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* hypre 2.26.0 (spack#33299) * Github Discussions can be used for Q&A (spack#33364) * Support spackbot rebuilding all specs from source (spack#32596) Support spackbot rebuilding all specs from source when asked (with "rebuild everything") - Allow overriding --prune-dag cli opt with env var - Use job variable to optionally prevent rebuild jobs early exit behavior - ci rebuild: Use new install argument to insist deps are always installed from binary, but package is only installed from source. - gitlab: fix bug w/ untouched pruning - ci rebuild: install from hash rather than json file - When doing a "rebuild everything" pipeline, make sure that each install job only consumes binary dependencies from the mirror being populated by the current pipeline. This avoids using, e.g. binaries from develop, when rebuilding everything on a PR. - When running a pipeline to rebuild everything, do not die because we generated a hash on the broken specs list. Instead only warn in that case. - bugfix: Replace broken no-args tty.die() with sys.exit(1) * python: add 3.10.7, 3.9.14, 3.8.14, 3.7.14 (spack#32623) * Add checksum for py-secretstorage 3.3.3 (spack#33366) * Add checksum for py-ipykernel 6.15.2 (spack#33360) * GnuPG: add v2.3.8 and update stack (spack#33368) * installer.py: traverse_dependencies has local deptype (spack#33367) Currently `traverse_dependencies` fixes deptypes to traverse once and for all in the recursion, but this is incorrect, since deptypes depend on the node (e.g. if it's a dependency and cache-only, don't follow build type edges, even if the parent is build from sources and needs build deps.) * py-horovod: add v0.26 (spack#33311) * py-horovod: add v0.26 * py-petastorm: add v0.12.0 * database: don't warn adding missing build deps (spack#33361) When installing an individual spec `spack --only=package --cache-only /xyz` from a buildcache, Spack currently issues tons of warnings about missing build deps (and their deps) in the database. This PR disables these warnings, since it's fine to have a spec without its build deps in the db (they are just "missing"). * Classic Intel compilers do not support gcc-toolchain (spack#33281) * Classic Intel compilers do not support gcc-toolchain This fix removes `--gcc-toolchain=` from the ~.fcg` files for the classic Intel compilers. AFAIK this option is only supported for Clang based compilers. This lead to an issue when installing cmake. Reproducer: ``` spack install cmake@3.24.2%intel@2021.7.0~doc+ncurses+ownlibs~qt build_type=Release arch=linux-amzn2-skylake_avx512 ``` Tagging maintainer @rscohn2 * Add `-gcc-name` for icc .. and `-gxx-name` for icpc. AFAIK this is used for modern C++ support, so we can ignore `ifort`. Co-authored-by: Stephen Sachs <stesachs@amazon.com> * py-xopen: version bump to 1.6.0 (spack#33231) * version bump to 1.6.0 * added py-isal, updated URL * Initial contribution of LibPressio ecosystem (spack#32630) * Add libpressio and dependencies; some of these packages are maintained as forks of the original repositories and in those cases the docstring mentions this. * Add optional dependency in adios2 on libpressio * cub package: set CUB_DIR environment variable for dependent installations * Clear R_HOME/R_ENVIRON before Spack installation (avoid sources outside of Spack from affecting the installation in Spack) * Rename dlib to dorian3d-dlib and update dependents; add new dlib implementation. Pending an official policy on how to handle packages with short names, reviewer unilaterally decided that the rename was acceptable given that the new Spack dlib package is referenced more widely (by orders of magnitude) than the original Co-authored-by: Samuel Li <shaomeng@users.noreply.github.com> * New packages: libbigwig, methyldackel (spack#33273) * libbigwig: adding new package libbigwig * methyldackel: adding new package methyldackel * libbigwig: tighten up curl variant * grid: reference `fftw-api` instead of `fftw` (spack#33374) This makes it possible to compile with, e.g., `cray-fftw`, not just `fftw`. * Bugfix HIP and aluminum rocm build (spack#33344) * Fixed two bugs in the HIP package recipe. The first is that the HIP_PATH was being set to the actual spec, and not the spec prefix. The second bug is that HIP is expected to be in /opt/rocm-x.y.z/hip but it's libraries can exist at both /opt/rocm-x.y.z/hip/lib and /opt/rocm-x.y.z/lib. This means that the external detection logic may find it in either and it turns out that some modules only expose one of those two locations. Logic is added to ensure that the internal HIP_PATH and associated ROCM_PATH are correctly set in both cases. * Added support for Aluminum to use the libfabric plugin with either RCCL or NCCL. * lz4: add 1.9.4 (spack#33334) * e4s ci stack: add trilinos +rocm (spack#31601) * py-fiona: add v1.8.22 (spack#33372) * intel-oneapi-compilers: fix Python 2.7 compliance (spack#33383) * build(deps): bump docker/setup-buildx-action from 2.1.0 to 2.2.0 (spack#33384) Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 2.1.0 to 2.2.0. - [Release notes](https://github.com/docker/setup-buildx-action/releases) - [Commits](docker/setup-buildx-action@95cb08c...c74574e) --- updated-dependencies: - dependency-name: docker/setup-buildx-action dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * mothur: add v1.48.0 and variants (spack#33326) * vsearch: add v2.22.1 (spack#33327) * papi: fix for Intel OneAPI compiler (spack#33225) Without this patch one hits this error trying to compiler papi with Intel OneAPI: icx: error: Note that use of '-g' without any optimization-level option will turn off most compiler optimizations similar to use of '-O0' [-Werror,-Wdebug-disables-optimization] Signed-off-by: Howard Pritchard <howardp@lanl.gov> Signed-off-by: Howard Pritchard <howardp@lanl.gov> * go,gcc: Support external go compilers for Go bootstrap (spack#27769) For ARM64, fallback to gccgo. (go-bootstrap@1.4 can't support ARM64) * Reusable --use-buildcache with better validation (spack#33388) Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com> * Docs: Spack info option updates (spack#33376) * intel-oneapi-compilers: do not pass -Wno-unused-command-line-argument to icc + refactor (spack#33389) * spack checksum: warn if version is deprecated (spack#32438) Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com> * Update the binary index before attempting direct fetches (spack#32137) "spack install" will not update the binary index if given a concrete spec, which causes it to fall back to direct fetches when a simple index update would have helped. For S3 buckets in particular, this significantly and needlessly slows down the install process. This commit alters the logic so that the binary index is updated whenever a by-hash lookup fails. The lookup is attempted again with the updated index before falling back to direct fetches. To avoid updating too frequently (potentially once for each spec being installed), BinaryCacheIndex.update now includes a "cooldown" option, and when this option is enabled it will not update more than once in a cooldown window (set in config.yaml). Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> * Relocate "run" type dependencies too (spack#33191) When downloading from binary cache not only replace RPATHs to dependencies, but also text references to dependencies. Example: `autoconf@2.69` contains a text reference to the executable of its dependency `perl`: ``` $ grep perl-5 /shared/spack/opt/spack/linux-amzn2-x86_64_v3/gcc-7.3.1/autoconf-2.69-q3lo/bin/autoreconf eval 'case $# in 0) exec /shared/spack/opt/spack/linux-amzn2-x86_64_v3/gcc-7.3.1/perl-5.34.1-yphg/bin/perl -S "$0";; *) exec /shared/spack/opt/spack/linux-amzn2-x86_64_v3/gcc-7.3.1/perl-5.34.1-yphg/bin/perl -S "$0" "$@";; esac' ``` These references need to be replace or any package using `autoreconf` will fail as it cannot find the installed `perl`. Co-authored-by: Stephen Sachs <stesachs@amazon.com> * Add a command to bootstrap Spack right now (spack#33407) * axom: python only reliably available when +python, +devtools (spack#33414) * pilercr: new package (spack#33251) * new package * fixed style * actually building now * raja +rocm: use hipcc as CMAKE_CXX_COMPILER (spack#33375) Signed-off-by: dependabot[bot] <support@github.com> Signed-off-by: Howard Pritchard <howardp@lanl.gov> Co-authored-by: Rui Peng Li <li50@llnl.gov> Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com> Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com> Co-authored-by: Carlos Bederián <carlos.bederian@unc.edu.ar> Co-authored-by: iarspider <iarspider@gmail.com> Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Stephen Sachs <stephenmsachs@gmail.com> Co-authored-by: Stephen Sachs <stesachs@amazon.com> Co-authored-by: Robert Underwood <robertu94@users.noreply.github.com> Co-authored-by: Samuel Li <shaomeng@users.noreply.github.com> Co-authored-by: snehring <7978778+snehring@users.noreply.github.com> Co-authored-by: Mosè Giordano <giordano@users.noreply.github.com> Co-authored-by: Brian Van Essen <vanessen1@llnl.gov> Co-authored-by: Michael Kuhn <michael.kuhn@ovgu.de> Co-authored-by: eugeneswalker <38933153+eugeneswalker@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Howard Pritchard <howardp@lanl.gov> Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com> Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> Co-authored-by: Robert Cohn <robert.s.cohn@intel.com> Co-authored-by: Jonathon Anderson <17242663+blue42u@users.noreply.github.com>
luke-dt
added a commit
to dantaslab/spack
that referenced
this pull request
Oct 19, 2022
* hypre 2.26.0 (spack#33299) * Github Discussions can be used for Q&A (spack#33364) * Support spackbot rebuilding all specs from source (spack#32596) Support spackbot rebuilding all specs from source when asked (with "rebuild everything") - Allow overriding --prune-dag cli opt with env var - Use job variable to optionally prevent rebuild jobs early exit behavior - ci rebuild: Use new install argument to insist deps are always installed from binary, but package is only installed from source. - gitlab: fix bug w/ untouched pruning - ci rebuild: install from hash rather than json file - When doing a "rebuild everything" pipeline, make sure that each install job only consumes binary dependencies from the mirror being populated by the current pipeline. This avoids using, e.g. binaries from develop, when rebuilding everything on a PR. - When running a pipeline to rebuild everything, do not die because we generated a hash on the broken specs list. Instead only warn in that case. - bugfix: Replace broken no-args tty.die() with sys.exit(1) * python: add 3.10.7, 3.9.14, 3.8.14, 3.7.14 (spack#32623) * Add checksum for py-secretstorage 3.3.3 (spack#33366) * Add checksum for py-ipykernel 6.15.2 (spack#33360) * GnuPG: add v2.3.8 and update stack (spack#33368) * installer.py: traverse_dependencies has local deptype (spack#33367) Currently `traverse_dependencies` fixes deptypes to traverse once and for all in the recursion, but this is incorrect, since deptypes depend on the node (e.g. if it's a dependency and cache-only, don't follow build type edges, even if the parent is build from sources and needs build deps.) * py-horovod: add v0.26 (spack#33311) * py-horovod: add v0.26 * py-petastorm: add v0.12.0 * database: don't warn adding missing build deps (spack#33361) When installing an individual spec `spack --only=package --cache-only /xyz` from a buildcache, Spack currently issues tons of warnings about missing build deps (and their deps) in the database. This PR disables these warnings, since it's fine to have a spec without its build deps in the db (they are just "missing"). * Classic Intel compilers do not support gcc-toolchain (spack#33281) * Classic Intel compilers do not support gcc-toolchain This fix removes `--gcc-toolchain=` from the ~.fcg` files for the classic Intel compilers. AFAIK this option is only supported for Clang based compilers. This lead to an issue when installing cmake. Reproducer: ``` spack install cmake@3.24.2%intel@2021.7.0~doc+ncurses+ownlibs~qt build_type=Release arch=linux-amzn2-skylake_avx512 ``` Tagging maintainer @rscohn2 * Add `-gcc-name` for icc .. and `-gxx-name` for icpc. AFAIK this is used for modern C++ support, so we can ignore `ifort`. Co-authored-by: Stephen Sachs <stesachs@amazon.com> * py-xopen: version bump to 1.6.0 (spack#33231) * version bump to 1.6.0 * added py-isal, updated URL * Initial contribution of LibPressio ecosystem (spack#32630) * Add libpressio and dependencies; some of these packages are maintained as forks of the original repositories and in those cases the docstring mentions this. * Add optional dependency in adios2 on libpressio * cub package: set CUB_DIR environment variable for dependent installations * Clear R_HOME/R_ENVIRON before Spack installation (avoid sources outside of Spack from affecting the installation in Spack) * Rename dlib to dorian3d-dlib and update dependents; add new dlib implementation. Pending an official policy on how to handle packages with short names, reviewer unilaterally decided that the rename was acceptable given that the new Spack dlib package is referenced more widely (by orders of magnitude) than the original Co-authored-by: Samuel Li <shaomeng@users.noreply.github.com> * New packages: libbigwig, methyldackel (spack#33273) * libbigwig: adding new package libbigwig * methyldackel: adding new package methyldackel * libbigwig: tighten up curl variant * grid: reference `fftw-api` instead of `fftw` (spack#33374) This makes it possible to compile with, e.g., `cray-fftw`, not just `fftw`. * Bugfix HIP and aluminum rocm build (spack#33344) * Fixed two bugs in the HIP package recipe. The first is that the HIP_PATH was being set to the actual spec, and not the spec prefix. The second bug is that HIP is expected to be in /opt/rocm-x.y.z/hip but it's libraries can exist at both /opt/rocm-x.y.z/hip/lib and /opt/rocm-x.y.z/lib. This means that the external detection logic may find it in either and it turns out that some modules only expose one of those two locations. Logic is added to ensure that the internal HIP_PATH and associated ROCM_PATH are correctly set in both cases. * Added support for Aluminum to use the libfabric plugin with either RCCL or NCCL. * lz4: add 1.9.4 (spack#33334) * e4s ci stack: add trilinos +rocm (spack#31601) * py-fiona: add v1.8.22 (spack#33372) * intel-oneapi-compilers: fix Python 2.7 compliance (spack#33383) * build(deps): bump docker/setup-buildx-action from 2.1.0 to 2.2.0 (spack#33384) Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 2.1.0 to 2.2.0. - [Release notes](https://github.com/docker/setup-buildx-action/releases) - [Commits](docker/setup-buildx-action@95cb08c...c74574e) --- updated-dependencies: - dependency-name: docker/setup-buildx-action dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * mothur: add v1.48.0 and variants (spack#33326) * vsearch: add v2.22.1 (spack#33327) * papi: fix for Intel OneAPI compiler (spack#33225) Without this patch one hits this error trying to compiler papi with Intel OneAPI: icx: error: Note that use of '-g' without any optimization-level option will turn off most compiler optimizations similar to use of '-O0' [-Werror,-Wdebug-disables-optimization] Signed-off-by: Howard Pritchard <howardp@lanl.gov> Signed-off-by: Howard Pritchard <howardp@lanl.gov> * go,gcc: Support external go compilers for Go bootstrap (spack#27769) For ARM64, fallback to gccgo. (go-bootstrap@1.4 can't support ARM64) * Reusable --use-buildcache with better validation (spack#33388) Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com> * Docs: Spack info option updates (spack#33376) * intel-oneapi-compilers: do not pass -Wno-unused-command-line-argument to icc + refactor (spack#33389) * spack checksum: warn if version is deprecated (spack#32438) Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com> * Update the binary index before attempting direct fetches (spack#32137) "spack install" will not update the binary index if given a concrete spec, which causes it to fall back to direct fetches when a simple index update would have helped. For S3 buckets in particular, this significantly and needlessly slows down the install process. This commit alters the logic so that the binary index is updated whenever a by-hash lookup fails. The lookup is attempted again with the updated index before falling back to direct fetches. To avoid updating too frequently (potentially once for each spec being installed), BinaryCacheIndex.update now includes a "cooldown" option, and when this option is enabled it will not update more than once in a cooldown window (set in config.yaml). Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> * Relocate "run" type dependencies too (spack#33191) When downloading from binary cache not only replace RPATHs to dependencies, but also text references to dependencies. Example: `autoconf@2.69` contains a text reference to the executable of its dependency `perl`: ``` $ grep perl-5 /shared/spack/opt/spack/linux-amzn2-x86_64_v3/gcc-7.3.1/autoconf-2.69-q3lo/bin/autoreconf eval 'case $# in 0) exec /shared/spack/opt/spack/linux-amzn2-x86_64_v3/gcc-7.3.1/perl-5.34.1-yphg/bin/perl -S "$0";; *) exec /shared/spack/opt/spack/linux-amzn2-x86_64_v3/gcc-7.3.1/perl-5.34.1-yphg/bin/perl -S "$0" "$@";; esac' ``` These references need to be replace or any package using `autoreconf` will fail as it cannot find the installed `perl`. Co-authored-by: Stephen Sachs <stesachs@amazon.com> * Add a command to bootstrap Spack right now (spack#33407) * axom: python only reliably available when +python, +devtools (spack#33414) * pilercr: new package (spack#33251) * new package * fixed style * actually building now * raja +rocm: use hipcc as CMAKE_CXX_COMPILER (spack#33375) Signed-off-by: dependabot[bot] <support@github.com> Signed-off-by: Howard Pritchard <howardp@lanl.gov> Co-authored-by: Rui Peng Li <li50@llnl.gov> Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com> Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com> Co-authored-by: Carlos Bederián <carlos.bederian@unc.edu.ar> Co-authored-by: iarspider <iarspider@gmail.com> Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Stephen Sachs <stephenmsachs@gmail.com> Co-authored-by: Stephen Sachs <stesachs@amazon.com> Co-authored-by: Robert Underwood <robertu94@users.noreply.github.com> Co-authored-by: Samuel Li <shaomeng@users.noreply.github.com> Co-authored-by: snehring <7978778+snehring@users.noreply.github.com> Co-authored-by: Mosè Giordano <giordano@users.noreply.github.com> Co-authored-by: Brian Van Essen <vanessen1@llnl.gov> Co-authored-by: Michael Kuhn <michael.kuhn@ovgu.de> Co-authored-by: eugeneswalker <38933153+eugeneswalker@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Howard Pritchard <howardp@lanl.gov> Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com> Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> Co-authored-by: Robert Cohn <robert.s.cohn@intel.com> Co-authored-by: Jonathon Anderson <17242663+blue42u@users.noreply.github.com>
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Adding methyldackel and a dependency.