Fujitsu-MPI wrapper commands aren't recognized from 'FindMPI'
function of 'cmake'. If we are using the Fujitsu compiler and Fujitsu MPI,
specify the MPI path information explicitly.
Flux requires `build` for python and many of the python packages because
it builds python bindings. Beyond the bindings, the Flux front-end
commands now use python too, hence the `run` type. Finally, Flux's
`pymod` module is linked against the python interpreter, so the package
requires a `link` dependency on python too.
* IWYU: fix 0.14 build
The CMake patch used for 0.13 hadn't been applied to the master when
0.14 was released, and this version of IWYU requires C++14 or higher.
* Flake8
```
'/var/folders/fy/x2xtwh1n7fn0_0q2kk29xkv9vvmbqb/T/s3j/spack-stage/spack-stage-valgrind-3.15.0-mtir7ubjz7mqmjbb7bogze2qm35hl4ze/spack-src/configure' '--prefix=/ornldev/code/spack/opt/spack/clang-11.0.0-apple/valgrind/mtir7ub' '--enable-only64bit' '--build=amd64-darwin'
1 error found in build log:
43 checking host system type... x86_64-pc-darwin
44 checking for a supported CPU... ok (x86_64)
45 checking for a 64-bit only build... yes
46 checking for a 32-bit only build... no
47 checking for a supported OS... ok (darwin)
48 checking for the kernel version... unsupported (18.7.0)
>> 49 configure: error: Valgrind works on Darwin 10.x, 11.x, 12.x, 13.x, 14.x, 15.x, 16.x and 17.x (Mac OS X 10.6/7/8/9/10/11 and macOS 10.12/13)
```
* ffr: add flag to use fixed format in which the length of one line of the source code is 255 when building with Fujitsu compiler.
* ffr: changed to elif.
The dev branch of UnifyFS now depends on the latest release of
GOTCHA, and will future releases.
This updates our spackage to depend on the correct version of GOTCHA
depending on the version of UnifyFS being installed.
* Create VMD recipe
This is a new recipe to install VMD on Spack-managed hosts.
* Fix lint errors.
* Use plain Package
As per peer-review:
- Use Package to build
- Use configure to create a Makefile
- Use install to copy files to prefix directory
* Move VMD package to correct path, duh...
* Restructure description so first short paragraph can be used by module files.
* Add an empty line as suggested by peer-review. That's how you separate paragraphs.
* Remove extra spaces.
* Use setup_build_environment since that's where you're supposed to export OS variblaes. Thanks to peer-review for spotting this.
* Create VMD recipe
This is a new recipe to install VMD on Spack-managed hosts.
* Fix lint errors.
* Use plain Package
As per peer-review:
- Use Package to build
- Use configure to create a Makefile
- Use install to copy files to prefix directory
* Move VMD package to correct path, duh...
* Add Cubist (#16069)
* Add Cubist
* enhance recipe
* Not using OS module anymore
* remove white space
* Fix build shell
* make Flake8 happy
* use bash shell for build
* Convert it To MakefilePackage as per peer-review
* dbcsr: expose all options, check openblas feats (#16034)
* dbcsr: expose all options, check openblas feats
* dbcsr: use Ninja to build, ensure serialized tests
* dbcsr: add myself as maintainer
* MPark.Variant: GCC 7.3.1 Conflict (#16081)
* MPark.Variant: GCC 7.3.1 Conflict
Due to an ICE in this specific patch-release of GCC, compile
errors in downstream packages should be avoided with a clean
conflict.
* Fix superfluous spaces
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Fix typo
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Move VMD package to correct path, duh...
* Add an empty line as suggested by peer-review. That's how you separate paragraphs.
* New matlab versions (#16086)
* Add new version 1.1.1 (#16087)
* New package bonniepp added (#16091)
* openbabel: fix compilation errors (#16090)
- Disable maeparser as it is broken with CMake
- Added missing dependencies
* singularity: updated maintainer list (#16093)
* New version xrootd-4.11.3 (#16092)
* I added Gaussian 16. I also execute bsd/install to fix scripts instead of filtering them.
* revert VMD so only Gaussian is in my PR.
* revert VMD so only Gaussian is in my PR.
* revert VMD so only Gaussian is in my PR.
* I added myself as a package maintainer.
Co-authored-by: asmaahassan90 <31959389+asmaahassan90@users.noreply.github.com>
Co-authored-by: Tiziano Müller <tiziano.mueller@chem.uzh.ch>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
Co-authored-by: Amjad Kotobi <amjadkotbi@gmail.com>
Co-authored-by: athanasio <athanasio@users.noreply.github.com>
Co-authored-by: Carlos Arango Gutierrez <arangogutierrez@gmail.com>
The openssl build process can use the wrong perl for
various reasons, including:
* Wrong value in PERL env var
* The build process first looks for `perl5`, which the
spack system does not provide, but some other
distributions provide it. That way, the build process can
end up using the wrong perl.
Stop all of these problems by explicitly setting PERL to
the to be used dependency.
* Updated versions of COSMA.
* Added an empty line for formatting.
* Switched to sha256.
* Renamed gpu variant to cuda. Extending the CudaPackage base class.
This change also adds a code path through the spack ci pipelines
infrastructure which supports PR testing on the Spack repository.
Gitlab pipelines run as a result of a PR (either creation or pushing
to a PR branch) will only verify that the packages in the environment
build without error. When the PR branch is merged to develop,
another pipeline will run which results in the generated binaries
getting pushed to the binary mirror.
* Fixing the build directory for cardioid.
* These imports are no longer needed due to deletions.
Co-authored-by: Robert Blake <rob.c.blake.3@gmail.com>
* [maloc] created template
* [maloc] added some build dependencies
* [maloc] added homepage and description
* [maloc] added doc variant in an attempt to disable documentation. Still builds doc though... at least when there is a system doxygen found. Having doxygen being a dependency here can bring python in and cause issues for dependents, even when listed as only a build dependency. Maybe this is a bug?
* [maloc] flake8 and fixme removal
* [maloc] shorted description
The pkg-config file of newer versions of at-spi2-core includes
dependencies for xtst, recordproto, inputproto and fixesproto, so they
have to be available at runtime as well.
* Adding varient for python interface in HELICS
* Append python interface to pythonpath
* cleaning up blank lines
* Update var/spack/repos/builtin/packages/helics/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Clarify comments about QMCPACK-to-QE converter.
* Allow hdf5=serial with QE 6.4.1 + qmcpack, but apply filter_file.
* Ammend comments about the use of the filter_file.
-[x] `z3` needs a dependency on `py-setuptools`
-[x] `z3` has a run dependency on `python`, so we might as well make
building with the python bindings default
`clingo` has some undocumented dependencies:
- `bison`, for which the default macos version is too old
- `re2c`, which isn't always available
Also, the python installation was not set up properly. Clingo by default
does an install in `~/.local`, so we need to disable that and add a few
other options to get things right.
- [x] add `bison` dependency
- [x] add `re2c` dependency
- [x] make `doxygen` dependency optional (and patch if needed)
- [x] add options to fix `python` build
- [x] make python build optional but on by default
* Add pmi support (required by ucx, ofi, and gni backends)
* Add support for ucx backend
* Add dependency on MPI for pmi=simplepmi, slurmpmi, or slurmpmi2
* Remove charmpp as an MPI provider since the changes in this PR can
add MPI as a dependency (mentioned previously)
* Install into transport_protocol-OS-arch subdirectory to match
default charmpp installation behavior (which helps dependents find it)
SKX includes AVX-512 extensions that consumer Skylake processors do
not have. Therefore, map Skylake to the prior arch to work on
these systems. Skylake-X processors will still map as the
skylake_avx512 spack arch and get the correct optimzations.
* Add maintainers.
Add variants for building with default earlier api versions.
* Update var/spack/repos/builtin/packages/hdf5/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add naromero77 as a maintainer for QMCPACK Spack package.
* Add QMCPACK 3.9.2
* Remove QE-to-QMCPACK wave function converter from QMCPACK Spack package. Already been moved to QE Spack package.
* Fix dependency of geant4 (amends #16497)
* Update geant4-data dependencies
* Reviewer comments (part 1/2)
* Reviewer comments (part 2/2)
* Update var/spack/repos/builtin/packages/geant4-data/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Adapt to the latest Acts developments
A long time ago, the Acts project (whose name was then capitalized ACTS) used
to maintain multiple software repositories:
- The heart of the tracking toolkit was located in the `acts-core` repository
- Fast simulation extensions were located in the `acts-fatras` repository
- Advanced usage examples were located in the `acts-framework` repository
This multi-repository organization, however, has been a source of constant
pain, which is why the various projects were gradually merged into a single
mono-repo, called `acts`. Today, with the integration of `acts-framework`,
this merging process is reaching completion.
The present pull request adapts the Acts package to this evolution by...
- Renaming the package to `acts`, reflecting the new repository name
- Renaming the `test` variant to `unit_tests`, reflecting current CMake naming
- Adding the new build variants that were inherited from `acts-framework`
- Acknowledging the change of semantics of the `examples` variant, and only
supporting the new ones (as the former variant was almost unused)
- Liberally using alphabetical order to make the package code more readable
- Recording a large number of conflicts, some of which are introduced by the
merging of `acts-framework` and some of which already existed before
- Using the new capitalization of "Acts"
* Add acts v0.23
* Update dd4hep version requirement
* Add acts v0.22.1 bugfix
* openfoam: correspond to build with Fujitsu compiler.
* openfoam: add rules for Fujitsu compiler (on linuxARM64)
- the Fujitsu compiler is a clang derivative, so use a modified
version of the clang rules if upstream does not supply anything
If using mpirun, the R sessions can be started with a wrapper script
that helps set up the R session cluster. Put this wrapper in the PATH so
it is easily accessible.
Add a `spack external find` command that tries to populate
`packages.yaml` with external packages from the user's `$PATH`. This
focuses on finding build dependencies. Currently, support has only been
added for `cmake`.
For a package to be discoverable with `spack external find`, it must define:
* an `executables` class attribute containing a list of
regular expressions that match executable names.
* a `determine_spec_details(prefix, specs_in_prefix)` method
Spack will call `determine_spec_details()` once for each prefix where
executables are found, passing in the path to the prefix and the path to
all found executables. The package is responsible for invoking the
executables and figuring out what type of installation(s) are in the
prefix, and returning one or more specs (each with version, variants or
whatever else the user decides to include in the spec).
The found specs and prefixes will be added to the user's `packages.yaml`
file. Providing the `--not-buildable` option will mark all generated
entries in `packages.yaml` as `buildable: False`
Cray has two machine types. "XC" machines are the larger
machines more common in HPC, but "Cluster" machines are
also cropping up at some HPC sites. Cluster machines run
a slightly different form of the CrayPE programming environment,
and often come without default modules loaded. Cluster
machines also run different versions of some software, and run
a linux distro on the backend nodes instead of running Compute
Node Linux (CNL).
Below are the changes made to support "Cluster" machines in
Spack. Some of these changes are semi-related general upkeep
of the cray platform.
* cray platform: detect properly after module purge
* cray platform: support machines running OSs other than CNL
Make Cray backend OS delegate to LinuxDistro when no cle_release file
favor backend over frontend OS when name clashes
* cray platform: target detection uses multiple strategies
This commit improves the robustness of target
detection on Cray by trying multiple strategies.
The first one that produces results wins. If
nothing is found only the generic family of the
frontend host is used as a target.
* cray-libsci: add package from NERSC
* build_env: unload cray-libsci module when not explicitly needed
cray-libsci is a package in Spack. The cray PrgEnv
modules load it implicitly when we set up the compiler.
We now unload it after setting up the compiler and
only reload it when requested via external package.
* util/module_cmd: more robust module parsing
Cray modules have documentation inside the module
that is visible to the `module show` command.
Spack module parsing is now robust to documentation
inside modules.
* cce compiler: uses clang flags for versions >= 9.0
* build_env: push CRAY_LD_LIBRARY_PATH into everything
Some Cray modules add paths to CRAY_LD_LIBRARY_PATH
instead of LD_LIBRARY_PATH. This has performance benefits
at load time, but leads to Spack builds not finding their
dependencies from external modules.
Spack now prepends CRAY_LD_LIBRARY_PATH to
LD_LIBRARY_PATH before beginning the build.
* mvapich2: setup cray compilers when on cray
previously, mpich was the only mpi implementation to support
cray systems (because it is the MPI on Cray XC systems).
Cray cluster systems use mvapich2, which now supports cray
compiler wrappers.
* build_env: clean pkgconf from environment
Cray modules silently add pkgconf to the user environment
This can break builds that do not user pkgconf.
Now we remove it frmo the environment and add it again if it
is in the spec.
* cray platform: cheat modules for rome/zen2 module on naples/zen node
Cray modules for naples/zen architecture currently specify
rome/zen2. For now, we detect this and return zen for modules
named `craype-x86-rome`.
* compiler: compiler default versions
When detecting compiler default versions for target/compiler
compatibility checks, Spack previously ran the compiler without
setting up its environment. Now we setup a temporary environment
to run the compiler with its modules to detect its version.
* compilers/cce: improve logic to determine C/C++ std flags
* tests: fix existing tests to play nicely with new cray support
* tests: test new functionality
Some new functionality can only be tested on a cray system.
Add tests for what can be tested on a linux system.
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Since #9481 Python's None is not permitted as a value for
MV variants. The string 'none' is used instead.
Add the same fix for the amgx and lammps packages
* CMake: fix https://github.com/spack/spack/issues/16453 with a patch addressing both libhugetlbfs and icpc warnings on Cray XC40 systems
* Including CMake v3.17.2 in the patched versions
* libspatialite
* flake8
* Added proper version constrain
* Update var/spack/repos/builtin/packages/libspatialite/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/libspatialite/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Otherwise, if I run `xenv` after `spack load py-xenv` it fails with:
```
Traceback (most recent call last):
File "/home/vavolkl/spack/opt/spack/linux-centos7-broadwell/gcc-8.3.0/py-xenv-develop_2018-12-20-lqbxakapsepqo5w3sjhhokj5o7c5jei2/bin/xenv", line 6, in <module>
from pkg_resources import load_entry_point
ModuleNotFoundError: No module named 'pkg_resources'
```
* [gaudi] fixes and patches
* Update var/spack/repos/builtin/packages/gaudi/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/gaudi/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Apply suggestions from code review
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* [gaudi] add older versions and fold +tests into +optional
* [gaudi] set run environment
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* grass
* Update var/spack/repos/builtin/packages/grass/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
We can control the shared/static build of CMake and the default in
Spack is to build shared libraries. The old, uncontrolled default
of this package is a static build.
* Revise description of patch variant.
* Add qmcpack variant. Apply QE-to-QMCPACK wave function converter patch.
* Clean-up, document, and re-organize.
* ELPA patches did not nead when=`+patch` variant.
* Need to be more precise here with QE version numbers.
* satisfies seems to be necessary here in order to get correct behaviour.
* Buglet with zlib link line.
* Update var/spack/repos/builtin/packages/quantum-espresso/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/quantum-espresso/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Fix for QE-to-QMCPACK wave function converter w.r.t. QE 6.3. Also adjust comments to reflect changes in code.
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
