Merge pull request #85636 from matthewbauer/blas-lapack-fix-fallout-from-83888
BLAS/LAPACK fix fallout from #83888
This commit is contained in:
Frederik Rietdijk
GitHub
commit
ec21df329a
@ -1290,32 +1290,9 @@ self: super: {
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### How to use Intel's MKL with numpy and scipy?
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A `site.cfg` is created that configures BLAS based on the `blas` parameter of
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the `numpy` derivation. By passing in `mkl`, `numpy` and packages depending on
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`numpy` will be built with `mkl`.
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The following is an overlay that configures `numpy` to use `mkl`:
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```nix
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self: super: {
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python37 = super.python37.override {
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packageOverrides = python-self: python-super: {
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numpy = python-super.numpy.override {
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blas = super.pkgs.mkl;
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};
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};
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};
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}
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```
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`mkl` requires an `openmp` implementation when running with multiple processors.
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By default, `mkl` will use Intel's `iomp` implementation if no other is
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specified, but this is a runtime-only dependency and binary compatible with the
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LLVM implementation. To use that one instead, Intel recommends users set it with
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`LD_PRELOAD`.
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Note that `mkl` is only available on `x86_64-{linux,darwin}` platforms;
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moreover, Hydra is not building and distributing pre-compiled binaries using it.
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MKL can be configured using an overlay. See the section “[Using
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overlays to configure
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alternatives](#sec-overlays-alternatives-blas-lapack)”.
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### What inputs do `setup_requires`, `install_requires` and `tests_require` map to?
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@ -137,4 +137,118 @@ self: super:
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Overlays are similar to other methods for customizing Nixpkgs, in particular the <literal>packageOverrides</literal> attribute described in <xref linkend="sec-modify-via-packageOverrides"/>. Indeed, <literal>packageOverrides</literal> acts as an overlay with only the <varname>super</varname> argument. It is therefore appropriate for basic use, but overlays are more powerful and easier to distribute.
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</para>
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</section>
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<section xml:id="sec-overlays-alternatives">
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<title>Using overlays to configure alternatives</title>
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<para>
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Certain software has different implementations of the same
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interface. Other distributions have functionality to switch
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between these. For example, Debian provides <link
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xlink:href="https://wiki.debian.org/DebianAlternatives">DebianAlternatives</link>.
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Nixpkgs has what we call <literal>alternatives</literal>, which
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are configured through overlays.
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</para>
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<section xml:id="sec-overlays-alternatives-blas-lapack">
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<title>BLAS/LAPACK</title>
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<para>
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In Nixpkgs, we have multiple implementations of the BLAS/LAPACK
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numerical linear algebra interfaces. They are:
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</para>
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<itemizedlist>
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<listitem>
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<para>
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<link xlink:href="https://www.openblas.net/">OpenBLAS</link>
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</para>
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<para>
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The Nixpkgs attribute is <literal>openblas</literal> for
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ILP64 and <literal>openblasCompat</literal> for LP64. This
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is the default.
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</para>
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</listitem>
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<listitem>
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<para>
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<link xlink:href="http://www.netlib.org/lapack/">LAPACK
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reference</link> (also provides BLAS)
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</para>
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<para>
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The Nixpkgs attribute is <literal>lapack-reference</literal>.
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</para>
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</listitem>
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<listitem>
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<para>
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<link
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xlink:href="https://software.intel.com/en-us/mkl">Intel
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MKL</link> (only works on x86 architecture, unfree)
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</para>
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<para>
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The Nixpkgs attribute is <literal>mkl</literal>.
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</para>
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</listitem>
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</itemizedlist>
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<para>
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Introduced in <link
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xlink:href="https://github.com/NixOS/nixpkgs/pull/83888">PR
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#83888</link>, we are able to override the ‘blas’ and ‘lapack’
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packages to use different implementations, through the
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‘blasProvider’ and ‘lapackProvider’ argument. This can be used
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to select a different provider. For example, an overlay can be
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created that looks like:
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</para>
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<programlisting>
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self: super:
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{
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blas = super.blas.override {
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blasProvider = self.mkl;
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}
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lapack = super.lapack.override {
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lapackProvider = self.mkl;
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}
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}
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</programlisting>
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<para>
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This overlay uses Intel’s MKL library for both BLAS and LAPACK
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interfaces. Note that the same can be accomplished at runtime
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using <literal>LD_PRELOAD</literal> of libblas.so.3 and
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liblapack.so.3.
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</para>
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<para>
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Intel MKL requires an <literal>openmp</literal> implementation
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when running with multiple processors. By default,
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<literal>mkl</literal> will use Intel’s <literal>iomp</literal>
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implementation if no other is specified, but this is a
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runtime-only dependency and binary compatible with the LLVM
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implementation. To use that one instead, Intel recommends users
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set it with <literal>LD_PRELOAD</literal>. Note that
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<literal>mkl</literal> is only available on
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<literal>x86_64-linux</literal> and
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<literal>x86_64-darwin</literal>. Moreover, Hydra is not build
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and distributing pre-compiled binaries using it.
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</para>
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<para>
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For BLAS/LAPACK switching to work correctly, all packages must
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depend on <literal>blas</literal> or <literal>lapack</literal>.
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This ensures that only one BLAS/LAPACK library is used at one
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time. There are two versions versions of BLAS/LAPACK currently
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in the wild, <literal>LP64</literal> (integer size = 32 bits)
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and <literal>ILP64</literal> (integer size = 64 bits). Some
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software needs special flags or patches to work with
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<literal>ILP64</literal>. You can check if
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<literal>ILP64</literal> is used in Nixpkgs with
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<varname>blas.isILP64</varname> and
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<varname>lapack.isILP64</varname>. Some software does NOT work
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with <literal>ILP64</literal>, and derivations need to specify
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an assertion to prevent this. You can prevent
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<literal>ILP64</literal> from being used with the following:
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</para>
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<programlisting>
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{ stdenv, blas, lapack, ... }:
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assert (!blas.isILP64) && (!lapack.isILP64);
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stdenv.mkDerivation {
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...
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}
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</programlisting>
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</section>
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</section>
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</chapter>
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@ -2,7 +2,7 @@
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, libyaml, libxc, fftw, blas, lapack, gsl, netcdf, arpack, autoreconfHook
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}:
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assert (!blas.is64bit) && (!lapack.is64bit);
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assert (!blas.isILP64) && (!lapack.isILP64);
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stdenv.mkDerivation rec {
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pname = "octopus";
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@ -13,7 +13,7 @@
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assert pythonSupport -> pythonPackages != null;
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assert opencvSupport -> opencv != null;
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assert (!blas.is64bit) && (!lapack.is64bit);
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assert (!blas.isILP64) && (!lapack.isILP64);
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let
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pname = "shogun";
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@ -9,7 +9,7 @@
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, static ? false
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}:
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assert (!blas.is64bit) && (!lapack.is64bit);
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assert (!blas.isILP64) && (!lapack.isILP64);
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stdenv.mkDerivation rec {
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name = "R-3.6.3";
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@ -5,7 +5,7 @@
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}:
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assert enableGUI -> libGLU != null && libGL != null && xorg != null && fltk != null;
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assert (!blas.is64bit) && (!lapack.is64bit);
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assert (!blas.isILP64) && (!lapack.isILP64);
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stdenv.mkDerivation rec {
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pname = "giac${lib.optionalString enableGUI "-with-xcas"}";
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@ -1,7 +1,7 @@
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{ stdenv, fetchurl, cmake, blas, lapack, gfortran, gmm, fltk, libjpeg
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, zlib, libGL, libGLU, xorg, opencascade-occt }:
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assert (!blas.is64bit) && (!lapack.is64bit);
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assert (!blas.isILP64) && (!lapack.isILP64);
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stdenv.mkDerivation rec {
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pname = "gmsh";
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@ -54,7 +54,7 @@
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, less
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}:
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assert (!blas.is64bit) && (!lapack.is64bit);
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assert (!blas.isILP64) && (!lapack.isILP64);
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# This generates a `sage-env` shell file that will be sourced by sage on startup.
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# It sets up various environment variables, telling sage where to find its
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@ -23,7 +23,7 @@
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}:
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# lots of segfaults with (64 bit) blas
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assert (!blas.is64bit) && (!lapack.is64bit);
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assert (!blas.isILP64) && (!lapack.isILP64);
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# Wrapper that combined `sagelib` with `sage-env` to produce an actually
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# executable sage. No tests are run yet and no documentation is built.
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@ -53,7 +53,7 @@
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, pplpy
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}:
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assert (!blas.is64bit) && (!lapack.is64bit);
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assert (!blas.isILP64) && (!lapack.isILP64);
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# This is the core sage python package. Everything else is just wrappers gluing
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# stuff together. It is not very useful on its own though, since it will not
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@ -1,7 +1,7 @@
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{ lib, stdenv
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, lapack-reference, openblasCompat, openblas
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, is64bit ? false
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, blasProvider ? if is64bit then openblas else openblasCompat }:
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, isILP64 ? false
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, blasProvider ? if isILP64 then openblas else openblasCompat }:
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let
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blasFortranSymbols = [
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@ -31,12 +31,12 @@ let
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else stdenv.hostPlatform.extensions.sharedLibrary;
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is64bit = blasProvider.blas64 or false;
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isILP64 = blasProvider.blas64 or false;
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blasImplementation = lib.getName blasProvider;
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in
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assert is64bit -> (blasImplementation == "openblas" && blasProvider.blas64) || blasImplementation == "mkl";
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assert isILP64 -> (blasImplementation == "openblas" && blasProvider.blas64) || blasImplementation == "mkl";
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stdenv.mkDerivation {
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pname = "blas";
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@ -49,7 +49,7 @@ stdenv.mkDerivation {
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};
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passthru = {
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inherit is64bit;
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inherit isILP64;
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provider = blasProvider;
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implementation = blasImplementation;
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};
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@ -58,6 +58,8 @@ stdenv.mkDerivation {
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dontConfigure = true;
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unpackPhase = "src=$PWD";
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dontPatchELF = true;
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installPhase = (''
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mkdir -p $out/lib $dev/include $dev/lib/pkgconfig
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@ -132,6 +134,8 @@ Libs: -L$out/lib -lcblas
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EOF
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'' + stdenv.lib.optionalString (blasImplementation == "mkl") ''
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mkdir -p $out/nix-support
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echo 'export MKL_INTERFACE_LAYER=${lib.optionalString is64bit "I"}LP64,GNU' > $out/nix-support/setup-hook
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echo 'export MKL_INTERFACE_LAYER=${lib.optionalString isILP64 "I"}LP64,GNU' > $out/nix-support/setup-hook
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ln -s $out/lib/libblas${canonicalExtension} $out/lib/libmkl_rt${stdenv.hostPlatform.extensions.sharedLibrary}
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ln -sf ${blasProvider}/include/* $dev/include
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'');
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}
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@ -1,7 +1,7 @@
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{ lib, stdenv
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, lapack-reference, openblasCompat, openblas
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, is64bit ? false
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, lapackProvider ? if is64bit then openblas else openblasCompat }:
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, isILP64 ? false
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, lapackProvider ? if isILP64 then openblas else openblasCompat }:
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let
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@ -14,7 +14,7 @@ let
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in
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assert is64bit -> (lapackImplementation == "openblas" && lapackProvider.blas64) || lapackImplementation == "mkl";
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assert isILP64 -> (lapackImplementation == "openblas" && lapackProvider.blas64) || lapackImplementation == "mkl";
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stdenv.mkDerivation {
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pname = "lapack";
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@ -27,7 +27,7 @@ stdenv.mkDerivation {
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};
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passthru = {
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inherit is64bit;
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inherit isILP64;
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provider = lapackProvider;
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implementation = lapackImplementation;
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};
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@ -36,6 +36,8 @@ stdenv.mkDerivation {
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dontConfigure = true;
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unpackPhase = "src=$PWD";
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dontPatchELF = true;
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installPhase = (''
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mkdir -p $out/lib $dev/include $dev/lib/pkgconfig
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@ -106,6 +108,8 @@ Libs: -L$out/lib -llapacke
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EOF
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'' + stdenv.lib.optionalString (lapackImplementation == "mkl") ''
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mkdir -p $out/nix-support
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echo 'export MKL_INTERFACE_LAYER=${lib.optionalString is64bit "I"}LP64,GNU' > $out/nix-support/setup-hook
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echo 'export MKL_INTERFACE_LAYER=${lib.optionalString isILP64 "I"}LP64,GNU' > $out/nix-support/setup-hook
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ln -s $out/lib/liblapack${canonicalExtension} $out/lib/libmkl_rt${stdenv.hostPlatform.extensions.sharedLibrary}
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ln -sf ${lapackProvider}/include/* $dev/include
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'');
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}
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@ -12,7 +12,7 @@
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, CoreServices, ApplicationServices
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}:
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assert (!blas.is64bit) && (!lapack.is64bit);
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assert (!blas.isILP64) && (!lapack.isILP64);
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with stdenv.lib;
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@ -88,7 +88,7 @@ stdenv.mkDerivation rec {
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"SHELL=${stdenv.shell}"
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"USE_SYSTEM_BLAS=1"
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"USE_BLAS64=${if blas.is64bit then "1" else "0"}"
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"USE_BLAS64=${if blas.isILP64 then "1" else "0"}"
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"USE_SYSTEM_LAPACK=1"
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@ -22,7 +22,7 @@
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with stdenv.lib;
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assert (!blas.is64bit) && (!lapack.is64bit);
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assert (!blas.isILP64) && (!lapack.isILP64);
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let
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dsfmtVersion = "2.2.3";
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@ -137,7 +137,7 @@ stdenv.mkDerivation rec {
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"SHELL=${stdenv.shell}"
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"USE_SYSTEM_BLAS=1"
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"USE_BLAS64=${if blas.is64bit then "1" else "0"}"
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"USE_BLAS64=${if blas.isILP64 then "1" else "0"}"
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"USE_SYSTEM_LAPACK=1"
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@ -53,7 +53,7 @@
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, darwin
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}:
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assert (!blas.is64bit) && (!lapack.is64bit);
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assert (!blas.isILP64) && (!lapack.isILP64);
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stdenv.mkDerivation rec {
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version = "5.2.0";
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@ -125,12 +125,12 @@ stdenv.mkDerivation rec {
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enableParallelBuilding = true;
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|
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# See https://savannah.gnu.org/bugs/?50339
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F77_INTEGER_8_FLAG = if blas.is64bit then "-fdefault-integer-8" else "";
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F77_INTEGER_8_FLAG = if blas.isILP64 then "-fdefault-integer-8" else "";
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|
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configureFlags = [
|
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"--with-blas=blas"
|
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"--with-lapack=lapack"
|
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(if blas.is64bit then "--enable-64" else "--disable-64")
|
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(if blas.isILP64 then "--enable-64" else "--disable-64")
|
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]
|
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++ (if stdenv.isDarwin then [ "--enable-link-all-dependencies" ] else [ ])
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++ stdenv.lib.optionals enableReadline [ "--enable-readline" ]
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|
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@ -2,7 +2,7 @@
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, gmpxx
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}:
|
||||
|
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assert (!blas.is64bit) && (!lapack.is64bit);
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assert (!blas.isILP64) && (!lapack.isILP64);
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|
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stdenv.mkDerivation rec {
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pname = "fflas-ffpack";
|
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|
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@ -10,7 +10,7 @@
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, withSage ? false # sage support
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}:
|
||||
|
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assert (!blas.is64bit) && (!lapack.is64bit);
|
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assert (!blas.isILP64) && (!lapack.isILP64);
|
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|
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stdenv.mkDerivation rec {
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pname = "linbox";
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@ -18,7 +18,7 @@ stdenv.mkDerivation {
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-e 's,^LAPACK=.*,LAPACK=-L${lapack}/lib -llapack,' \
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Makeconf
|
||||
''
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+ stdenv.lib.optionalString blas.is64bit
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+ stdenv.lib.optionalString blas.isILP64
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''
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sed -i Makeconf -e '/^FFLAGS=.*/ s/$/-fdefault-integer-8/'
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'';
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|
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@ -27,7 +27,7 @@ stdenv.mkDerivation {
|
||||
|
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cmakeFlags = [
|
||||
"-DBUILD_SHARED_LIBS=ON"
|
||||
"-DINTERFACE64=${optionalString blas.is64bit "1"}"
|
||||
"-DINTERFACE64=${optionalString blas.isILP64 "1"}"
|
||||
];
|
||||
|
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preCheck = if stdenv.isDarwin then ''
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
{ stdenv, fetchurl, unzip, blas, lapack, gfortran }:
|
||||
|
||||
assert (!blas.is64bit) && (!lapack.is64bit);
|
||||
assert (!blas.isILP64) && (!lapack.isILP64);
|
||||
|
||||
stdenv.mkDerivation rec {
|
||||
pname = "ipopt";
|
||||
|
||||
@ -1,8 +1,4 @@
|
||||
{ stdenv, fetchurl, cmake, gfortran, cudatoolkit, libpthreadstubs, lapack, blas
|
||||
, mklSupport ? false, mkl ? null
|
||||
}:
|
||||
|
||||
assert !mklSupport || mkl != null;
|
||||
{ stdenv, fetchurl, cmake, gfortran, cudatoolkit, libpthreadstubs, lapack, blas }:
|
||||
|
||||
with stdenv.lib;
|
||||
|
||||
@ -17,13 +13,10 @@ in stdenv.mkDerivation {
|
||||
name = "magma-${version}.tar.gz";
|
||||
};
|
||||
|
||||
buildInputs = [ gfortran cudatoolkit libpthreadstubs cmake ]
|
||||
++ (if mklSupport then [ mkl ] else [ lapack blas ]);
|
||||
buildInputs = [ gfortran cudatoolkit libpthreadstubs cmake lapack blas ];
|
||||
|
||||
doCheck = false;
|
||||
|
||||
MKLROOT = optionalString mklSupport mkl;
|
||||
|
||||
preConfigure = ''
|
||||
export CC=${cudatoolkit.cc}/bin/gcc CXX=${cudatoolkit.cc}/bin/g++
|
||||
'';
|
||||
|
||||
@ -2,7 +2,7 @@
|
||||
, gfortran, mpi, blas, lapack
|
||||
} :
|
||||
|
||||
assert (!blas.is64bit) && (!lapack.is64bit);
|
||||
assert (!blas.isILP64) && (!lapack.isILP64);
|
||||
|
||||
stdenv.mkDerivation rec {
|
||||
pname = "scalapack";
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
{ stdenv, fetchFromGitHub, blas, lapack, gfortran, fixDarwinDylibNames }:
|
||||
|
||||
assert (!blas.is64bit) && (!lapack.is64bit);
|
||||
assert (!blas.isILP64) && (!lapack.isILP64);
|
||||
|
||||
stdenv.mkDerivation rec {
|
||||
pname = "scs";
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
{ stdenv, fetchurl, gfortran, blas, lapack }:
|
||||
|
||||
let
|
||||
int_t = if blas.is64bit then "int64_t" else "int32_t";
|
||||
int_t = if blas.isILP64 then "int64_t" else "int32_t";
|
||||
in
|
||||
stdenv.mkDerivation rec {
|
||||
version = "4.2.1";
|
||||
|
||||
@ -6,7 +6,7 @@ let
|
||||
version = "4.4.4";
|
||||
name = "suitesparse-${version}";
|
||||
|
||||
int_t = if blas.is64bit then "int64_t" else "int32_t";
|
||||
int_t = if blas.isILP64 then "int64_t" else "int32_t";
|
||||
SHLIB_EXT = stdenv.hostPlatform.extensions.sharedLibrary;
|
||||
in
|
||||
stdenv.mkDerivation {
|
||||
|
||||
@ -44,7 +44,7 @@ stdenv.mkDerivation rec {
|
||||
"BLAS=-lblas"
|
||||
"LAPACK=-llapack"
|
||||
"MY_METIS_LIB=-lmetis"
|
||||
] ++ stdenv.lib.optionals blas.is64bit [
|
||||
] ++ stdenv.lib.optionals blas.isILP64 [
|
||||
"CFLAGS=-DBLAS64"
|
||||
] ++ stdenv.lib.optionals enableCuda [
|
||||
"CUDA_PATH=${cudatoolkit}"
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
{ stdenv, fetchurl, cmake,
|
||||
gfortran, blas, lapack}:
|
||||
|
||||
assert (!blas.is64bit) && (!lapack.is64bit);
|
||||
assert (!blas.isILP64) && (!lapack.isILP64);
|
||||
|
||||
stdenv.mkDerivation rec {
|
||||
version = "5.2.1";
|
||||
|
||||
@ -8,7 +8,7 @@
|
||||
, gfortran
|
||||
, lapackSupport ? true }:
|
||||
|
||||
assert (!blas.is64bit) && (!lapack.is64bit);
|
||||
assert (!blas.isILP64) && (!lapack.isILP64);
|
||||
|
||||
stdenv.mkDerivation rec {
|
||||
pname = "sundials";
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
, gfortran
|
||||
, lapackSupport ? true }:
|
||||
|
||||
assert (!blas.is64bit) && (!lapack.is64bit);
|
||||
assert (!blas.isILP64) && (!lapack.isILP64);
|
||||
|
||||
stdenv.mkDerivation rec {
|
||||
pname = "sundials";
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
{ stdenv, fetchFromGitHub, darwin, ocaml, findlib, dune, base, stdio, lapack, blas }:
|
||||
|
||||
assert stdenv.lib.versionAtLeast (stdenv.lib.getVersion ocaml) "4.05.0";
|
||||
assert (!blas.is64bit) && (!lapack.is64bit);
|
||||
assert (!blas.isILP64) && (!lapack.isILP64);
|
||||
|
||||
stdenv.mkDerivation rec {
|
||||
pname = "ocaml${ocaml.version}-lacaml";
|
||||
|
||||
@ -11,7 +11,7 @@
|
||||
, npy
|
||||
}:
|
||||
|
||||
assert (!blas.is64bit) && (!lapack.is64bit);
|
||||
assert (!blas.isILP64) && (!lapack.isILP64);
|
||||
assert blas.implementation == "openblas" && lapack.implementation == "openblas";
|
||||
|
||||
buildDunePackage rec {
|
||||
|
||||
@ -14,7 +14,7 @@
|
||||
, withFftw ? true
|
||||
}:
|
||||
|
||||
assert (!blas.is64bit) && (!lapack.is64bit);
|
||||
assert (!blas.isILP64) && (!lapack.isILP64);
|
||||
|
||||
buildPythonPackage rec {
|
||||
pname = "cvxopt";
|
||||
|
||||
@ -12,18 +12,16 @@
|
||||
, setuptoolsBuildHook
|
||||
}:
|
||||
|
||||
assert (!blas.is64bit) && (!lapack.is64bit);
|
||||
assert (!blas.isILP64) && (!lapack.isILP64);
|
||||
|
||||
let
|
||||
cfg = writeTextFile {
|
||||
name = "site.cfg";
|
||||
text = (lib.generators.toINI {} {
|
||||
${blas.implementation} = {
|
||||
include_dirs = "${blas}/include:${lapack}/include";
|
||||
include_dirs = "${lib.getDev blas}/include:${lib.getDev lapack}/include";
|
||||
library_dirs = "${blas}/lib:${lapack}/lib";
|
||||
} // lib.optionalAttrs (blas.implementation == "mkl") {
|
||||
mkl_libs = "mkl_rt";
|
||||
lapack_libs = "";
|
||||
libraries = "lapack,lapacke,blas,cblas";
|
||||
};
|
||||
});
|
||||
};
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
{ stdenv, fetchurl, blas, lapack, mpi } :
|
||||
|
||||
assert (!blas.is64bit) && (!lapack.is64bit);
|
||||
assert (!blas.isILP64) && (!lapack.isILP64);
|
||||
|
||||
stdenv.mkDerivation rec {
|
||||
pname = "hpl";
|
||||
|
||||
@ -59,7 +59,7 @@ in
|
||||
{
|
||||
blas = mapListToAttrs supportedSystems (system': let system = lib.systems.elaborate { system = system'; };
|
||||
in mapListToAttrs (blasProviders system) (provider: let
|
||||
is64bit = builtins.elem provider (["mkl64"] ++ lib.optional system.is64bit "openblas");
|
||||
isILP64 = builtins.elem provider (["mkl64"] ++ lib.optional system.is64bit "openblas");
|
||||
pkgs = pkgsFun {
|
||||
config = { inherit allowUnfree; };
|
||||
system = system';
|
||||
@ -68,13 +68,13 @@ in
|
||||
lapackProvider = if provider == "mkl64"
|
||||
then super.mkl
|
||||
else builtins.getAttr provider super;
|
||||
inherit is64bit;
|
||||
inherit isILP64;
|
||||
};
|
||||
blas = super.blas.override {
|
||||
blasProvider = if provider == "mkl64"
|
||||
then super.mkl
|
||||
else builtins.getAttr provider super;
|
||||
inherit is64bit;
|
||||
inherit isILP64;
|
||||
};
|
||||
})];
|
||||
};
|
||||
|
||||
Loading…
Reference in New Issue
Block a user