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  • 5 commits
  • 6 files changed
  • 2 contributors

Commits on Apr 22, 2020

  1. blas,lapack: use correct name for library 

    To match the soname, we need to use libblas.so.3, liblapack.so.3.
    @matthewbauer
    matthewbauer committed Apr 22, 2020

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    vbgl Vincent Laporte
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    5a500ff View commit details

  2. python.pkgs.scipy: set SCIPY_USE_G77_ABI_WRAPPER=1 

    To avoid segmentation fault on MKL, we need to use the CBLAS ABI.
Normally, scipy will autodetect this, but here we don’t link using the
‘libmkl_rt.so’ name. So we need to manually set this.

See https://github.com/scipy/scipy/blob/50012918db47f0ec3418dd53f0277daa589f82e3/doc/source/building/linux.rst#fortran-abi-mismatch
    @matthewbauer
    matthewbauer committed Apr 22, 2020
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    3d18975 View commit details

  3. doc/overlays.xml: fix missing documentation for blas/lapack 

    This adds some more information to the documentation as well as
addressing review from #85636.
    @matthewbauer
    matthewbauer committed Apr 22, 2020
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Commits on Apr 23, 2020

  1. doc/using/overlays.xml: update LD_LIBRARY_PATH example

    @bhipple
    bhipple authored Apr 23, 2020
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    480a55a View commit details

  2. Merge pull request #85799 from matthewbauer/blas-lapack-expand-docs 

    BLAS/LAPACK fixup and expand docs
    @bhipple
    bhipple authored Apr 23, 2020
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31 changes: 21 additions & 10 deletions doc/using/overlays.xml
View file
Original file line number Diff line number Diff line change
@@ -140,8 +140,8 @@ self: super:
<section xml:id="sec-overlays-alternatives">
<title>Using overlays to configure alternatives</title>
<para>
Certain software has different implementations of the same
interface. Other distributions have functionality to switch
Certain software packages have different implementations of the
same interface. Other distributions have functionality to switch
between these. For example, Debian provides <link
xlink:href="https://wiki.debian.org/DebianAlternatives">DebianAlternatives</link>.
Nixpkgs has what we call <literal>alternatives</literal>, which
@@ -160,8 +160,9 @@ self: super:
</para>
<para>
The Nixpkgs attribute is <literal>openblas</literal> for
ILP64 and <literal>openblasCompat</literal> for LP64. This
is the default.
ILP64 (integer width = 64 bits) and
<literal>openblasCompat</literal> for LP64 (integer width =
32 bits). <literal>openblasCompat</literal> is the default.
</para>
</listitem>
<listitem>
@@ -190,8 +191,15 @@ self: super:
#83888</link>, we are able to override the ‘blas’ and ‘lapack’
packages to use different implementations, through the
‘blasProvider’ and ‘lapackProvider’ argument. This can be used
to select a different provider. For example, an overlay can be
created that looks like:
to select a different provider. BLAS providers will have
symlinks in <literal>$out/lib/libblas.so.3</literal> and
<literal>$out/lib/libcblas.so.3</literal> to their respective
BLAS libraries. Likewise, LAPACK providers will have symlinks
in <literal>$out/lib/liblapack.so.3</literal> and
<literal>$out/lib/liblapacke.so.3</literal> to their respective
LAPCK libraries. For example, Intel MKL is both a BLAS and
LAPACK provider. An overlay can be created to use Intel MKL
that looks like:
</para>
<programlisting>
self: super:
@@ -208,9 +216,12 @@ self: super:
<para>
This overlay uses Intel’s MKL library for both BLAS and LAPACK
interfaces. Note that the same can be accomplished at runtime
using <literal>LD_PRELOAD</literal> of libblas.so.3 and
liblapack.so.3.
using <literal>LD_LIBRARY_PATH</literal> of libblas.so.3 and
liblapack.so.3. For instance:
</para>
<programlisting>
$ LD_LIBRARY_PATH=$(nix-build -A mkl)/lib:$LD_LIBRARY_PATH nix-shell -p octave --run octave
</programlisting>
<para>
Intel MKL requires an <literal>openmp</literal> implementation
when running with multiple processors. By default,
@@ -221,8 +232,8 @@ self: super:
set it with <literal>LD_PRELOAD</literal>. Note that
<literal>mkl</literal> is only available on
<literal>x86_64-linux</literal> and
<literal>x86_64-darwin</literal>. Moreover, Hydra is not build
and distributing pre-compiled binaries using it.
<literal>x86_64-darwin</literal>. Moreover, Hydra is not
building and distributing pre-compiled binaries using it.
</para>
<para>
For BLAS/LAPACK switching to work correctly, all packages must
4 changes: 2 additions & 2 deletions pkgs/build-support/alternatives/blas/default.nix
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Original file line number Diff line number Diff line change
@@ -63,7 +63,7 @@ stdenv.mkDerivation {
installPhase = (''
mkdir -p $out/lib $dev/include $dev/lib/pkgconfig
libblas="${lib.getLib blasProvider}/lib/libblas${stdenv.hostPlatform.extensions.sharedLibrary}"
libblas="${lib.getLib blasProvider}/lib/libblas${canonicalExtension}"
if ! [ -e "$libblas" ]; then
echo "$libblas does not exist, ${blasProvider.name} does not provide libblas."
@@ -100,7 +100,7 @@ Libs: -L$out/lib -lblas
Cflags: -I$dev/include
EOF
libcblas="${lib.getLib blasProvider}/lib/libcblas${stdenv.hostPlatform.extensions.sharedLibrary}"
libcblas="${lib.getLib blasProvider}/lib/libcblas${canonicalExtension}"
if ! [ -e "$libcblas" ]; then
echo "$libcblas does not exist, ${blasProvider.name} does not provide libcblas."
4 changes: 2 additions & 2 deletions pkgs/build-support/alternatives/lapack/default.nix
View file
Original file line number Diff line number Diff line change
@@ -41,7 +41,7 @@ stdenv.mkDerivation {
installPhase = (''
mkdir -p $out/lib $dev/include $dev/lib/pkgconfig
liblapack="${lib.getLib lapackProvider}/lib/liblapack${stdenv.hostPlatform.extensions.sharedLibrary}"
liblapack="${lib.getLib lapackProvider}/lib/liblapack${canonicalExtension}"
if ! [ -e "$liblapack" ]; then
echo "$liblapack does not exist, ${lapackProvider.name} does not provide liblapack."
@@ -74,7 +74,7 @@ Cflags: -I$dev/include
Libs: -L$out/lib -llapack
EOF
liblapacke="${lib.getLib lapackProvider}/lib/liblapacke${stdenv.hostPlatform.extensions.sharedLibrary}"
liblapacke="${lib.getLib lapackProvider}/lib/liblapacke${canonicalExtension}"
if ! [ -e "$liblapacke" ]; then
echo "$liblapacke does not exist, ${lapackProvider.name} does not provide liblapacke."
8 changes: 4 additions & 4 deletions pkgs/development/libraries/science/math/mkl/default.nix
View file
Original file line number Diff line number Diff line change
@@ -114,10 +114,10 @@ in stdenvNoCC.mkDerivation {
'') + ''
# Setup symlinks for blas / lapack
ln -s $out/lib/libmkl_rt${stdenvNoCC.hostPlatform.extensions.sharedLibrary} $out/lib/libblas${stdenvNoCC.hostPlatform.extensions.sharedLibrary}
ln -s $out/lib/libmkl_rt${stdenvNoCC.hostPlatform.extensions.sharedLibrary} $out/lib/libcblas${stdenvNoCC.hostPlatform.extensions.sharedLibrary}
ln -s $out/lib/libmkl_rt${stdenvNoCC.hostPlatform.extensions.sharedLibrary} $out/lib/liblapack${stdenvNoCC.hostPlatform.extensions.sharedLibrary}
ln -s $out/lib/libmkl_rt${stdenvNoCC.hostPlatform.extensions.sharedLibrary} $out/lib/liblapacke${stdenvNoCC.hostPlatform.extensions.sharedLibrary}
ln -s $out/lib/libmkl_rt${stdenvNoCC.hostPlatform.extensions.sharedLibrary} $out/lib/libblas${stdenvNoCC.hostPlatform.extensions.sharedLibrary}${stdenvNoCC.lib.optionalString stdenvNoCC.hostPlatform.isLinux ".3"}
ln -s $out/lib/libmkl_rt${stdenvNoCC.hostPlatform.extensions.sharedLibrary} $out/lib/libcblas${stdenvNoCC.hostPlatform.extensions.sharedLibrary}${stdenvNoCC.lib.optionalString stdenvNoCC.hostPlatform.isLinux ".3"}
ln -s $out/lib/libmkl_rt${stdenvNoCC.hostPlatform.extensions.sharedLibrary} $out/lib/liblapack${stdenvNoCC.hostPlatform.extensions.sharedLibrary}${stdenvNoCC.lib.optionalString stdenvNoCC.hostPlatform.isLinux ".3"}
ln -s $out/lib/libmkl_rt${stdenvNoCC.hostPlatform.extensions.sharedLibrary} $out/lib/liblapacke${stdenvNoCC.hostPlatform.extensions.sharedLibrary}${stdenvNoCC.lib.optionalString stdenvNoCC.hostPlatform.isLinux ".3"}
'';

# fixDarwinDylibName fails for libmkl_cdft_core.dylib because the
8 changes: 4 additions & 4 deletions pkgs/development/libraries/science/math/openblas/default.nix
View file
Original file line number Diff line number Diff line change
@@ -178,10 +178,10 @@ EOF
done
# Setup symlinks for blas / lapack
ln -s $out/lib/libopenblas${stdenv.hostPlatform.extensions.sharedLibrary} $out/lib/libblas${stdenv.hostPlatform.extensions.sharedLibrary}
ln -s $out/lib/libopenblas${stdenv.hostPlatform.extensions.sharedLibrary} $out/lib/libcblas${stdenv.hostPlatform.extensions.sharedLibrary}
ln -s $out/lib/libopenblas${stdenv.hostPlatform.extensions.sharedLibrary} $out/lib/liblapack${stdenv.hostPlatform.extensions.sharedLibrary}
ln -s $out/lib/libopenblas${stdenv.hostPlatform.extensions.sharedLibrary} $out/lib/liblapacke${stdenv.hostPlatform.extensions.sharedLibrary}
ln -s $out/lib/libopenblas${stdenv.hostPlatform.extensions.sharedLibrary} $out/lib/libblas${stdenv.hostPlatform.extensions.sharedLibrary}${stdenv.lib.optionalString stdenv.hostPlatform.isLinux ".3"}
ln -s $out/lib/libopenblas${stdenv.hostPlatform.extensions.sharedLibrary} $out/lib/libcblas${stdenv.hostPlatform.extensions.sharedLibrary}${stdenv.lib.optionalString stdenv.hostPlatform.isLinux ".3"}
ln -s $out/lib/libopenblas${stdenv.hostPlatform.extensions.sharedLibrary} $out/lib/liblapack${stdenv.hostPlatform.extensions.sharedLibrary}${stdenv.lib.optionalString stdenv.hostPlatform.isLinux ".3"}
ln -s $out/lib/libopenblas${stdenv.hostPlatform.extensions.sharedLibrary} $out/lib/liblapacke${stdenv.hostPlatform.extensions.sharedLibrary}${stdenv.lib.optionalString stdenv.hostPlatform.isLinux ".3"}
'';

meta = with stdenv.lib; {
2 changes: 2 additions & 0 deletions pkgs/development/python-modules/scipy/default.nix
View file
Original file line number Diff line number Diff line change
@@ -53,6 +53,8 @@ in buildPythonPackage rec {

setupPyBuildFlags = [ "--fcompiler='gnu95'" ];

SCIPY_USE_G77_ABI_WRAPPER = 1;

meta = {
description = "SciPy (pronounced 'Sigh Pie') is open-source software for mathematics, science, and engineering. ";
homepage = "https://www.scipy.org/";