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721 Commits

Author SHA1 Message Date
Daniël de Kok
da115b4c56
Merge pull request #103120 from danieldk/libtorch-bin-cmake-fix-lib-paths 
libtorch-bin: fix CMake library paths for split outputs
 2020-11-10 12:10:38 +01:00
Frederik Rietdijk
20f001c01e Merge master into staging-next 2020-11-09 14:33:52 +01:00
Daniël de Kok
2802a021e3 libtorch-bin: modify passthru test to capture CMake misconfiguration 2020-11-09 07:49:54 +01:00
Daniël de Kok
e8721af065 libtorch-bin: fix CMake library paths for split outputs 
The libtorch CMake files are in the `dev` output and used relative
paths to locate the shared libraries. This fails, because the
libraries are in the `out` output. This change patches the CMake files
to use library paths from `out`.

See #102146.
 2020-11-09 07:49:54 +01:00
Daniël de Kok
d36077239c
Merge pull request #103078 from danieldk/cleanup-libtorch-bin-test 
libtorch-bin: cleanup passthru test
 2020-11-09 07:49:03 +01:00
Daniël de Kok
a71f07694c libtorch-bin: cleanup passthru test 
- Make passthru.tests an attrset.
- Remove CMake VERBOSE option.
- Remove spurious `cat CMakeLists.txt`.
- Run the test as well.
- Actually test some functionality.
 2020-11-07 13:50:23 +01:00
Frederik Rietdijk
99fb79ae84 Merge master into staging-next 2020-11-06 12:51:56 +01:00
Daniël de Kok
b5d27eb87c mkl: Add a small test program 
The MKL pkg-config files often change and are then incorrect for our
paths. pkg-config validation finds some issues, but not incorrect
paths. So, add a small test program to test whether the generated
pkg-config files can actually be used to build a functioning
binary. Hopefully this catches future regressions.
 2020-11-06 12:18:56 +01:00
Daniël de Kok
702b626570 mkl: Fix pkg-config file 
There was a spurious `intel64` in some library paths.
 2020-11-06 09:55:12 +01:00
R. RyanTM
4d507f9002 petsc: 3.13.4 -> 3.14.0 2020-11-04 07:59:18 +00:00
TredwellGit
d1d536cc07 openblas: 0.3.10 -> 0.3.12 
https://github.com/xianyi/OpenBLAS/releases/tag/v0.3.11
https://github.com/xianyi/OpenBLAS/releases/tag/v0.3.12
 2020-11-01 10:58:02 +01:00
Renato Alves
019fa5f608
htslib: 1.10.2 -> 1.11 (#100812) 2020-10-29 11:18:29 +01:00
eyjhb
4ce6364e29 ns-3: 3.30 -> 3.32 2020-10-28 20:22:15 +01:00
Daniël de Kok
442ba6668f libtorch-bin: 1.6.0 -> 1.7.0 
Changelog:

https://github.com/pytorch/pytorch/releases/tag/v1.7.0
 2020-10-28 13:23:35 +01:00
Ben Siraphob
db74029e3e treewide: remove package names from prefix of descriptions 2020-10-27 09:15:07 -07:00
R. RyanTM
1007e8140a openlibm: 0.7.1 -> 0.7.2 2020-10-26 00:47:50 +00:00
Robert Scott
c873f13eac
Merge pull request #101031 from r-burns/spooles 
spooles: fix build on darwin
 2020-10-19 19:07:03 +01:00
Ryan Burns
c04219a9d5 spooles: fix build on darwin 2020-10-18 13:32:45 -07:00
Timo Kaufmann
e9f8c385c0
Merge pull request #100870 from r-ryantm/auto-update/brial 
brial: 1.2.8 -> 1.2.10
 2020-10-18 10:37:47 +02:00
R. RyanTM
57738e9b6f brial: 1.2.8 -> 1.2.10 2020-10-17 19:37:17 +00:00
Ben Darwin
e20652da9b elastix: 5.0.0 -> 5.0.1; unbreak OS X build 2020-10-17 11:36:31 -07:00
Ben Siraphob
683a87dbeb treewide: remove periods from end of package descriptions 2020-10-17 08:22:31 -07:00
Vladimír Čunát
338b25697c
Merge branch 'master' into staging-next 
Quite many rebuilds from master:
> Estimating rebuild amount by counting changed Hydra jobs.
>    3926 x86_64-darwin
>    4645 x86_64-linux
 2020-10-10 11:32:10 +02:00
Frederik Rietdijk
ec28e32c9e Merge master into staging-next 2020-10-08 21:47:26 +02:00
Lassulus
f849b13978
Merge pull request #98571 from bcdarwin/gifticlib 
gifticlib: init at unstable-2020-07-07
 2020-10-08 21:48:31 +02:00
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