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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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* 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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* 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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machine. (#4596)
Use spack install meshkit ^cgm+oce, for geometry engine support, by default cgm is facet-based
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- previously restricted everything to QT-4, but now only have that
restriction for older paraview versions.
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* Remove unneeded patch lines which fail for the most recent CNTK version on the head of the git repo
* Really check for NVML/GDK
* Fix some violations
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* gtkplus: set XDG_DATA_DIRS
* shared-mime-info: database of common MIME types
* gtkplus: needs shared-mime-info for correct handling of stock icons
* shared-mime-info: builds with newer intltool than provided by some platforms
* atk: set XDG_DATA_DIRS at run-time
* gdk-pixbuf: set XDG_DATA_DIRS at run-time
* gtkplus: set XDG_DATA_DIRS at run-time
* pango: set XDG_DATA_DIRS at run-time
* shared-mime-info: set XDG_DATA_DIRS at run-time
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* caliper: Update caliper package
* caliper: Explicitly enable/disable cmake options for all variants
* caliper: Fix flake8 warnings
* caliper: Modify defaults for Mac
* caliper: Fix some more flake8 warnings
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* enable some of the tools
do not make zoltan default
* modify moab package
add shared, debug options to cgm, too
build some tools by default (mbsize, mbconvert)
add hdf5, netcdf dependency
add pnetcdf variant (dependency), metis, parmetis, zoltan
add shared, debug, fortran options to moab
* few kinks for moab
zoltan should be built without fortran api, otherwise moab
complains (need to fix)
also, notice that when built with cgm, shared can't find
cgm libraries for the new tools/geometry execs
install in serial for the time being (because of example makefile
duplicate?)
for example, these builds are successful:
spack install moab+mpi+hdf5+zoltan ^mpich@3.2
spack install moab+mpi+hdf5+shared ^mpich@3.2
* force hdf5+mpi if both are specified
also, something like this works:
spack install moab+mpi+hdf5+cgm ^mpich@3.2 ^cgm+oce+mpi ^oce@0.17.2
use mpich32, and cgm built with oce 0.17.2
* forgot about irel, fbigeom, mbcoupler
* add meshkit package
simple build so far, moab and cgm deps only
also, an example of complex build for cgm
spack install moab+mpi+hdf5+cgm+irel+fbigeom ^mpich@3.2 ^cgm+oce+mpi ^oce@0.17.2
* for meshkit, moab needs to have irel, fbigeom
* forgot to self.spec
after building moab with cgm with oce 0.17.2, we can build
meshkit with something like this
spack install meshkit ^moab/tsb75zk
cgm depencency is found out from moab
moab has to be built with irel and fbigeom
* add netgen package and review
do not support yet older versions of meshkit
(which depend on lasso, etc)
add netgen package; tested with meshkit (netgen has to be built without
occ, for meshkit)
We are not enforcing that yet, we may have to test
* use conflicts where needed, suggested by review
remove release candidates
* flake8 alignment errors
* flake8
* reviews
flake8 alignment
explicit options, even for default variants
variant for netgen should be "gui", with the default ~gui (False)
FIXME: with-occ does not work right for netgen ; maybe it should be disabled?
also, with +gui, it should depend on a lot more, like tk, tcl?
* flake8 issues
whitespaces and a comment in netgen
* add more explicit options
--without-mpi needs fixing for cgm, moab and meshkit
add variable url for netgen (although we don''t know if other
versions will appear)
* flake8, trailing whitespace
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* ninja-fortran: a Fortran-capable fork of ninja build tool
* Use url_for_version for clarity
* Clean ninja-fortran
* Cleanup in the original ninja package
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* Remove test dependencies from Python packages
* Make test deptype more clear for a couple more packages
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Fixes #4549.
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- new version 2.6.4 as well
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* augustus: adding augustus
* augustus: fixing flake8 things
* augustus: simplifying verbose
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