The tcl module for r-dorng will fail to load due to the [] characters in
the description. This happens for Tcl formatted modules loaded by Lmod
at least.
```
module load r-dorng-1.7.1-gcc-9.2.0-wtq7bne
Lmod has detected the following error: .../spack/share/spack/modules/linux-centos7-broadwell/r-dorng-1.7.1-gcc-9.2.0-wtq7bne:(r-dorng-1.7.1-gcc-9.2.0-wtq7bne):
invalid command name "L'Ecuyer"
```
Split text for short and long descriptions.
* Add variants to petsc
This PR adds the follolwing variants to the petsc package
- gmp
- jpeg
- libpng
- giflib
- mpfr
- netcdf
- pnetcdf (parallel-netcdf)
- moab
- eigen
- random123
- exodusii
- mstk
- cgns
- memkind
- muparser
- p4est
- saws
- libyaml
- zstd
* Fix flake8 errors
* Additional changes to Petsc recipe
This commit addresses the issues with dependencies that were brought up
in the comments. There are also a few other enhancements.
- the language of the new variant descriptions was changed to be more
consistent with what was already in the recipe
- an explicit '+mpi' was added to the depends_on('hypre...') directives
- an explicit '+mpi' was added to the depends_on('trilinos...')
directives
- the run time error checking for '~mpi' was replaced with 'conflicts()'
directives that will cause the install to fail sooner
- additional variants that were 'parallel only' were added to the '~mpi'
check
* Set the '~mpi`' conflicts msg to a variable
* Changing raja, chai, and umpire packages so all will compile with each other.
* Need a CUDA version of CHAI when compiling with raja+cuda+chai
* Updating checks for commit.
* Adding comments explaining why chai+umpire tests were disabled
* Reactivating tests for CHAI and Umpire
* reordering versions
* Unified handling of Cuda Arch
* Adding latest versions
* Unused/Untested: removed
* Aesthetic and test mode in Chai
* Unified handling of Cuda Arch
* Using 'ON' consistently, instead of 'On'
* Apply suggestions from code review
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Fix, suggestion and patch:
Chai depends on RAJA, not the other way.
Apply suggested master-main version mapping.
Add Umpire version 3.0.0 and patch.
Co-authored-by: Robert Blake <blake14@llnl.gov>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* New package - REDItools
This PR adds the REDItools package, along with a new package dependency,
py-fisher. This contains a patch generated from the python 2to3 script
as well as some other fixes. I am not sure if the project is ready to
support python-3 yet but I submitted the other patches upstream.
* Update var/spack/repos/builtin/packages/reditools/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* new version 2020.3; new variants nosuffix and fft; version selections for plumed
* fixed too long lines
* fixed whitespaces
* revised fft interface according to @haampie 's suggestions
Co-authored-by: lu64bag3 <gerald.mathias@lrz.de>
* new package Wonton
* remove the flecsi variant because flecsi-sp does not have a spackage
* fix url, clean up whitespaces
* formatting
* put in explicit else clauses for variants in CMake section because CMake's behavior is system-dependent
Co-authored-by: Rao Garimella <rao@abyzou.lanl.gov>
* update version: intel packages daal, ipp, mkl-dnn, mkl, mpi, parallel-studio, pin, tbb and makes url parameter consistent and always use single quote.
* Fixes a typo with one of the sha256 checksum..
* Adds version entries for new versions of Intel packages.
* Adds hashes for new versions of Intel packages.
* Adds missing hash of Intel compiler.
* Adds the newest version of Intel MPI 2019.8.
* Fixes hash for intel-parallel-studio and intel-tbb.
* Fixes version number of Intel MPI.
* Adds GPI-2 package.
* Fixes flake8 noticed issues.
* Second try to fix flake8 comment
* Fixes some issues adamjstewart noticed.
* Fixes package according to flake8 complains.
* Fixes flake8 issue.
* Renames next version to master and removes master.
* Adds maintainer into gpi-2 and returns master branch for the git
repository.
Co-authored-by: Robert Mijakovic <robert.mijakovic@lrz.de>
* Dyninst: 10.2 release
* Use 'elf' instead of 'elfutils'
* Use v10.2.0 tag
* Change minimum elfutils to 0.173
* Move STERILE_BUILD option to correct cmake_args
* make a sacrifice to the flake8 gods
* Add maintainer
* Revert to using elf@1 for elfutils
* Allow all ParaView versions to depend on Python 2
* Keep conflict for 5.9 and up with python 2
* Fix line too long
* Don't use backslash
* Try fixing indent
* Clean logic for python cmake flags
* Try fixing indent
Previously the python package for vim used static linking, and depending
on what system libraries were available and linked against could cause
symbol conflicts for python leading to segfaults in loading c modules in
the standard library (i.e. heapq). This patch address this issue by
dynamically linking them.
If you use git to clone a repository ssh, git transfers control the ssh
binary available on your path, if that ssh binary was built with
contradictory version of openssl/kerberos, then your git commands will
fail.
* sirius, update versions, fixes, add missing options
- sirius/spfft: depend on fftw-api
- cleanup +shared option
- sirius add option for memory pool
- sirius add version 6.5.3 and 6.5.4
- sirius: add spfft dependency for @master, @develop
* add nlcglib package
Robust wave function optimization for SIRIUS.
* add q-e-sirius package
based on q-e package
* Update var/spack/repos/builtin/packages/q-e-sirius/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* nlcglib: pass nvcc_wrapper to cmake
* Add 6.5.6
* Make flake8 happy
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
* canu: fix depends issue & using java instead of jdk
* Update var/spack/repos/builtin/packages/canu/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* typo error correction
* Adding recipe for `colorspacious` (a python package)
* Copyright year changed
* revert last commit on basic_usage.rst
* better with a good description
* fix according to failed test
* Update var/spack/repos/builtin/packages/py-colorspacious/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-colorspacious/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Additional versions of py-jsonschema.
* Tweak to force Maestro to use jsonschema@3.2.0:
* Correction of whitespace (flake8 error).
* Merges importlib's Python version conditons
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add new versions of spfft
* Extend CudaPackage and use virtual fftw package
Co-authored-by: Simon Pintarelli <simon.pintarelli@cscs.ch>
* Add CUDA 11 compatibility note
* Depend on older cuda <= 10 for spfft <= 0.9.11
Co-authored-by: Simon Pintarelli <simon.pintarelli@cscs.ch>
* introduce logic for boost+context dependency and generic_context variant
* fix OTF2 instrumentation minor problem
* default coroutine impl depends on platform
* fix flake8
* add reference to ~generic_coroutines conflict info
* Update var/spack/repos/builtin/packages/hpx/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Octopus: Add support for version 10.0.
Fix compilation when using the MKL as a provider for BLAS/LAPACK. Octopus will now detect that the MKL also provides the FFTW API and will refuse to compile when both the FFTW library and the MKL are given to the configure script.
* Octopus: Add supported version range for libxc.
* berkeley-db: add version 18.1.40, update build options in package
* combine adamjstewart's changes
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* [kassiopeia] New package
* [kassiopeia] Remove master branch, update dependencies
* Update var/spack/repos/builtin/packages/kassiopeia/package.py
Unable to test since I do not have a license to intel-parallel-studio, but I see no reason why it would not work if.
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* [kassiopeia] depends_on mpi
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* [kassiopeia] cmake_args with self.spec.satisfies and elses
* [kassiopeia] args.extend -> args.append
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* h5py: explicitly specify version
hdf5@1.10.5 on Cray is wrongly detected as 1.8.4.
* Update var/spack/repos/builtin/packages/py-h5py/package.py
Thanks. Also had this first, then CI was complaining about line length ...
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update LBANN, Hydrogen, Aluminum to inherit CudaPackage
* Update CMake constraints: LBANN, Hydrogen, and Aluminum now require
cmake@3.16.0: (better support for pthreads with nvcc)
* Aluminum: add variants for host-enabled MPI and RMA features in a
MPI-GPU RDMA-enabled library
* NCCL: add versions 2.7.5-1, 2.7.6-1, and 2.7.8-1
* Hydrogen: add version 1.4.0
* LBANN: add versions 0.99 and 0.100
* Aluminum: add versions 0.4.0 and 0.5.0
* new package(s): py-gql
and related dependencies:
py-aiohttp
py-async-timeout
py-graphql-core
py-idna-ssl
py-multidict
py-websockets
py-yarl
new versions:
py-requests
* fixes
Co-authored-by: Andrew W Elble <aweits@skl-a-00.rc.rit.edu>
* NWChem 7.0.0
* add python2 for 6.8.1. removed 6.8 https://github.com/spack/spack/pull/17779#discussion_r462700413
* nwchem 6.8.1 breaks with gcc 10 and later
* restored extra python bits for version 6.8.1. add env. definition of basis libraries
* changes for flake8
* url fixed
* prevent 6.8.1 being compiled with gcc 10
* Ferret: Add missing dependency with curl.
* Ferret: Don't force using the static version of libgfortran.
* Ferret: Ensure Spack's compiler wrappers are used.
This allows properly setting the rpaths.
* Ferret: Add support for versions 7.3 to 7.6.
* Ferret: Add a variant to install Ferret standard datasets.
* Ferret: Define some useful runtime environnement variables.
* Ferret: Fix flake8.
Also add myself as a maintainer as suggested by @alalazo.
As discussed in issue #17638, wherein kahip fails to build when
scons is dependent on python@3.
This converts the print statements in various SConstruct files
into python3 friendly print functions.
I found most of the affected SConstruct files in both @2.00 and
the later versions I found on web, but some files were only in @2.00.
I split the patches into two files for that reason, but have not
tried the later versions.
* LAMMPS: Use LATTE 1.2.2 starting with version 20200602.
Version 20200602 and upper requires Latte 1.2.2. This caused the internal Latte distribution to be used instead of the Latte install provided by Spack.
* LAMMPS: Add new versions 20200630 and 20200721.
* dcmtk: fixed type error
* Update var/spack/repos/builtin/packages/dcmtk/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* New package: IDL
* Update var/spack/repos/builtin/packages/idl/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/idl/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* added license header and changed url_for_version to just url
* removed unused imports, addressed comments
* removed trailing whitespace on line 14
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
During configure lhapdf5 searches for python. On one system
I tested on (ubuntu 19.10) it finds a system installed python3
and fails to create the python extension.
Variant named to make explicit that this is only a python2 extension.
* update version: intel packages daal, ipp, mkl-dnn, mkl, mpi, parallel-studio, pin, tbb and makes url parameter consistent and always use single quote.
* Fixes a typo with one of the sha256 checksum..
* Adds version entries for new versions of Intel packages.
* Adds hashes for new versions of Intel packages.
* Adds missing hash of Intel compiler.
* Adds the newest version of Intel MPI 2019.8.
* Fixes hash for intel-parallel-studio and intel-tbb.
* Fixes version number of Intel MPI.
Co-authored-by: Robert Mijakovic <robert.mijakovic@lrz.de>
* openfoam: use MPI 'headers' property (fixes#17730)
* openfoam: +spdp variant, usable for OpenFOAM 1906 and later
in contrast to +float32, which uses single-precision throughout, +spdp
uses the following:
- single-precision for most internals
- double-precision for linear solver
* openfoam: add m4 as build dependency
* scotch: update to 6.0.9 released Oct 2019
Co-authored-by: Mark Olesen <Mark.Olesen@esi-group.com>
Libunwind already builds a shared library. The +pic variant adds the
compiler pic flag to the static archive so that it can be linked into
another shared library.
Eospac's build breaks on gcc@10: due to dependence on -fcommon behavior
and gnu changing to -fno-common. Added conditional argument to support
bleeding edge compilers
This PR adds the r-dss package and the r-bsseq package, also new, as a
dependency. This includes the latest versions, which required updates to
the following dependencies:
- r-biocgenerics
- r-iranges
- r-s4vectors
- r-summarizedexperiment
Older versions of r-dss and r-bsseq are included as well to ensure
compatibility with older versions of the above dependencies.
* WHIZARD: add versions 2.8.4 and 2.8.3
* New package: LCIO
* WHIZARD: add optional dependency on LCIO
* WHIZARD: add optional dependency on Openloops
* WHIZARD: allow building with either hepmc or hepmc3 dependencies
* Openloops: set process_lib_dir in configure
* Openloops: fix reference to variant
astropy 3.2.1 fails to build with python 3.8.3 with
errors similar to this:
astropy/stats/_stats.c:318:11: error: too many arguments to function 'PyCode_New'
PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
These are files that are generated by cython, but are included in the
tarball. Since there's apparently been an API change to PyCode_New, they will
need to be re-cythonized to compile correctly.
