* 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:.
```
* libcircle: add develop version from git master branch
* Update var/spack/repos/builtin/packages/libcircle/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* libcircle: flake8 fix i think
* libcircle: naming things
* libcircle: 🐑 my sacrifice to the flake8 gods
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add 20181226 release of pgmath
* 20190329 release of pgmath requires match for CMPLX macro.
* Add llvm-flang package for Flang fork of LLVM
* Add new and old flang releases.
* Add cmake and python dependencies.
* Update dependencies on llvm-flang and pgmath.
* Fix cmake args and change spec to reflect llvm-flang package.
* change copyright date through 2020.
* Reference Flang package more explicitly.
* More robust support for python executable.
* import os no longer needed, picked up by flake8.
* Use built-in target spec. Variant and targets follow style in main LLVM package.
* Get rid of targets list and only support one target for now.
* Sparc does not appear to be supported in Flang.
* Raise InstallError if architecture not supported.
* fixes#967
* Version bump to 0.9.1
- Bugfixes for spack find
- 0.9.1 can read specs from current develop.
* Don't assume spack is in the path when building docs.
* Quick fix for relocation issues.
* elf relocation fix: cherry-picked from develop branch (#6889)
* Revert "Quick fix for relocation issues."
This reverts commit 57608a6dc4.
* Buildcache: relocate fixes (#6512)
* Updated function which checks if a binary file needs relocation.
Previously this was incorrectly identifying ELF binaries as symbolic
links (so they were being excluded from relocation). Added test to
check that ELF binaries are not considered symlinks.
* relocate_text was not replacing paths in text files. Added test to
check that text files are relocated properly (i.e. paths in the file
are converted to the new prefix).
* Exclude backup files created by filter_file when installing from
binary cache.
* Update write_buildinfo_file method signature to distinguish between
the spec prefix and the working directory for the binary cache
package.
* Final changes for v0.11.0 (#6318)
* Fix logo link in README.md to point to the develop branch. (#6969)
* Compiler flag handlers (#6415)
This adds the ability for packages to apply compiler flags in one of
three ways: by injecting them into the compiler wrapper calls (the
default in this PR and previously the only automated choice);
exporting environment variable definitions for variables with
corresponding names (e.g. CPPFLAGS=...); providing them as arguments
to the build system (e.g. configure).
When applying compiler flags using build system arguments, a package
must implement the 'flags_to_build_system_args" function. This is
provided for CMake and autotools packages, so for packages which
subclass those build systems, they need only update their flag
handler method specify which compiler flags should be specified as
arguments to the build system.
Convenience methods are provided to specify that all flags be applied
in one of the 3 available ways, so a custom implementation is only
required if more than one method of applying compiler flags is
needed.
This also removes redundant build system definitions from tutorial
examples
* Fix type issues with setting flag handlers (#6960)
The flag_handlers method was being set as a bound method, but when
reset in the package.py file it was being set as an unbound method
(all python2 issues). This gets the underlying function information,
which is the same in either case.
The bug was uncovered for parmetis in #6858. This is a partial fix.
Included are changes to the parmetis package.py file to make use of
flag_handlers.
* Bump version to 0.11.1
* Added flags to unit tests + OSX build done once per day (#6988)
* Adding flags to codecov reports
* OSX builds are triggered once a day
* Pull R list_urls from upstream.
* travis: removed /usr/local/include/c++ before installing gcc on OSX (#6515) (#7027)
"brew install gcc" fails for travis build because of an existing
/usr/local/include/c++. This commit removes the offending file
as suggested by brew.
* Fix gfortran 7 detection (#7017)
* Add NameError to exceptions caught from configure_args in module generation (#7173)
* Revert "Binary caching: remove symlinks, copy files instead (#9747)"
This reverts commit 058cf81312.
* Make Spack relocate text files in build caches with relative binaries
* add the tfel package
* fix the tfel package
* fix the tfel package
* fix the tfel package
* Taking Adam J. Steward' remarks into account
* fixes trailing white spaces
* Update description
* Update dependencies following @adamjstewart adices
* Style fixes
* Style fixes
* Add java optional support
* add the maintainers attribute (following @alalazo advice), disable interface not selected (following @adamjstewart advice)
* flake8 fixes
* Fix Cast3M and python-bindings support. Python detection is made compatible with cmake'FindPythonLibs module (at least how it is used in TFEL)
* Style fixes
* Style fixes
* Fix test on python version
* Follow @adamjstewart advices: code is much cleaner and readable
* Small fix
* Small fix
* Add comment
* Small fix in cmake option
* try again (trying to overcome Travis CI unstable build process)
* Add support for the MFrontGenericInterfaceSupport project (MGIS)
* Style fixes
* Package documentation update
* Package documentation update
* Fix a typo thanks to Andreas Baumbach review
* Follow Adam J. Stewart advices
* Fix type
* bugfix: add back r's for invalid regexes
* tutorial basics section: fix gcc install version
* version bump: v0.12.1
* bugfix: bring in .travis.yml from develop
* Add new TFEL' versions (3.0.4, 3.1.4 and 3.2.1). Add new MGIS version (1.0.1). Fix MGIS dependency
* merge with spack:develop
* add missing dependency
* new versions of and
* Fix MGIS url. Fix duplicate variant in TFEL
* Fix tfel packaging according to Adam J. Stewart' advices
* Fix flake8 warning
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
Co-authored-by: Peter Scheibel <scheibel1@llnl.gov>
Co-authored-by: Greg Becker <becker33@llnl.gov>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add ADF
* Fix typo and lint
* fix lint again
* one more lint fix
* fix identation
* still stying to fix identation
* one final fix
* import needed libraries
* changes as per reviewer's request
fix setup environment function, enhance recipe
* add import os once again
* chnages as per reviewer's request
* Set conflicts for qt5 and the Intel compiler
This PR sets a `conflicts` statement for QT5 and the Intel compiler.
* New patches for intel compiles
This commit adds two patches to get QT5 to compile with the intel
compilers. The two patches are very similar but the file being patched
was changed substantially between qt-5.11 and qt-5.12. The patch checks
versions of both GCC and Intel compilers to know when to use overflow
builtis. Essentially, GCC must be >= 5 and Intel must be >= 18.
The sqlite dependency needs the `+column_metadata` variant when the
Intel compiler is used. That is made conditional on the compiler but it
might make sense to make that the default for the sqlite dependency.
Some other changes were made based on testing builds of various QT5
versions with several Intel compilers.
- The libxext dependency is still needed for QT5
- A dependency on libxrender is needed
- The gtk option format needs to be constrained at the qt@5.7 level, not
qt@5.8.
- An extra configure option is needed for the sql plugins RPATH
* Adding a new package, scikit-build, which is very useful for building python extensions
* Update package.py
* Update package.py
Trying to address flake8 corrections
* Update var/spack/repos/builtin/packages/py-scikit-build/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-scikit-build/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-rapidjson: new package at 0.9.1
* py-rapidjson: rename to py-python-rapidjson, use PyPI mirror
* py-python-rapidjson: add missing deps
* python-rapidjson: use short PyPI url
* py-python-rapidjson: remove extra dependencies
* Add platform flag to QT for linux+clang
* Extend QT platform support to more compilers and systems
* Unify QT5 configure options
* fixup! Unify QT5 configure options
* fixup! Unify QT5 configure options
* fixup! Unify QT5 configure options
* Fix newer flake8 and mac qt5 configure
* Add Thirdorder recipe
* Remove white spaces
* Converting recipe to a PythonPackage base class
* remove trailing spaces
* remove line at end of file
* enhance recipe as per reviewer
* fix post_install as requested by reviewer
* rename dir to py-thirderorder
* change checksum to sha256
* py-intervaltree: new package at 3.0.2
* py-intervaltree: fix checksum
* py-intervaltree: add py-setuptools dep
* py-intervaltree: use inclusive ranges
* py-intervaltree: change py-test dep type
Beginning with numpy > 1.16 when using older versions of gcc the
`std=c99` flag must be used. The Intel compiler depends on gcc for its
language extensions so the version of gcc is important. If the version
of gcc used by the Intel compiler is one that requires the `-std=c99`
flag then that flag will have to be used for a build with the Intel
compiler as well.
This PR tests the version of gcc used by the Intel compiler and will
abort the build if the gcc version is < 4.8 and inject the `-std=c99`
flag if >= 4.8 and < 5.1. This will cover the system gcc compiler and
any gcc environment module loaded at build time.
Due to formatting differences, the older version of perl-bioperl was
getting picked up as the preferred version. This PR explicitly sets the
newer version to be preferred.
Because of a bug in the current concretizer,
spack install gromacs
fails because gromacs depends on hwloc (default is v2), and Open MPI
(the default MPI library) depends on hwloc v1.
As discussed in https://github.com/spack/spack/issues/14339, this
workaround should be removed once the concretizer is fixed
Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
