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* Merge pull request #87866 from danieldk/validate-pkgconfig-hookBenjamin Hipple2020-06-02
|\ | | | | validatePkgConfig: init
| * mkl: use validatePkgConfig hookDaniël de Kok2020-05-31
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* | Merge pull request #82180 from bcdarwin/bppcoreBenjamin Hipple2020-05-26
|\ \ | |/ |/| bppsuite: init at 2.4.1
| * bpp-popgen: init at 2.4.1Ben Darwin2020-05-25
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| * bpp-phyl: init at 2.4.1Ben Darwin2020-05-25
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| * bpp-seq: init at 2.4.1Ben Darwin2020-05-25
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| * bpp-core: init at 2.4.1Ben Darwin2020-05-25
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* | mkl: fix expectation of MKLROOT being set in pkg-config filesDaniël de Kok2020-05-14
|/ | | | | | | | | The Intel MKL pkg-config files did not work, because they expect that the MKLROOT environment variable is set. This change replaces occurences by the actual path of MKL in the Nix store. Since the pkg-config files seem to break quite frequently after upgrades, add a post-install check to validate the pkg-config files.
* Merge pull request #87518 from r-ryantm/auto-update/sympowTimo Kaufmann2020-05-11
|\ | | | | sympow: 2.023.5 -> 2.023.6
| * sympow: 2.023.5 -> 2.023.6R. RyanTM2020-05-10
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* | Merge master into staging-nextFrederik Rietdijk2020-05-10
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| * Merge pull request #86142 from bcdarwin/itk-5.1.0Dmitry Kalinkin2020-05-09
| |\ | | | | | | Itk: 5.0.1 -> 5.1.0
| | * elastix: update for ITK 5.1.0Ben Darwin2020-05-05
| | | | | | | | | | | | | | | - fetch patches to build elastix 5.0 with ITK 5.1 - update 'platforms': builds on Darwin, fails on aarch64
* | | Merge master into staging-nextFrederik Rietdijk2020-05-09
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| * | petsc: 3.13.0 -> 3.13.1R. RyanTM2020-05-08
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* | | mkl: include symlinks to versioned libblas.so.3 namesBenjamin Hipple2020-05-08
| | | | | | | | | | | | Some build systems look for this specifically.
* | | openblas: also export unversioned libraries for linuxJonathan Ringer2020-05-08
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* | Merge pull request #86755 from andersk/abseil-ortoolsMario Rodas2020-05-07
|\ \ | | | | | | abseil-cpp: 20191119 -> 20200225.2; or-tools: 7.5 -> 7.6
| * | or-tools: 7.5 -> 7.6R. RyanTM2020-05-04
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* | Merge staging into staging-nextFrederik Rietdijk2020-05-01
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| * openblas: 0.3.8 -> 0.3.9Markus Kowalewski2020-05-01
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* | suitesparse-graphblas: 3.2.1 -> 3.2.2R. RyanTM2020-05-01
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* Merge pull request #85799 from matthewbauer/blas-lapack-expand-docsBenjamin Hipple2020-04-22
|\ | | | | BLAS/LAPACK fixup and expand docs
| * blas,lapack: use correct name for libraryMatthew Bauer2020-04-22
| | | | | | | | To match the soname, we need to use libblas.so.3, liblapack.so.3.
* | Merge pull request #85636 from matthewbauer/blas-lapack-fix-fallout-from-83888Frederik Rietdijk2020-04-21
|\| | | | | BLAS/LAPACK fix fallout from #83888
| * magma: remove mklSupport flagMatthew Bauer2020-04-20
| | | | | | | | This now relies on the "blas" and "lapack" packages.
| * blas,lapack: use isILP64 instead of is64bitMatthew Bauer2020-04-20
| | | | | | | | | | | | | | | | This is a better name since we have multiple 64-bit things that could be referred to. LP64 : integer=32, long=64, pointer=64 ILP64 : integer=64, long=64, pointer=64
* | elastix: enable testsBen Darwin2020-04-21
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* | elastix: python -> python3Ben Darwin2020-04-21
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* scs: breaks on 64bit blasMatthew Bauer2020-04-17
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* treewide: use blas and lapackMatthew Bauer2020-04-17
| | | | | | | | | | | | This makes packages use lapack and blas, which can wrap different BLAS/LAPACK implementations. treewide: cleanup from blas/lapack changes A few issues in the original treewide: - can’t assume blas64 is a bool - unused commented code
* blas/lapack: add wrapper for “alternative”s of BLAS/LAPACK providerMatthew Bauer2020-04-17
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This is based on previous work for switching between BLAS and LAPACK implementation in Debian[1] and Gentoo[2]. The goal is to have one way to depend on the BLAS/LAPACK libraries that all packages must use. The attrs “blas” and “lapack” are used to represent a wrapped BLAS/LAPACK provider. Derivations that don’t care how BLAS and LAPACK are implemented can just use blas and lapack directly. If you do care what you get (perhaps for some CPP), you should verify that blas and lapack match what you expect with an assertion. The “blas” package collides with the old “blas” reference implementation. This has been renamed to “blas-reference”. In addition, “lapack-reference” is also included, corresponding to “liblapack” from Netlib.org. Currently, there are 3 providers of the BLAS and LAPACK interfaces: - lapack-reference: the BLAS/LAPACK implementation maintained by netlib.org - OpenBLAS: an optimized version of BLAS and LAPACK - MKL: Intel’s unfree but highly optimized BLAS/LAPACK implementation By default, the above implementations all use the “LP64” BLAS and LAPACK ABI. This corresponds to “openblasCompat” and is the safest way to use BLAS/LAPACK. You may received some benefits from “ILP64” or 8-byte integer BLAS at the expense of breaking compatibility with some packages. This can be switched at build time with an override like: import <nixpkgs> { config.allowUnfree = true; overlays = [(self: super: { lapack = super.lapack.override { lapackProvider = super.lapack-reference; }; blas = super.blas.override { blasProvider = super.lapack-reference; }; })]; } or, switched at runtime via LD_LIBRARY_PATH like: $ LD_LIBRARY_PATH=$(nix-build -E '(with import <nixpkgs> {}).lapack.override { lapackProvider = pkgs.mkl; is64bit = true; })')/lib:$(nix-build -E '(with import <nixpkgs> {}).blas.override { blasProvider = pkgs.mkl; is64bit = true; })')/lib ./your-blas-linked-binary By default, we use OpenBLAS LP64 also known in Nixpkgs as openblasCompat. [1]: https://wiki.debian.org/DebianScience/LinearAlgebraLibraries [2]: https://wiki.gentoo.org/wiki/Blas-lapack-switch
* lapack: enable shared libraries, cblas, and testsMatthew Bauer2020-04-17
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* suitesparse: 5.7.1 -> 5.7.2R. RyanTM2020-04-10
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* Merge pull request #84451 from robertodr/update-mklBenjamin Hipple2020-04-10
|\ | | | | mkl: 2020.0.166 -> 2020.1.217 (Linux only)
| * mkl: 2020.0.166 -> 2020.1.217Roberto Di Remigio2020-04-06
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* | treewide: Per RFC45, remove all unquoted URLsMichael Reilly2020-04-10
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* | Merge pull request #84455 from r-ryantm/auto-update/petscMario Rodas2020-04-08
|\ \ | | | | | | petsc: 3.12.4 -> 3.13.0
| * | petsc: fix build on darwinMario Rodas2020-04-06
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| * | petsc: 3.12.4 -> 3.13.0R. RyanTM2020-04-06
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* / openblas: Add `singleThreaded` option. Off by default.Niklas Hambüchen2020-04-08
|/ | | | See https://github.com/xianyi/OpenBLAS/issues/2543
* mkl: 2019.5.281 -> 2020.0.166 (Linux only)Roberto Di Remigio2020-03-27
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* Merge pull request #82274 from jtojnar/suitesparese-5.6Jan Tojnar2020-03-22
|\ | | | | suitesparse: 5.4.0 → 5.7.1 + clean up
| * suitesparse: ultimate clean-upJan Tojnar2020-03-11
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Switch to default buildPhase & installPhase * In preConfigure * Do not add -DNPARTITION to CHOLMOD_CONFIG. That would disable the use of Metis but we already have that. * Do not remove -lrt on Darwin, Darwin compiler can handle that and the code no longer exists anyway. * With CUDA enabled * Do not replace CUDA_ROOT. It does not exist any more. Instead we are setting CUDA_PATH in makeFlags. * Do not replace GPU_BLAS_PATH, it defaults to CUDA_PATH so it will end up with the same value. * Do not add -DCHOLMOD_OMP_NUM_THREADS to GPU_CONFIG. Why would be having the library use the same number of threads as the builder a good idea? * Do not replace CUDA_PATH, we are setting it in makeFlags now. * Do not replace CUDART_LIB and CUBLAS_LIB. They were being replaced incorrectly (cuda libs are located in lib directory, not lib64). Instead set the correct paths in makeFlags. * Do not replace CUDA_INC_PATH. Its default looks like it will end up with the same value. * Do not replace NV20, NV30, NV35 – not used any more. * Do not replace NVCC, defaults to the same. * Do not replace NVCCFLAGS, we just used the default from SourceSparse 4.4.7 with -gencode=arch=compute_60,code=compute_60 tacked on top. Current upstream default looks much better. * Stop adding -DNTIMER to CFLAGS on Darwin – clock_gettime is supported by macOS 10.12 SDK. * In buildPhase * Move the make arguments to makeFlags and library to buildFlags, allowing us to drop the manual make call. I did not verify all of these are still needed. * Remove the creation of libsuitesparse.so. As far as I could tell it is some kind of remnant of our old expression – perhaps due to past deficiencies of the build scripts, we created the individual libraries as symlinks to libsuitesparse.so: https://github.com/NixOS/nixpkgs/commit/e36b3ec0a56c3b06152a205a46804733b88695d6 But since the build script can now build individual .so libraries, there should be no need for this abomination. No other distros do this either. * In installPhase * No need to copy things manually, there is an install target. We just need to pass INSTALL=$out flag to make to let it know where to install the files. * I do not have means of verifying the darwin dylib name fix but it looks like it might be fixed in an upcoming release. * I dropped the rpath fixup as it does not seem to be needed any more (ldd does not report any unresolved libraries).
| * suitesparse: do not build Mongoose & GraphBLASJan Tojnar2020-03-11
| | | | | | | | We already have package for them
| * suitesparse: link against system metisJan Tojnar2020-03-10
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| * suitesparse: 5.4.0 → 5.7.1Jan Tojnar2020-03-10
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| * suitesparse-graphblas: init at 3.1.2Jan Tojnar2020-03-10
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| * mongoose: init at 2.0.4Jan Tojnar2020-03-10
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| * suitesparse: clean upJan Tojnar2020-03-10
| | | | | | | | | | | | | | * Split to multiple outputs * Fetch source from GitLab (the only source for future releases) * Re-order attrset to be more idiomatic * Format with nixpkgs-fmt
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