## Summary
This PR updates and improves the Spack package for [UPC++](https://upcxx.lbl.gov).
I'm an LBL employee and developer on the UPC++ team, as well as the maintainer of this Spack package.
### Key Improvements:
* Adding new 2020.3.0 release and support for use of develop/master branches
- Our build infrastructure underwent a major change in this release, switching from a hand-rolled Python2 script to a bash-based autoconf work-alike.
- The new build system is NOT using autotools (nor does it support some of the more esoteric autoconf options), but the user interface for common builds is similar.
* Add explicit support for an MPI optional dependency
- New `mpi` variant enables use of the MPI-based spawner (most relevant on loosely coupled clusters), and the (unofficial) mpi-conduit backend
- This variant is OFF by default, since UPC++ works fine without MPI on many systems, increasing the likelihood first-time Spack users get a working build without needing to correctly setup MPI
* Add support for post-install testing using the test support deployed in the new build infrastructure
* Fix or workaround a few bugs observed during testing
### Status
The new package has been validated with a variety of specs across over seven different systems, including: NERSC cori, ALCF Theta, OLCF Summit, an in-house Linux cluster, and macOS laptops (Mojave and Catalina).
Expose serial/parallel build (MPI), CUDA/OpenMP backends, Clang, and
Ascent bindings.
Interestingly, `warpx +ascent` currently leads to an infinite loop in
the Spack concretizer.
Git-based conditions database for HEP and other experiments.
Use latest release version and current master to support Linux and
macOS. Add core known dependencies and conflicts related to C++17
support.
cxxstd variant added to help transitive dependencies, and for future
support for newer standards in future.
Update WarpX for recent developments:
- add openPMD I/O (default: ON)
- remove electro-static solver option (now a runtime option)
- enable tiny profiler by default
- depend on new CXX std support in make scripts for C++14
- WarpX only supports 2D and 3D in cartesian dims
* davix: add cxxstd variant
Davix is written in C++, so add this variant to allow dependents to specify
this so a consistent ABI is used.
* davix: fix flake8 errors
* Add gmsh v4.5.4 with new options
This adds OpenCASCADE as an alternative to the oce package.
A new variant 'privateapi' is added to enable the gmsh private API.
* Make oce conflict with opencascade in gmsh
* Add version 6.20.{00,02}, don't yet mark it preferred
* It needs zstd
* It needs numpy (at least for 6.20.00:6.20.03)
* Reorder python dependencies a bit
* Add mlp variant, default False
Older versions always include mlp, so no conflicts there.
* Disable tmva, because it needs mlp
* tmva needs mlp, so add conflict
* Add sources and resources for each version of Rust
* install bootstrapping compiler into stage
* Add libgit2
* Install bootstrapping compiler correctly
* implement full rust bootstrap
* Remove support for Rust pre-1.14
Also add lots of comments
* Support only Rust 1.17 and newer
* Remove < 1.23 versions of Rust
* Change the layout of rust_releases for maintainability
* Remove LLVM variant
* Address flake8 issues
* Make libgit2 curl variant default False, conflict 0.28 and newer
* Remove binutils dependency
* Add ARM64 while we're at it
* flake8
* use the 'python' routine rather than relying on the correct python to be picked up
* petsc: add checksum for 3.12.4
* petsc: constrain hdf5 to <= 1.10.x
Current petsc will error when being build with hdf5 1.12, so this ensures that
a compatible hdf5 will be used. Fix suggested by @balay.
Hpctoolkit master was recently updated to test for and allow old
binutils <= 2.33.1 and/or new binutils 2.34. Older hpctoolkit up to
2030.03.01 will forever require :2.33.1.
Adjust the libunwind dependency for safety with the current
concretizer.
Fabtests provides runtime analysis tools and examples of libfabric.
As with other projects that are tightly version-bound, e.g.
`py-adios` and `adios`, the fact that releases stem from the same
repo does not imply they should be the same package.
Remove resources, which complicate the libfabric build, and update
the fabtests package accordingly.
* Trilinos: Add more variants
+ Provide three new variants to allow building trilinos without netcdf, matio,
or glm.
+ No change to defaults.
* Fix style issue.
* py-tuiview: Source has moved to github
* py-tuiview: Explicitly require +python on gdal dependency
* py-tuiview: Versions up to 1.1.99 are qt4 only
* py-tuiview: Add version 1.2.6, which is qt5 only
* Explicit version range on gdal dependency
* adol-c:updating sources location
* Update var/spack/repos/builtin/packages/adol-c/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* try extend path to solve PyQt5.sip not found issue
* disable private sip installation in sippackage class
* undo manual PyQt5 dir creation in py-sip site-packages dir
* fix typo
* fix typo
* also apply fix to PyQt4
* tidy up
* flake8 and tidy up
* tidy and undo hardcoding of python_include_dir
* replace hardcoded python inc dir
* fix minor issues
* rethink include dir variable name
* improve style
* add new versions
* implement new sip setup to qsci installation
* set sip-incdir correctly for the new setup
* setup extend_path thing before qsci python bindings
* take care of conflict
* flake8
* also extend for PyQt4
* improve style
* improve style
* SipPackage build sys should depend on py-sip
* consolidate extend_path fixes into SipPackage
* fix typo
* fix bugs
* flake8
* revert sip doc to pre-resource setup
* import os module
* flake8
Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
* CGNS: Version update
The CGNS library has several new versions. There was a format-changing change in 3.4.0 which was removed for 3.4.1. The change was then added again and released with a change to the major version (4.0.0). Note that 4.0.0 should be close to the functionality of 3.4.0.
* CGNS: Add shared variant
Added the `shared`variant to make the CMake build correctly pick up the RPATH settings.
* Added a package for the DiHydrogen distributed linear algebra library.
* Updated recipe to provide cuda architecture constaints.
* Addressed reviewer comments
* Fixed flake 8
* Previous qt changes broke the openspeedshop gui build. This puts back the changes that caused the breakage.
* Update the qt version to be more robust.
Co-authored-by: Galarowicz, James <jgalarowicz@newmexicoconsortium.org>
* Add patches when building with NAG
* Make libxml2 support optional. Also include conflict for
@:3.2~hydra+libxml2 since @:3.2~hydra does not require libxml2
support
* Add '--disable-silent-rules' to get more verbose output during
the build
* Implemented working file filtering to replace spack compiler wrapper with real compiler.
* Using string=True instead of re.escape. Using self.prefix.lib instead of appending /lib.
Co-authored-by: Wyatt Spear <wspear@cs.uoregon.edu>
* Add new vecgeom versions, add cuda support, automate target options
* Add ROOT, GDML, and external VecCore support to VecGeom
* Address reviewer comments
* Update vecgeom for CUDA
* Update versions
Add a 'define_from_variant` helper function to CMake-based Spack
packages to convert package variants into CMake arguments. For
example:
args.append('-DFOO=%s' % ('ON' if '+foo' in self.spec else 'OFF'))
can be replaced with:
args.append(self.define_from_variant('foo'))
The following conversions are handled automatically:
* Flag variants will be converted to CMake booleans
* Multivalued variants will be converted to semicolon-separated strings
* Other variant values are converted to CMake string arguments
This also adds a 'define' helper method to convert any variable to
a CMake argument. It has the same conversion rules as
'define_from_variant' (but operates directly on values rather than
requiring the user to supply the name of a package variant).
PR #15212 added a new connect_timeout option that can be overridden
using fetch_options but had to specified per-version. This adds a new
per-package variable that can be used to override fetch_options for
all versions in the package. This includes connect_timeout as well
as 'cookie' (e.g. for the jdk package).
Packages can combine package-level fetch_options with per-version
fetch_options, in which case the version fetch_options completely
override the package-level fetch_options.
This commit includes tests for the added behavior.
* Change py-merlinwf to py-merlin to match PyPi.
Change py-merlin to py-merlin-info.
Move to py-merlin_info.
Add py-merlin-info back in.
* Update dependent packages for the new merlin name.
* Remove non-working pyre and the associated packages, exchanger,
py-pythia and py-mlerin-info from citcoms.
* Remove blank line.
* scr: add develop, legacy branches; version 2.0.0
squash! scr: add develop and legacy versions
* filo: package for SCR component
* spath: package for SCR component
* axl: update for versions 0.3 and 0.2
* scr: build with components
* spath: structure of +mpi if/else
* 👌 capitalization of ecp-veloc
* scr: branches are always greater than any version
* Parallel-netcdf: update package.
* Add a temporary patch for version 'develop'.
* Rename version 'develop' to 'master'.
* Drop the patch for 'master'.
includes fixes for likwid-mpirun, better support for ARM and POWER,
other bugfixes.
For full support of ARM and POWER, #14183 has to be merged, too.
Added TomTheBear as maintainer. He is the current main developer of
LIKWID.
* new package: GunRock
* Update var/spack/repos/builtin/packages/gunrock/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* improve
Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Sinan81 <Sinan81@github>
* add --skip-unstable-versions option to 'spack mirror create' which skips sources/resource for packages if their version is not stable (i.e. if they are the head of a git branch rather than a fixed commit)
* '--skip-unstable-versions' should skip all VCS sources/resources, not just those which are not cachable
* New package: bat
Add package for bat:
A cat(1) clone with wings.
* Update copyright date
* Embiggen comment re build env settings
Provide a bit more explanatory text about why setup_build_environment
needs to set LLVM_CONFIG_PATH and LIBCLANG_PATH.
Co-authored-by: George Hartzell <ghartzell@audentestx.com>
* eigen: updated url to point to gitlab
fixes#13890
Eigen migrated from bitbucket to gitlab
* eigen: simplified package (no dependencies other than stdlib)
* Added TODO list for future improvements
* libunwind: remove version 2018.10.12, add stable branch
Finish cleaning up the libunwind version numbers. The 2018.10.12
snapshot number didn't fit well with spack's ordering (my bad), and
1.4-rc1 is a near identical replacement.
Add a version for the 1.4-stable branch.
Add a variant for zlib compressed symbol tables (develop branch only).
Adjust packages caliper and hpctoolkit to adapt to the changes.
Add myself as maintainer.
* Flake
* Settle on renaming 'develop' to 'master' (to match the branch name)
and name the 'v1.4-stable' branch as '1.4-head'. 'stable' or
'1.4-stable' is a better name, but '1.4-head' (an infinity version)
sorts better.
* explicitly link against libtinfo
* Update to v15.9
* fixed indentation
* fixed url definition
* added url vor current version again
* fixed indentation
* moving url_version to the bottom
* Add version 0.5.14
* Add variant to allow setting the localstatedir: See below
* Add bzip2 dependency
* Add myself to maintainers (I just think, I can care for
this package)
About localstatedir:
munge has a server and a client.
They communicate via unix domain sockets.
This socket is in PREFIX/var.
This package provides the client, the server, and
development part (headers, libraries).
Let's assume one has the server part installed as a system
package. This generally is a good idea, so that the server
gets started during boot. This means, that the socket is in
the system's /var.
If one now wants to use the client part (library!) via
spack, one has a problem: spack's munge looks in
SPACK-PACKAGE-PREFIX/var for the socket.
There needs to be a way to let the spack installed package
use the system's socket.
So add a variant to override the path during build:
localstatedir=/var.
* Add Checksum for 1.4.1.4 Release
Add checksum for 1.4.1.4 release. Mark myself as maintainer. List develop version.
* Update var/spack/repos/builtin/packages/libhio/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
It was reported that UnifyFS had a bug with the --enable-mpi-mount
config option, which corresponds to the auto-mount variant. This bug
was fixed in the UnifyFS dev branch, however remains broken for the
0.9.0 version.
This adds a patch to the unifyfs package to fix the auto-mount
variant when installing with version 0.9.0.
This also removes the openssl dependency as unifyfs does not directly
depend on it. This was said to be a non-explicit dependency in #15258.
However, if it is needed, it is likely a non-explicit dependency of
one of unifyfs's dependencies and should be added there.
Fixes: #15292
* lammps: add most recent stable release
* Update var/spack/repos/builtin/packages/lammps/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Add package for ripgrep:
ripgrep is a line-oriented search tool that recursively searches
your current directory for a regex pattern. ripgrep is similar to
other popular search tools like The Silver Searcher, ack and grep.
* [opensubdiv] created stub for opensubdiv
* [opensubdiv] added homepage and description
* [opensubdiv] removed boilerplate
* [opensubdiv] working on dependencies and variants
* [opensubdiv] fixed syntax error
* [opensubdiv] defined spec
* [opensubdiv] added dev version
* [opensubdiv] building on CudaPackage
* [opensubdiv] always build with open gl and depends_on('gl')
* [opensubdiv] applying cuda flags
* [opensubdiv] worked on doc variant
* [opensubdiv] added some x11 libraries
* [opensubdiv] depends on glfw
* [opensubdiv] locating glew
* [opensubdiv] added openmp variant
* [opensubdiv] flake8 fixing
* [opensubdiv] fixed develop version name
* [opensubdiv] fixed description to not need @
* ADIOS2: Version `master`
Rename branch version to supported, real development branch `master`.
The old name is legacy Spack when alternative development branch
names were not yet supported.
* ADIOS: Simplify via spec Variable
use the already defined local variable `spec` to shorten
lines
Since 1.9.0 is broken for Darwin, which impacts many developers, and
the fix is still a RC, let's keep the previous release as default.
This avoids distruption for OSX developers and CI.
* @develop needs the full git repo to use "git describe"
properly
* If not specifying the cxxstd variant, let cmake use its
default
* Improve fmt dependencies: fairlogger < 1.6.2 does not
work with fmt >= 6.
* Small other stuff
Just `depend_on('ncurses')`, pkgconfig seems to cause the right thing
to happen if the package is built +termlib or ~termlib (tested both
ways on a CentOS 7 system).
Additional details in: https://github.com/spack/spack/issues/15281
Tested by building all of the releases of tmux on a CentOS 7 box.
* add preliminary afqmc support in qmcpack
* afqmc updates
* fix spack typos
* edit AFQMC to only allow up 3.7 or above
* added NCCL library support for AFQMC build
* add CMAKE args for BUILD_AFQMC_WITH_NCCL
* update for just AFQMC support. No AFQMC+GPU support
* remove nccl for afqmc
* flake8 whitespace fix
* Update flag_handler for 'netcdf-fortran'.
* Refactoring.
* Enable old versions of netcdf-fortran for NAG.
* Disable parallel 'make check' for versions before 4.5.0.
* Fix shared libraries built with NAG instead of conflicting it.
* Add 'skosukhin' as a maintainer of 'netcdf-fortran'.
This PR adds some fixes for the tcsh package.
- Adds new version
- adds list_url so fetching works for current and old tarballs
- sets ncurses dependency explicitly to `ncurses+termlib`
If `+termlib` is not set then it will link against the system libtinfo.
* Quantum-Espresso: qe-6.5 fails to detect MKL for FFT
qe-6.5 fails to detect MKL for FFT if BLAS_LIBS is set due to
an unfortunate upsteam change in their autoconf/configure:
- qe-6.5/install/m4/x_ac_qe_blas.m4 only sets 'have_blas'
but no 'have_mkl' if BLAS_LIBS is set (which seems to be o.k.)
- however, qe-6.5/install/m4/x_ac_qe_fft.m4 in 6.5 unfortunately
relies on x_ac_qe_blas.m4 to detect MKL and set 'have_mkl'
- qe-5.4 up to 6.4.1 had a different logic and worked fine with
BLAS_LIBS being set
However, MKL is correctly picked up by qe-6.5 for BLAS and FFT if
MKLROOT is set (which SPACK does automatically for ^intel-mkl).
Thus, do not set BLAS_LIBS when compiling qe-6.5 with intel-mkl.
* replace all '^intel-mkl' by '^mkl' to match other packages which also provide MKL
e.g. intel-parallel-studio+mkl as mentioned by @adamjstewart in #15276
* Filter problematic flag from std_cmake_args
Including '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON' in the cmake args causes
bits of cmake's output to end up in the autoconf-generated configure
script. See https://github.com/spack/spack/issues/15274 and
* Don't build in parallel (sigh)
* Constrain hackery for newer versions...
... to newer versions.
* [WIP] new package: qgis
* add maintainer
* further improvements
* reflect improvements to qscintilla installation paths
* comment out qtkeychain dependency as the package is created
* uncomment qtkeychaing dependency, since this package is now created
* a comment on webkit
* specify versions of dependencies, add variant
* fix variant description
* fix proj dependency logic
* adjust conflicts and dependencies so that one can compile qgis@2 with qt4, python2.7
* minor improvement
* fix some build errors, improve dependency specs
* qsci python bindings will be build by py-pyqt
* cmake variable QSCINTILLA_LIBRARY should point to library itself not the parent folder
* turn grass off explicitly, fix typo, turn qspatialite off explicitly
* fix typo
* specify more cmake options that doesn"t seem to be set properly, and use spack provided pkg-config
* fix libzip
* fix build issue with sqlite variant, add runtime dependencies
* add more runtime python package dependencies
* reflect variant name change in sqlite
* add maintainer, correct typo
* add TODO's
* add more versions
* improve style
* add latest versions
* netcdf -> netcdf-c
* add variants as shown in cmake config
* add conflict: v3.8.1 won't build if qt@5.13:
* change preferred version to latest long term release, 3.10.3
* add a zillion of build options
* improve style
* add descriptions for variants
* remove and already implemented compilation tip
* add "when" statements for optional dependencies
* make flake8 happy
* Update var/spack/repos/builtin/packages/qgis/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/qgis/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/qgis/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/qgis/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/qgis/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* convert conflicts to depends_on
* undo str conversion for path objects
* fix flake8 E131
* fix flake8 E128, E124
* improve style
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Caliper depends on python3.
The package needs to be told where to find it.
* More flake8 formatting edits.
* Change explicit python3 to spec['python'].command.path
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Removing defunct import for flake8
* Flake8 trailing whitespace warning.
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
This PR adds 'http://' to the homepage setting of a few packages that do
not have it set. Not having that set can cause problems with some wiki
apps when embedding the homepage value into markdown syntax.
- bowtie2
- exuberant-ctags
- perl-want
- samtools
- add version info for v1.8.0
- v1.8.0 adds a new source file, `file.c`, which need to be included
in our hardcoded list of objects to link.
I discovered this while demonstrating "how easy it is to add a new
package to Spack", only to scratch my head when it failed `spack
install` but worked when I ran `make` in the stage dir. Finally
looked at tree/package.py and it All Became Clear.
Perhaps someone should rewrite this to use MakefilePackage, but the
Makefile starts off with a bunch of twisty turny "uncomment these
lines to run on this platform", so it might not be worth it.
* Added package py-versioneer
* Update python version
* Added python2 to versioneer
* Added python2 to versioneer
* Update var/spack/repos/builtin/packages/py-versioneer/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Cleaning comments
* Removed temporarily @warner as a maintainer, waiting for answer
* Removed line
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* gromacs: add v2019.6
* Update var/spack/repos/builtin/packages/gromacs/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
- Tell make about the source code path
- Install actual header files, not a wrapper with wrong paths
- Add a patch to prevent compiler warnings
- Improve description
* Fixups for jupyter
This PR fixes a few things for some jupyter related packages.
py-ipython:
- make the python depends_on statements reflect needs of different
versions
- remove an unneeded conflicts directive
py-ipywidgets:
- add new version
- set version constraints for py-widgetsnbextension
py-jupyter-console
- add new version
- set python dependencies for versions as needed
- set version constraint for py-ipython
- set version constraints for py-prompt-toolkit
py-pyqt5
- build with py-sip
py-qtconsole
- add dependency on py-pyqt5
* Update var/spack/repos/builtin/packages/py-jupyter-console/package.py
Tweak version ranges.
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-jupyter-console/package.py
Tweak version range.
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Make py-pyqt5 a run dependency
Also, make formatting more consistent.
* Fix site_packages_dir
Change reference of site_packages_dir to self.site_packages_dir. Oddly,
this did not show up as a problem until I regenerated the module.
* Restore py-pyqt5 to previous state
* Explicitly set path to site_packages_dir
This change prevents an error when regenerating the py-pyqt5 module
file.
* Fix flake8 errors
* Make sure prefix is in join_path
* Fix flake8 errors
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* New package: py-librosa
This PR adds the py-librosa package, along with new dependency packages
and some updates of existing dependency packages.
- new package: py-audioread
- new package: py-resampy
- new package: py-soundfile
- update package: py-numba
- update package: py-llvmlite
py-numba:
- add updated version
- adjust constraints
py-llvmlite:
- add updated version
- adjust constraints
- fix version specifications for llvm
- add environment function to set PIC
* Update var/spack/repos/builtin/packages/py-numba/package.py
Ah, yes, I see that `setuptools` is listed in the `install_requires` array. I missed that before.
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Fix dependency
- Add dependency of py-soundfile depends on libsndfile
- Add new libsndfile package
* Add py-pytest-runner build dep
* Make numpy a variant for py-soundfile
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
