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2022-10-19py-pandas: add v1.5.1 (#33412)Adam J. Stewart1-0/+1
2022-10-19mpich: enable building when @3.4~cuda (#33325)Sergey Kosukhin1-1/+1
2022-10-19patch std::filesystem check as done in llnl/umpire pr#784 (#33250)eugeneswalker2-0/+34
2022-10-19umpire +rocm: use hipcc as CMAKE_CXX_COMPILER (#33377)eugeneswalker1-0/+3
2022-10-19raja +rocm: use hipcc as CMAKE_CXX_COMPILER (#33375)eugeneswalker1-0/+7
2022-10-19pilercr: new package (#33251)Luke Diorio-Toth1-0/+28
* new package * fixed style * actually building now
2022-10-19axom: python only reliably available when +python, +devtools (#33414)eugeneswalker1-1/+1
2022-10-19Add a command to bootstrap Spack right now (#33407)Massimiliano Culpo2-1/+17
2022-10-19Relocate "run" type dependencies too (#33191)Stephen Sachs1-2/+2
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>
2022-10-19Update the binary index before attempting direct fetches (#32137)Jonathon Anderson4-19/+48
"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>
2022-10-18spack checksum: warn if version is deprecated (#32438)Tamara Dahlgren5-2/+42
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2022-10-18intel-oneapi-compilers: do not pass -Wno-unused-command-line-argument to icc ↵Robert Cohn1-27/+21
+ refactor (#33389)
2022-10-18Docs: Spack info option updates (#33376)Tamara Dahlgren3-10/+27
2022-10-18Reusable --use-buildcache with better validation (#33388)Harmen Stoppels4-31/+76
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2022-10-18go,gcc: Support external go compilers for Go bootstrap (#27769)Bernhard Kaindl4-11/+56
For ARM64, fallback to gccgo. (go-bootstrap@1.4 can't support ARM64)
2022-10-18papi: fix for Intel OneAPI compiler (#33225)Howard Pritchard1-0/+5
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>
2022-10-18vsearch: add v2.22.1 (#33327)snehring1-0/+4
2022-10-18mothur: add v1.48.0 and variants (#33326)snehring1-20/+63
2022-10-18build(deps): bump docker/setup-buildx-action from 2.1.0 to 2.2.0 (#33384)dependabot[bot]1-1/+1
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](https://github.com/docker/setup-buildx-action/compare/95cb08cb2672c73d4ffd2f422e6d11953d2a9c70...c74574e6c82eeedc46366be1b0d287eff9085eb6) --- 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>
2022-10-18intel-oneapi-compilers: fix Python 2.7 compliance (#33383)Massimiliano Culpo1-2/+2
2022-10-17py-fiona: add v1.8.22 (#33372)Adam J. Stewart1-1/+2
2022-10-17e4s ci stack: add trilinos +rocm (#31601)eugeneswalker1-0/+5
2022-10-17lz4: add 1.9.4 (#33334)Michael Kuhn1-0/+1
2022-10-17Bugfix HIP and aluminum rocm build (#33344)Brian Van Essen2-7/+31
* 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.
2022-10-17grid: reference `fftw-api` instead of `fftw` (#33374)Mosè Giordano1-1/+1
This makes it possible to compile with, e.g., `cray-fftw`, not just `fftw`.
2022-10-17New packages: libbigwig, methyldackel (#33273)snehring2-0/+66
* libbigwig: adding new package libbigwig * methyldackel: adding new package methyldackel * libbigwig: tighten up curl variant
2022-10-17Initial contribution of LibPressio ecosystem (#32630)Robert Underwood35-26/+1410
* 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>
2022-10-17py-xopen: version bump to 1.6.0 (#33231)Luke Diorio-Toth2-1/+28
* version bump to 1.6.0 * added py-isal, updated URL
2022-10-17Classic Intel compilers do not support gcc-toolchain (#33281)Stephen Sachs1-15/+26
* 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>
2022-10-17database: don't warn adding missing build deps (#33361)Harmen Stoppels1-27/+48
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").
2022-10-17py-horovod: add v0.26 (#33311)Adam J. Stewart2-0/+6
* py-horovod: add v0.26 * py-petastorm: add v0.12.0
2022-10-17installer.py: traverse_dependencies has local deptype (#33367)Harmen Stoppels1-9/+19
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.)
2022-10-17GnuPG: add v2.3.8 and update stack (#33368)Massimiliano Culpo6-1/+12
2022-10-17Add checksum for py-ipykernel 6.15.2 (#33360)iarspider1-0/+1
2022-10-17Add checksum for py-secretstorage 3.3.3 (#33366)iarspider1-0/+1
2022-10-17python: add 3.10.7, 3.9.14, 3.8.14, 3.7.14 (#32623)Carlos Bederián1-2/+6
2022-10-17Support spackbot rebuilding all specs from source (#32596)Scott Wittenburg2-21/+66
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)
2022-10-17Github Discussions can be used for Q&A (#33364)Harmen Stoppels1-0/+1
2022-10-17hypre 2.26.0 (#33299)Rui Peng Li1-0/+1
2022-10-17Add checksum for py-prompt-toolkit 3.0.31 (#33362)iarspider1-0/+1
2022-10-17Add checksum for py-grpcio-tools 1.48.1 (#33358)iarspider1-2/+5
2022-10-17installer.py: fix/test get_deptypes (#33363)Harmen Stoppels2-1/+40
Fixing an oversight in https://github.com/spack/spack/pull/32537 `get_deptypes` should depend on new `package/dependencies_cache_only` props.
2022-10-17gitlab ci: Do not force protected build jobs to run on aws runners (#33314)Scott Wittenburg1-1/+1
2022-10-17Add checksum for py-astroid 2.12.7, py-astroid 2.12.10, py-setuptools ↵iarspider4-30/+46
62.6.0, py-wrapt 1.14.1, py-pylint 2.15.0 (#32976) * Add checksum for py-astroid 2.12.7, py-setuptools 62.6.0 * Also add checksum for py-wrapt * Update package.py * Update package.py (#57) * Update package.py * Update package.py * Update package.py
2022-10-17installer.py: show timers for binary install (#33305)Harmen Stoppels1-23/+57
Print a message of the form ``` Fetch mm:ss. Build: mm:ss. Total: mm:ss ``` when installing from buildcache. Previously this only happened for source builds.
2022-10-17py-jupyterlab-pygments: install from wheel to avoid cyclic dependency (#33278)iarspider1-7/+21
* py-jupyterlab-pygments: avoid cyclic dependency * Fix style * Update package.py * Update package.py * [@spackbot] updating style on behalf of iarspider * Update package.py * Flake-8 * fix Co-authored-by: iarspider <iarspider@users.noreply.github.com>
2022-10-17py-numpy: add v1.23.4 (#33260)Adam J. Stewart1-0/+1
2022-10-17Add checksum for py-sniffio 1.3.0 (#32975)iarspider1-0/+2
2022-10-17py-tensorflow-hub: zlib, again. (#33359)Harmen Stoppels2-5/+31
2022-10-17mariadb-c-client: add 3.3.2, 3.2.7, 3.1.18, 3.0.10 (#33335)Michael Kuhn1-0/+4