Fixes#10361Fixes#6634
When mkl isnt in the spec, still write an explicit mkl entry to
prevent numpy from looking in system dirs and using a system install
of mkl. Do the same for openblas and atlas (although mkl was the only
system install reported to interfere with Spack's choice).
* Updating nalu-wind, nalu, openfast, and tioga packages. Includes
improved handling of +shared variant.
* Add fftw and catalyst support to nalu-wind.
* Restrict ParaView to use matplotlib versions before 3 (which
require Python 3)
* py-modred: New package
Parallelized python module for finding modal decompositions and
reduced order models.
* fix license
I think?
* Add dependency on py-numpy
and remove commented out code
* vigra: new package
* Better constraints and types on some depends_on. Use site_packages_dir variable for Python install dir. Explicit switch-offs where available. Change some local variables to suit style checks.
* Take care of lines too long
* Explicit WITH_HDF5=ON
* docbook processing works correctly for gdk-pixbuf
1. The various bits of documentation in gdk-pixbuf include hardcoded
references to dtd's and stuff at their canonical, Internet,
locations. BUT, gdk-pixbuf runs xslt-proc with the `--nonet`
option, which forbids it from using the network. Sadness ensues.
Traditionally folks use XML Catalogs to map these to local copies.
Our docbook-xsl package wasn't setting the appropriate env var in
its dependents environments to use our catalog.
Now it does. Less sadness ensues.
2. If we're going to use these things, we should depend on them.
* Add gdk-pixbuf's bin to build environment
The "post-install.sh" script uses gdk-pixbuf-query-loaders, which was
installed earlier.
If py-psyclone can set its own bin on its PATH, so can we...
* Make gdk-pixbuf use recognizable docbook location
Our docbook-xsl package assumes that the canonical location is
`http://cdn.docbook.org/release/xsl/current/manpages/docbook.xsl`, but
the gdk-pixbuf's meson build script uses
`http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl`.
This means that our XML Catalog doesn't fix the reference and sadness
happens.
Just patch the build that we see what we want to see, then we can make
it all go away.
* Add commentary re docbook patch
* Make catalog helper a property
Thanks @adamjstewart!
* Run tests if/when run_tests is true
Thanks @adamjstewart!
* Tune up dependencies
Thanks @adamjstewart!
* Wordsmit commentary
This adds a lot of fixes and updates for alpine ascent and its dependencies:
* add support for static (via ~shared) and use vtk-m 1.2
* update vtkh package to output cmake configure file and pinning it to vtkm 1.2
* make conduit respect ~python
* fix ascent python logic
* consistant cmake usage
* conditionally add tbb in ascent if vtkh
* enable openmp
* more robust handling of variants
* update ascent and conduit for static builds
* add optional support for mfem in ascent
* enable mfem conduit support for ascent
* add optional adios dep to conduit
* remove ver req from conduit
* ascent: remove confusing comment
* tweaks to conduit and ascent pkg recipes
* fix typo in conduit package
* pref conduit master
* changing mfem to depend on conduit@master to get updated relay
* restore use of conduit 0.3.1 or greater for mfem
* set master as preferred conduit version
* allow mfem to use conduit master
* adding rover package and editing ascent
* updating vtkm cmake dep
* guard ascent python support on +shared
* removing rover to simply ascent package
* add fortran variant to conduit, to allow us to turn off conduit support even when a fortran compiler is specified
* fix fortran compiler check so it can work on cray systems
* working towards cuda fix for vtkm lagrange filter
* update ascent package with more variants, and patch to avoid nvcc issue
* hdf5 flags fix for BGQ
* add post install test
* add testing to ascent
* add testing of the using-with-make example
* add ctest output on error for run_tests
* Remove Cray CC compilers causing problems on case-insensitive filesystems
* cray -> cce
* Ensure that compiler-specific directory comes first in build-env
* Point to compiler-specific symlinks
Binary caches of packages with absolute symlinks had broken symlinks.
As a stopgap measure, #9747 addressed this by replacing symlinks with
copies of files when creating binary cached packages.
This reverts #9747 and instead, either relative-izes the symlink or
rewrites the target. If the binary cache is created using '--rel' (as
in "spack buildcache create --rel...") then absolute symlinks will be
replaced with relative symlinks (in addition to making RPATHs relative
as before); otherwise they are rewritten (when the binary cache is
unpacked and installed).
The current output of buildcache list is very verbose and I feel like
some details are getting lost. By making the output similar to find, I
think users will be able to get a better overview of what is stored in
the cache.
* dealii: fix concretization of xsdk package
* tests: add concretization tests for deal.II and xSDK, which are often broken due to limitations in the concretizer
* use pytest.mark.parametrize
Updated LBANN, Hydrogen, and Aluminum to not require CUDA-aware MPI
even when using CUDA. Fixed small bugs within both LBANN and Hydrogen
packages. Added requirements for breathe and cereal to LBANN.
Fixes issues #9613 and #3209.
Remove the spack wrapper directories from PATH for the bootstrap step.
This was breaking the build for Cray (and other cross-compile) because
bjam was built for the BE and died on SIGILL on the FE.
This only affects building bjam. The boost libraries are still built
the normal spack way with the spack wrappers.
Add variants 'cray' and 'bgq' to build for Cray and Blue Gene compute
nodes. These systems need separate options to find the MPI compiler
for hpcprof-mpi.
The 4.0.1 release is the culmination of the SUNDIALS 4.0.0 preview releases,
i.e. the 4.0.0-dev versions. As such, the 4.0.0-dev releases are now
being removed.
* Explicitly listing blas and lapack sections in site.cfg for numpy when using netlib-lapack so that scipy can find them as well.
* Reducing code to use a function call instead of copying and pasting.
* Fixing flake8 errors.
* Fixing python 3.6 error when site.cfg lists library_dirs multiple times.
* Formatting.
* Verifying blas and lapack are enabled before writing to site.cfg.
* Fixing flake8 errors.
* Fixing conflicts since this package file has been updated.
* Fixing flake8 stuff.
* Handling blas and lapack variants for netlib-lapack in site.cfg for py-numpy.
* Don't write netlib-lapack site.cfg file if no blas or lapack variants enabled in py-numpy.
* Removing redundant if statement.
* Fixing mistake in py-numpy site.cfg generation.
* Separating blas and lapack further in site.cfg for netlib-lapack in py-numpy.
Allow customizing views with Spec-formatted directory structure
Allow views to specify projections that are more complicated than
merging every package into a single shared prefix. This will allow
sites to configure a view for the way they want to present packages
to their users; for example this can be used to create a prefix for
each package but omit the DAG hash from the path.
This includes a new YAML format file for specifying the simplified
prefix for a spec in a view. This configuration allows the use of
different prefix formats for different specs (i.e. specs depending
on MPI can include the MPI implementation in the prefix).
Documentation on usage of the view projection configuration is
included.
Depending on the projection configuration, paths are not guaranteed
to be unique and it may not be possible to add multiple installs of
a package to a view.
