When building eospac with %clang, spack's Fortran compiler wrapper is called
'flang', which is rejected by the eospac build system..Allow compilation with
%clang by patching the eospac build system.
My testing only covers %clang where flang is actually gfortran. However, this
patch only registers 'flang' as a known Fortran compiler and does not set any
flags or options that are compiler specific.
.
Add configurable HTTP, Python and readline support.
Add previously missing dependencies.
Minor patch to improve Python support (see https://github.com/xrootd/xrootd/pull/695).
* Use GitLab's API endpoint for fetching a git snapshot.
* More GitLab packages use the API.
* find_list_url for GitLab's API URLs.
* Flake8
* Url for 'hacckernels'.
* Check GitLab API regexps before the non-API ones.
* Add Trinity package
New package to install Trinity - another odd installer (assumes installation to /usr/local/bin and doesn't copy dot files hence deleting them)
* Update package.py
added dependencies from https://github.com/trinityrnaseq/trinityrnaseq/wiki/Installing-Trinity
* Update package.py
Copy tree to prefix.bin so that PATH can correctly be set for the Trinity command - can't split it off as it seems everything needs to stay together.
* Update package.py
Fixed over-length lines and space before comma
This commit fixes#7900.
In short: in the absence of constraints to the contrary, spack will
download the preferred version of a package, which is usually the most
recent non-develop version. On a clean spack installation without
hypre installed, `spack install mfem` will download hypre 2.14.0,
which is API-incompatible with mfem 3.3.2 (and earlier versions of
mfem), so spack will throw compiler errors re: the API mismatch.
This commit fixes that error by restricting mfem release versions
3.3.2 and earlier to hypre version 2.10.b to 2.13.999 (only 2.13.0
currently exists, but if it has a non-2.14.x maintenance release,
these versions of hypre should also be permitted).
* automake: added version 1.16.1
* lmod: added version 7.7.29
* git: added version 2.17.0
* tmux: added version 2.7
* scala: added version 2.12.5, fixed typo in version 2.10.6
* Added spark@2.3.0, hadoop@3.1.0, jdk@8u172-b11
* picard: added version 2.18.3
* tar: added version 1.30
Added OpenMP variant for kokkos that can be disabled to build and test
on platforms where OpenMP is not available or desired. Also updated
version list
* Committer: sajid <sajid@xrmlite.phys.northwestern.edu>
modified: var/spack/repos/builtin/packages/py-numpy/package.py
* Corrected typo
* removing whitespace
* remove whitespace
* remove whitespace, if not will do this in vim
* fabtests: new package
* fabtests: fix hashes for github archive behavior & add libfabric dep
* fabtests: both versions confirmed working
* fabtests: use developer provided archive
* Fix build issue with PMIx on aarch64
Work around a bug in PMIx that causes build issues on aarch64. Bug was
fixed in PMIx 2.1.1, so the spack package checks both the architecture
and the PMIx version. Workaround is to just not build the PMIx test and
example code.
* Minor code cleanups
Minor corrections to make 'spack flake8' happy.
* Add support for version 2.1.1
* r-matr: Create new package.
* shocklibs: Create new package.
* r-biom-utils: Create new package.
* r-mgraster: Create new package
* py-poster: Create new package.
* py-requests-toolbelt: Create new package.
* perl-libwww-perl: Create new package.
* py-mg-rast-tools: Create new package.
* mg-rast-tools: Fix version constraints for dependencies.
* Change dependency type of py-setuptools.
* openPMD-api
Add a new package for openPMD-api.
openPMD is a meta-data standard (markup, schema) for hierarchical,
scientific particle and mesh based data.
openPMD-api is a library wrapping the underlying backends (HDF5,
ADIOS, ...) into a single, object-aware API.
* Repository: https://github.com/openPMD/openPMD-api
* Project: https://github.com/openPMDhttp://www.openPMD.org
* mpi variant forwarding: fix concretization
+ I am unable to build suite-sparse@5.2.0 with clang@6.0.0. The build fails
with the error:
```
2397 [ 99%] Linking C executable wildtype_demo
2398 make[4]: Leaving directory
`/tmp/kellyt/spack-stage/spack-stage-w0XYhK/SuiteSparse/GraphBLAS/build'
>> 2399 libgraphblas.so.2.0.1: undefined reference to `__fpclassify'
>> 2400 clang-6.0: error: linker command failed with exit code 1 (use -v to
see invocation)
>> 2401 make[4]: *** [wildtype_demo] Error 1
```
+ This error appears because libgraphblas.so requires `-lm`, but that link
dependency is not explicitly listed in GraphBLAS\CMakeLists.txt.
+ A patch file is provided to add this dependency. The patch is only applied
when the compiler is `%clang`.
* ADIOS 1.13.1
ADIOS 1.13.1 fixes several issues with zero-sized block
reading and writing when compression transports are used.
* SZ 1.4.12.3
Add the lastest SZ release used in ADIOS1.
* geopm: Added initial files for package geopm
and py-natsort dependency
* geopm: Updated variants for hwloc and mpi defaults
* geopm: Cleaned up unwanted hyphenation in description.
* geopm: updates according to change request.
* geopm: Updated minor change requests.
Clarification for ruby-ronn dependency included as a TODO.
This requires changes in the current configure and build process
which will be changed in a future version.
* geopm: changed to AutotoolsPackage and fixed hwloc
The changes for hwloc required to add a specific version bc of a
conflicting version of openmpi's hwloc dependency being below
1.99. This works but updates to this package should check if this
restriction is still required. (Thus TODO added)
* geopm: Added link dependencies (thanks for pointing this out).
Also removed empty line below class definition.
* geopm: Fixed depends_on according to package guide.
Removed wrong type 'run' and removed types for numactl, mpi and hwloc
to use default build & link type.
* geopm: Fixed and updated +doc dependencies
new pacakge ruby-ronn (package specified as in ruby-narray package)
Updated second +doc dependency doxygen.
* geopm: Changed args for Autotools specific feature.
Added enable_or_disable and with_or_without instead of if cascade.
Added overhead variant.
Also added missing dependency (default: build&link) for json-c).
* glvis@3.3: new package
* mesa-glu: now provides 'glu' (GL Utility library)
* openglu: add package, provides glu
* [GLVis] Use MakefilePackage as base. Add 'develop' version.
Small tweaks in the makefile arguments.
* [GLVis] Locate the X11, GL and GLU libraries within their respective
prefixes. Set the C compiler in the makefile arguments.
* [GLVis] Fix a bug: the same variable was used for two different things.
* [libx11] Add the libs property
* [OpenGL] Add the libs property
* [OpenGLU] Add the libs property
* [GLVis] Use the libs properties of libx11, opengl, and openglu
* opengl: make error throw on install, not fetch
* opengl: add configuration advice for darwin
* opengl: add more versions of GL/OpenGL
* opengl: improve documentation in comments
* [OpenGL] Fix formatting
* 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!
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.
* 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
* 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
* 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)
* 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
* 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
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
* [hypre] Add the 'headers' property plus a small tweak in the 'libs'
property.
* [hypre] Add fallbacks for searching for '.libs' in 'prefix.lib64' and
in all of 'prefix'.
* [hypre] Fix style.
* [hypre] Use find_headers instead of find + HeaderList.
* added a new package file for PHIST (Pipelined, Hybrid-parallel Iterative Solver Toolkit)
* packages/phist: fix some formatting errors (too long lines etc)
and set allowed values for option "outlev"
* packages/phist: fix some more flake8 errors
* add headers property to netlib-lapack and intel-mkl
* ghost: fix finding cblas header and libs (at least for mkl and netlib-lapack, which provide headers())
* added a new package file for PHIST (Pipelined, Hybrid-parallel Iterative Solver Toolkit)
* packages/phist: fix some formatting errors (too long lines etc)
and set allowed values for option "outlev"
* packages/phist: fix some more flake8 errors
* phist: use headers property to find lapacke include dir
* phist: fix flake8 error
* phist: be more specific about dependencies and update version
* phist: state trilinos minimum version when building with Tpetra kernels
* gmp: add oldish version 5.1.3 with checksum
* phist: get rid of the 'petsc+complex' variant, it can be installed by kernel_lib=petsc ^petsc+complex
* phist: new version
* phist: fix version checksum
* Revert "add headers property to netlib-lapack and intel-mkl"
This reverts commit d8cb62905ebfb2cba186fd2d736d54a88a49d089.
* Revert "ghost: fix finding cblas header and libs (at least for mkl and netlib-lapack, which provide headers())"
This reverts commit d406a77ed7879c124fbaf1d757d002b9f0771620.
* phist: remove unused function
* phist: reorder package file versions/variants/depends_on/rest
* phist: some minor changes requested by @adamjsteward
* Add latest version of MPFR and patches for older versions
* Fetch and checksum patches instead of storing them
* Fix bug, version attribute was being overridden
* meme: added perl-xml-parser dependency, resolved issue. still need to fix ghostscript or image-magick, conversion not working.
* meme: fixed issue with libxslt/libxml2 conflict, and added imagemagick support
* meme: removing libxslt/libxml2 dependency lines
* meme: configure args
* meme: separating configure args
* meme: removing a comment, and hoping for travis to rebuild. site seems back up.
* meme: make image-magick optional
* meme: add comment referencing PR
* meme: bah flake8
* Promote to Autotools for simplicity; broaden Intel CPU opt targeting from SSE4.2 to AVX2
* make Intel CPU opt targeting same as in ../libxc
* flake8 W291
* use canonical means to pass (ahem) the test phase, h/t @adamjstewart
* revert f25d598 (unrelated merge)
* re-merge
* make py-setuptools a run-time-only dep for py-basemap and patch python package to only apply setuptools flag for build deps
* py-qtconsole does not require setuptools
* intel-xed: new package
The Intel X86 Encoder Decoder library for encoding and decoding
x86 machine instructions.
* intel-xed: style fixes for flake8.
* intel-xed: better style fix
* intel-xed: update to version 2018.02.14, add PYTHONPATH for
building with python 3, cleanup the opt flag.
The restrict compilation option with icc causes deadlock when multithreading is used. This issue has already been reported to the Scotch development team, but for current versions it is more reliable not to use the restrict compilation option.
* libtool: actually do symlinking correctly on darwin
Version 4 of the libtool/darwin debacle:
AutotoolsPackage hardcodes libtool & libtoolize into the autoreconf
stage, so the commands `libtool` and `libtoolize` MUST be present, and
shimming in glibtoolize into AutotoolsPackage when sys.platfrom ==
'darwin' does not work.
join_path(spec['libtool'].prefix.bin, 'libtool') still shadows system
BSD libtool (in apple-cctools, see PR #7177), but this shadowing could
be okay, depending on the combination of dependent specs.
* librom: new package
* Adding unzip package.
* Removing bzip2 dependency in unzip and raising an error when on Cray.
* Fixing error.
* Using conflicts statement for Cray detection in unzip package.
* add headers property to netlib-lapack and intel-mkl
* ghost: fix finding cblas header and libs (at least for mkl and netlib-lapack, which provide headers())
* fix flake8 errors
* ghost: remove unnecessary query parameter
* fix flake8 errors
* ghost: make it a CudaPackage (as suggested by @davydden, thanks!)
* ghost: missing whitespace
* Fix a bug when checking for 'xl' or 'xl_r' compiler.
* Add support for parallel build - the 's', 'c', 'd', and 'z' targets
are build separately allowing parallel builds.
* When build '+shared', inject all dependencies into the link lines of
the mumps libraries.
* Run the examples only when installing with the '--test' Spack option.
It seems there has been a change in concretization that resulted in
a request for a llvm latest (5.0.1) while not satisfying the later
more precise request for a version.
Remove the first line and only rely on the last.
A build of python@3.X had the following in the logs:
```
The necessary bits to build these optional modules were not found:
_dbm _gdbm _tkinter
```
As Tkinter is already a variant, we adopt the same strategy for dbm.
This includes:
* Added latest available versions (1.11.9, 2.0.0)
* Added variants to enable graphical output from lstopo
* Enabled build of the bundled netloc package if @2.0.0:
* Added dependency from numactl if @:1.11.9
* Added a constraint to avoid using hwloc@2.0.0 with openmpi
cube's configure only recognizes qt versions with single digit version
components and breaks with qt 5.10. Patch the configure files directly
to avoid having to regenerate them.
Mscgen is a small program that parses Message Sequence Chart descriptions and
produces PNG, SVG, EPS or server side image maps (ismaps) as the output.
See http://www.mcternan.me.uk/mscgen/
