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Change-Id: I67b9e4eb4dfd3a962b7fe8840f5eb012fcd009cc
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Fixes #7548
This updates the "spack view" command to use the same parsing logic
as "spack install" on the user-provided specs. For example you can
provide a DAG hash to refer to an exact installed spec instead of
specifying name, compiler, etc.
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* mvapich2: added version 2.3rc1 + variant to use alloca if available
* mvapich2: removed version 1.9 + cleaned recipe
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When an invalid spec is encountered by `parse_specs()` we now raise a
`SpackError` instead of calling `sys.exit()`
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* soapdenovo-trans: Create new package.
* change header
* soapdenovo-trans: change package type to makefile.
* soapdenovo-trans: fix flake8 error.
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* 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
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Open MPI 3.0.1 bug fix release is out the door!
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
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* 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
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* 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
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* 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
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* 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)
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* 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
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[MUMPS] Various improvements in the package
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* added htslib 1.7 and checksum
* mindthegap: New package
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* Add ignore_conflicts to package activation
includes:
* with_dependency flag for do_activate
* ignore_conflicts flag for do_activate
* start of cleanup of activate cmd
* ensure that apr is picked up
* Update package.py
* add apr explicitly as dependency
* remove unnecessary newlines
* Update package.py
fixing dependencies
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* ltrace: create new package
* Update package.py
* Update package.py
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* Fix Python3 bug in tut
* Revert URL change
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* gurobi: new pacakge
* fixed flake8 errors
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Fixes #7593
By default MacOS concretizes using the clang compiler. The unit tests
include a call to "spack spec mpileaks", which has elfutils as a
dependency; #7096 added a conflict in elfutils to avoid building
with clang, which lead to the MacOS unit tests to start failing.
This updates the concretization to force using gcc when concretizing
mpileaks.
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spack brought out some configury/make issues with
libhio, so some patches come along for the ride.
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
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Use `$HOME` for cli commands in `mirrors.yaml` and add
"username" example strings in the file itself.
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* r-snowfall: dep for phantompeakqualtools
* r-snowfall: fix version number
* r-snowfall: fix hash
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* --enable-shared *additionally* builds shared libraries
(and it builds fast, so no variant here)
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Modifications:
* Added zlib dependency, starting from version 3.0.0
* Added memchecker support for debugging
* Remove mpirun and similar links if slurm is selected as a scheduler
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