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lib (#9023)
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Final fix for v2.1 (hopefully)
Test build on LANL CCSCS4, Desktop
Signed-off-by: Daniel Topa <dantopa@lanl.gov>
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* Add latest release 3.0.2
https://www.open-mpi.org/software/ompi/v3.0/:x
Signed-off-by: Daniel Topa <dantopa@lanl.gov>
* 1. Added correct md5 sum for Open MPI v3.1.1 (https://www.open-mpi.org//software/ompi/v3.1/)
2. Made v3.1.1 the default version
3. Added libmpiso versions for v3.1.1 and 3.0.2
Signed-off-by: Daniel Topa <dantopa@lanl.gov>
* Added Open MPI v2.14 to version list; Tested build; Added libmpi.so version
Signed-off-by: Daniel Topa <dantopa@lanl.gov>
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* QMCPACK now supports QE 6.3. Dropped QE 5.3 due to incompatibilities.
* QMCPACK general clean-up of depends_on.
* Add QMCPACK 3.5.0
* More robust support of MKL detection in QMCPACK.
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* scorep: make optional packages variants
add packages for cube sub-components: cubew, cubelib
* fix style errors
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Fixes #9001
#8289 added support for install_tree and copy_tree to merge into an existing
directory structure. However, it did not properly handle relative symlinks and
also removed support for the 'ignore' keyword. Additionally, some of the tests
were overly-strict when checking the permissions on the copied files.
This updates the install_tree/copy_tree methods and their tests:
* copy_tree/install_tree now preserve relative link targets (if the symlink in the
source directory structure is relative, the symlink created in the destination
will be relative)
* Added support for 'ignore' argument back to copy_tree/install_tree (removed
in #8289). It is no longer the object output by shutil.ignore_patterns: you pass a
function that accepts a path relative to the source and returns whether that
path should be copied.
* The openfoam packages (currently the only ones making use of the 'ignore'
argument) are updated for the new API
* When a symlink target is absolute, copy_tree and install_tree now rewrite the
source prefix to be the destination prefix
* copy_tree tests no longer check permissions: copy_tree doesn't enforce
anything about permissions so its tests don't check for that
* install_tree tests no longer check for exact permission matching since it can add
file permissions
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libmongoc requires pkg-config to detect several of its dependencies.
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* libunwind: add version 1.3-rc1 and variant xz
Version 1.3-rc1 is the latest published snapshot from libunwind.
Variant xz adds spack-built support for reading compressed symbol
tables, or else disables this feature. Without the variant, libunwind
will look for liblzma in /usr/lib.
* Add preferred=True to version 1.2.1 as the last official stable
release.
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* gperftools@2.7: new version
* gperftools: update homepage & url
The URL in the homepage field of the gperftools package redirects to
its GitHub repo, and the URL for version 2.3 returns a 404 error. This
commit updates both fields to the most recent sensible values.
* gperftools: update commit hashes to sha256
This commit deletes the url field for all listed versions because it
is no longer needed as a result of updating the package url field. In
addition, all commit hashes are updated to SHA256.
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* initial atk update
* Add coreqs
* Fixed flake8 errors
* corrected gnome's version URLs
* Added correct list_url's
* Changed list_depth
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* added relion 3 beta - WIP
* added relion 3 beta - WIP
* more relion changes - still WIP
* more changes for relion
* more changes
* now correctly handling cuda_arch
* now correctly handling cuda_arch
* fixed flake8 syntax errors
* fixed flake8 syntax errors
* merge
* fixed flake8 errors again
* relion 3 finished
* added print message to cuda_arch exception
* relion - shortened explination
* still need tag=2.0.3 for v 2.0.3 - removed @develop since it no longer exists
* correct cuda versions now used properly
* relion 3 done
* added tags back
* fixed exception message
* relion - added develop back as master
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- foam_add_lib() must be used instead of the undefined foamAddLib()
for adding VTK
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* add gcc8 patch for python 2.7.14
Change-Id: I48cb5e717577d8158d1f7f1fe270156a01940d8a
* add explaining comment
Change-Id: Ia46168e2269d7de47d7ec8d0bf9e3b7696ea8e31
* remove unnecessary part of the patch
Change-Id: Iee763effe2439f0f160c1547640eca4bb9451a68
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Replace use of `shutil.copytree` with `copy_tree` and `install_tree` functions in `llnl.util.filesystem`.
- `copy_tree` copies without setting permissions. It should be used to copy files around in the build directory.
- `install_tree` copies files and sets permissions. It should be used to copy files into the installation directory.
- `install` and `copy` are analogous single-file functions.
- add more extensive tests for these functions
- update packages to use these functions.
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* zoltan: fix building with Intel compilers
- building with the Intel compilers may require explicit linking
with the Intel Fortran library (libifcore)
* simplify code; get rid of format() for static strings
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- dependency patching test didn't attempt to apply patches; just to see
whether they were on the spec.
- it applies the patch now and verifies that that patch was applied.
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* Change bzip2 download URL
* bzip2.org -> bzip.org
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* r-rots: new package
* r-rots: hash is a commit
* r-rots: dep types
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* r-argparse: new package
* r-argparse: dep types
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* r-genelendatabase: new package
* r-genelendatabase: git not url
* r-genelendatabase: add runtime deps and fix package type
* r-genelendatabase: dep type
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* r-glimma: new package
* r-glimma: git not url
* r-glimma: adding runtime deps
* r-glimma: dep types
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* r-ctc: new package
* r-ctc: fixing package directory name
* r-ctc: git not url
* r-ctc: dep types
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* Add smtools 1.9.
* Add hstlib 1.9.
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* Install sam.h and libbam.a for legacy apps.
* Install bam.h.
* Remove which(mkdir).
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* Add package for fasta
Add a package for the fasta sequence alignment tools.
The build system is novel (fasta is "venerable", so...). The source
tree includes nearly 50 variant Makefiles, the installer is expected
to pick one that's appropriate and then edit the "XDIR" variable to
specify the installation path. I can only test 64 bit darwin and
linux, so that's all I've included. I'm also assuming that every
64bit x86 system we'll see supports the SSE2 extensions. Other
situations can be dealt with when someone has a test case.
* Switch to MakefilePackage and clean up a bit
- Clean up the description
- Switch to MakefilePackage
- generalize the path to the chosen Makefile
- implement separate `edit`, `build`, and `install` phases.
* Fix call to format()
* Fix broken if logic
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