Commit graph

796 commits

Author SHA1 Message Date
Ben Darwin 44d854af30 bicgl: update LIBMINC_DIR due to libminc CMake changes 2020-10-06 15:31:19 -04:00
Ben Darwin 85946918ac oobicpl: update LIBMINC_DIR due to libminc CMake changes 2020-10-06 15:31:17 -04:00
Ben Darwin 2c33e9d1a4 bicpl: fix LIBMINC_DIR due to libminc CMake changes 2020-10-06 15:31:15 -04:00
Ben Darwin da69e470f2 EBTKS: update LIBMINC_DIR due to libminc update 2020-10-06 15:31:15 -04:00
Frederik Rietdijk 692d219a93 Merge staging-next into staging 2020-10-06 10:25:58 +02:00
Jonathan Ringer 7902256cfd openblas: enable multiple outputs 2020-10-05 16:15:14 -07:00
Doron Behar 6bbfd17e34 suitesparse: assert that compatible lapack and blas are used 2020-10-01 21:53:44 +03:00
Doron Behar b34ca89335 suitesparse: 5.7.2 -> 5.8.1
Update dependencies. Remove not needed `BLAS` and `LAPACK` makeFlags for
non darwin systems.
2020-10-01 21:53:21 +03:00
Timo Kaufmann 27f084d817
Merge pull request #98779 from r-ryantm/auto-update/libbraiding
libbraiding: 1.0 -> 1.1
2020-09-28 11:11:06 +02:00
R. RyanTM f175cb4478 libbraiding: 1.0 -> 1.1 2020-09-25 18:52:32 +00:00
R. RyanTM ced2c4a0ec cliquer: 1.21 -> 1.22 2020-09-25 02:29:32 +00:00
Ben Darwin 8a3c9812cc gifticlib: init at unstable-2020-07-07 2020-09-23 12:07:37 -04:00
Matthew Bauer c85fc341b0 pytorch: update to use passthru's for checks
This makes the checks a little easier to understand - we can just
check it in the passthru. Also increase major check for cuda 11.
2020-09-10 14:23:15 -05:00
Ben Darwin 98512f3eaa nifticlib: 2.0.0 -> 3.0.1 2020-09-09 15:26:04 -04:00
Daniël de Kok 466522c919
Merge pull request #97137 from danieldk/blis-0.7.0
blis: init at 0.7.0
2020-09-08 14:55:39 +02:00
Benjamin Hipple 3c4335723c
Merge pull request #97019 from danieldk/mkl-2020.2
mkl: 2020.2.254 -> 2020.3.279
2020-09-07 13:28:27 -04:00
Jan Tojnar 87ec0fb5f3
Merge pull request #96982 from graham33/fix/96981_suitesparse_dylib_names
suitesparse: rename fixDarwinDylibNames override
2020-09-07 16:51:07 +02:00
Graham Bennett e10228defa suitesparse: remove custom fixDarwinDylibNames postInstall
This shadows the regular fixDarwinDylibNames function, which is a
nativeBuildInput, and prevents it from converting some relative paths to
absolute.  According to the comment this can be removed as of 5.7.2.
2020-09-06 19:57:21 +01:00
Daniël de Kok 383075f38b openblas: re-enable AVX512 support
AVX512 support was disabled due to an issue in the AVX512 DGEMM
kernel:

https://github.com/NixOS/nixpkgs/issues/59708

However, this kernel has been replaced upstream a while ago:

https://github.com/xianyi/OpenBLAS/releases/tag/v0.3.8

And they have enabled AVX512 kernels since then.
2020-09-06 20:46:35 +02:00
R. RyanTM bd9c787dfd openlibm: 0.7.0 -> 0.7.1 2020-09-05 09:19:39 +00:00
Daniël de Kok 863724b3f3 blis: init at 0.7.0 2020-09-04 18:44:01 +02:00
Daniël de Kok 405f49dc4a mkl: 2020.2.254 -> 2020.3.279
Release notes:

https://software.intel.com/content/www/us/en/develop/articles/intel-math-kernel-library-release-notes-and-new-features.html
2020-09-03 15:29:10 +02:00
Matthew Bauer 8e6f466967
Merge pull request #96563 from obsidiansystems/skip-cudnn_cnn_infer-instead-of-removing
cudnn: skip libcudnn_cnn_infer.so, instead of removing
2020-09-02 16:29:28 -05:00
R. RyanTM 5f28c07087 suitesparse-graphblas: 3.3.0 -> 3.3.3 2020-09-01 23:31:10 +02:00
Daniël de Kok 35e19d22c1 libtorch-bin: init at 1.6.0 2020-08-30 13:22:09 +02:00
Matthew Bauer ed950bb104 cudnn: skip libcudnn_cnn_infer.so, instead of removing
This is needed to build the CUDNN samples, so we should make sure it
winds up in $out/lib. The library is too big to support patchelf, so
we need to skip it. Most programs will still get the opengl path
because it also links to other libraries.
2020-08-28 15:16:15 -05:00
R. RyanTM 5af070fb0c petsc: 3.13.3 -> 3.13.4 2020-08-27 04:53:49 +00:00
Benjamin Hipple d41c129198
Merge pull request #95727 from obsidiansystems/cuda11
cudatoolkit: init v11.0.3
2020-08-26 15:09:08 -04:00
Frederik Rietdijk 0a874ff2a6 Merge master into staging-next 2020-08-24 11:50:58 +02:00
Daniël de Kok bebe5c963f
Merge pull request #95739 from danieldk/magma-2.5.3
magma: 2.5.0 -> 2.5.3
2020-08-23 10:58:21 +02:00
Jan Tojnar 91104b5417
Merge branch 'master' into staging-next 2020-08-23 02:00:50 +02:00
Silvan Mosberger 23962528ce
Merge pull request #93703 from taktoa/master
osqp: init at 0.6.0
2020-08-20 02:03:08 +02:00
Matthew Bauer abba9a2154 nccl: 2.4.8-1 -> 2.7.8-1 2020-08-19 13:34:56 -05:00
Matthew Bauer 164f8024e9 cudatoolkit: init v11.0.3 2020-08-19 13:34:52 -05:00
Daniël de Kok 147e24dcd6 magma: 2.5.0 -> 2.5.3
Other changes:

- Move gfortran and cmake to nativeBuildInputs.
- Magma now (only) generates dynamic libraries by default.
- Use ninja for faster builds.
2020-08-18 11:18:08 +02:00
Frederik Rietdijk d59c57f8a6
Merge pull request #92412 from matthewbauer/blas-cross
Blas/Lapack cross fixes
2020-08-15 08:55:57 +02:00
Daniël de Kok a49a59bc6c amd-libflame: init at 2.2
libflame is a protable library for dense matrix computations,
providing a complete LAPACK implementation. The AMD fork of libflame
is optimized for AMD CPUs.
2020-08-09 08:29:08 +02:00
Remy Goldschmidt c473490524
osqp: init at 0.6.0 2020-08-08 13:32:51 -07:00
Daniël de Kok 57d4c67fb8
Merge pull request #93052 from danieldk/amd-blis-zen-only
amd-blis: init at 2.2
2020-08-08 20:01:24 +02:00
R. RyanTM ca9c2e3548 petsc: 3.13.2 -> 3.13.3 2020-08-07 12:44:29 +10:00
Daniël de Kok 1474bfe27d
Merge pull request #93653 from danieldk/mkl-2020.2.254
mkl: 2020.1.217 -> 2020.2.254
2020-08-05 08:08:08 +02:00
Pavol Rusnak 7839270bb0
or-tools: 7.6 -> 7.7 2020-07-26 15:34:17 +02:00
Daniël de Kok 6a236f5410 mkl: 2020.1.217 -> 2020.2.254 2020-07-22 17:38:07 +02:00
markuskowa 533720caa9
Merge pull request #93031 from andrew-d/andrew/dsd
dsd: init at 2018-07-01
2020-07-18 23:18:23 +02:00
Jack Coughlin 8a65fe8da6 petsc: Fix install_name_tool patch
The PETSc library's config/install.py script checks whether
/usr/bin/install_name_tool is an existing file:

https://gitlab.com/petsc/petsc/-/blob/master/config/install.py#L368

Therefore, it is not enough to replace it with something that we expect
to be on the PATH, as this will cause the linked if statement to be
silently skipped. The consequence is that applications linked against
this version of petsc will fail at runtime on MacOS with a dynamic
loading error.

Instead, we should replace install_name_tool with the absolute path of a
binary we know will be present at build time.

Note that this should be fixed upstream as well, but this is sufficient
to fix the runtime error.
2020-07-18 08:47:24 -07:00
Andrew Dunham f856cb8a9e it++: init at 4.3.1 2020-07-16 17:59:24 -07:00
Daniël de Kok 4fbe92df09 amd-blis: init at 2.2
We compile specifically for Zen:

- Zen/Zen2 are not included in the x86_64 or amd64 configurations.
- Including them breaks AMD BLIS in other places, since some functions
  have Zen-specific definitions that fail on other platforms.

Non-Zen CI runners will succeed when they are Haswell or later, since
a Haswell kernel is compiled as a dependency.
2020-07-13 13:16:37 +02:00
Benjamin Hipple 2ec5479689
Merge pull request #89299 from wucke13/petsc
petsc: add fotran build argument
2020-07-07 13:50:29 -04:00
wucke13 dc5113fb06 petsc: 3.13.1 -> 3.13.2
+ add fortran build argument
2020-07-07 09:34:43 +02:00
Matthew Bauer 8a525d6a2b arpack: add blas, lapack to library path
Fixes #89215
2020-07-06 01:30:10 -04:00
R. RyanTM 669b2ab244 suitesparse-graphblas: 3.2.2 -> 3.3.0 2020-06-30 16:21:46 +00:00
R. RyanTM f79c05b113 openblas: 0.3.9 -> 0.3.10 2020-06-19 10:59:46 +02:00
Ryan Burns 92d7b38e89 openblas: enable on ppc64le 2020-10-02 18:10:44 -07:00
Doron Behar 60b4b396e5
Merge pull request #98501 from doronbehar/pkg/octave/arpack 2020-10-01 19:04:43 +03:00
Doron Behar bd77df6d6f arpack: assert that blas and lapack are compatible
Do it before buildInputs per:
https://github.com/NixOS/nixpkgs/pull/94892#discussion_r471110250

Remove unneed, BLAS_LIBS and LAPACK_LIBS from environment - the
libraries are detected just fine when in buildInputs.
2020-09-23 00:57:31 +03:00
Doron Behar e0d947c79c arpack: cosmetic changes
Don't use `with stdenv.lib` at the top of the expression, per:
https://nix.dev/anti-patterns/language.html#with-attrset-expression

Use rec and version inside `mkDerivation`, like almost any other
derivation.
2020-09-23 00:52:45 +03:00
Benjamin Hipple 4af635feff
Merge pull request #87866 from danieldk/validate-pkgconfig-hook
validatePkgConfig: init
2020-06-02 23:27:27 -04:00
Daniël de Kok 127cdd0cab mkl: use validatePkgConfig hook 2020-05-31 20:45:07 +02:00
Benjamin Hipple f04a5af0cc
Merge pull request #82180 from bcdarwin/bppcore
bppsuite: init at 2.4.1
2020-05-26 21:07:25 -04:00
Ben Darwin 7f656f3ef6 bpp-popgen: init at 2.4.1 2020-05-25 21:12:17 -04:00
Ben Darwin a53b27829c bpp-phyl: init at 2.4.1 2020-05-25 21:10:59 -04:00
Ben Darwin 8d712ccc16 bpp-seq: init at 2.4.1 2020-05-25 21:09:52 -04:00
Ben Darwin adc7b4c979 bpp-core: init at 2.4.1 2020-05-25 21:08:31 -04:00
Daniël de Kok e88673aa27 mkl: fix expectation of MKLROOT being set in pkg-config files
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.
2020-05-14 19:40:18 +02:00
Timo Kaufmann 346de1fb8c
Merge pull request #87518 from r-ryantm/auto-update/sympow
sympow: 2.023.5 -> 2.023.6
2020-05-11 21:35:40 +00:00
R. RyanTM f66d997a29 sympow: 2.023.5 -> 2.023.6 2020-05-10 16:42:21 +00:00
Frederik Rietdijk 303adc7697 Merge master into staging-next 2020-05-10 09:43:48 +02:00
Dmitry Kalinkin e80302dc7d
Merge pull request #86142 from bcdarwin/itk-5.1.0
Itk: 5.0.1 -> 5.1.0
2020-05-09 15:03:28 -04:00
Frederik Rietdijk d7cca0f356 Merge master into staging-next 2020-05-09 11:12:29 +02:00
R. RyanTM c0e63bc87e petsc: 3.13.0 -> 3.13.1 2020-05-08 15:57:25 +00:00
Benjamin Hipple 706642091e mkl: include symlinks to versioned libblas.so.3 names
Some build systems look for this specifically.
2020-05-08 06:52:02 +02:00
Jonathan Ringer c1e605dd6b openblas: also export unversioned libraries for linux 2020-05-08 06:52:02 +02:00
Mario Rodas a340a9f4d8
Merge pull request #86755 from andersk/abseil-ortools
abseil-cpp: 20191119 -> 20200225.2; or-tools: 7.5 -> 7.6
2020-05-07 06:53:54 -05:00
Ben Darwin 5caa76705b elastix: update for ITK 5.1.0
- fetch patches to build elastix 5.0 with ITK 5.1
- update 'platforms': builds on Darwin, fails on aarch64
2020-05-05 00:08:04 -04:00
R. RyanTM 7a17b13b48 or-tools: 7.5 -> 7.6 2020-05-04 03:12:00 -07:00
Frederik Rietdijk 00bbfccecf Merge staging into staging-next 2020-05-01 09:28:45 +02:00
R. RyanTM 51b1533b37 suitesparse-graphblas: 3.2.1 -> 3.2.2 2020-05-01 09:06:34 +02:00
Markus Kowalewski 15cd0bd993 openblas: 0.3.8 -> 0.3.9 2020-05-01 09:02:51 +02:00
Benjamin Hipple 21be830522
Merge pull request #85799 from matthewbauer/blas-lapack-expand-docs
BLAS/LAPACK fixup and expand docs
2020-04-22 21:56:20 -04:00
Matthew Bauer 5a500ff0ba blas,lapack: use correct name for library
To match the soname, we need to use libblas.so.3, liblapack.so.3.
2020-04-22 12:37:04 -05:00
Frederik Rietdijk ec21df329a
Merge pull request #85636 from matthewbauer/blas-lapack-fix-fallout-from-83888
BLAS/LAPACK fix fallout from #83888
2020-04-21 19:59:16 +02:00
Ben Darwin fe07e2b2ac elastix: enable tests 2020-04-21 07:54:59 +02:00
Ben Darwin 30cafee8b6 elastix: python -> python3 2020-04-21 07:54:59 +02:00
Matthew Bauer a6a502fca0 magma: remove mklSupport flag
This now relies on the "blas" and "lapack" packages.
2020-04-20 16:02:57 -05:00
Matthew Bauer ff2f2644f8 blas,lapack: use isILP64 instead of is64bit
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
2020-04-20 16:02:43 -05:00
Matthew Bauer fcf33e2499 scs: breaks on 64bit blas 2020-04-17 16:24:31 -05:00
Matthew Bauer 1c8aba8334 treewide: use blas and lapack
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
2020-04-17 16:24:09 -05:00
Matthew Bauer 43873351ff blas/lapack: add wrapper for “alternative”s of BLAS/LAPACK provider
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
2020-04-17 16:23:55 -05:00
Matthew Bauer 90326ba624 lapack: enable shared libraries, cblas, and tests 2020-04-17 16:17:12 -05:00
R. RyanTM 1450740470 suitesparse: 5.7.1 -> 5.7.2 2020-04-10 11:55:20 -07:00
Benjamin Hipple a1f6400fd5
Merge pull request #84451 from robertodr/update-mkl
mkl: 2020.0.166 -> 2020.1.217 (Linux only)
2020-04-10 13:54:49 -04:00
Michael Reilly 84cf00f980
treewide: Per RFC45, remove all unquoted URLs 2020-04-10 17:54:53 +01:00
Mario Rodas 2f41064d86
Merge pull request #84455 from r-ryantm/auto-update/petsc
petsc: 3.12.4 -> 3.13.0
2020-04-08 21:35:27 -05:00
Niklas Hambüchen df907c4786 openblas: Add singleThreaded option. Off by default.
See https://github.com/xianyi/OpenBLAS/issues/2543
2020-04-08 13:46:04 +02:00
Mario Rodas ad15e4e8a0
petsc: fix build on darwin 2020-04-06 12:00:00 +00:00
R. RyanTM 758e81662f petsc: 3.12.4 -> 3.13.0 2020-04-06 11:46:40 +00:00
Roberto Di Remigio 488527eaa6
mkl: 2020.0.166 -> 2020.1.217 2020-04-06 11:57:22 +02:00
Roberto Di Remigio 335e097352
mkl: 2019.5.281 -> 2020.0.166 (Linux only) 2020-03-27 08:45:20 +01:00
Jan Tojnar d951c534da
Merge pull request #82274 from jtojnar/suitesparese-5.6
suitesparse: 5.4.0 → 5.7.1 + clean up
2020-03-22 06:58:25 +01:00
Josef Kemetmüller fbb273c5fe fenics: 2017.1.0 -> 2019.1.0
Fixes: NixOS/nixpkgs#75886
2020-03-19 21:48:27 -07:00
Timo Kaufmann d8d0b60c22
Merge pull request #82766 from r-ryantm/auto-update/brial
brial: 1.2.7 -> 1.2.8
2020-03-17 14:29:02 +00:00
R. RyanTM 707e0b1e96 brial: 1.2.7 -> 1.2.8 2020-03-17 01:13:50 +00:00
Tom Hall c6c753668d openblas: disable optimisation pending fix
See https://github.com/xianyi/OpenBLAS/issues/2496
2020-03-14 18:06:59 +00:00
wucke13 4f58c15ee6 petsc: 3.8.4 -> 3.12.4
+ add cxx flag to configure, because getdp needs it
2020-03-13 04:10:20 +00:00
Jan Tojnar b552b84ae2
suitesparse: ultimate clean-up
* 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: e36b3ec0a5 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).
2020-03-11 03:45:25 +01:00
Jan Tojnar c16d5b6534
suitesparse: do not build Mongoose & GraphBLAS
We already have package for them
2020-03-11 02:33:06 +01:00
Jan Tojnar 306cf6091f
suitesparse: link against system metis 2020-03-10 21:16:28 +01:00
Jan Tojnar e9d7774b7b
suitesparse: 5.4.0 → 5.7.1 2020-03-10 21:16:27 +01:00
Jan Tojnar 559f02e208
suitesparse-graphblas: init at 3.1.2 2020-03-10 21:16:27 +01:00
Jan Tojnar b4e6293a8d
mongoose: init at 2.0.4 2020-03-10 20:35:44 +01:00
Jan Tojnar 40ae28791f
suitesparse: clean up
* 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
2020-03-10 20:35:44 +01:00
Josef Kemetmüller 1cc9b2501d suitesparse: Enable parallel building 2020-03-10 17:16:17 +01:00
Mario Rodas 99722af1d5
Merge pull request #81843 from OmnipotentEntity/cudnn-7.6.5
cudnn_cudatoolkit_10_2: init at 7.6.5
2020-03-10 07:19:50 -05:00
R. RyanTM e04fab644f osi: 0.108.4 -> 0.108.6 2020-03-06 07:22:33 +01:00
Michael Reilly 972db874b3 cudnn_cudatoolkit_10_2: init at 7.6.5 2020-03-05 15:14:10 -05:00
Frederik Rietdijk 9d88ee08f6 Merge master into staging-next 2020-02-18 16:09:19 +01:00
Dylan Simon e25f0b3e3d scalapack: 2.1 -> 2.1.0
2.1 seems to have disappeared
2020-02-17 18:31:13 -05:00
Frederik Rietdijk ec1184f461 Merge master into staging-next 2020-02-17 15:12:28 +01:00
Drew Risinger c71f63a337 ecos: 2.0.6 -> 2.0.7
Bump ecos module.
2020-02-16 19:12:52 -08:00
R. RyanTM 6222192872 openblas: 0.3.7 -> 0.3.8 2020-02-11 12:01:57 +00:00
Anders Kaseorg 1a32e383e6 or-tools: 7.3 -> 7.5
Signed-off-by: Anders Kaseorg <andersk@mit.edu>
2020-02-10 20:40:12 +01:00
R. RyanTM 5659946d6a m4ri: 20200115 -> 20200125 2020-02-08 16:16:48 +00:00
Drew Risinger c13bf84d45 libraries.science.math.scs: 2.0.2 -> 2.1.1 2020-01-31 16:05:05 -05:00
Frederik Rietdijk dce0ca29d9 Merge master into staging-next 2020-01-28 10:46:13 +01:00
Timo Kaufmann e39e304638
Merge pull request #78496 from r-ryantm/auto-update/brial
brial: 1.2.6 -> 1.2.7
2020-01-26 23:28:02 +01:00
R. RyanTM 2d172e6403 brial: 1.2.6 -> 1.2.7 2020-01-26 02:39:07 +00:00
Timo Kaufmann d62e410ccd
Merge pull request #78222 from r-ryantm/auto-update/m4ri
m4ri: 20140914 -> 20200115
2020-01-22 17:43:44 +01:00
R. RyanTM 813678058f m4ri: 20140914 -> 20200115 2020-01-21 23:46:57 +00:00
R. RyanTM 3937313195 m4rie: 20150908 -> 20200115 2020-01-21 23:24:43 +00:00
Anders Kaseorg 3cd8ce3bce treewide: Fix unsafe concatenation of $LD_LIBRARY_PATH
Naive concatenation of $LD_LIBRARY_PATH can result in an empty
colon-delimited segment; this tells glibc to load libraries from the
current directory, which is definitely wrong, and may be a security
vulnerability if the current directory is untrusted.  (See #67234, for
example.)  Fix this throughout the tree.

Signed-off-by: Anders Kaseorg <andersk@mit.edu>
2020-01-15 09:47:03 +01:00
Niklas Hambüchen de1e61f34d
Merge pull request #77104 from r-ryantm/auto-update/htslib
htslib: 1.9 -> 1.10.2
2020-01-13 01:51:32 +01:00
Mario Rodas 5ab4676d88
Merge pull request #77194 from r-ryantm/auto-update/primesieve
primesieve: 7.4 -> 7.5
2020-01-09 05:02:21 -05:00
R. RyanTM e28fe589d9 primesieve: 7.4 -> 7.5 2020-01-07 00:22:48 -08:00
R. RyanTM 940d12bf5d htslib: 1.9 -> 1.10.2 2020-01-06 09:16:51 -08:00
Mario Rodas e11aab8340
Merge pull request #76356 from r-ryantm/auto-update/openlibm
openlibm: 0.6.0 -> 0.7.0
2020-01-06 09:58:54 -05:00
Frederik Rietdijk 17ab5f9d88 Merge master into staging-next 2020-01-06 10:38:20 +01:00
Ryan Mulligan f8cd096aad
Merge pull request #54967 from volhovm/volhovm/clmagma
clmagma: init at 1.3
2020-01-05 08:18:12 -08:00
Frederik Rietdijk 828f93a326 Merge master into staging-next 2020-01-05 16:00:21 +01:00
markuskowa 1c55261574
Merge pull request #75526 from robertodr/more-mkl
Add GNU threading and Fortran libraries to MKL package
2020-01-04 20:36:43 +01:00
Frederik Rietdijk 867552957f openblas: fix static musl build 2020-01-03 12:50:47 +01:00
Frederik Rietdijk 960c24a996
Merge pull request #75798 from tobim/pkgsStatic/arrow
arrow-cpp: add pkgsStatic support
2020-01-03 10:13:31 +01:00
Frederik Rietdijk f08e3e38d4 Merge master into staging-next 2020-01-02 21:41:13 +01:00
Tobias Mayer db5d3cdfe2 openblas: partially fix static build 2019-12-31 15:05:13 +01:00
Robin Gloster 313da176d3
treewide: NIX_*_FLAGS -> string 2019-12-31 00:16:46 +01:00
Robin Gloster 5f2b92e3ec
treewide: NIX_*_COMPILE -> string 2019-12-31 00:13:29 +01:00
Robin Gloster 2157dcd141
treewide: installFlags is a list 2019-12-30 13:22:43 +01:00
Merijn Broeren 133103d709
treewide: replace make/build/configure/patchFlags with nix lists 2019-12-30 12:58:11 +01:00
Linus Heckemann 2c19725202 mirtk: enable tbb support for multithreading 2019-12-30 01:16:08 +01:00
R. RyanTM a2a56df6f8 openlibm: 0.6.0 -> 0.7.0 2019-12-23 20:42:29 -08:00
Roberto Di Remigio 153597a320
mkl: filter static libs in installPhase 2019-12-19 10:23:26 +01:00
Roberto Di Remigio 6cc9bbe2fd
mkl: extract static libraries optionally 2019-12-19 10:12:00 +01:00
Roberto Di Remigio e0605b3174
mkl: add GNU threading and Fortran libraries
Signed-off-by: Roberto Di Remigio <roberto.diremigio@gmail.com>
2019-12-19 10:12:00 +01:00
Timo Kaufmann 135081a538 brial: 1.2.5 -> 1.2.6
Motivation is mostly https://github.com/BRiAl/BRiAl/pull/37, which is a
pre-requiste for getting the sage tests to pass with python3.
2019-12-13 20:31:31 +01:00
Mateusz Kowalczyk 1451a52a38 Remove myself (fuuzetsu) from maintainer lists
I haven't been doing any maintenance for a long time now and not only
do I get notified, it also creates a fake impression that all these
packages had at least one maintainer when in practice they had none.
2019-12-05 16:29:48 +09:00
Dmitry Kalinkin aa7efea848
Merge pull request #73958 from markuskowa/upd-lapack
liblapack: 3.8.0 -> 3.9.0
2019-11-24 20:06:04 -05:00
John Ericson d0d5136cce Merge remote-tracking branch 'upstream/master' into wrapper-pname-support 2019-11-24 17:25:07 +00:00
John Ericson 9b090ccbca treewide: Get rid of most parseDrvName without breaking compat
That is because this commit should be merged to both master and
release-19.09.
2019-11-24 17:22:28 +00:00
Markus Kowalewski 7e44c6dee6
liblapack: 3.8.0 -> 3.9.0 2019-11-24 11:47:50 +01:00
Markus Kowalewski 8419bb2a20
scalapack: 2.0.2 -> 2.1 2019-11-20 22:44:33 +01:00
Renaud 5411dbda33
Merge pull request #71710 from bcdarwin/fix-elastix
elastix: 4.9.0 -> 5.0.0 (and mark unbroken)
2019-11-18 23:23:16 +01:00
Ben Darwin b618730708 elastix: 4.9.0 -> 5.0.0 (and mark unbroken) 2019-11-18 13:29:02 -05:00
markuskowa 7d728faea5
Merge pull request #73227 from markuskowa/fix-mkl
mkl: add scalapack libraries to output
2019-11-18 10:46:33 +01:00
Markus Kowalewski d817a49faa
mkl: add scalapack libraries to output 2019-11-18 09:05:03 +01:00
Ben Darwin 736860d34b nifticlib and niftseg: change platform from linux to unix since these build on OSX 2019-11-14 21:25:10 -05:00
Andreas Rammhold 1e72fa5158
Merge pull request #68954 from dguibert/dg/cudatoolkit_10_1
cudatoolkit: add 10.1.243
2019-11-06 08:58:30 +01:00
Benjamin Hipple fa1e275f31 mkl: 2019.3 -> 2019.5 (#71476)
Includes bugfixes, new features, and performance improvements.

Full release notes here:
https://software.intel.com/en-us/articles/intel-math-kernel-library-release-notes-and-new-features

Leave Darwin on 2019.3 pending resolution of DMG issues
2019-10-27 15:34:16 -04:00
Sam Stites f12199614d magma: use cudatoolkit 2019-10-23 10:57:43 -07:00
markuskowa f6d7f8ae16
Merge pull request #68927 from danieldk/mkl
mkl: include pkgconfig files
2019-10-13 19:16:49 +02:00
Linus Heckemann 5aa4b19946 treewide: mark some broken packages as broken
Refs:
e6754980264fe927320d5ff2dbd24ca4fac9a160
1e9cc5b9844ef603fe160e9f671178f96200774f
793a2fe1e8bb886ca2096c5904e1193dc3268b6d
c19cf65261639f749012454932a532aa7c681e4b
f6544d618f30fae0bc4798c4387a8c7c9c047a7c
2019-10-08 17:14:26 +02:00
Orivej Desh 2455b2e309 or-tools: 7.0 -> 7.3 2019-10-04 05:17:48 +00:00
Nikolay Amiantov 1c429acbff tensorflow: add OpenGL path to find libcudart 2019-10-02 10:33:31 +03:00
Timo Kaufmann 7a7e9c1b27
Merge pull request #64193 from timokau/sage-8.9
sage: 8.8 -> 8.9
2019-09-30 11:13:46 +00:00
Joachim F ad773d31e2
Merge pull request #69345 from joachifm/feat/split-version
Replace uses of splitString for splitting version strings
2019-09-27 06:19:18 +00:00
Joachim Fasting bad07dfac5
tree-wide: replace uses of splitString "." with lib.versions
Quoting from the splitString docstring:

   NOTE: this function is not performant and should never be used.

This replaces trivial uses of splitString for splitting version
strings with the (potentially builtin) splitVersion.
2019-09-26 17:42:49 +02:00
Timo Kaufmann 1797c9c295 sage: 8.9.beta9 -> 8.9.rc0
Sage now by default expects the lcalc library to be named Lfunction
(instead of libLfunction). This could be changed by an environment
variable (https://trac.sagemath.org/ticket/28224), but various distros
seem to agree on this standard
(https://groups.google.com/forum/#!topic/sage-packaging/xvh55IxHTZg) so
it's best just to follow it. The old standard was set by sage anyway and
sage is the only consumer of lcalc in nixpkgs.
2019-09-24 17:51:09 +02:00
Matthieu Coudron d70eba7ab3 ns-3: 3.29 -> 3.30
Fixes python bindings.
2019-09-24 00:30:12 +09:00
Daniël de Kok 9f25e95576 mkl: include pkgconfig files 2019-09-22 20:07:34 +02:00
David Guibert 92690a8937 cuddn: add 10.1 (version 7.6.3) 2019-09-17 15:19:41 +02:00
Markus Kowalewski ecd20d2166
liblapack: remove optimized blas flag.
This cmake flag has no effect since no external blas
library is provided in the build inputs.
2019-09-15 11:39:58 +02:00
Markus Kowalewski fc7374176f
liblapack: build LAPACKE C api 2019-09-15 11:39:58 +02:00
Vladimír Čunát 991c0e1618
treewide: mark packages as buildable on darwin (PR #45364)
vcunat amended the commit a bit; see the PR for details/discussion.
2019-09-15 10:50:08 +02:00
Miguel Madrid Mencía 148c82e07e
maintainer: mimadrid: update github username and personal data 2019-09-14 12:15:46 +02:00
volth 7b8fb5c06c treewide: remove redundant quotes 2019-09-08 23:38:31 +00:00
Frederik Rietdijk 5f4734b1dd Merge remote-tracking branch 'upstream/gcc-8' into staging-next
Earlier the gcc8 branch was merged instead of the gcc-8 branch (note the dash)...
2019-09-08 20:44:26 +02:00
Frederik Rietdijk 66bc7fc1b3 Merge master into staging-next 2019-09-06 22:46:05 +02:00
tbenst 6d7282d74a magma: 2.0.2 -> 2.5.0 2019-09-06 20:15:10 +02:00
Vladimír Čunát 4aad2947f8
Merge branch 'master' into staging-next 2019-09-04 11:00:56 +02:00
Franz Pletz de85797565
Merge remote-tracking branch 'origin/master' into gcc-8 2019-09-03 22:15:07 +02:00
idontgetoutmuch 739cdb368e Ensure blas produces pkg config files (#67629)
blas: produce pkgconfig file
2019-09-03 16:34:45 +02:00
Mikhail Volkhov 58dffa3459
clmagma: init at 1.3 2019-08-30 22:40:04 +02:00
volth 08f68313a4 treewide: remove redundant rec 2019-08-28 11:07:32 +00:00
Frederik Rietdijk 5061fe0c2c Merge staging-next into staging 2019-08-28 08:26:42 +02:00
volth 35d68ef143 treewide: remove redundant quotes 2019-08-26 21:40:19 +00:00
Robin Gloster 616b8343c4
Merge remote-tracking branch 'upstream/master' into gcc-8 2019-08-25 18:55:46 +02:00
Vladimír Čunát 2e6bf42a22
Merge branch 'master' into staging-next
There ver very many conflicts, basically all due to
name -> pname+version.  Fortunately, almost everything was auto-resolved
by kdiff3, and for now I just fixed up a couple evaluation problems,
as verified by the tarball job.  There might be some fallback to these
conflicts, but I believe it should be minimal.

Hydra nixpkgs: ?compare=1538299
2019-08-24 08:55:37 +02:00
R. RyanTM 0ff0c288a8 sympow: 2.023.4 -> 2.023.5
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/sympow/versions
2019-08-20 21:06:37 -07:00
Markus Kowalewski 6ff8958bef openblas: 0.3.6 -> 0.3.7 2019-08-18 11:49:24 +02:00
volth c814d72b51 treewide: name -> pname 2019-08-17 10:54:38 +00:00
Frederik Rietdijk fe9a3e3e63 Merge staging-next into staging 2019-08-17 09:39:23 +02:00
volth 46420bbaa3 treewide: name -> pname (easy cases) (#66585)
treewide replacement of

stdenv.mkDerivation rec {
  name = "*-${version}";
  version = "*";

to pname
2019-08-15 13:41:18 +01:00