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* added polypolish package, comfirmed builds
* added bwa dep
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* julia: don't look for the openlibm libraries when unneeded
Cause spack to *not* check for the existence of the openlibm libraries (by adding it to the pkgs list) when ~openlibm is specified.
* [@spackbot] updating style on behalf of downloadico
Co-authored-by: downloadico <downloadico@users.noreply.github.com>
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Co-authored-by: SoniaScard <SoniaScard@users.noreply.github.com>
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This reverts commit b1559cc831620ee2b2cf8e57fdecc5bb3bf8edfd.
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Packages should depend on the virtual provider, pkgconfig, not on its implementations pkg-config or pkgconf.
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- the updated OpenFOAM wmake rules now allow multiple locations for
compiler flags:
* wmake/General/common/c++Opt [central]
* wmake/linux64Gcc/c++Opt [traditional]
- match both '=' and ':=' make rule lines
Co-authored-by: Mark Olesen <Mark.Olesen@esi-group.com>
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Changes to improve locating shared libraries on Windows, which in
turn enables the use of Clingo. This PR attempts to establish a
proper distinction between linking on Windows vs. Linux/Mac: on
Windows, linking is always done with .lib files (never .dll files).
This somewhat complicates the model since the Spec.lib method could
return libraries that were used for both linking and loading, but
since these are not always the same on Windows, it was decided to
treat Spec.libs as being for link-time libraries. Additional functions
are added to help dependents locate run-time libraries.
* Clingo is now the default concretizer on Windows
* Clingo is now the concretizer used for unit tests on Windows
* Fix a permissions issue that can occur while moving Git files during
fetching/staging
* Packages can now implement "win_add_library_dependent" to register
files/directories that include libraries that would need to link
to dependency dlls
* Packages can now implement "win_add_rpath" to register the locations
of dlls that dependents would want to load
* "Spec.libs" on Windows is updated to return link-time libraries
(i.e. .lib files, rather than .dll files)
* PackageBase.rpath on Windows is now updated to return the most-likely
locations where .dlls will be found (which is generally in the bin/
directory)
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* Enable Cuda for AMReX smoke test.
* style fix
* more style fixes
* change /... to join_path
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
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* Nalu-Wind: Allow for standard versions of trilinos
This will allow us to utilize custom numeric versions for trilinos in `spack-manager` while we continue to develop `nalu-wind`.
Pinging @eugeneswalker @jrood-nrel @tasmith4
* Update var/spack/repos/builtin/packages/nalu-wind/package.py
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* exago: query and use MPI compilers from spack
* exago: requires explicit location of mpi.h for nvcc
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Currently there's a slow sequential step in binary relocation where all
strings of a binary are collected, with rpaths removed, and then
filtered for the old install root.
This is completely unnecessary, and also incorrect, since we replace
more than just the old install root in the prefix to prefix mapping. And
in fact the prefix to prefix mapping is parallel, and a single pass. So
even as an optimization, this filter makes no sense anymore.
Therefor we remove it
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- single pass over the binary data matching all prefixes
- collect offsets and replacement strings
- do in-place updates with `fseek` / `fwrite`, since typically our
replacement touch O(few bytes) while the file is O(many megabytes)
- be nice: leave the file untouched if some string can't be
replaced
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* New MFEM version: 4.5
Add new MFEM variants: ginkgo, hiop
* mfem: small tweaks
* mfem: tweak testing script
* mfem: try to resolve issue #30483
* mfem: fix style
* mfem: tweak for Spack-built hipsparse
Co-authored-by: eugeneswalker <38933153+eugeneswalker@users.noreply.github.com>
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* Deprecate spack bootstrap trust/untrust
* Update CI
* Update tests
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Co-authored-by: eugeneswalker <38933153+eugeneswalker@users.noreply.github.com>
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(#33587)
* phist: add/update conflicts with cray-libsci and/or python@3.11: for versions <1.11.2
* phist: style fix
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(#33586)
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Update `warpx` & `py-warpx` to the latest release, `22.10`.
Update `py-picmistandard` accordingly.
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py-pyspoa) and updates to others (py-scikit-build, py-ont-fast5-api) (#33541)
* Added py-medaka and dependencies
* fixed py-parasail build error
* medaka still doesn't have correct linked libdeflate
* fixed pyspoa deps
* added htslib.patch, confirmed builds and runs
* fixed style
* Update var/spack/repos/builtin/packages/py-auditwheel/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* made requested changes
* added targets for pyspoa dep
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
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/home/xsdk/spack.x/lib/spack/env/oneapi/icx -DAdd_ -Dscalapack_EXPORTS -I/opt/intel/oneapi/mpi/2021.7.0/include -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/scalapack.dir/BLACS/SRC/dgamx2d_.c.o -MF CMakeFiles/scalapack.dir/BLACS/SRC/dgamx2d_.c.o.d -o CMakeFiles/scalapack.dir/BLACS/SRC/dgamx2d_.c.o -c /home/xsdk/spack.x/spack-stage/spack-stage-netlib-scalapack-2.2.0-uj3jepiowz5is4hmdmjrzjltetgdr3lx/spack-src/BLACS/SRC/dgamx2d_.c
/home/xsdk/spack.x/spack-stage/spack-stage-netlib-scalapack-2.2.0-uj3jepiowz5is4hmdmjrzjltetgdr3lx/spack-src/BLACS/SRC/igsum2d_.c:154:7: error: call to undeclared function 'BI_imvcopy'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
BI_imvcopy(Mpval(m), Mpval(n), A, tlda, bp->Buff);
^
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Also adds 4.0 dev versions
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--Wno-error=implicit-function-declaration (#33576)
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Also: add type annotation to indicate that "phases" is always a
tuple of strings.
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* Add nextflow 22.10.1
* Add trailing comma (style)
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Currently the vasp package always enables the use of shmem to reduce algorithm memory usage (see
https://www.vasp.at/wiki/index.php/Precompiler_options). This is great,but on some systems gives compile errors with the interoperability of C and Fortran. This PR makes that shmem flag optional, but retains the
existing default on behavior.
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* ophidia-analytics-framework: new package at v1.7
* Fix code style in ophidia-analytics-framework
Co-authored-by: SoniaScard <SoniaScard@users.noreply.github.com>
Co-authored-by: Donatello Elia <eldoo@users.noreply.github.com>
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* Added support for building the DiHydrogen package and LBANN extensions
to DiHydrogen with ROCm libraries.
Fixed a bug on Cray systems where CMake didn't try hard enough to find
an MPI-compatible compiler wrapper. Make it look more.
Added support for the roctracer package when using ROCm libraries.
* Fixed how ROCm support is defined for pre-v0.3 versions.
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- hdf5-vfd-gds:
- Add new version 1.0.2 compatible with hdf5@1.13.
- CMake is a build dependency.
- Set `HDF5_PLUGIN_PATH` in the runtime environment, this plugin
is loaded dynamically.
- SDK:
- The VFD GDS driver only has utility when CUDA is enabled.
- Require hdf5-vfd-gds@1.0.2+ (1.0.1 and earlier do not compile).
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