* Update Dyninst package file for TBB dependency
Dyninst master and 10.0 release
versions require the tbb package. This mod
updates the tbb versions adding the one that
dyninst uses and adds the required spack package
changes to dyninst/package.py.
* Put new version of tbb in proper location, per reviewer comment.
* Only depend on tbb if building the development version.
* Changes for the release of Dyninst 10.0.0
* Introduce FFTW2 and FFT3 providers for Intel-MKL and FFTW Spack packages.
* make fftw default package for fftw-api virtual package
* virtual package test assertion now provides location of default virtual packages.
* Change name of virtual package to fftw-api and used versioned interface.
- `spack.util.environment` is the new home for routines that modify
environment variables.
- This is to make room for `spack.environment` to contain new routines
for dealing with spack environments
* modified tutorial packages
* update hint in hdf5 tutorial file (typo for suggested argument)
* add repo.yaml to tutorial repository
* update tutorial docs to refer user to tutorial package repository
* flake edits
* recommend site scope vs. defaults
* you don't specify the repo's name when adding a repo, just the path
* henson: new package
* henson: change github path to henson-insitu
* henson: make mpi-wrappers=off by default
* henson: remove unsued variable and spaces to make linter happy
* henson: rename version master to develop
* xeus: new package
cppzmq: add version 4.3.0
zeromq: make libsodium optional, on by default
* xeus: add patch so it builds, add new version
nlohmann-json: add more versions
cryptopp: add more versions
* xeus: flake8
* xeus: fix license
* Provide a newer doxygen version.
+ Also provide a patch that allows collaboration diagrams to work properly with
C++ std::shared_ptr<T>. Ref:
6c380ba91a
* Add the setting of CBTF_MPI_IMPLEMENTATION to the cbtf-krell
and openspeeedshop package files, so that the mpi implementation
can be found by the tool. This allows users to not have to
set this manually if only one mpi implementation is specified
in the build.
* Update version ranges for dependencies of cbtf packages
* GCC: constrain version 6, 7, and 8 to build with ISL version at
most 0.18
* GCC version 9 (not yet released) will be compatible with
ISL version 0.20 so future GCC releases are constrained to build
with ISL version at most 0.20
* ISL: Add v0.15, replace all md5 sums with sha256 sums for ISL
versions
* GCC versions before 6 were constrained to build with ISL 0.14
but have been confirmed to work with ISL 0.15
* GCC: Place an upper bound on GCC's mpfr dependency
* packages/phist: add variant 'fortran' to enable/disable building the Fortran bindings
* xsdk: add phist
* packages/xsdk: add a comment reg. updating phist dependency
* packages/phist: +fortran variant is only for versions 1.7:
* packages/phist: update comments
* xsdk: forgot to specify kernel library for phist (picked tpetra, assuming trilinos+tpetra will be installed)
* packages/phist: add variant 'openmp' to allow disabling OpenMP
* phist: fix compile error due to missing -lm
* flake8: fix warnings
* packages/phist: fix cmake flag: XSDK_ENABLE_Fortran (rather than XSDK_BUILD_Fortran)
* packages/phist: allow disabling building the scamac matrix generator (which causes trouble on some systems)
* packages/xsdk: disable scamac within phist because it caused problems for @balay and is not essential for now
* packages/phist: actually disable scamac via cmake if ~scamac
* phist: disable openmp from xsdk
This commit overhauls the libMesh package script in a number of ways:
* We now inherit from AutotoolsPackage.
* libMesh contains about a dozen third-party dependencies that can
only be provided by the copy bundled with libMesh. This patch
enumerates all such bundled dependencies and disables all of them
by default.
* libMesh supports compilation with external installations of boost,
eigen, hdf5, slepc, and tbb; this patch adds all of them to
package.py.
* libMesh will look for a few system executables (xz, bzip, gdb) by
default. This is now disabled.
* libMesh will now used a copy of perl installed by spack instead of
trying to find the system copy.
* Compilation with non-system MPI installations requires an additional
flag (--with-mpi=); this has been added.
The install() function in the miniconda2 & 3 package.py files referenced
self.url, which is hard-coded to 4.3.11. That's not necessary the
version that the user requested, though. Changed the install() function
to reference self.stage.archive_file. Also added a version string for
4.5.11.
Move suite-sparse gcc version constraint from dealii to suite-sparse
package and update it (gcc 4.9 is required as of version 5.2.0 rather
than 5.1.0). The constraint is now expressed as a conflict rather
than a dependency.
* updated visit package
* make hdf5 and silo conflict with ~gui variant
* Changed parallel => mpi and quotes in description
* Corrected +mpi variant in VisIt package
The previous commit introduced a bug (+parallel variant wasn't renamed +mpi), and the +mpi variant wasn't True by default. This is corrected.
arrow: add missing dependency for python build
The Parquet library moved into the Arrow organisation, hence add a
parquet flavor and adapt dependencies.
* flux: ensure git tags are always available
previous `--unshallow` would only run when `--depth 0` was used. If
1--single-branch` was used, then the `.git/shallow` file would not exist
and `--unshallow` would not work.
add v0.6.0 and update dependencies accordingly
update dependencies to match latest flux versions
adds support for python 3
increases precision of czmq version required for older flux versions
adds new lz4 dependency
* Add stat version 4.0.1
* stat 4.0.1: requires py-xdot
* stat versions at or above 4.0.0 dont require python 2 (it still
requires python but can build with 2 or 3)
* stat versions at or above 4.0.0 dont require py-pygtk and py-enum34
* Replace py-xdot version 0.9.1 with 1.0
* py-xdot: use lib directory vs. lib64 for atk dependency
* Add version 18.9.0 (w/CMake)
* Add version dependent install methods to handle transition from
Make-based package (17.1) to CMake-based package, using the NEST
package as an example
* Remove unnecessary build_targets method for older Make-based
version
* Don't retrieve just the C/Fortran interfaces for netlib-lapack -
blas/lapack libs are now handled the same for all implementations
* Remove netlib-lapack detection patch
* add new version 3.1.0
* add conflict for parmetis without mpi
* strumpack >= 3.1.0 uses -DTPL_ENABLE_<package> instead of
-DSTRUMPACK_USE_<package>
* require cmake at least 3.2
* Added support for the Aluminum library to LBANN and Hydrogen. Also
fixed several bugs in the grouping of dependencies of both packages.
* Updated the conduit package to have the proper dependency on the
python variant.
* Added new versions for NCCL
* Fixed a bug in how Hydrogen set the path for OpenBLAS.
* Added support for conduit in LBANN.
* vtk: add variants for Xdmf IO support, ffmpeg support, and MPI
* vtk: depends on boost when Xdmf support is enabled
* vtk: add backported patch for python3.7
* vtk: New policy only for cmake >= 3.12
* mesa: add py-argparse dependency (for build)
* lz4: use MOREFLAGS instead of LIBS to add -lrt
scalasca actually requires cubew, not the full cube bundle. However,
cubew@4.4 causes the build of previous versions to fail because there is
no cube-config script anymore.
- remove the old LGPL license headers from all files in Spack
- add SPDX headers to all files
- core and most packages are (Apache-2.0 OR MIT)
- a very small number of remaining packages are LGPL-2.1-only
- This is bundled into one commit to make it easy to revert if we do get
consent from peetsv's company to relicense these contributions.
- Revert "dialign-tx adding patch for gcc@5.4.0 (#6413)"
- This reverts commit 09eeb991a2.
- Remove the following LGPL-2.1 packages because we have not gotten
consent to relicense them:
- fast-gbs
- igv
- metasv
- perl-xml-libxml
- py-cnvkit
- py-crossmap
- py-pybedtools
- py-pyfaidx
- py-pyvcf
- py-vmd-python
- r-cghflasso
- r-dismo
- r-proc
- r-spatial
- r-utf8
* omega-h: fix dependencies
1. Remove Gmodel altogether. Omega_h doesn't
actually call Gmodel for anything, it was
more or less just doing additional unit
testing for Gmodel
2. Make Trilinos off by default. Most codes do
not need the ParameterList interface, and
Kokkos through Trilinos is not well explored
in Spack
3. Use modern CMake style to choose the zlib
dependency
getopts.pl is not listed as a Spack dependency of sspace-standard,
so without this change, this package was only working on systems
where getopts.pl was already installed.
* Added conflict in Trilinos for STK when building as shared on Darwin.
* Created shared variant for Nalu and Nalu-Wind to automatically build
Trilinos as static library on Darwin.
* Moved ECP tags from Nalu to Nalu-Wind (the latter is the official
ECP application).
* Remove py-setuptools dependency from py-spyder (fixes#9205)
* Add constraint on transitive qt dependency to build with webkit
extension (required for this package)
* Update pycodestyle dependency constraints
* reordered dependencies (py-zmq, py-chardet) to confirm to the
ordering in setup.py
* superlu-dist: Update package.py for superlu-dist v6.0.0 using CMake
* superlu_dist: Update the header of package.py
* Specify lapack_blas and DCMAKE_INSTALL_LIBDIR
disable support for superlu-dist before v5
current stable releases of PETSc and Trilinos have non-overlapping
requirements on Superlu-dist. For now turn it off by default in
Trilinos, which requires older versions.
* bison: Add missing build dependencies
bison also depends on cmp, which is currently not available in Spack.
* help2man: Add missing build dependency
* m4: Fix build with newer versions of glibc
* openssl: Add missing build dependency
openssl's configure script is actually a Perl script.
* texinfo: Add missing perl dependency
* diffutils: New package
* findutils: Fix build with newer versions of glibc
* mvapich2, mpich: Add missing findutils dependency
* Add option to disable threads for Geant4
* Add option to enable DagMC in MOAB
* Explicitly add OFF flag when threading is disabled
* Fix unintentional enabling of C++14 in Geant4
The following always evaluated to True:
'c++14' or 'c++1y' in spec:
* Push default flag handlers into module scope
* Preserve backwards compatibility of builtin flag handler names
Ensure Spack continues to work for packages using the `Package.env_flags` idiom and equivalent.
* update docs and tests to match
* Update packages to match new syntax
* xerces-c: Add variant for choice of transcoder (gnuiconv, iconv, icu,
macos, windows). It's important to specify a --enable-transcoder
option on the configure line or else xerces may make a different
choice when multiple transcoders are available.
* Pass the compile flags to configure. For cflags and cxxflags, this is
necessary to respect the value from the spack install line.
Otherwise, xerces (and any autotools package) will choose a default
value that overrides the spack compiler wrapper.
* Add xerces version 3.2.2.
* icu4c needs the --enable-rpath configure option on Darwin
* New package: tldd
* https://gitlab.com/miscripts/tldd
* Improvements
* make it prefetchable by specifying a hash based version
* specify the constraints on pstreams versions (from INSTALL)
* Improvements
* Make it a Makefile Package and only overwrite the install_targets
* Remove the URL as there's really no downloadable 'tar ball' version
* Initial commit for new package STRUMPACK, a linear solver library.
* Update to STRUMPACK version 3.0.3.
This adds a check for OpenMP task priority support (since OpenMP 4.5)
* treesub: new package starting at 0.2
* treesub: fix ant build, add exec script
* treesub: use portable octal format
* treesub: add license header
not sure how it even went missing.
The build process of Catalyst requires Python at build time (see line 86) even when the +python variant is not selected.
When the +python variant is selected, Python becomes required at build, link, and run time. There doesn't seem to be any restriction on the version of Python required when +python is not selected.
* Fix: bug in VTK package
Fix for issue 9423 (https://github.com/spack/spack/issues/9423): compilers other than clang don't have the `is_apple` property.
* VTK package: removing trailing whitespace
So flake8 stops complaining.
* Release 2.0 of the ECP Proxy Apps suite
* update laghos version
* make install dir structure consistent across all ecp-proxy-apps
* minor
* update macsio version
* patching p4est to select the proper openmp lib
* For when compiler.openmp_flag isn't supported
* authored by @nrichart, I only tested it
* Adding openmp variant
Signed-off-by: Ricardo Silva <ricardo.silva@epfl.ch>
Building bazel yielded errors since commit cd9691d. The first commit
fixes the build for older bazel versions, the second commit adds new
versions and ports the patches to these versions.
* petsc: add new versions 3.9.4 and 3.10.0
* petsc:update superlu_dist dependency for version 3.10 [might have to change this later for xsdk]
* slepc: add in new releases 3.9.2 and 3.10.0
* Catch2: 2.3.0+
Add the latest two releases of Catch2.
In 2.3.0+, the include changed to a future-proof
`<catch2/catch.hpp>` path which dependent projects will break upon.
* openPMD-api: Catch2 2.3.0+
openPMD-api just updated to use the new, future-proof Catch2
headers `<catch2/catch.hpp>`.
Adds 'code' to the list of suffixes that are excluded from version
parsing of URLs, such that if a URL contains the string
'cistem-1.0.0-beta-source-code', a version X will substitute in to
produce a URL with cistem-X-source-code ('source' was already excluded).
The 'cistem' package version is updated to make use of this (and fix
a fetching bug with the cistem package). A unit test is added to check
this parsing case.
Turns out that there was a configury problem in libhio
which caused issues building the package on non-cray
systems, aka when using mpicc and friends.
Signed-off-by: Howard Pritchard <hppritcha@gmail.com>
This commit adds a patch that prevents the package from hanging. The package would hang because CMakeLists would look for a system MPI. This patch changes the behavior.
* add version 1.3.0
* change build parameters, install process
* mxnet will not compile against spack's nnvm and dmlc so we must use
the distributions provided by the source package.
* also removed 'bin' installation as mxnet is just a shared library.
* improve BLAS linking
* remove unnecessary args
* added variant for python bindings
* r-nloptr: Explicit depends_on(nlopt). Previously there was a hidden dependency, masked by the package's configure script.
* r-nloptr: Change spelling of variables to satisfy pyflake8
* r-nloptr: Break a long line to satisfy pyflake8
* r-nloptr: larger indent on continuation, to satisfy pyflake8
* r-nloptr: another attempt at larger indent on continuation, to satisfy pyflake8
* r-nloptr: now a smaller indent on continuation, to satisfy pyflake8
* r-nloptr: Another attempt at right amount of indent.
* r-nloptr: Another attempt at right amount of indent.
* Use the correct attributes for finding the nlopt includes and libs.
* Lines too long, split into pieces
This patch does not apply cleanly anymore and breaks clang/Mac builds
balay@asterix /home/balay/git-repo/github/trilinos (develop=)
$ patch -Np1 < /home/balay/git-repo/github/spack/var/spack/repos/builtin/packages/trilinos/xlf_tpetra.patch
can't find file to patch at input line 3
Perhaps you used the wrong -p or --strip option?
The text leading up to this was:
--------------------------
|--- a/packages/tpetra/core/src/Tpetra_Details_libGemm.cpp
|+++ b/packages/tpetra/core/src/Tpetra_Details_libGemm.cpp
--------------------------
File to patch:
* Added jdk version, added r-ks and r-multicool packages, made some r packages less conservative in their r version requirement
* flake8 fixes
* fix formatting in jdk version cmd
* Added type=('build', 'run') to some R package dependencies,
added some missing dependencies to r-ks. Thanks Adam.
* fix flake8 error
Due to an internal bug regarding the handling of scalars
(ndim must be 0) in numpy prior to 1.15.0, openPMD-api
will require the latest numpy 1.15+.
Since there is a small regression with datetime pickling in
1.15.0 from the required fix and spack only packages 1.15.1
currently, we depend on 1.15.1 in the recipe.
* add 5 most recent versions and git master branch
* add trilinos, gmodel, throw, examples, optimize, symbols,
and warnings variants
* disable XSDK so that Trilinos dependencies are found.
* added py-pycogent
* flake8 edits
* added type=('build', 'run') to deps, changed py-matplotlib and mpi4py
* changed python min version to 2.6
* fixed cython to py-cython dep
* fixed mpi4py to py-mpi4py
* fixed py-sqlalchemy
* added 1.5.3 version
* fixed version 1.5.3 install
* changed deps names to reflect convention
* added variants
* changed download URL and added SHA256 hash
* fixed deps
* added github url for 1.5.3
* removed unneeded deps
* doesn't require py-setuptools
* fixed url and added py-setuptools specific to version 1.9
* fixed variant names and changed cython to normal dependency instead of variant
* removed cython dep, failed to build when it was present. Changed variant name 'mpi4py' to 'mpi' and changed sqlalchemy variant name to mpi
* fixed dependencies and added py-pymysql dep
* added setup-environment step
* changed download url for 1.5.3 to pypi
* fixed flake8 issue
* updated
* added changes
* Addition of latest maestrowf releases.
* Addition of filelock to dependencies.
* Addition of when clause to depends_on for filelock and tabulate.
* Correction of the tar url.
Update the version numbers and now depend on
the develop version of dyninst because of a
feature in openspeedshop depends on new code
in the dyninst develop tree. Without dyninst
develop, openspeedshop will not build.
* py-matplotlib: Add patch to fix FreeType library detection
Adds patch to add $CPATH to locations searched for FreeType header file
Patch has been upstreamed:
https://github.com/matplotlib/matplotlib/pull/11457
* py-matplotlib: Add patch to fix FreeType library detection
* Make patch only apply to versin 2.2.2 (as already upstreamed)
* Fix flake8 format issue
* py-matplotlib: add range to freetype patch
* py-matplotlib: whitespace
1. I presently get errors of the sort
==> Error: KeyError: 'No spec with name mpi in silo@4.10.2%gcc@8.1.0+fortran+mpi
[...]
$HOME/spack/var/spack/repos/builtin/packages/silo/package.py:84, in configure_args:
81 'FCFLAGS={0}'.format(self.compiler.pic_flag)]
82
83 if '+mpi' in self.spec:
>> 84 config_args.append('CC=%s' % self.spec['mpi'].mpicc)
85 config_args.append('CXX=%s' % self.spec['mpi'].mpicxx)
86 config_args.append('FC=%s' % self.spec['mpi'].mpifc)
without the extra explicit MPI dependency.
2. Silo uses zlib, so we should explicitly depend on it.
Added SUNDIALS 3.1.2 and 4.0.0-dev.1 versions and relevant dependencies
(3.1.2 requires CMake 2.8.12). Updated all versions to use sha256 hashes.
Addressed issue specific to clang compiler on macOS.
* Addition of py-filelock and first page of versions.
* Addition of setup.py patch for setuptools.
* flake8 failure fixes.
* Reduced url declaration to a single line.
* Correction to py-filelock to use distutils.
