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* ampliconnoise: new package
* ampliconnoise: fixed installation
* ampliconnoise: fixing install again
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* libint: factored parts of configure_args into their own functions
* libint: added -xSSE2, as suggested by @lee218llnl
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* Dataspaces spack package, hard-wired for ubuntu VM
* Initial commit of dataspaces spack package
* Made changes and additions necessary to install on Cori and Titan
* Added temp 1.6.2.1 for testing
* Updated tar file for 1.6.2
* Fixed formatting
* Set the type of build dependencies
* Changed the way autogen.sh is called for compatibility
* Use append instead of extend to add configure flags
* Various syntax fixes
* Switched string checking to method for compatibility
Now using the six library for Python 3 compatibility. Thanks @adamjstewart
* Made MPI variant default
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- Lock test can be run either as a node-local test or as an MPI test.
- Lock test is now parametrized by filesystem, so you can test the
locking capabilities of your NFS, Lustre, or GPFS filesystem. See docs
for details.
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- Uses O_CREAT for touch (for guaranteed atomic open on NFS, multi-node)
- Ignore concurrent create errors in mkdirp
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- renamed develop version from 'plus' to 'develop'
- patches now prefixed by corresponding OpenFOAM version number.
This makes it easier to sort and see what old/junk exists.
- remove MPI_BUFFER_SIZEk env variable (for all openfoam variants).
The OpenFOAM shell setup addresses this and there is no reason
to pollute the module environment at this stage.
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* sabre initial commit, works but test does not
* removing test until I have time to fix it
* sabre: fixing flake8 errors
* sabre: changing to MakefilePackage
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See - https://github.com/Microsoft/CNTK/issues/62
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Commit-type: bug-fix, portability-fix
Funded-by: IDEAS
Project: xSDK
Time: .4 hours
Reported-by: Stanislav Y Sergienko <ssergien@anl.gov>
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The tarball used until now is not available anymore.
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* go-bootstrap: Update to 1.4-bootstrap-20170531
Clean up empty patch method.
* go: Update to 1.8.3
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5.9.0 fails to build with disabled OpenGL.
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* mpifileutils: update to v0.7
* mpifileutils: disable --enable-experimental in v0.6 and earlier
* mpifileutils: list newest version first, avoid experimental switch unless at v0.7 or later
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* Update hdfgroup packages to new URL structure
* Update docs now that HDF5 URL isn't that complicated
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Make it possible to pass addition arguments to the
JVM.
Apparently there are two vars and they are [commonly *both* used][1].
Go figure.
[1]: https://stackoverflow.com/questions/23507639/is-it-same-mean-java-args-and-java-opts
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* albacore 1.24 requires numpy 1.13 - added numpy 1.13
* added numpy 1.13
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* Add package for lftp
* Avoid expensive list processing
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* allpathslg: adding package. compiler specs iffy, will fix
* allpaths-lg: adding new package
* allpaths-lg: fixing conflicts
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* * add mpii* wrappers for use with intel compilers
* in mumps package, scotch is compiled without metis option when
ptscotch variant is selected. This removes confusion over which
metis.h to use
* for intel mkl, add SPACK_COMPILER_EXTRA_RPATHS ending in 'intel64'
* scotch lib requires libz when compression is turned on. This
caused a link issue on some Ubuntu distributions (not
redhat). Change Scotch package to add -lz when needed
* * intel-mkl append to SPACK_COMPILER_EXTRA_RPATHS rather than setting
* use more concise method to obtain libz libraries for scotch
* remove changes to intel mpi
* remove commented out depends_on
* fix flake8 errors
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* Add package for primer3
Built and mildly tested on CentOS 7.
* Convert to MakefilePackage
I always forget about this...
* Set build_directory the easy way
Life's not always complicated. Don't go out of my way
to make it so....
* Fix Flake8 issue
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* Add package for muscle
Minimally tested on CentOS7.
* Convert to MakefilePackage
Do it the easy way...
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Minimally tested on CentOS 7.
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* pegtl: version bump
* pegtl: added 2.1.4
* pegtl: reorder versions
* pegtl: fix flake8
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* Return an error exit code if spack cd does not succeed.
* Reducing amount of return statements in spack cd exit code.
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* added perl-star-fusion and perl-intervaltree
* added perl-star-fusion and all dependencies
* changes
* made changes as requested to perl-star-fusion dependencies
* changed perl-intervaltree dependency
* changes to star fusion
* now using perl properly
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* Added magma package
* Incorporated Serban's change
* fix-xl/trilinos: add -qfixed to Fortran flags in seacas package
* fix-xl/trilinos: fixed spack flake8 errors
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- Thanks to pointer from @adamjstewart - can avoid this either by
avoiding an external mxml dependency, or by making certain that they
both use consistent code generation.
The adios package uses '-fPIC' for python linkage and this seems to
require the same for mxml too. If the adios-internal version of mxml
is used, it has the same flags for both.
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* added py-multiqc and dependencies
* added requested changes per #4381
* added colormath dependency per https://github.com/jsvine/spectra/blob/master/requirements.txt
* py-multiqc changes
* py-multiqc does not need colormath - spectra does
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* adding clhep 2.3.4.4, etc and modernizing package.py
* add remaining 2.3.x.y clhep releases
* setting list_depth to 1 is sufficient
* remove whitespace
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(#4600) (#4601)
- The buggy flex-2.6.2 was blacklisted in the corresponding flex
package, but now also removed the md5sum to avoid suggesting that
this version should be revived.
The 2.6.3 has similar problems (at least for scotch), but 2.6.4
seems to work.
- Rejig flex restriction for scotch to exclude 2.6.2-2.6.3 only. Since
flex-2.6.4 appears to be okay again, we can remove the flex version
restriction that trickled through into the openfoam packages as a
consequent of an spack spec bug.
- Make flex a build dependency for the openfoam packages
(seems to have been an earlier oversight).
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* Don't immediately raise an error when an editor is not found
* If no editor is found, raise an error only if we try to use it.
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* Allow arbitrary Prefix attributes
* Test attribute type as well
* Flake8 fixes
* Remove __new__ method
* Fewer uses of join_path in the docs
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