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2022-11-09updates and fixes for libpressio (#33789)Robert Underwood6-2/+77
* updates and fixes for libpressio * differentiate between standalone and build tests * add e4s tags Co-authored-by: Robert Underwood <runderwood@anl.gov>
2022-11-09New package: py-darshan (#33430)Jean Luca Bez1-0/+45
* include py-darshan * include requested changes * fix required versions * fix style * fix style * Update package.py * Update var/spack/repos/builtin/packages/py-darshan/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-11-09Adding libpfm 4.12.0 (#33779)Filippo Spiga1-1/+2
2022-11-09sentieon-genomics: adding version 202112.06 (#33786)snehring1-0/+1
2022-11-09Update package.py (#33787)James Willenbring1-1/+1
Proposing to add myself as a maintainer of the Trilinos Spack package after a related conversation with @kuberry.
2022-11-09Boost: Change comment to conflict for MPI/Python (#33767)kwryankrattiger1-4/+7
Boost 1.64.0 has build errors when building the python and MPI modules. This was previously just a comment in the package.py which allowed broken specs to concretize. The comments are now expressed in conflicts to prevent this.
2022-11-09postgresql: fix weird spack message (#33770)snehring1-1/+1
2022-11-08MFEM: more updates for v4.5 (#33603)Veselin Dobrev3-48/+113
* [mfem] updates related to building with cuda * [hypre] tweak to support building with external ROCm/HIP * [mfem] more tweaks related to building with +rocm * [mfem] temporary (?) workaround for issue #33684 * [mfem] fix style * [mfem] fix +shared+miniapps install
2022-11-08Add checksum for py-protobuf 4.21.7, protobuf 21.7; remove protobuf and ↵iarspider4-175/+59
py-protobuf 2.x (#32977) * Add checksum for py-protobuf 4.21.7, protobuf 21.7 * Update var/spack/repos/builtin/packages/protobuf/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update package.py * Update var/spack/repos/builtin/packages/protobuf/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/protobuf/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update package.py * Update package.py * Delete protoc2.5.0_aarch64.patch * Update package.py * Restore but deprecate py-protobuf 3.0.0a/b; deprecate py-tensorflow 0.x * Fix audit Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-11-08Patch `fmt` for hipcc/dpcpp (#33733)Mikael Simberg1-0/+8
* Patch fmt for hipcc/dpcpp * Add msimberg as fmt maintainer
2022-11-08environment-modules: add version 5.2.0 (#33762)Xavier Delaruelle1-1/+2
2022-11-08hepmc3: new version 3.2.5 (#33748)Wouter Deconinck1-0/+1
Changelog at https://gitlab.cern.ch/hepmc/HepMC3/-/tags/3.2.5 Maintainer: @vvolkl
2022-11-08hypre +rocm: needs explicit rocprim dep (#33745)eugeneswalker1-0/+1
2022-11-08python: 3.11.0 (#33507)Harmen Stoppels3-8/+293
2022-11-08cosma: Add shared option (#33751)Dave Love1-4/+6
2022-11-08gromacs: enable linking with armpl-gcc FFT (#33750)Annop Wongwathanarat1-0/+7
2022-11-08r: fix order of execution for Makeconf filtering (#33752)Massimiliano Culpo1-2/+3
fixes #33747
2022-11-07intel oneapi classic bootstrapping (#31285)Greg Becker3-4/+71
The `intel` compiler at versions > 20 is provided by the `intel-oneapi-compilers-classic` package (a thin wrapper around the `intel-oneapi-compilers` package), and the `oneapi` compiler is provided by the `intel-oneapi-compilers` package. Prior to this work, neither of these compilers could be bootstrapped by Spack as part of an install with `install_missing_compilers: True`. Changes made to make these two packages bootstrappable: 1. The `intel-oneapi-compilers-classic` package includes a bin directory and symlinks to the compiler executables, not just logical pointers in Spack. 2. Spack can look for bootstrapped compilers in directories other than `$prefix/bin`, defined on a per-package basis 3. `intel-oneapi-compilers` specifies a non-default search directory for the compiler executables. 4. The `spack.compilers` module now can make more advanced associations between packages and compilers, not just simple name translations 5. Spack support for lmod hierarchies accounts for differences between package names and the associated compiler names for `intel-oneapi-compilers/oneapi`, `intel-oneapi-compilers-classic/intel@20:`, `llvm+clang/clang`, and `llvm-amdgpu/rocmcc`. - [x] full end-to-end testing - [x] add unit tests
2022-11-07mpich: patch @3.4 to fix checking whether the datatype is contiguous (#33328)Sergey Kosukhin2-1/+144
Co-authored-by: Thomas Jahns <jahns@dkrz.de> Co-authored-by: Thomas Jahns <jahns@dkrz.de>
2022-11-07PyTorch: add v1.13.0 (#33596)Adam J. Stewart7-65/+186
* PyTorch: add v1.13.0 * py-torchaudio: add v0.13.0 * py-torchaudio: add all versions * py-torchvision: jpeg required for all backends * py-torchtext: add v0.14.0 * py-torchtext: fix build * py-torchaudio: fix build * py-torchtext: update version tag * Use Spack-built sox * Explicitly disable sox build * https -> http
2022-11-07Add zstd support for elfutils (#33695)Cédric Chevalier1-0/+4
* Add zstd support for elfutils Not defining `+zstd` implies `--without-zstd` flag to configure. This avoids automatic library detection and thus make the build only depends on Spack installed dependencies. * Use autotools helper "with_or_without" * Revert use of with_or_without Using `with_or_without()` with `variant` keyword does not seem to work.
2022-11-08Fix missing "*.spack*" files in views (#30980)Jordan Galby1-0/+46
All files/dirs containing ".spack" anywhere their name were ignored when generating a spack view. For example, this happened with the 'r' package.
2022-11-072022.3.1 oneAPI release promotion (#33742)akhursev15-0/+95
2022-11-07eckit: fix underlinking (#33739)Sergey Kosukhin1-0/+8
2022-11-07Rust: don't apply constraints to nightly/beta versions (#33723)Adam J. Stewart2-4/+6
2022-11-07quantum-espresso: improve concretization for intel libraries (#33312)Laura Bellentani1-0/+1
2022-11-07singularity: add new versions (#33462)Yang Zongze2-0/+7
2022-11-07GLVis: new versions: v4.1, v4.2 (#33728)Veselin Dobrev2-17/+50
2022-11-07openblas confuses flang/flang-new, so do not set TIME with ~fortran (#33163)Sajid Ali1-2/+3
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com> Co-authored-by: eugeneswalker <38933153+eugeneswalker@users.noreply.github.com>
2022-11-07netcdf-c: add variant optimize (#33642)Sergey Kosukhin1-3/+5
2022-11-07socat: new package (#33713)Michael Kuhn1-0/+31
2022-11-07py-modin: add new package (#33724)Adam J. Stewart4-42/+119
Co-authored-by: adamjstewart <adamjstewart@users.noreply.github.com>
2022-11-07elfutils: add version 0.188 (#33715)Tim Haines1-0/+1
2022-11-06py-vermin: add latest version 1.5.0 (#33727)Morten Kristensen1-1/+2
2022-11-06CMake: add versions 3.24.3, 3.23.4, and 3.23.5 (#33700)John W. Parent1-0/+3
2022-11-06Add version 4.2.2 to R (#33726)Glenn Johnson1-0/+1
2022-11-06z3: New version 4.11.2 (#33725)Erik Schnetter1-0/+1
2022-11-05ADD version 0.19.0 in py-gym recipe (#33701)Emilio J. Padrón González1-5/+5
* ADD version 0.19.0 in py-gym recipe * Fix py-gym download url and dependencies for v0.19.0 * Fix stupid error in previous commit: no change in py-cloudpickle dep * Yes, I should've paid more attention! O:) I think now it is right, thanks!
2022-11-05py-transformers: add v4.24.0 (#33716)Adam J. Stewart3-10/+23
* py-transformers: add v4.24.0 * Internet access still required
2022-11-05openssh: New version 9.1p1 (#33668)Erik Schnetter1-0/+1
Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
2022-11-05Fix relocation to avoid overwriting merged constant strings (#32253)Tom Scogland2-2/+12
Compilers and linker optimize string constants for space by aliasing them when one is a suffix of another. For gcc / binutils this happens already at -O1, due to -fmerge-constants. This means that we have to take care during relocation to always preserve a certain length of the suffix of those prefixes that are C-strings. In this commit we pick length 7 as a safe suffix length, assuming the suffix is typically the 7 characters from the hash (i.e. random), so it's unlikely to alias with any string constant used in the sources. In general we now pad shortened strings from the left with leading dir seperators, but in the case of C-strings that are much shorter and don't share a common suffix (due to projections), we do allow shrinking the C-string, appending a null, and retaining the old part of the prefix. Also when rewiring, we ensure that the new hash preserves the last 7 bytes of the old hash. Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2022-11-04py-matplotlib: add v3.6.2 (#33683)Adam J. Stewart1-0/+1
2022-11-04Updated tau 2.32 hash (#33718)wspear1-1/+1
2022-11-04openssl: New version 1.1.1s (#33664)Erik Schnetter1-2/+12
This is a security update.
2022-11-05py-pytorch-lightning: add conflicts for py-torch~distributed (#33710)Adam J. Stewart1-0/+5
2022-11-04Cray support: use linux platform for newer craype versions (#29392)Greg Becker7-17/+17
Newer versions of the CrayPE for EX systems have standalone compiler executables for CCE and compiler wrappers for Cray MPICH. With those, we can treat the cray systems as part of the linux platform rather than having a separate cray platform. This PR: - [x] Changes cray platform detection to ignore EX systems with Craype version 21.10 or later - [x] Changes the cce compiler to be detectable via paths - [x] Changes the spack compiler wrapper to understand the executable names for the standalone cce compiler (`craycc`, `crayCC`, `crayftn`).
2022-11-04package/py-pykml: add new py3 compatible version (#33631)Sinan1-0/+3
* package/py-pykml: add new py3 compatible version * fix bugs Co-authored-by: sbulut <sbulut@3vgeomatics.com>
2022-11-04arm-forge: add 22.1 and 22.1.1. (#33584)kent-cheung-arm1-0/+12
2022-11-04add justbuild package (#33689)Alberto Sartori1-0/+82
2022-11-04Python package: fix .libs on macOS with external Python (#33410)Dom Heinzeller1-4/+21
For some instances of externally-provided Python (e.g. Homebrew), the LDLIBRARY/LIBRARY config variables don't actually refer to libraries and should therefore be excluded from ".libs".