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2022-11-01superlu-dist: fix rocm variant for the master branch (#33624)liuyangzhuan1-2/+5
* superlu-dist: fix rocm variant for the master branch * simplify superlu-dist * add mpi include to HIP_HIPCC_FLAGS Co-authored-by: liuyangzhuan <liuyangzhuan@users.noreply.github.com>
2022-11-01Add tracy 0.9 (#33638)Mikael Simberg3-0/+3
* Add tracy 0.9 * Add conflict for pika and tracy@0.9:
2022-11-01py-pytorch-lightning: add v1.8.0 (#33643)Adam J. Stewart3-4/+72
2022-11-01py-ilmbase: add dependency to py-numpy (#33633)Qian Jianhua1-0/+1
* py-ilmbase: add dependency to py-numpy * fix style
2022-11-01package/py-simplekml_add_new_versions (#33632)Sinan1-0/+2
Co-authored-by: sbulut <sbulut@3vgeomatics.com>
2022-11-01Relocate links using prefix to prefix map (#33636)Harmen Stoppels3-58/+58
Previously symlinks were not relocated when they pointed across packages
2022-10-31hpctoolkit: adjust rocm dependency types (#33627)Mark W. Krentel1-4/+6
Drop the link dependency type for the rocm packages. We don't actually link, and that adds rpaths that conflict with the app.
2022-10-31py-torchmetrics: add v0.10.2 (#33630)Adam J. Stewart1-0/+1
2022-10-31ParaView: ParaView needs to set the HDF5 API (#33617)kwryankrattiger1-0/+9
When building ParaView with a newer HDf5 than 1.10, it needs to select the 1.10 API using flags.
2022-10-31GDAL: add v3.5.3 (#33623)Adam J. Stewart1-0/+1
2022-10-31new package: polypolish (#33601)Luke Diorio-Toth1-0/+29
* added polypolish package, comfirmed builds * added bwa dep
2022-10-31julia: don't look for the openlibm libraries when unneeded (#33626)downloadico1-1/+2
* 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>
2022-10-31ophidia-server: new package at v1.7 (#33581)SoniaScard1-0/+47
Co-authored-by: SoniaScard <SoniaScard@users.noreply.github.com>
2022-10-31Revert "gitlab: when_possible -> false (#33443)" (#33552)Massimiliano Culpo2-2/+2
This reverts commit b1559cc831620ee2b2cf8e57fdecc5bb3bf8edfd.
2022-10-31Fix pkgconfig dependencies (#33614)Michael Kuhn7-6/+7
Packages should depend on the virtual provider, pkgconfig, not on its implementations pkg-config or pkgconf.
2022-10-31openfoam: update mechanism for creating spack-specific wmake rules (#33615)Mark Olesen1-23/+51
- 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>
2022-10-31Windows: fix library loading and enable Clingo bootstrapping (#33400)John W. Parent8-73/+115
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)
2022-10-31Enable Cuda for AMReX smoke test. (#28576)Erik1-2/+7
* 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>
2022-10-31rsync: New version 3.2.7 (#33618)Erik Schnetter1-0/+3
2022-10-31Nalu-Wind: Allow for standard versions of trilinos (#33620)psakievich1-1/+1
* 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
2022-10-31gmake: add a patch so dirs are not executed (#33578)Harmen Stoppels2-0/+135
2022-10-31exago: query and use MPI compilers from spack (#33598)Satish Balay1-0/+11
* exago: query and use MPI compilers from spack * exago: requires explicit location of mpi.h for nvcc
2022-10-31Make --backtrace show non-SpackError backtraces (#33540)Harmen Stoppels1-3/+8
2022-10-31remove sequential filter in binary relo (#33608)Harmen Stoppels1-16/+4
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
2022-10-31_replace_prefix_bin performance improvements (#33590)Harmen Stoppels2-26/+51
- 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
2022-10-31utf8proc: add v2.8.0 (#33611)Mosè Giordano1-0/+1
2022-10-30openjdk: add 11.0.16.1+1, 11.0.17+8, 17.0.4.1+1, 17.0.5+8 (#33355)Diego Alvarez1-0/+72
2022-10-30libgit2: add v1.4.4 and v1.5.0 (#33604)Mosè Giordano1-0/+2
2022-10-29e4s ci: add mfem +rocm (#31604)eugeneswalker1-0/+1
2022-10-29New MFEM version: 4.5 (#33480)Veselin Dobrev2-41/+124
* 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>
2022-10-29unifyfs %oneapi: -Wno-error=deprecated-non-prototype,unused-function (#33602)eugeneswalker1-0/+3
2022-10-29gettext: constrain nvhpc patch to @:0.20.0 (#33489)eugeneswalker1-1/+1
2022-10-29Deprecate spack bootstrap trust/untrust (#33600)Massimiliano Culpo8-70/+113
* Deprecate spack bootstrap trust/untrust * Update CI * Update tests
2022-10-29mpich: fix rpath flags in mpif90 when building with oneapi (#33319)Sergey Kosukhin4-32/+23
Co-authored-by: eugeneswalker <38933153+eugeneswalker@users.noreply.github.com>
2022-10-29phist: add/update conflicts with cray-libsci and/or python@3.11: for … ↵Jonas Thies1-1/+7
(#33587) * phist: add/update conflicts with cray-libsci and/or python@3.11: for versions <1.11.2 * phist: style fix
2022-10-29czmq %oneapi: -Wno-error: gnu-null-pointer-arithmetic, strict-prototypes ↵eugeneswalker1-0/+8
(#33586)
2022-10-29json-c %oneapi: add -Wno-error=implicit-function-declaration (#33585)eugeneswalker1-0/+7
2022-10-29mumps: update URLs, and add versions 5.5.0, 5.5.1 (#33597)Satish Balay2-3/+31
2022-10-29WarpX 22.10 & PICMI-Standard (#33594)Axel Huebl3-3/+12
Update `warpx` & `py-warpx` to the latest release, `22.10`. Update `py-picmistandard` accordingly.
2022-10-29libtiff: CMake support, internal codecs variants (#33591)Adam J. Stewart1-23/+74
2022-10-28Fixed a bad variant when statement for including cuDNN. (#33595)Brian Van Essen1-1/+1
2022-10-28new packages (py-auditwheel, py-medaka, py-parasail, py-progressbar33, ↵Luke Diorio-Toth8-0/+172
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>
2022-10-28netlib-scalapack: fix build error with oneapi compilers (#33539)Satish Balay1-1/+1
/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); ^
2022-10-28starpu: add papi and blocking variants (#33580)Lucas Nesi1-0/+7
2022-10-28ReFrame: add versions up to v3.12.0 (#33446)Vasileios Karakasis1-0/+13
Also adds 4.0 dev versions
2022-10-28gitlab ci: patched make 4.3.0 (#33583)Harmen Stoppels16-31/+33
2022-10-28patchelf: add v0.16.1 (#33579)Harmen Stoppels1-0/+1
2022-10-28openblas %oneapi: extend application of ↵eugeneswalker1-1/+1
--Wno-error=implicit-function-declaration (#33576)
2022-10-27CachedCMakePackage: Add back initconfig as a defined phase (#33575)Chris White3-4/+7
Also: add type annotation to indicate that "phases" is always a tuple of strings.
2022-10-27py-scikit-learn: add v1.1.3 (#33534)Adam J. Stewart1-0/+1
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