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2023-04-04PyTorch: fix ppc64le patching (#36621)Adam J. Stewart1-1/+1
2023-04-03eospac: expose version 6.5.6 (#36615)Daryl W. Grunau1-1/+6
Co-authored-by: Daryl W. Grunau <dwg@lanl.gov>
2023-04-03added new packages (#36608)Andrey Perestoronin15-0/+90
2023-04-03gromacs: make package inherit from CudaPackage (#36551)Daniel Ahlin1-2/+1
To conform to spack way of specifying cuda_arch. This commit does not change version-specific gencode handling for older gromacs versions
2023-04-03py-pillow: add v9.5.0 (#36593)Adam J. Stewart1-0/+2
2023-04-03py-pandas: add v2.0.0 (#36617)Adam J. Stewart3-28/+62
2023-04-03modules: remove default symlink on uninstall (#36454)Xavier Delaruelle2-0/+16
When app is uninstalled, if it matches a default, then remove the default symlink targeting its modulefile. Until now, when a default were uninstalled, the default symlink were left pointing to a nonexistent modulefile.
2023-04-03Bump required CMake version for stdexec (#36605)Mikael Simberg1-1/+1
2023-04-03Improve Dockerfile recipe generation (#35187)Massimiliano Culpo6-15/+163
- Update default image to Ubuntu 22.04 (previously was still Ubuntu 18.04) - Optionally use depfiles to install the environment within the container - Allow extending Dockerfile Jinja2 template - Allow extending Singularity definition file Jinja2 template - Deprecate previous options to add extra instructions
2023-04-03New package py-pycorenlp (#36609)Benjamin Meyers1-0/+24
2023-04-03hip: mathlibs inherit CudaPackage and ROCmPackage (#34586)Cory Bloor8-68/+253
Unless the amdgpu_target is overriden, the libraries will default to being built for cuda, since amdgpu_target=none is both default and in conflict with +rocm. This requires a custom Disjoint set to include both the 'auto' variant used by the rocm mathlibs and the 'none' variant used by ROCmPackage. * Fix search for hip+cuda in hipcub@5.1 and later This patch is not strictly necessary, but it may fix the search for HIP in certain environments. * Backport fix for CUDA 11.5 to hipsparse
2023-04-03Updated homepage URL (#36519)vijay kallesh7-7/+7
2023-04-03Automated deployment to update package flux-sched 2023-04-01 (#36591)Vanessasaurus1-0/+1
Co-authored-by: github-actions <github-actions@users.noreply.github.com>
2023-04-03Rework error handling within the ASP logic program (#36536)Massimiliano Culpo4-123/+122
* Reduce effort on grounding by employing cardinality constraints If we use a cardinality constraint instead of a rule using pair of values, we'll end up grounding 1 rule instead of all the possible pair combinations of the allowed values. * Display all errors from concretization, instead of just one If clingo produces multiple "error" facts, we now print all of them in the error message. Before we were printing just the one with the least priority. Consolidate a few common patterns in concretize.lp to ensure that certain node attributes have one and only one value assigned. All errors are displayed, so use a single criterion instead of three. * Account for weights in concretize.lp To recover the optimization order we had before, account for weights of errors when minimizing. The priority is mapped to powers of 10, so to effectively get back the same results as with priorities.
2023-04-03openPMD-api: 0.15.1 (#36604)Axel Huebl1-1/+2
Latest patch release, fixing build issues.
2023-04-03namd: add oneapi support (#36139)Robert Cohn1-2/+11
2023-04-03External Detection for llvm-amdgpu (#36595)Matin Raayai1-0/+15
* Added external detection of llvm-amdgpu. * Style cleaning for llvm-amdgpu.
2023-04-03zstd: fix makefile build, default to makefile (#36606)Harmen Stoppels1-3/+3
2023-04-03openblas: use "all" target since it's marked sequential (#35905)Harmen Stoppels2-25/+1
openblas likes to concurrently writes to the same archive from different targets, and solves that through .NOTPARALLEL: all We run `make x y z` which is not affected by `NOTPARALLEL`, running into races.
2023-04-03modules: correctly detect explicit installation (#36533)Xavier Delaruelle16-47/+78
When generating modulefile, correctly detect software installation asked by user as explicit installation. Explicit installation status were previously fetched from database record of spec, which was only set after modulefile generation. Code is updated to pass down the explicit status of software installation to the object that generates modulefiles. Fixes #34730. Fixes #12105. A value for the explicit argument has to be set when creating a new installation, but for operations on existing installation, this value is retrieved from database. Such operations are: module rm, module refresh, module setdefaults or when get_module function is used. Update on the way tests that mimics an installation, thus explicit argument has to be set under such situation.
2023-04-03binutils 2.40: add missing zstd dep (#36598)Harmen Stoppels1-0/+5
2023-04-02sublime-text: Fix the dependencies of the recent update (#36562)Laura Weber1-7/+9
2023-04-02petsc: simplify dependencies with hypre (#36573)Tristan Carel1-18/+10
* petsc: simplify dependencies with hypre * add propagation of `complex` variant to hypre
2023-04-02papyrus: disable tests (#36599)Harmen Stoppels1-2/+2
2023-04-01New package: py-mike and dependency. (#36587)Leonard-Anderson-NNL2-0/+43
Co-authored-by: Cloud User <leonardanderson@leonardander004.hzterscemazurawp3xenxzahla.bx.internal.cloudapp.net>
2023-04-01root: vc variant: root accepts only vc version 1.3.0 (#36594)Juan Miguel Carceller1-1/+1
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-04-01yafyaml: Add fismahigh variant to comply with FISMA standards (#36471)Alex Richert1-0/+8
2023-04-01petsc,py-petsc4py,slepc,py-slepc4py: add version 3.19.0 (#36588)Satish Balay6-30/+12
2023-04-01CMake: add version 3.26.2 (#36567)John W. Parent1-0/+1
2023-04-01libxpm: Fix linking with libintl (#36568)Bernhard Kaindl1-2/+2
Original Author of this change: Chris Green <greenc@fnal.gov> Two changes: - Remove adding the library path using -L: It is obsolete now that we have the library paths in before the system paths. - Link with -linto only if the gettext recipe provides it: When we are on a glibc system, we can use external gettext, which means we use the libintl inside libc.so: no -lintl then. This change was already submitted in #35450 and reviewed but is stuck in this big PR which is trying to do too in a single PR.
2023-03-31Perl package: change attr to method (#36580)John W. Parent1-2/+1
This fixes a bug in the Windows build of Perl. An attribute defined in package class is inaccessible from the install method due to builder: refactor it to be a method.
2023-03-31netcdf-c package: fix patch applied on Windows (#36581)John W. Parent1-1/+1
2023-03-31MDAnalysis 2.4.3 (#36541)Rocco Meli3-23/+62
* mda 2.4.3 * black * mda update and reshuffle * add tidynamics
2023-03-31Allow configurable stage names (#36509)John W. Parent5-6/+21
Add `config:stage_name` which is a Spec format string that can customize the names of stages created by Spack. This was primarily created to allow generating shorter stage names on Windows (along with `config:build_stage`, this can be used to create stages with short absolute paths). By default, this is not set and the prior name stage format is used. This also removes the username component that is always added to Stage paths on Windows (if users want to include this, they can add it to the `build_stage`).
2023-03-31py-aioitertools: add v0.11.0 (#36540)Alec Scott1-1/+3
* py-aioitertools: add v0.11.0 * Update var/spack/repos/builtin/packages/py-aioitertools/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update package.py --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-03-31compiler wrapper: fix -Xlinker parsing (#35929)Harmen Stoppels2-35/+123
* compiler wrapper: fix -Xlinker parsing * handle the case of -rpath without value; avoid that we drop the flag * also handle the -Xlinker -rpath -Xlinker without further args case... * fix test * get rid of global $rp var, reduce branching
2023-03-31petsc: builds break with gnu-make-4.4.1 (#35906)Satish Balay1-1/+5
Use 'make' detected by spack within petsc build
2023-03-31Ascent: Drop VTK-h dependency for 0.9 (#36458)kwryankrattiger1-4/+5
* Ascent: Drop VTK-h dependency for 0.9 * Ascent: Remove duplicate OpenMP constraints * Ascent: 0.9.0 cannot build with vtk-m@2 * Ascent: Only needs vtkm when using vtkh * Ascent: Require fides when building with ADIOS2
2023-03-31rocsparse: exclude v5.4 from being patched (#36571)renjithravindrankannath1-2/+2
2023-03-31hiop: add v0.7.2 (#36570)Cameron Rutherford1-0/+1
2023-03-31steps: add variants gmsh and kokkos (#36543)Tristan Carel1-4/+19
2023-03-31OpenMC: add v0.13.3 (#36564)Paul Romano2-2/+5
* OpenMC: add v0.13.3 * Add missing version in list for py-openmc
2023-03-31hdf5: add a map variant (#35523)H. Joe Lee1-0/+2
* hdf5: add map variant * hdf5: add mininum version for map variant * hdf5: fix black error
2023-03-31New: py-dalib, py-qdldl, py-qpsolvers; Update: py-ecos, py-scs, py-osqp (#36549)Benjamin Meyers6-1/+93
* New: py-dalib, py-qdldl, py-qpsolvers; Update: py-ecos, py-scs, py-osqp * [@spackbot] updating style on behalf of meyersbs * Update py-qpsolvers homepage * Add when clause to py-future
2023-03-31New package py-json2html (#36111)Benjamin Meyers1-0/+20
* New package py-json2html * Remove deprecated python deps
2023-03-31Add latet CMake release (#36119)John W. Parent1-0/+1
2023-03-31octopus: Add sparskit variant (#36494)Ashwin Kumar Karnad1-2/+10
Co-authored-by: Hans Fangohr <fangohr@users.noreply.github.com> Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
2023-03-31goma: add additional versions up to 7.4.3 (#36561)Weston Ortiz1-0/+4
2023-03-31Deprecate old tasmanian (#36534)Miroslav Stoyanov1-6/+23
* deprecated old versions and deps * syntax fix --------- Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-03-31typehint a few globals (#36544)Harmen Stoppels6-8/+20