nixpkgs/doc/using/overlays.xml
Matthew Bauer 3c41d61514 doc/overlays.xml: update documentation for BLAS/LAPACK
This expands the documentation and explains how to assert LP64.
2020-04-21 11:03:10 -05:00

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<chapter xmlns="http://docbook.org/ns/docbook"
xmlns:xlink="http://www.w3.org/1999/xlink"
xml:id="chap-overlays">
<title>Overlays</title>
<para>
This chapter describes how to extend and change Nixpkgs using overlays. Overlays are used to add layers in the fixed-point used by Nixpkgs to compose the set of all packages.
</para>
<para>
Nixpkgs can be configured with a list of overlays, which are applied in order. This means that the order of the overlays can be significant if multiple layers override the same package.
</para>
<!--============================================================-->
<section xml:id="sec-overlays-install">
<title>Installing overlays</title>
<para>
The list of overlays can be set either explicitly in a Nix expression, or through <literal>&lt;nixpkgs-overlays></literal> or user configuration files.
</para>
<section xml:id="sec-overlays-argument">
<title>Set overlays in NixOS or Nix expressions</title>
<para>
On a NixOS system the value of the <literal>nixpkgs.overlays</literal> option, if present, is passed to the system Nixpkgs directly as an argument. Note that this does not affect the overlays for non-NixOS operations (e.g. <literal>nix-env</literal>), which are <link xlink:href="#sec-overlays-lookup">looked</link> up independently.
</para>
<para>
The list of overlays can be passed explicitly when importing nixpkgs, for example <literal>import &lt;nixpkgs> { overlays = [ overlay1 overlay2 ]; }</literal>.
</para>
<para>
Further overlays can be added by calling the <literal>pkgs.extend</literal> or <literal>pkgs.appendOverlays</literal>, although it is often preferable to avoid these functions, because they recompute the Nixpkgs fixpoint, which is somewhat expensive to do.
</para>
</section>
<section xml:id="sec-overlays-lookup">
<title>Install overlays via configuration lookup</title>
<para>
The list of overlays is determined as follows.
</para>
<para>
<orderedlist>
<listitem>
<para>
First, if an <link xlink:href="#sec-overlays-argument"><varname>overlays</varname> argument</link> to the Nixpkgs function itself is given, then that is used and no path lookup will be performed.
</para>
</listitem>
<listitem>
<para>
Otherwise, if the Nix path entry <literal>&lt;nixpkgs-overlays></literal> exists, we look for overlays at that path, as described below.
</para>
<para>
See the section on <literal>NIX_PATH</literal> in the Nix manual for more details on how to set a value for <literal>&lt;nixpkgs-overlays>.</literal>
</para>
</listitem>
<listitem>
<para>
If one of <filename>~/.config/nixpkgs/overlays.nix</filename> and <filename>~/.config/nixpkgs/overlays/</filename> exists, then we look for overlays at that path, as described below. It is an error if both exist.
</para>
</listitem>
</orderedlist>
</para>
<para>
If we are looking for overlays at a path, then there are two cases:
<itemizedlist>
<listitem>
<para>
If the path is a file, then the file is imported as a Nix expression and used as the list of overlays.
</para>
</listitem>
<listitem>
<para>
If the path is a directory, then we take the content of the directory, order it lexicographically, and attempt to interpret each as an overlay by:
<itemizedlist>
<listitem>
<para>
Importing the file, if it is a <literal>.nix</literal> file.
</para>
</listitem>
<listitem>
<para>
Importing a top-level <filename>default.nix</filename> file, if it is a directory.
</para>
</listitem>
</itemizedlist>
</para>
</listitem>
</itemizedlist>
</para>
<para>
Because overlays that are set in NixOS configuration do not affect non-NixOS operations such as <literal>nix-env</literal>, the <filename>overlays.nix</filename> option provides a convenient way to use the same overlays for a NixOS system configuration and user configuration: the same file can be used as <filename>overlays.nix</filename> and imported as the value of <literal>nixpkgs.overlays</literal>.
</para>
<!-- TODO: Example of sharing overlays between NixOS configuration
and configuration lookup. Also reference the example
from the sec-overlays-argument paragraph about NixOS.
-->
</section>
</section>
<!--============================================================-->
<section xml:id="sec-overlays-definition">
<title>Defining overlays</title>
<para>
Overlays are Nix functions which accept two arguments, conventionally called <varname>self</varname> and <varname>super</varname>, and return a set of packages. For example, the following is a valid overlay.
</para>
<programlisting>
self: super:
{
boost = super.boost.override {
python = self.python3;
};
rr = super.callPackage ./pkgs/rr {
stdenv = self.stdenv_32bit;
};
}
</programlisting>
<para>
The first argument (<varname>self</varname>) corresponds to the final package set. You should use this set for the dependencies of all packages specified in your overlay. For example, all the dependencies of <varname>rr</varname> in the example above come from <varname>self</varname>, as well as the overridden dependencies used in the <varname>boost</varname> override.
</para>
<para>
The second argument (<varname>super</varname>) corresponds to the result of the evaluation of the previous stages of Nixpkgs. It does not contain any of the packages added by the current overlay, nor any of the following overlays. This set should be used either to refer to packages you wish to override, or to access functions defined in Nixpkgs. For example, the original recipe of <varname>boost</varname> in the above example, comes from <varname>super</varname>, as well as the <varname>callPackage</varname> function.
</para>
<para>
The value returned by this function should be a set similar to <filename>pkgs/top-level/all-packages.nix</filename>, containing overridden and/or new packages.
</para>
<para>
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.
</para>
</section>
<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
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
are configured through overlays.
</para>
<section xml:id="sec-overlays-alternatives-blas-lapack">
<title>BLAS/LAPACK</title>
<para>
In Nixpkgs, we have multiple implementations of the BLAS/LAPACK
numerical linear algebra interfaces. They are:
</para>
<itemizedlist>
<listitem>
<para>
<link xlink:href="https://www.openblas.net/">OpenBLAS</link>
</para>
<para>
The Nixpkgs attribute is <literal>openblas</literal> for
ILP64 and <literal>openblasCompat</literal> for LP64. This
is the default.
</para>
</listitem>
<listitem>
<para>
<link xlink:href="http://www.netlib.org/lapack/">LAPACK
reference</link> (also provides BLAS)
</para>
<para>
The Nixpkgs attribute is <literal>lapack-reference</literal>.
</para>
</listitem>
<listitem>
<para>
<link
xlink:href="https://software.intel.com/en-us/mkl">Intel
MKL</link> (only works on x86 architecture, unfree)
</para>
<para>
The Nixpkgs attribute is <literal>mkl</literal>.
</para>
</listitem>
</itemizedlist>
<para>
Introduced in <link
xlink:href="https://github.com/NixOS/nixpkgs/pull/83888">PR
#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:
</para>
<programlisting>
self: super:
{
blas = super.blas.override {
blasProvider = self.mkl;
}
lapack = super.lapack.override {
lapackProvider = self.mkl;
}
}
</programlisting>
<para>
This overlay uses Intels 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.
</para>
<para>
Intel MKL requires an <literal>openmp</literal> implementation
when running with multiple processors. By default,
<literal>mkl</literal> will use Intels <literal>iomp</literal>
implementation if no other is specified, but this is a
runtime-only dependency and binary compatible with the LLVM
implementation. To use that one instead, Intel recommends users
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.
</para>
<para>
For BLAS/LAPACK switching to work correctly, all packages must
depend on <literal>blas</literal> or <literal>lapack</literal>.
This ensures that only one BLAS/LAPACK library is used at one
time. There are two versions versions of BLAS/LAPACK currently
in the wild, <literal>LP64</literal> (integer size = 32 bits)
and <literal>ILP64</literal> (integer size = 64 bits). Some
software needs special flags or patches to work with
<literal>ILP64</literal>. You can check if
<literal>ILP64</literal> is used in Nixpkgs with
<varname>blas.isILP64</varname> and
<varname>lapack.isILP64</varname>. Some software does NOT work
with <literal>ILP64</literal>, and derivations need to specify
an assertion to prevent this. You can prevent
<literal>ILP64</literal> from being used with the following:
</para>
<programlisting>
{ stdenv, blas, lapack, ... }:
assert (!blas.isILP64) &amp;&amp; (!lapack.isILP64);
stdenv.mkDerivation {
...
}
</programlisting>
</section>
</section>
</chapter>