In some cases the FindHDF5.cmake returnd a wrong value for the HDF5 library names and path. For example it returns hdf5-shared as library name without a search path or checking if this is really an existing shared library. By HDF5_NO_FIND_PACKAGE_CONFIG_FILE=True/ON to the cmake options, the FindHDF5 module does not rely on a properly install hdf5-config.cmake and thus searches for the library and its paths. This results in a usable return value and fenics works afterwards.
* Updates for dependencies in main branch
* Add more depends
* Make CMake available at runtime for fenics-dolfinx
* Add maintainer
Co-authored-by: Garth N. Wells <gnw20@cam.ac.uk>
Although `cpio` is present in many environments, it may not be always
available.
The failure to build this package can be reproduced in a fresh Docker
image `debian:10`.
* trilinos: rename basker variant
The Basker solver is part of amesos2 but is clearer without the extra
scoping.
* trilinos: automatically enable teuchos and remove variant
Basically everything in trilinos needs teuchos
* trilinos: group top-level dependencies
* trilinos: update dependencies, removing unused
- GLM, X11 are unused (x11 lacks dependency specs too)
- Python variant is more like a TPL so rearrange that
- Gtest internal package shouldn't be compiled or exported
- Add MPI4PY requirement for pytrilinos
* trilinos: remove package meta-options
- XSDK settings and "all opt packages" are not used anywhere
- all optional packages are dangerous
* trilinos: Use hwloc iff kokkos
See #19119, also the HWLOC tpl name was misspelled so this was being ignored before.
* Flake
* Fix trilinos +netcdf~mpi
* trilinos: default to disabling external dependencies
* Remove teuchos from downstream dependencies
* fixup! trilinos: Use hwloc iff kokkos
* Add netcdf requirements to packages with ^trilinos+exodus
* trilinos: disable exodus by default
* fixup! Add netcdf requirements to packages with ^trilinos+exodus
* trilinos: only enable hwloc when @13: +kokkos
* xyce: propagate trilinos dependencies more simply
* dtk: fix missing boost dependency
* trilinos: remove explicit metis dependency
* trilinos: require metis/parmetis for zoltan
Disable zoltan by default to minimize default dependencies
* trilinos: mark mesquite disabled and fix kokkos arch
* xsdk: fix trilinos to also list zoltan [with zoltan2]
* ci: remove nonexistent variant from trilinos
* trilinos: add missing boost dependency
Co-authored-by: Satish Balay <balay@mcs.anl.gov>
Third-party Python libraries may be installed in one of several directories:
1. `lib/pythonX.Y/site-packages` for Spack-installed Python
2. `lib64/pythonX.Y/site-packages` for system Python on RHEL/CentOS/Fedora
3. `lib/pythonX/dist-packages` for system Python on Debian/Ubuntu
Previously, Spack packages were hard-coded to use the (1). Now, we query the Python installation itself and ask it which to use. Ever since #21446 this is how we've been determining where to install Python libraries anyway.
Note: there are still many packages that are hard-coded to use (1). I can change them in this PR, but I don't have the bandwidth to test all of them.
* Python: handle dist-packages and site-packages
* Query Python to find site-packages directory
* Add try-except statements for when distutils isn't installed
* Catch more errors
* Fix root directory used in import tests
* Rely on site_packages_dir property
* Change url and checksums for libpng to official sourceforge archives
* Update url scheme from http to https
* switch to .xz archives
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
* Add py-h5py version 3.3.0
The mpi4py dependency was bumped to 3.0.2 in setup.py. I'm not sure if that's actually required or not, but nothing lower is still tested.
* Use environment variable to stop h5py using setuptools setup_requires feature
* Add myself as a maintainer for py-h5py
* [py-transformers] can now use newer versions of tokenizers
* [py-transformers] Added version 4.6.1
* [py-transformers] removing old patch
* [py-transformers] boto3 no longer needed
* first build of py-torchmeta
* updated versions for torchvision and torch
* [py-torchmeta] using pil provider
Co-authored-by: Sid Pendelberry <sid@rit.edu>
The Makefile for the MAGMA smoke tests uses pkg-config to find
the MAGMA compile flags, but the test() routine in the spack
package was not configured to provide the location of the
pkg-config file. This modification sets PKG_CONFIG_PATH correctly
to allow the smoketests to successfully compile. It also removes
the *_dir variables which were unused by the magma
examples/Makefile.
Using the original concretizer, trying to concretize py-jupyterlab fails
with
```
==> Error: Invalid Version range: 6.1.0:6.1
```
because py-tornado does not have a 6.1.0 version but only a 6.1 one.
Makefiles for libtirpc have hardcoded the -pipe flag to the compiler
nvhpc compilers do not recognize that flag.
This PR provides a patch to remove the -pipe flag from the Makefile.
Patch should work with libtirpc@1.2.6 and @1.1.4
jupyterlab was looking for its application directory inside the python
prefix instead its own one. This was fixed by setting the according
environment variable.
* openPMD-api: rename develop
Rename to match known Spack version comparison schemes:
```
develop>main>master>head>trunk>9999>0>z>a
```
Currently, the hdf5 patch that is pre-0.14.0 is also applied to
`dev`, which naturally fails (already applied).
* fix dev in warpx
* py-markupsafe: add 2.0.1
* Update var/spack/repos/builtin/packages/py-markupsafe/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Ideally a test-only dependency won't be in the build, but until then
mark the requirement of gtest up to 1.10.
See e4s job failure at https://gitlab.spack.io/spack/spack/-/jobs/349959 .
Looks like 1.11 introduces some breaking incompatibilities, so perhaps
we should transition later.
* fix remaining flake8 errors
* imports: sort imports everywhere in Spack
We enabled import order checking in #23947, but fixing things manually drives
people crazy. This used `spack style --fix --all` from #24071 to automatically
sort everything in Spack so PR submitters won't have to deal with it.
This should go in after #24071, as it assumes we're using `isort`, not
`flake8-import-order` to order things. `isort` seems to be more flexible and
allows `llnl` mports to be in their own group before `spack` ones, so this
seems like a good switch.
* Fix compiler test
Use `self.spec.satisfies` on compiler to determine if a flag should be
applied or not. This approach avoids issues with the strings `gcc`
or `clang` appearing in the full path to the compiler executables, as
happens with spack-installed compilers (e.g. `nvhpc%gcc`).
* Limit compiler name search to last path component
@skosukhin pointed out that the cflag modification should happen for any
clang or gcc compiler, regardless of what compiler spec provides them.
This commit reverts to searching for a compiler name containing "gcc"
or "clang", but limits the search to the last path component, which
avoids matching spack-installed compilers built with gcc (e.g.
`nvhpc%gcc`), which will have "gcc" in the compiler path.
* Use `os.path` rather than `pathlib`
Co-authored-by: Paul Henning <phenning@lanl.gov>
This PR configures the spack docbook packages
- docbook-xsl
- docbook-xml
The public entities are now mapped to the locally installed files of the
respective packages. The example catalogs are left in place and
XML_CATALOG_FILES points to the newly created catalogs.
Perl keeps copies of the bzip2 and zlib source code in its own source
tree and by default uses them in favor of outside libraries. Instead,
put these dependencies under control of spack and tell perl to use the
spack-built versions.
