WarpX removed the `dev` branch in favor of a simpler,
`master`-centric development model.
`master` is the new development branch and there is no
stable branch anymore (we use tags and release branches
instead).
* Hydrogen now depends on `aluminum +nccl` vs. `aluminum +mpi_cuda`
* Hydrogen: Simplify Mac OS OpenMP-detection logic
* Aluminum: Add Mac OS OpenMP-detection logic
* LBANN: depend on conduit@0.4.0: instead of conduit@master
Fixes#10019
If multiple instances of a package were installed in a single
instance of Spack, and they differed in terms of dependencies, then
"spack find" would not distinguish specs based on their dependencies.
For example if two instances of X were installed, one with Y and one
with Z, then "spack find X ^Y" would display both instances of X.
This PR creates the r-watermelon package, along with dependencies.
- new package: r-fdb-infiniummethylation-hg19
- new package: r-illuminahumanmethylation450kanno-ilmn12-hg19
- new package: r-lumi
- new package: r-methylumi
- new package: r-roc
- new package: r-txdb-hsapiens-ucsc-hg19-knowngene
- updated package: r-matrixstats, new version needed as a dependency
This PR adds the r-pscbs package along with new dependencies and updates.
- new package: r-aroma-light
- new package: r-r-cache
- updated package: r-r-oo
This PR adds the r-copula package and dependencies.
- new package: r-adgoftest
- new package: r-gsl
- new package: r-pspline
- new package: r-stabledist
* New package - r-rmariadb
This PR creates the r-rmariadb package. It also includes an update to
the r-dbi package as a newer version of that is needed.
* Update var/spack/repos/builtin/packages/r-rmariadb/package.py
Argh, copy/paste. I wish the mirror would list itself as the archive site as well, but it just mirrors that data field from CRAN site. Thanks for catching that, I will make sure to look for that in the future.
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Use mariadb-client
Use mariadb-client so people can set a preferred provider.
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Fixes#14850. Commit 6b1958219 added versions 2020 and 2020.1 for
intel-tbb as part of updating several intel packages but added the
wrong sha256 sums for the github/01org repository.
Also, version 2020 is 2020, not 2020.0.
Add patch makefile-debug to restore the debug targets.
Python depends on gettext. Packages that depend on gettext and Python
together will encounter a concretizer bug which incorrectly detects
a constraint conflict. This sets the default value of +libxml2 in
Python to be the same as gettext so that packages which depend on
both (like mesa) can successfully concretize without adding manual
constraints.
* 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..
This PR adds a new version of llvm and fixes the dependency specs.
- This package depends on libtinfo in all cases so change the ncurses
dependency to reflect that
- if +lldb is in the spec but +python is not then do not build the lldb
python support
- build lldb python support only if +python is in the spec with +lldb
- install the llvm python bindings if +python is in the spec
- install the clang python bindings if +clang and +python are in the spec
- Fixes for conflicts with ~clang
- Fix typo in conflict of compiler-rt and flang
- More robustly handle compiler version switching between QT4 and 5, and
mac/linux, and gcc/intel/clang
- Remove assumption about intel linker being in path
* Convert libmng to use CMake rather than autoconf
The autoconf script failed to recognize the intel compiler; it was
harwired to use gcc.
* Simplify cmake logic and remove unused variant
Add an optional 'submodules_delete' field to Git versions in Spack
packages that allows them to remove specific submodules.
For example: the nervanagpu submodule has become unavailable for the
PyTorch project (see issue 19457 at
https://github.com/pytorch/pytorch/issues/). Removing this submodule
allows 0.4.1 to build.
* Octave: moved the short description in its own paragraph
* Octave: patch mkoctfile.in.cc to avoid using compiler wrappers
* Added a check to ensure mkoctfile works correctly
* update libarchive and fix version of libarchive cmake dependency
* (at least) libarchive 3.3.3 dependency from cmake 3.15.0
* cmake depends on libarchive 3.1.0 if not specified differently
currently it is applied to cmake <3.15.0
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* draco: update versions
+ Added versions 7.3.0 and 7.4.0.
+ Change several variants to be default TRUE since most consumers need these
variants enabled (eospac, lapack, parmetis, superlu-dist). Change variant name
for `+superlu_dist` to use hyphen instead of underscore. This makes the
variant name consistent with the spackage name for `superlu-dist`.
+ Clean up `depends_on` instructions and avoid specifying `type` when possible.
+ Provide patch files that are necessary for some machines (mostly Cray
machines).
* Remove trailing whitespace.
* Revert variant name to use underscore.
* add maintainer information.
Previously, the install stage would compile in things that were
disabled during the build_ext phase. This would also result in the
build pulling in locally installed versions of libraries that were
disabled. The install process doesn't honor the same command-line
flags that build_ext does, but does call build_ext again. Avoid the
whole issue by just writing the options to setup.cfg
Also, add the Imagemagick dependency for tests.
* pumi: sim version check, meshes via submodule, ctest
* Apply suggestions from code review
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* pumi: update comment on master version string
* pumi: description of simmodsuite_version_check variant
* pumi: add white space to variant description
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* git: add version 2.25.0 and fixup pcre dependency
pcre2 became optional in 2.14 and the default in 2.18. I noticed this
as git was compiling against the system pcre2 (spack was
specifying pcre as the dependency).
* missed a chunk from my internal repo
* Set netcdf-fortran to build serially with Intel compiler
This PR turns off parallel builds when the Intel compiler is used.
Builds with the Intel compiler will fail otherwise.
* Change how parallel build is handled
Use patch from netcdf-fortran project to turn off parallel buildi for
version 4.5.2.
* diffutils: Changed the handling of undeclared functions from warning to error.
* diffutils: Change the handling of warnings or error
* Delete '-Werror=implicit-function-declaration'
* Add '-Qunused-arguments'
Replace the deprecated ADIOS1 backend default with ADIOS2 default.
Disable sz since we do not need it and it conflicts with supported
version ranges between ADIOS2 and ADIOS1 if someone enables both.
* intel-tbb: Fix install names on Darwin
Intel-TBB's libraries on Darwin are installed with "@rpath" prefixed
to their install names. This was found to cause issues building the root
package on Darwin due to libtbb not being found when running some of the
generated tools linking to it.
Follow example from other packages with the same issue and fixup up install
names for intel-tbb post install.
* intel-tbb: fix flake8 errors
* Dirty hack to fix#14148
* A better way of checking if a package is taken from system
* Update var/spack/repos/builtin/packages/qt/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update qt/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add the py-merlinwf package
* Fix importlib-resources package name for spack naming convention.
* Add build to dependencies and add updated versions.
* Remove pytest-runner dependency.
* Fix typo.
* Add the py-tabulate dependency.
* Add sha256 for version 1.0.0
* Change to maestro version 1.1.5.
* Increase to version 1.0.4.
* Bump maestrowf version and prepare for new pypi version.
* Add sha256sum for version 1.1.5
* Add version 1.1.1.
Update maestrowf version to 1.1.7
* Add versions 1.0.5, 1.1.0, 1.1.1 and potential 1.2.0.
* Add version 1.2.0 and when on maestrowf@1.1.6.
* Add version 1.2.2 , remove 1.2.1 and 1.1.0.
* Update var/spack/repos/builtin/packages/py-merlinwf/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-merlinwf/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Remove mysql variant until new mysql interface module is enabled.
The mysql code may be removed.
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Get py-torch to build caffe2
This PR gets the py-torch package to build with caffe2, and closes
issue #14576. If building on a machine with CUDA but no GPU the build
will try to build with all compute capabilities. Older compute
capabilities are not supported so the build will fail. The list of
capabilities can be passed to the build using values set in the
cuda_arch variant. Likewise, conflicts are also set to catch if the
unsupported capabilities are listed in cuda_arch.
This PR also sets version constraints on using an external mkldnn for
newer versions. Currenly, only versions up to 0.4 use an external mkldnn
library. Also, the cuda variant is set to True, which restores
previous behavior.
* Update var/spack/repos/builtin/packages/py-torch/package.py
Fix typo.
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Adjust conflicts
This commit adjusts the conflicts. There is an issue with the
cuda_arch=20 conflicts directive as there is a conflicting dependency
with any version >=1.1 and a cuda_arch=20 dependency specified in
CudaPackage that gets trapped first.
* Use a common message for conflicts
This commit adds a variable to contain the bulk of the message stringi
for the cuda_arch conflicts. This is used along with a version string
in the conflicts directives messages.
* Fix the strings
- Use a multiline string for the cuda_arch_conflict variable.
- No need for format() in the msg value.
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Openblas target is now determined automatically upon inspection of
`TargetList.txt`. If the spack target is a generic architecture family
(like x86_64 or aarch64) the DYNAMIC_ARCH setting is used
instead of targeting a specific microarchitecture.
* Try to switch to a newer fork of ftgl
* Allow ROOT to be more flexible about ftgl versions
* Turn ftgl into a CMakePackage
* Update ROOT ftgl dep since 2.1.3 isn't a thing anymore
* Please flake8
* Try to bring back the doc variant
* Comment it out instead of removing it
* Fix root+x breakage from #11129
* Separate out +opengl breakage
* Not strictly X11-related, but more breakage from #11129
* Another X11 breakage found while building 6.08.x
* Don't put system headers in SPACK_INCLUDE_DIRS + deduplicate
* xextproto is only a dependency in +x builds
Rework Spack's continuous integration workflow to be environment-based.
- Add the `spack ci` command, which replaces the many scripts in `bin/`
- `spack ci` decouples the CI workflow from the spack instance:
- CI is defined in a spack environment
- environment is in its own (single) git repository, separate from Spack
- spack instance used to run the pipeline is up to the user
- A new `gitlab-ci` section in environments allows users to configure how
specs in the environment should be mapped to runners
- Compilers can be bootstrapped in the new pipeline workflow
- Add extensive documentation on pipelines (see `pipelines.rst` for further details)
- Add extensive tests for pipeline code
* Update and fix samtools
This PR adds samtools-1.10 and sets the htlib directory so that the
spack built htslib can be used. This PR also arranges the dependencies
so that the htslib sequence is grouped on its own. Finally, the bzip2
dependency is removed and python and perl run dependencies are added.
* Fix samtools when built with ncurses+termlib
* The CI flake8 tests require lowercase variable
Interestingly, this did not show up when I ran `spack flake8` locally.
Unfortunately UCX 1.7.0 is appearing in RPMS before it's officially released.
There's a problem with Open MPI 4.0.x where x < 3 and this version of UCX,
namely that the UCT BTL fails to compile.
See https://github.com/open-mpi/ompi/issues/7128
This patch works around the problem by disabling the build of the UCT BTL
for releases 4.0.0 to 4.0.2.
add hppritcha (me) as maintainer
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
* Add +cfitsio variant to wcslib dependency
* Replace ncurses dependency with readline dependency
casacore explicitly may depend on readline, not ncurses
* Add workaround for casacore's readline dependency
casacore optionally depends upon readline, but it's CMakeLists.txt provides no
user control over whether or not readline becomes a dependency. As readline is
often present by default on systems, it's better for this package to explicitly
depend on readline in order to prevent linking to whatever system version of the
library happens to be found during the build process. This should be considered
a workaround until casacore's CMakeLists.txt is fixed.
* Apply workaround for casacore's dependency on SOFA
Similar to the issues with casacore's readline dependency, casacore's optional
dependency on SOFA does not provide the user with a means of controlling the
dependency during build time. Unlike the readline library, the SOFA library is
unlikely to exist on most systems by default. As the SOFA dependency is only
optionally used for testing casacore, requiring it by default is not a good
workaround. Until casacore's CMakeLists.txt is fixed, this variant has been
removed to avoid unexpected library dependencies in the installed package.
* Add newer casacore versions
* Add mpokorny to maintainer field
- The suite-sparse author publishes new versions starting with 5.5.0 on GitHub, see https://github.com/DrTimothyAldenDavis/SuiteSparse/releases and http://faculty.cse.tamu.edu/davis/SuiteSparse/
- change spack to download from there
- updated sha256 checksums from GitHub for all available releases
- For versions 5.4.0, 5.5.0, 5.6.0 there is a slightly different compilation necessary: first `make default` then `make install`.
Summary of the version changes (+ added, -removed [because not available on GitHub]):
```
+ 5.6.0
+ 5.5.0
+ 5.4.0
5.3.0
5.2.0
+ 5.1.2
5.1.0
+ 5.0.0
+ 4.5.6
4.5.5
- 4.5.4
4.5.3
- 4.5.1
```
to disabled use of libunwind. Without this mesa fails to build
using recent Cray compilers - cce 9 and higher - on aarch64 systems.
Signed-off-by: Howard Pritchard <hppritcha@gmail.com>
It seems that stable versions of perl also install a `perlX.Y.Z` binary.
However, it seems that this binary can hang if used in conjunction with
Spack's sbang workaround, as observed during automake's build.
* Update py-csvkit
This PR updates the py-csvkit package. This version requires a python
stack based on agate and this PR includes the new dependency packages.
- py-agate-dbf
- py-agate-excel
- py-agate-sql
- py-agate
- py-dbfread
- py-isodate
- py-leather
- py-parsedatetime
- py-python-slugify
- py-pytimeparse
- py-text-unidecode
* Replace the copy/pasted apostrophes
Python 2 can not process the copy/pasted apostrophes so replace them
with standard single quote character.
* Add version constraints on dependencies
* Add version contraint to graphviz patches
This PR restricts the graphviz version that the patches for building
with the Intel compiler apply to. The two patches that were needed for
building graphviz-2.40.1 with the Intel compiler are not needed for
graphviz-2.42.2.
* Adjust the qt dependencies
The qt5 patch is only needed for graphviz-2.40.1. However, that version
will only compile with GCC-6 or greater.
* add variant for enabling testing
* add variant for enabling testing
* enable tests and clean up other options
* enable tests and clean up other options
* add numbered versions
* add numbered versions
* updates to avoid enable_tests variant; correct versioning
* updates to avoid enable_tests variant; correct versioning
* fixes for style
* appropriate partitioners are enabled if 'all' is specified - so no need to check in spec
* revert accidental change to copyright
* remove erroneously re-introduced line about tests
* new spack recipe for build Jali - unstructured mesh infrastructure for multiphysics applications
* remove the +parallel condition for mstk, update 1.1.1 sha256sum and whitespace cleanup
* reformat description
* cut down description
* Fixes:
1. MPI_THREAD_MULTIPLE problem with OpenMPI and UCX.
Changes:
1. OpenMPI provides two new depends_on options which result in UCX being compiled with multiple threads support. One implicit when OpenMPI 3.x is used, MPI_THREAD_MULTIPLE is enabled by default, and one explicit for OpenMPI <= 2.x, MPI_THREAD_MULTIPLE is disabled by default.
2. Extends UCX package to allow "Enable thread support in UCP and UCT" option.
3. Adds sha256 sums of UCX releases 1.6.1 and 1.2.0.
More details:
Fixes the issue with OpenMPI where programs which use MPI_THREAD_MULTIPLE will fail to execute because UCP worker didn't support it.
During the OpenMPI package installation it's the +thread_multiple spec was not propagated to UCX nor UCX handled it at all.
Now, the OpenMPI package is capable of handling +thread_multiple spec when UCX is request and the UCX package correctly handles +thread_multiple and compiles with the --enable-mt option.
Error message during runtime:
pml_ucx.c:226 Error: UCP worker does not support MPI_THREAD_MULTIPLE
* Adapts check of specs to read better and is the suggested form in the docs.
* Explicitly disables multithreading of UCX if +thread_multiple option is not used.
* Rework texlive package to install from source
This PR reworks the texlive package so that it installs from versioned
source distibution files. This is preferred over installing the binary
package for several reasons. For the binary installation:
1. Each component is downloaded, so can not use a spack mirror.
2. Changes in components over time are not reflected in spack hash.
3. Some of the binaries do not run due to glibc issues, depending on OS.
This PR keeps the binary installation as an option but it should be
considered deprecated, and probably rewmoved at some point.
This PR depends on zziplib from PR #14318.
* Fix flake8 issues
One of the perl scripts was encoded with ISO-8859-1, which caused the
sbang replacement process to fail when spack uses python3. This PR
converts the ps_scan script to UTF-8 encoding.
This PR converts ISO-8859 encoding to UTF-8 encoding for three scripts in
repeatmasker.
- the main RepeatMasker script
- SimpleBatcher.pm
- wublastToCrossmatch.pl
The ISO-8859 encoding prevented the sbang replacement of long paths when
spack uses python3.
* Update the icu4c package
This PR makes several changes to the icu4c package
1. add updated version to 65.1
2. modify the default url as project has moved to github
3. set UTF-8 locale to support building from source files in UTF-8
format
Note that the older versions are not available on github so explicit urls
were used. This PR will close#14399.
* Consolidate the urls
Consolidate the URLs in the `version` directives by using an if test in
`url_for_version`.
* Put version and sha256 on same line
* Put top level url back
* Update and fix bcftools package
This PR updates bcftools to 1.10.2 and is dependent on PR #14504.
This PR also fixes builds of other versions. Versions 1.2-1.4 did not
use autotools so when the packaeg was converted to use autotools with
version 1.6 those older versions could no longer build. Also, those
versions needed to be patched to use an external htsllib. The method of
finding the external htslib is also different for those older versions.
In addition, this PR adds two variants to bcftools:
- libgsl
- perl-filters
Finally, dependencies for perl and python are added, and an unused
dependency for libzip was removed.
* Do not use '@' in variant description
The '@' character in a variant description will cause a problem with
`spack info`.
```
==> Error: Incomplete color format: '@' in
expressions, for @1.8:
```
* Fix error with python2 processing this package
* Update htslib and add libcurl variant
This PR updates htslib to version 1.10.2 and adds a libcurl variant. The
libcurl variant defaults to True because, while it is optional, it is
highly recommended by the project developers.
Other things done:
- be consistent with quotes
* Change version in variant description
Apparently, `spack info` does not like the `@` character in a variant
description.
```
==> Error: Incomplete color format: '@' in
@1.3:.
```
