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2022-08-26Add pic variant to bacio (#32388)Dom Heinzeller1-0/+7
* Add pic variant to bacio * Fix black style error
2022-08-26add eztrace 2.0 release (#32350)François Trahay1-1/+1
* [EZTrace] Version uptate to 2.0 * Update var/spack/repos/builtin/packages/eztrace/package.py Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-08-26calculate make_jobs in ninja (#32384)Tom Scogland1-2/+4
This is in case ninja's setup_dependent_package is called before its module is initialized by build_environment
2022-08-25libzmq: add patch for gcc-12; conflict for older gcc-11 versions (#32381)Wouter Deconinck1-2/+9
Per #32214, the existing patch `92b2c...` for `gcc@11:` only applies cleanly for `libzmq@4.3.3:4.3.4`. This PR adds a conflict for earlier versions, as they cannot be patched due to different context. For `gcc@11`, this leaves the most recent two versions available (a satisfactory compromise). For `gcc@12`, however, there is another existing conflict that makes these most recent two versions unavailable. This PR adds an upstream patch for the single most recent version that allows compilation with `gcc@12` for that most recent version. Starting point: - `gcc@11` concretizes on all versions, attempts to apply patch on `@4.2.3:4.3.4`, and only succeeds to apply patch on `@4.3.3:4.3.4`, - `gcc@12` concretizes on `@:4.3.1` (and `@master`), attempts to apply patch on `@4.2.3:4.3.1`, fails to apply patch on all. Ending point: - `gcc@11` concretizes on `@4.3.3:4.3.4` (and `@master`), attempts and succeeds to apply patch on `@4.3.3:4.3.4`, - `gcc@12` concretizes on `@4.3.4` (and `@master`), attempts and succeeds to apply patch on `@4.3.4`. Verified with environment build: ```yaml spack: specs: - libzmq@4.3.4%gcc@12.1.0 - libzmq@4.3.4%gcc@11.3.0 - libzmq@4.3.3%gcc@11.3.0 view: false ``` which returns the following: ```console 16:14:47 wdconinc@menelaos ~/git/spack (libzmq-patch-gcc12 *+$%=) $ spack install --fresh ==> Installing environment libzmq [+] /opt/software/linux-ubuntu22.04-skylake/gcc-12.1.0/libmd-1.0.4-egpgd6eoaqtsl5fja2iwsl6gyc4o32p5 [+] /opt/software/linux-ubuntu22.04-skylake/gcc-12.1.0/libsodium-1.0.18-af3rsfnvck6anxf7eeog3f2bph44tjia [+] /opt/software/linux-ubuntu22.04-skylake/gcc-12.1.0/pkgconf-1.8.0-z5of2hj2c6ygd3kxr4cwv7u7t42sxair [+] /opt/software/linux-ubuntu22.04-skylake/gcc-11.3.0/libmd-1.0.4-tec234gco2sd7n52dkwbrad43sdhaw4o [+] /opt/software/linux-ubuntu22.04-skylake/gcc-11.3.0/libsodium-1.0.18-uljf675u3yrn5c7fdjdpa5c7qnnkynke [+] /opt/software/linux-ubuntu22.04-skylake/gcc-11.3.0/pkgconf-1.8.0-l4hzc2g4pnn7dwyttphmxivt3xghvpoq [+] /opt/software/linux-ubuntu22.04-skylake/gcc-12.1.0/libbsd-0.11.5-fi3ri64moy45ksr4sf5pcwd6k23dsa4o [+] /opt/software/linux-ubuntu22.04-skylake/gcc-11.3.0/libbsd-0.11.5-2matmm7im7oygrr77k7wznttv4rbupfz ==> Installing libzmq-4.3.4-t7ad54q3atrnte4rzq7g7cfjcw5227pr ==> No binary for libzmq-4.3.4-t7ad54q3atrnte4rzq7g7cfjcw5227pr found: installing from source ==> Fetching https://mirror.spack.io/_source-cache/archive/c5/c593001a89f5a85dd2ddf564805deb860e02471171b3f204944857336295c3e5.tar.gz ==> Fetching https://mirror.spack.io/_source-cache/archive/31/310b8aa57a8ea77b7ac74debb3bf928cbafdef5e7ca35beaac5d9c61c7edd239 ==> Fetching https://github.com/zeromq/libzmq/pull/4334.patch?full_index=1 ==> Applied patch https://github.com/zeromq/libzmq/commit/92b2c38a2c51a1942a380c7ee08147f7b1ca6845.patch?full_index=1 ==> Applied patch https://github.com/zeromq/libzmq/pull/4334.patch?full_index=1 ==> libzmq: Executing phase: 'autoreconf' ==> libzmq: Executing phase: 'configure' ==> libzmq: Executing phase: 'build' ==> libzmq: Executing phase: 'install' ==> libzmq: Successfully installed libzmq-4.3.4-t7ad54q3atrnte4rzq7g7cfjcw5227pr Fetch: 0.61s. Build: 1m 31.57s. Total: 1m 32.18s. [+] /opt/software/linux-ubuntu22.04-skylake/gcc-12.1.0/libzmq-4.3.4-t7ad54q3atrnte4rzq7g7cfjcw5227pr ==> Installing libzmq-4.3.3-pxrd6piprucu65bkro2ixms6d3x2eudz ==> No binary for libzmq-4.3.3-pxrd6piprucu65bkro2ixms6d3x2eudz found: installing from source ==> Fetching https://mirror.spack.io/_source-cache/archive/9d/9d9285db37ae942ed0780c016da87060497877af45094ff9e1a1ca736e3875a2.tar.gz ==> Using cached archive: /home/wdconinc/.spack/cache/_source-cache/archive/31/310b8aa57a8ea77b7ac74debb3bf928cbafdef5e7ca35beaac5d9c61c7edd239 ==> Applied patch https://github.com/zeromq/libzmq/commit/92b2c38a2c51a1942a380c7ee08147f7b1ca6845.patch?full_index=1 ==> libzmq: Executing phase: 'autoreconf' ==> libzmq: Executing phase: 'configure' ==> libzmq: Executing phase: 'build' ==> libzmq: Executing phase: 'install' ==> libzmq: Successfully installed libzmq-4.3.3-pxrd6piprucu65bkro2ixms6d3x2eudz Fetch: 0.93s. Build: 11.55s. Total: 12.48s. [+] /opt/software/linux-ubuntu22.04-skylake/gcc-11.3.0/libzmq-4.3.3-pxrd6piprucu65bkro2ixms6d3x2eudz ==> Installing libzmq-4.3.4-hiil6dzy2reb4nk555zztwh44rpbyv4h ==> No binary for libzmq-4.3.4-hiil6dzy2reb4nk555zztwh44rpbyv4h found: installing from source ==> Using cached archive: /home/wdconinc/.spack/cache/_source-cache/archive/c5/c593001a89f5a85dd2ddf564805deb860e02471171b3f204944857336295c3e5.tar.gz ==> Using cached archive: /home/wdconinc/.spack/cache/_source-cache/archive/31/310b8aa57a8ea77b7ac74debb3bf928cbafdef5e7ca35beaac5d9c61c7edd239 ==> Applied patch https://github.com/zeromq/libzmq/commit/92b2c38a2c51a1942a380c7ee08147f7b1ca6845.patch?full_index=1 ==> libzmq: Executing phase: 'autoreconf' ==> libzmq: Executing phase: 'configure' ==> libzmq: Executing phase: 'build' ==> libzmq: Executing phase: 'install' ==> libzmq: Successfully installed libzmq-4.3.4-hiil6dzy2reb4nk555zztwh44rpbyv4h Fetch: 0.01s. Build: 10.77s. Total: 10.78s. [+] /opt/software/linux-ubuntu22.04-skylake/gcc-11.3.0/libzmq-4.3.4-hiil6dzy2reb4nk555zztwh44rpbyv4h ```
2022-08-25py-pytorch-lightning: add v1.7.3 (#32383)Adam J. Stewart1-0/+1
2022-08-25phylip: adding workarounds for gcc10+ (#32376)snehring1-0/+16
* phylip: adding workarounds for gcc10+ * phylip: switch to spec.satisfies
2022-08-25zig: add v0.9.1 (#32380)Massimiliano Culpo1-1/+13
2022-08-25charliecloud: add versions 0.28 and 0.29 (#32378)Richard Berger1-1/+3
2022-08-25New package: py-mkdocs (#32363)Ryan Marcellino1-0/+30
2022-08-25fixed cp2k libcp2k.pc (#32349)AMD Toolchain Support1-10/+11
Co-authored-by: Prasanthi <pdonthir@amd.com>
2022-08-25new packages: r-cmdstanr and cmdstan (#32364)Glenn Johnson2-0/+117
2022-08-25new package: r-glmgampoi (#32366)Glenn Johnson1-0/+29
* new package: r-glmgampoi * Remove duplicate depends_on directive
2022-08-25new packages: r-scdblfinder and dependencies (#32367)Glenn Johnson4-0/+134
- r-bluster - r-metapod - r-scran
2022-08-25[ycsb] fixes build process and installation of YCSB (#32213)Matthieu Dorier1-15/+39
* [ycsb] fixes build process and installation of YCSB * [ycsb] fixing style * [ycsb] removed extra newline
2022-08-25New package: glab (#32251)Wileam Y. Phan1-0/+23
2022-08-25ddt: Initial commit (#32338)robgics1-0/+33
* ddt: Initial commit * ddt: Minor change to license date to appease the CI gods * Get rid of unattractive extra line * Switch to sha256 instead of md5
2022-08-25Adding e3sm-kernels to Spack (#32341)Robert Pavel1-0/+57
* Initial Draft of E3SM-Kernels Spackage Initial draft of E3SM-Kernels. Currently no support for nested_loops due to build system limitations * Style Check and Fixed gfortran Check Fixed style issues and changed gnu toolchain check to a gfortran check due to hybrid compilers (e.g. clang+gfortran) * Fixed Style Issues
2022-08-25lammps: added build dependency to py-setuptools (#32351)Lucas Frérot1-0/+1
LAMMPS' setup.py uses setuptools as of lammps/lammps@2ed8e5cf022
2022-08-25Add patch for missing template instantiation in pika 0.7.0 on macOS (#32370)Mikael Simberg1-0/+7
2022-08-25tixi: new variants (fortran,shared) (#32356)Melven Roehrig-Zoellner1-0/+13
* tixi: new variants (fortran,shared) Since some tixi 3 versions, additional CMake flags are needed to build tixi with shared libraries, respectively with Fortran support. * tixi: fix style
2022-08-25snap-berkeley: update to version 2.0.1 (#32358)snehring1-9/+6
2022-08-25fish: adding v3.5.1 (#32362)Tyler Funnell1-1/+2
2022-08-25libfabric: adding missing dep for opx fabric (#32377)snehring1-0/+1
2022-08-25Changes for ROCm-5.2.0 changes and new recipe rocwmma (#31667)Sreenivasa Murthy Kolam4-11/+148
* Changes for ROCm-5.2.0 changes and new recipe rocwmma * modify the maintainers for hipify-clang * address review comments * update the rocwmma new recipe as per latest syntax * fix style errors * modify the patch file to provide the details about the patch * fix style errors
2022-08-25Python: add new maintainer (#31755)Adam J. Stewart2-2/+2
2022-08-25libfabric: Match main version. (#32342)H. Joe Lee1-5/+5
* Match main version. `develop` no loger exists. * Change develop to main.
2022-08-25cplex: add package.py (#32337)robgics1-0/+77
* cplex: add package.py * Update var/spack/repos/builtin/packages/cplex/package.py Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-08-25Update ESMF: bug fix for esmf@8.3.0b09 with PIO (#32360)Dom Heinzeller1-1/+13
2022-08-25py-pynn: add version 0.10.0 (#32307)Christian Mauch1-2/+12
2022-08-24whizard: Fix passing of build options, update versions (#32326)Graeme A Stewart1-0/+4
* whizard: Fix passing of build options, update versions The dependency of whizard on libtirpc is now correctly passed down as an autotools option. Update known versions of package with 3.0.2 and 3.0.3. * Express path to headers via spec object methods
2022-08-24fujitsu-fftw: add option for enabling thread support (#31426)otsukay1-0/+6
Co-authored-by: Yuichi Otsuka <otsukay@riken.jp> Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com> Co-authored-by: otsukay <otsukay@users.noreply.github.com>
2022-08-24process-in-process: overhaul package recipe (#32347)Atsushi Hori1-118/+134
2022-08-23New package: py-mkdocs-material-extensions (#32334)Ryan Marcellino1-0/+19
2022-08-23New package: py-griffe and new build backend: py-pdm-pep517 (#32335)Ryan Marcellino2-0/+40
* New package: py-griffe and new build backend: py-pdm-pep517 * add pdm to build backend docs
2022-08-23add conduit 0.8.4 release (#32343)Cyrus Harrison1-0/+1
2022-08-23minc-toolkit: add runtime flex dependency (#32345)Ben Darwin1-1/+1
Some programs such as `minccalc` depend on libfl.so at runtime.
2022-08-23[WRF] Version update to 4.4 (#32046)Timothy Brown3-2/+84
* [WRF] Update to version 4.4. * [WRF] Patches for v4.4. * Fixing style. * [@spackbot] updating style on behalf of t-brown
2022-08-23Add new package for MUST runtime correctness analysis tool (#32329)Jim Galarowicz1-0/+106
* Add new package for MUST runtime correctness analysis tool * Fix encryption to SHA256 to fix with spack convention.
2022-08-23New package: py-pyyaml-env-tag (#32333)Ryan Marcellino1-0/+20
2022-08-23cpu-features: fix fetch failure (#32325)iarspider1-1/+2
* cpu-features: fix fetch failure `master` branch was renamed to `main` * Update var/spack/repos/builtin/packages/cpu-features/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-08-23intel-oneapi-compilers-classic: fix paths (#32305)Robert Cohn1-1/+7
* Fix intel-oneapi-compilers-classic bin path * Update package.py * intel-oneapi-compilers-classic fix path Co-authored-by: OfirGan <offirgan@gmail.com>
2022-08-23minc-toolkit: add MINC_TOOLKIT environment variable at runtime (#32331)Ben Darwin1-0/+3
This variable is used by some programs both internal and external to the toolkit itself to discover shared objects, data, etc.
2022-08-23py-scipy: Fortran compiler specify code is change to setup.cfg for Fujitsu ↵Toyohisa Kameyama1-6/+7
compiler (#32142) * py-numpy: Change Fortran detect order for Fujitsu Compiler. * create setup.cfg instead of command line.
2022-08-23New package: py-loguru (#32074)Jen Herting1-0/+25
* [py-loguru] New package * [py-loguru] Removed commented out line * [py-loguru] Added types removed extra dependencies * [py-loguru] missing windows dependency. listing windows as a conflict for now * [py-loguru] depends on py-colorama when platform=windows * [py-loguru] flake8 * [py-loguru] Import update * [py-loguru] - python is a runtime dependency - setuptools is a build dependency * [@spackbot] updating style on behalf of qwertos Co-authored-by: James A Zilberman <jazrc@rit.edu> Co-authored-by: qwertos <qwertos@users.noreply.github.com>
2022-08-23New package: py-python-javabridge (#32075)Jen Herting1-0/+21
* [py-python-javabridge] New package * [py-python-javabridge] Added dependencies * [py-python-javabridge] Added types * [py-python-javabridge] py-setuptools and java are dependencies * [py-python-javabridge] Import update * [@spackbot] updating style on behalf of qwertos Co-authored-by: James A Zilberman <jazrc@rit.edu> Co-authored-by: qwertos <qwertos@users.noreply.github.com>
2022-08-23libfabric: new versions (#32083)Martin Pokorny1-1/+5
* libfabric: add new versions 1.15.0, 1.15.1, main (previously named master) * Add OPX fabric option, with conflict for versions before v1.15.0 Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-08-23SDK: Quick fix to allow SDK to build with HIP (#32321)kwryankrattiger1-1/+5
2022-08-23Add cxxstd flag to googletest and default mock to true (#32171)Seth R. Johnson2-17/+23
2022-08-23Geant4: update cmake defines and add support for nvhpc (#32185)Seth R. Johnson1-17/+27
* geant4: use define function * geant4: Change new feature from conflicts to when * geant4: add support/conflicts for nvhpc * fixup! geant4: add support/conflicts for nvhpc
2022-08-23remove compiler optimize level limit of O2 for GCC (#32303)Zhilin Zheng1-5/+0
gfortran can make it with O3, it might be better to remove this limitation.
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