atlas: remove #49776

matthewbauer · 2018-11-05T02:27:49Z

atlas is broken and can apparently be removed.

atlas is broken and can apparently be removed. Fixes NixOS#49594

markuskowa · 2018-11-05T10:38:20Z

blas and liblapack may be replaced by openblasCompat here but this step requires further testing.
CC @symphorien @veprbl

veprbl · 2018-11-05T10:48:26Z

pkgs/top-level/all-packages.nix

  liblapack = callPackage ../development/libraries/science/math/liblapack {};
-  liblapackWithoutAtlas = liblapackWithAtlas.override { atlas = null; };
-  liblapackWithAtlas = liblapack;


liblapackWithoutAtlas would need to go to aliases.nix

matthewbauer · 2018-11-06T02:31:15Z

@GrahamcOfBorg build petsc openmodelica shogun giac openblas

GrahamcOfBorg · 2018-11-07T08:17:18Z

Failure on x86_64-darwin (full log)

Attempted: petsc, shogun, openblas

The following builds were skipped because they don't evaluate on x86_64-darwin: openmodelica, giac

Partial log (click to expand)

make PETSC_DIR=/nix/store/mzlyphzrjqs1g6yjmi6dpbxblfi7spq2-petsc-3.8.4 PETSC_ARCH="" test
====================================
/nix/store/f5aw0jl41r3nydav2mprvd2zyb76hg92-gnumake-4.2.1/bin/make  --no-print-directory PETSC_ARCH=arch-darwin-c-debug PETSC_DIR=/private/tmp/nix-build-petsc-3.8.4.drv-0/petsc-3.8.4 mpi4py-install petsc4py-install
make[1]: Nothing to be done for 'mpi4py-install'.
make[1]: Nothing to be done for 'petsc4py-install'.
post-installation fixup
strip is /nix/store/g5r4apl0za012ffs6ladinwa5w0m1l3k-cctools-binutils-darwin/bin/strip
stripping (with command strip and flags -S) in /nix/store/mzlyphzrjqs1g6yjmi6dpbxblfi7spq2-petsc-3.8.4/lib  /nix/store/mzlyphzrjqs1g6yjmi6dpbxblfi7spq2-petsc-3.8.4/bin
patching script interpreter paths in /nix/store/mzlyphzrjqs1g6yjmi6dpbxblfi7spq2-petsc-3.8.4
error: build of '/nix/store/ij8pl9nda6kfl48s1d4g8x2iw15nzv0b-shogun-6.0.0.drv' failed

GrahamcOfBorg · 2018-11-07T08:18:48Z

Failure on x86_64-linux (full log)

Attempted: petsc, shogun, giac, openblas

The following builds were skipped because they don't evaluate on x86_64-linux: openmodelica

Partial log (click to expand)

In file included from /build/source/src/shogun/classifier/svm/NewtonSVM.cpp:19:0:
/build/source/src/shogun/mathematics/lapack.h:37:10: fatal error: cblas.h: No such file or directory
 #include <cblas.h>
          ^~~~~~~~~
compilation terminated.
make[2]: *** [src/shogun/CMakeFiles/libshogun.dir/build.make:1381: src/shogun/CMakeFiles/libshogun.dir/classifier/svm/NewtonSVM.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:204: src/shogun/CMakeFiles/libshogun.dir/all] Error 2
make: *** [Makefile:152: all] Error 2
builder for '/nix/store/3wrvkrv5hg5rjlv8j2zqn0ancwms8gga-shogun-6.0.0.drv' failed with exit code 2
error: build of '/nix/store/3wrvkrv5hg5rjlv8j2zqn0ancwms8gga-shogun-6.0.0.drv' failed

GrahamcOfBorg · 2018-11-07T08:54:26Z

Failure on aarch64-linux (full log)

Attempted: petsc, shogun, giac, openblas

The following builds were skipped because they don't evaluate on aarch64-linux: openmodelica

Partial log (click to expand)

strip is /nix/store/p9akxn2sfy4wkhqdqa3li97pc6jaz3r1-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/nhx8pb4n2pilbi2aq2621y4m7g0wy3mm-giac-1.4.9-59/lib  /nix/store/nhx8pb4n2pilbi2aq2621y4m7g0wy3mm-giac-1.4.9-59/bin
patching script interpreter paths in /nix/store/nhx8pb4n2pilbi2aq2621y4m7g0wy3mm-giac-1.4.9-59
/nix/store/nhx8pb4n2pilbi2aq2621y4m7g0wy3mm-giac-1.4.9-59/bin/pgiac: interpreter directive changed from "/usr/bin/perl" to "/nix/store/bzgcpj9fijmlxgjaa72fjys7m3ycijy8-perl-5.28.0/bin/perl"
checking for references to /build in /nix/store/nhx8pb4n2pilbi2aq2621y4m7g0wy3mm-giac-1.4.9-59...
shrinking RPATHs of ELF executables and libraries in /nix/store/k09lcz1hwbind8nmsqxmzj1jcxv7ypq3-giac-1.4.9-59-doc
strip is /nix/store/p9akxn2sfy4wkhqdqa3li97pc6jaz3r1-binutils-2.30/bin/strip
patching script interpreter paths in /nix/store/k09lcz1hwbind8nmsqxmzj1jcxv7ypq3-giac-1.4.9-59-doc
checking for references to /build in /nix/store/k09lcz1hwbind8nmsqxmzj1jcxv7ypq3-giac-1.4.9-59-doc...
error: build of '/nix/store/ld2f5bph5s5iv4z0bmdl7nxwy9a5smvs-shogun-6.0.0.drv' failed

markuskowa · 2018-11-07T12:14:35Z

Using openblas instead of blas seems to work here (I can compile it locally).

--- a/pkgs/applications/science/machine-learning/shogun/default.nix
+++ b/pkgs/applications/science/machine-learning/shogun/default.nix
@@ -2,7 +2,7 @@
 # data, compression
 , bzip2, curl, hdf5, json_c, lzma, lzo, protobuf, snappy
 # maths
-, blas, eigen, nlopt, lp_solve, colpack
+, openblasCompat, eigen, nlopt, lp_solve, colpack
 # libraries
 , libarchive, liblapack, libxml2
 # extra support
@@ -41,7 +41,7 @@ stdenv.mkDerivation rec {
   CCACHE_DIR=".ccache";
 
   buildInputs = with lib; [
-      blas bzip2 ccache cmake colpack curl ctags eigen hdf5 json_c lp_solve lzma lzo
+      openblasCompat bzip2 ccache cmake colpack curl ctags eigen hdf5 json_c lp_solve lzma lzo
       protobuf nlopt snappy swig (libarchive.dev) liblapack libxml2
     ]
     ++ optionals (pythonSupport) (with pythonPackages; [ python ply numpy ])

shogun needs the cblas.h header file to be available. It used to get it from liblapack, but that is not available anymore. Instead we can use openblasCompat to get it.

matthewbauer · 2018-11-07T19:23:06Z

Thanks! A few more packages may need that as well. Lots of them must have been getting it from liblapack.

matthewbauer · 2018-11-07T19:24:29Z

@GrahamcOfBorg build magma scs gmsh csdp mxnet scalapack

This doesn’t make any sense to keep - we don’t have a liblapack with atlas anymore.

GrahamcOfBorg · 2018-11-07T19:34:11Z

Failure on x86_64-darwin (full log)

Attempted: scs, gmsh, csdp, scalapack

The following builds were skipped because they don't evaluate on x86_64-darwin: magma, mxnet

Partial log (click to expand)

         91 - xssyevr (Failed)
         92 - xdsyevr (Failed)
         93 - xcheevr (Failed)
         94 - xzheevr (Failed)
         95 - xshseqr (Failed)
         96 - xdhseqr (Failed)
Errors while running CTest
make: *** [Makefile:130: test] Error 8
builder for '/nix/store/8yj4dl5z3f506q37zbqifyjqscqdp89j-scalapack-2.0.2.drv' failed with exit code 2
error: build of '/nix/store/099w05ms0hg2yiwwai676f9vyh8224dk-gmsh-4.0.2.drv', '/nix/store/8yj4dl5z3f506q37zbqifyjqscqdp89j-scalapack-2.0.2.drv' failed

GrahamcOfBorg · 2018-11-07T19:35:22Z

Failure on aarch64-linux (full log)

Attempted: liblapack, shogun

Partial log (click to expand)

[  2%] Building CXX object src/shogun/CMakeFiles/libshogun.dir/base/Parallel.cpp.o
[  2%] Building CXX object src/shogun/CMakeFiles/libshogun.dir/base/Parameter.cpp.o
[  2%] Building CXX object src/shogun/CMakeFiles/libshogun.dir/base/SGObject.cpp.o
/build/ccQ1RdXJ.s: Assembler messages:
/build/ccQ1RdXJ.s:3821: Error: unknown mnemonic `pause' -- `pause'
make[2]: *** [src/shogun/CMakeFiles/libshogun.dir/build.make:1030: src/shogun/CMakeFiles/libshogun.dir/base/SGObject.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:204: src/shogun/CMakeFiles/libshogun.dir/all] Error 2
make: *** [Makefile:152: all] Error 2
builder for '/nix/store/1p9mbllmfzgvl0p8s82kyc2hc2f7p8vl-shogun-6.0.0.drv' failed with exit code 2
error: build of '/nix/store/1p9mbllmfzgvl0p8s82kyc2hc2f7p8vl-shogun-6.0.0.drv' failed

GrahamcOfBorg · 2018-11-07T19:40:38Z

Failure on x86_64-darwin (full log)

Attempted: liblapack, shogun

Partial log (click to expand)

./Main/ColPackHeaders.h:61:11: fatal error: 'omp.h' file not found
        #include <omp.h>
                 ^~~~~~~
1 error generated.
make[1]: *** [Makefile:1489: SampleDrivers/Basic/color_bipartite_graph_using_BipartiteGraphBicoloringInterface.o] Error 1
make[1]: Leaving directory '/private/tmp/nix-build-ColPack-1.0.10.drv-0/source'
make: *** [Makefile:859: all] Error 2
builder for '/nix/store/2qdwr8gif8qixqvn5xfh0y6hvqg2q4f1-ColPack-1.0.10.drv' failed with exit code 2
cannot build derivation '/nix/store/bmabvfgglparcmcjcr6ygyl2wvs6843b-shogun-6.0.0.drv': 1 dependencies couldn't be built
error: build of '/nix/store/bmabvfgglparcmcjcr6ygyl2wvs6843b-shogun-6.0.0.drv' failed

GrahamcOfBorg · 2018-11-07T19:41:02Z

Failure on aarch64-linux (full log)

Attempted: liblapack, shogun

Partial log (click to expand)

[  2%] Building CXX object src/shogun/CMakeFiles/libshogun.dir/base/Parallel.cpp.o
[  2%] Building CXX object src/shogun/CMakeFiles/libshogun.dir/base/Parameter.cpp.o
[  2%] Building CXX object src/shogun/CMakeFiles/libshogun.dir/base/SGObject.cpp.o
/build/ccHhNgMD.s: Assembler messages:
/build/ccHhNgMD.s:3821: Error: unknown mnemonic `pause' -- `pause'
make[2]: *** [src/shogun/CMakeFiles/libshogun.dir/build.make:1030: src/shogun/CMakeFiles/libshogun.dir/base/SGObject.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:204: src/shogun/CMakeFiles/libshogun.dir/all] Error 2
make: *** [Makefile:152: all] Error 2
builder for '/nix/store/1p9mbllmfzgvl0p8s82kyc2hc2f7p8vl-shogun-6.0.0.drv' failed with exit code 2
error: build of '/nix/store/1p9mbllmfzgvl0p8s82kyc2hc2f7p8vl-shogun-6.0.0.drv' failed

GrahamcOfBorg · 2018-11-07T19:41:39Z

Failure on x86_64-darwin (full log)

Attempted: liblapack, shogun

Partial log (click to expand)

-- Installing: /nix/store/d4qsxly2syvlji6likwl53yxb1b6j5bw-liblapack-3.8.0/lib/cmake/lapack-3.8.0/lapack-config-version.cmake
-- Installing: /nix/store/d4qsxly2syvlji6likwl53yxb1b6j5bw-liblapack-3.8.0/lib/pkgconfig/blas.pc
-- Installing: /nix/store/d4qsxly2syvlji6likwl53yxb1b6j5bw-liblapack-3.8.0/lib/libblas.a
-- Installing: /nix/store/d4qsxly2syvlji6likwl53yxb1b6j5bw-liblapack-3.8.0/lib/liblapack.a
post-installation fixup
strip is /nix/store/g5r4apl0za012ffs6ladinwa5w0m1l3k-cctools-binutils-darwin/bin/strip
stripping (with command strip and flags -S) in /nix/store/d4qsxly2syvlji6likwl53yxb1b6j5bw-liblapack-3.8.0/lib
patching script interpreter paths in /nix/store/d4qsxly2syvlji6likwl53yxb1b6j5bw-liblapack-3.8.0
cannot build derivation '/nix/store/bmabvfgglparcmcjcr6ygyl2wvs6843b-shogun-6.0.0.drv': 1 dependencies couldn't be built
error: build of '/nix/store/bmabvfgglparcmcjcr6ygyl2wvs6843b-shogun-6.0.0.drv' failed

GrahamcOfBorg · 2018-11-07T20:02:26Z

Success on x86_64-linux (full log)

Attempted: liblapack, shogun

Partial log (click to expand)

shrinking /nix/store/c4xi5qa6jnnz3aj8sjp8rwb3vn7374ds-shogun-6.0.0/share/shogun/examples/libshogun/classifier_mkl_svmlight_modelselection_bug
shrinking /nix/store/c4xi5qa6jnnz3aj8sjp8rwb3vn7374ds-shogun-6.0.0/share/shogun/examples/libshogun/serialization_basic_tests
shrinking /nix/store/c4xi5qa6jnnz3aj8sjp8rwb3vn7374ds-shogun-6.0.0/share/shogun/examples/libshogun/classifier_multiclasslinearmachine
shrinking /nix/store/c4xi5qa6jnnz3aj8sjp8rwb3vn7374ds-shogun-6.0.0/share/shogun/examples/libshogun/parameter_set_from_parameters
shrinking /nix/store/c4xi5qa6jnnz3aj8sjp8rwb3vn7374ds-shogun-6.0.0/lib/python2.7/site-packages/_modshogun.so
shrinking /nix/store/c4xi5qa6jnnz3aj8sjp8rwb3vn7374ds-shogun-6.0.0/lib/libshogun.so.18.0
strip is /nix/store/vcc4svb8gy29g4pam2zja6llkbcwsyiq-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/c4xi5qa6jnnz3aj8sjp8rwb3vn7374ds-shogun-6.0.0/lib
patching script interpreter paths in /nix/store/c4xi5qa6jnnz3aj8sjp8rwb3vn7374ds-shogun-6.0.0
checking for references to /build in /nix/store/c4xi5qa6jnnz3aj8sjp8rwb3vn7374ds-shogun-6.0.0...

GrahamcOfBorg · 2018-11-07T20:10:33Z

Timed out, unknown build status on x86_64-linux (full log)

Attempted: scs, gmsh, csdp, mxnet, scalapack

The following builds were skipped because they don't evaluate on x86_64-linux: magma

Partial log (click to expand)

-- Installing: /nix/store/jmsv8761d3ycpwghfmzg56i56rpy6c5a-gmsh-4.0.2/share/man/man1/gmsh.1
post-installation fixup
shrinking RPATHs of ELF executables and libraries in /nix/store/jmsv8761d3ycpwghfmzg56i56rpy6c5a-gmsh-4.0.2
shrinking /nix/store/jmsv8761d3ycpwghfmzg56i56rpy6c5a-gmsh-4.0.2/bin/gmsh
gzipping man pages under /nix/store/jmsv8761d3ycpwghfmzg56i56rpy6c5a-gmsh-4.0.2/share/man/
strip is /nix/store/vcc4svb8gy29g4pam2zja6llkbcwsyiq-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/jmsv8761d3ycpwghfmzg56i56rpy6c5a-gmsh-4.0.2/bin
patching script interpreter paths in /nix/store/jmsv8761d3ycpwghfmzg56i56rpy6c5a-gmsh-4.0.2
checking for references to /build in /nix/store/jmsv8761d3ycpwghfmzg56i56rpy6c5a-gmsh-4.0.2...
error: build of '/nix/store/zcllzj9ifvfgf4307i2gmhr7inf2aqkg-mxnet-1.2.1.drv' failed

GrahamcOfBorg · 2018-11-07T20:41:20Z

Timed out, unknown build status on x86_64-linux (full log)

Attempted: liblapack, shogun

Partial log (click to expand)

[ 63%] Building CXX object src/shogun/CMakeFiles/libshogun.dir/structure/FactorGraphModel.cpp.o
[ 64%] Building CXX object src/shogun/CMakeFiles/libshogun.dir/structure/FactorType.cpp.o
[ 64%] Building CXX object src/shogun/CMakeFiles/libshogun.dir/structure/GEMPLP.cpp.o
[ 64%] Building CXX object src/shogun/CMakeFiles/libshogun.dir/structure/GraphCut.cpp.o
[ 64%] Building CXX object src/shogun/CMakeFiles/libshogun.dir/structure/HMSVMModel.cpp.o
[ 64%] Building CXX object src/shogun/CMakeFiles/libshogun.dir/structure/HashedMultilabelModel.cpp.o
[ 64%] Building CXX object src/shogun/CMakeFiles/libshogun.dir/structure/HierarchicalMultilabelModel.cpp.o
[ 64%] Building CXX object src/shogun/CMakeFiles/libshogun.dir/structure/IntronList.cpp.o
building of '/nix/store/cxm6pncgw12yrs2cr5rp98w5p4f9hjxs-shogun-6.0.0.drv' timed out after 3600 seconds
error: build of '/nix/store/cxm6pncgw12yrs2cr5rp98w5p4f9hjxs-shogun-6.0.0.drv' failed

GrahamcOfBorg · 2018-11-07T21:04:16Z

Failure on aarch64-linux (full log)

Attempted: scs, gmsh, csdp, mxnet, scalapack

The following builds were skipped because they don't evaluate on aarch64-linux: magma

Partial log (click to expand)

cannot build derivation '/nix/store/by5p7vlw6p1hsixyliy85dim5r8xqzq5-conduit-1.3.1.drv': 14 dependencies couldn't be built
cannot build derivation '/nix/store/q3pv07v48jyh8qzgpm1r8wjv6yc5va57-tls-1.4.1.drv': 17 dependencies couldn't be built
cannot build derivation '/nix/store/x94qhdgjjn6pi5zhcnbxp6csmndvyvrh-connection-0.2.8.drv': 11 dependencies couldn't be built
cannot build derivation '/nix/store/793ymrxpa1nmc0h9qbyb705hzaqpc6aa-yaml-0.8.32.drv': 15 dependencies couldn't be built
cannot build derivation '/nix/store/qcpay92v35qx4jgpckq7krz513ah3sdv-http-client-tls-0.3.5.3.drv': 13 dependencies couldn't be built
cannot build derivation '/nix/store/a1snaj0bpwzl00skil0a6xz97i0mkilf-pandoc-2.2.1.drv': 40 dependencies couldn't be built
cannot build derivation '/nix/store/2r6n4ij8p62869sx23fkhd6w9jy9nmap-rdma-core-20.1.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/lbbwcz4vcny5s1byc5r3q09078ww6db6-openmpi-3.1.2.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/84m4d732z0bljyk7n92z56km3hqvzxwz-scalapack-2.0.2.drv': 1 dependencies couldn't be built
error: build of '/nix/store/1xwavjqb73zdv68jdca499nkdvfh1lr6-mxnet-1.2.1.drv', '/nix/store/84m4d732z0bljyk7n92z56km3hqvzxwz-scalapack-2.0.2.drv', '/nix/store/vnlhzv942a7wvc3xy3n7djpp5n33qw1l-gmsh-4.0.2.drv' failed

markuskowa · 2018-11-07T22:20:45Z

This turns out to be more work than though.

colpack has never been built before on darwin.
liblapack can be removed from shogun. It's not used anymore. Doesn't solve the aarch64 build failure though (?).
scalapack has never been built successfully on darwin (set platforms.linux should be fine here).

not needed anymore

GrahamcOfBorg · 2018-11-08T21:07:19Z

Failure on x86_64-darwin (full log)

Attempted: liblapack, shogun

Partial log (click to expand)

./Main/ColPackHeaders.h:61:11: fatal error: 'omp.h' file not found
        #include <omp.h>
                 ^~~~~~~
1 error generated.
make[1]: *** [Makefile:1489: SampleDrivers/Basic/color_bipartite_graph_using_BipartiteGraphBicoloringInterface.o] Error 1
make[1]: Leaving directory '/private/tmp/nix-build-ColPack-1.0.10.drv-0/source'
make: *** [Makefile:859: all] Error 2
builder for '/nix/store/2qdwr8gif8qixqvn5xfh0y6hvqg2q4f1-ColPack-1.0.10.drv' failed with exit code 2
cannot build derivation '/nix/store/gf67ngnfckz7y2xk345vbhqwhlsc4biv-shogun-6.0.0.drv': 1 dependencies couldn't be built
error: build of '/nix/store/gf67ngnfckz7y2xk345vbhqwhlsc4biv-shogun-6.0.0.drv' failed

GrahamcOfBorg · 2018-11-08T21:11:00Z

Failure on aarch64-linux (full log)

Attempted: liblapack, shogun

Partial log (click to expand)

[  2%] Building CXX object src/shogun/CMakeFiles/libshogun.dir/base/Parallel.cpp.o
[  2%] Building CXX object src/shogun/CMakeFiles/libshogun.dir/base/Parameter.cpp.o
[  2%] Building CXX object src/shogun/CMakeFiles/libshogun.dir/base/SGObject.cpp.o
/build/ccIHndXN.s: Assembler messages:
/build/ccIHndXN.s:3821: Error: unknown mnemonic `pause' -- `pause'
make[2]: *** [src/shogun/CMakeFiles/libshogun.dir/build.make:1030: src/shogun/CMakeFiles/libshogun.dir/base/SGObject.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:204: src/shogun/CMakeFiles/libshogun.dir/all] Error 2
make: *** [Makefile:152: all] Error 2
builder for '/nix/store/yfwy7ndnk7viw6fwlahmfycjm81w883d-shogun-6.0.0.drv' failed with exit code 2
error: build of '/nix/store/yfwy7ndnk7viw6fwlahmfycjm81w883d-shogun-6.0.0.drv' failed

GrahamcOfBorg · 2018-11-08T21:36:33Z

Success on x86_64-linux (full log)

Attempted: liblapack, shogun

Partial log (click to expand)

shrinking /nix/store/byylcimd0g2lvg51ks58fn2h11c5mvk4-shogun-6.0.0/share/shogun/examples/libshogun/library_map
shrinking /nix/store/byylcimd0g2lvg51ks58fn2h11c5mvk4-shogun-6.0.0/share/shogun/examples/libshogun/library_mldatahdf5
shrinking /nix/store/byylcimd0g2lvg51ks58fn2h11c5mvk4-shogun-6.0.0/share/shogun/examples/libshogun/modelselection_apply_parameter_tree
shrinking /nix/store/byylcimd0g2lvg51ks58fn2h11c5mvk4-shogun-6.0.0/share/shogun/examples/libshogun/modelselection_grid_search_string_kernel
shrinking /nix/store/byylcimd0g2lvg51ks58fn2h11c5mvk4-shogun-6.0.0/share/shogun/examples/libshogun/evaluation_cross_validation_mkl_weight_storage
shrinking /nix/store/byylcimd0g2lvg51ks58fn2h11c5mvk4-shogun-6.0.0/share/shogun/examples/libshogun/classifier_multiclass_ecoc_discriminant
strip is /nix/store/vcc4svb8gy29g4pam2zja6llkbcwsyiq-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/byylcimd0g2lvg51ks58fn2h11c5mvk4-shogun-6.0.0/lib
patching script interpreter paths in /nix/store/byylcimd0g2lvg51ks58fn2h11c5mvk4-shogun-6.0.0
checking for references to /build in /nix/store/byylcimd0g2lvg51ks58fn2h11c5mvk4-shogun-6.0.0...

GrahamcOfBorg · 2018-11-11T01:35:09Z

Success on x86_64-darwin (full log)

Attempted: liblapack

The following builds were skipped because they don't evaluate on x86_64-darwin: colpack, scalapack, shogun

Partial log (click to expand)

a) For `nixos-rebuild` you can set
  { nixpkgs.config.allowUnsupportedSystem = true; }
in configuration.nix to override this.

b) For `nix-env`, `nix-build`, `nix-shell` or any other Nix command you can add
  { allowUnsupportedSystem = true; }
to ~/.config/nixpkgs/config.nix.


/nix/store/d4qsxly2syvlji6likwl53yxb1b6j5bw-liblapack-3.8.0

GrahamcOfBorg · 2018-11-11T02:01:36Z

Success on x86_64-linux (full log)

Attempted: colpack, liblapack, scalapack, shogun

Partial log (click to expand)

shrinking /nix/store/byylcimd0g2lvg51ks58fn2h11c5mvk4-shogun-6.0.0/share/shogun/examples/libshogun/parameter_set_from_parameters
shrinking /nix/store/byylcimd0g2lvg51ks58fn2h11c5mvk4-shogun-6.0.0/lib/python2.7/site-packages/_modshogun.so
shrinking /nix/store/byylcimd0g2lvg51ks58fn2h11c5mvk4-shogun-6.0.0/lib/libshogun.so.18.0
strip is /nix/store/vcc4svb8gy29g4pam2zja6llkbcwsyiq-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/byylcimd0g2lvg51ks58fn2h11c5mvk4-shogun-6.0.0/lib
patching script interpreter paths in /nix/store/byylcimd0g2lvg51ks58fn2h11c5mvk4-shogun-6.0.0
checking for references to /build in /nix/store/byylcimd0g2lvg51ks58fn2h11c5mvk4-shogun-6.0.0...
cannot link '/nix/store/.links/10hani3vqnr0g1ckdaz7lfpg354afd0hcrvbdd5d9d5fn49l8ds0' to '/nix/store/byylcimd0g2lvg51ks58fn2h11c5mvk4-shogun-6.0.0/share/shogun/examples/libshogun/streaming_onlineliblinear_dense': No space left on device
copying path '/nix/store/ydl44v6sxijhrd63xnq9gswkqz52jn0p-scalapack-2.0.2' from 'https://cache.nixos.org'...
warning: unable to download 'https://cache.nixos.org/nar/1f63x497xk4z3l3xg1j1z1hb7nxrhdgijdz6c1xmailc6kk289rn.nar.xz': Error in the HTTP2 framing layer (16); retrying in 255 ms

GrahamcOfBorg · 2018-11-11T02:41:13Z

Timed out, unknown build status on aarch64-linux (full log)

Attempted: colpack, liblapack, scalapack, shogun

Partial log (click to expand)

cannot build derivation '/nix/store/by5p7vlw6p1hsixyliy85dim5r8xqzq5-conduit-1.3.1.drv': 14 dependencies couldn't be built
cannot build derivation '/nix/store/q3pv07v48jyh8qzgpm1r8wjv6yc5va57-tls-1.4.1.drv': 17 dependencies couldn't be built
cannot build derivation '/nix/store/x94qhdgjjn6pi5zhcnbxp6csmndvyvrh-connection-0.2.8.drv': 11 dependencies couldn't be built
cannot build derivation '/nix/store/793ymrxpa1nmc0h9qbyb705hzaqpc6aa-yaml-0.8.32.drv': 15 dependencies couldn't be built
cannot build derivation '/nix/store/qcpay92v35qx4jgpckq7krz513ah3sdv-http-client-tls-0.3.5.3.drv': 13 dependencies couldn't be built
cannot build derivation '/nix/store/a1snaj0bpwzl00skil0a6xz97i0mkilf-pandoc-2.2.1.drv': 40 dependencies couldn't be built
cannot build derivation '/nix/store/2r6n4ij8p62869sx23fkhd6w9jy9nmap-rdma-core-20.1.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/lbbwcz4vcny5s1byc5r3q09078ww6db6-openmpi-3.1.2.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/84m4d732z0bljyk7n92z56km3hqvzxwz-scalapack-2.0.2.drv': 1 dependencies couldn't be built
error: build of '/nix/store/84m4d732z0bljyk7n92z56km3hqvzxwz-scalapack-2.0.2.drv', '/nix/store/yfwy7ndnk7viw6fwlahmfycjm81w883d-shogun-6.0.0.drv' failed

atlas: remove

95373d3

atlas is broken and can apparently be removed. Fixes NixOS#49594

matthewbauer mentioned this pull request Nov 5, 2018

atlas fails to build #49594

Closed

GrahamcOfBorg added 8.has: clean-up 10.rebuild-darwin: 11-100 10.rebuild-linux: 11-100 labels Nov 5, 2018

markuskowa added this to To do in Picking up garbage via automation Nov 5, 2018

veprbl reviewed Nov 5, 2018

View reviewed changes

liblapack: add compat aliases

6ba2b84

shogun: use openblas

349f3df

shogun needs the cblas.h header file to be available. It used to get it from liblapack, but that is not available anymore. Instead we can use openblasCompat to get it.

aliases: remove liblapackWithAtlas

f2c49bd

This doesn’t make any sense to keep - we don’t have a liblapack with atlas anymore.

GrahamcOfBorg added 10.rebuild-linux: 1-10 and removed 10.rebuild-linux: 11-100 labels Nov 7, 2018

shogun: remove liblapack

3dcb8c1

not needed anymore

markuskowa added 3 commits November 11, 2018 02:17

scalapack: set platform to linux

06f3676

colpack: set platform to linux

6533d75

Merge branch 'master' into atlas-remove

45a4adb

GrahamcOfBorg added 2.status: merge conflict 8.has: package (new) and removed 2.status: merge conflict labels Nov 11, 2018

jtojnar moved this from To do to In progress in Picking up garbage Nov 13, 2018

matthewbauer merged commit 2e18ba6 into NixOS:master Nov 14, 2018

Picking up garbage automation moved this from In progress to Done Nov 14, 2018

matthewbauer deleted the atlas-remove branch February 22, 2019 04:23

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atlas: remove #49776

atlas: remove #49776

matthewbauer commented Nov 5, 2018

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atlas: remove #49776

atlas: remove #49776

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