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<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE guide SYSTEM "/dtd/guide.dtd">
<!-- $Header: /var/cvsroot/gentoo/xml/htdocs/proj/en/science/blas-lapack.xml,v 1.3 2007/12/27 19:35:25 bicatali Exp $ -->
<guide link="/proj/en/science/blas-lapack.xml">
<title>Using multiple versions of BLAS and LAPACK with Gentoo/Linux</title>
<author title="Author">
<mail link="bicatali@gentoo.org">Sébastien Fabbro</mail>
</author>
<author title="Author">
<mail link="markusle@gentoo.org">Markus Dittrich</mail>
</author>
<author title="Editor">
<mail link="nightmorph@gentoo.org">Joshua Saddler</mail>
</author>
<abstract>
This guide explains the use of the different implementations of the BLAS
and LAPACK libraries that are available via Portage.
</abstract>
<!-- The content of this document is licensed under the CC-BY-SA license -->
<!-- See http://creativecommons.org/licenses/by-sa/2.5 -->
<license/>
<version>1.0</version>
<date>2007-10-22</date>
<chapter>
<title>Introduction</title>
<section>
<body>
<p>
The Basic Linear Algebra Subroutines (BLAS) and Linear Algebra PACKage (LAPACK)
are well designed linear algebra software libraries developed by the
High Performance Computing (HPC) community. BLAS
implements dense matrix and vectors products, while LAPACK provides routines for
solving systems of linear equations. Both are widely used in
many scientific applications and it is, therefore, important to
have efficient implementations available.
</p>
<p>
Originally written in FORTRAN 77, a number of additional language
wrappers have been developed for languages like C, C++, FORTRAN 95, and others.
The following legacy libraries are available via the reference ebuilds:
</p>
<ul>
<li>
<uri link="http://netlib.org/blas">BLAS</uri>: FORTRAN 77 implementation of
BLAS
</li>
<li>
<uri link="http://netlib.org/blas">CBLAS</uri>: C implementation of BLAS
</li>
<li>
<uri link="http://netlib.org/lapack">LAPACK</uri>: FORTRAN 77 implementation
of LAPACK
</li>
</ul>
<p>
In addition, Gentoo provides a number of optimized BLAS and LAPACK implementations
that will be described below. Different implementations are bundled together with
Gentoo's <c>eselect</c> system and the widely used <c>pkg-config</c> tool.
</p>
<p> It is important to note that if you require, e.g., a well performing
BLAS implementation, simply emerging X over Y often is not enough. Rather, you will have
to carefully benchmark your applications since performance may depend
on many factors,
such as hardware or network.
If you are simply looking for a well performing and well tested
implementation, the reference ebuilds will likely be your best choice.
</p>
</body>
</section>
</chapter>
<chapter>
<title>For Users</title>
<section>
<title>Installing</title>
<body>
<p>
If best possible performance is not of paramount importance for you
and you simply
need BLAS and/or LAPACK, just emerge the virtual packages:
</p>
<pre caption="Installing">
# <i>emerge blas cblas lapack</i>
</pre>
<p>
These will install the reference legacy packages from
<uri>http://netlib.org</uri>. They are well tested, easy to debug
implementations. They should satisfy most users; if they're all you need, you're
done reading.
</p>
<p>
However, if:
</p>
<ul>
<li>BLAS/LAPACK are critical for the speed of your applications</li>
<li>you absolutely need to build the fastest computer</li>
<li>you want to help Gentoo sci project to improve their packages</li>
</ul>
<p>
... then read on, and be sure to file bugs both to Gentoo and upstream.
</p>
<p>
There is a number of optimized implementations of these libraries in the Portage
tree:
</p>
<ul>
<li>
<uri link="http://math-atlas.sourceforge.net">ATLAS</uri>: Automatically
Tuned Linear Algebra Software is an open-source package that empirically
tunes the library to the machine it is being compiled on. It provides BLAS
(FORTRAN 77 and C), and LAPACK implementations on various architectures.
</li>
<li>
<uri
link="http://www.tacc.utexas.edu/resources/software/software.php">GotoBLAS</uri>:
Goto BLAS provide open-source, free for academic use, hand-coded
machine language, processor optimized versions of the FORTRAN 77 BLAS
routines. Claims to be the fastest BLAS.
</li>
<li>
<uri link="http://developer.amd.com/acml.jsp">ACML</uri>: AMD Core Math
Library is a closed-source but free package containing BLAS (FORTRAN 77
only) and LAPACK for x86 and amd64 architectures, but also other math tools
such as statistical libraries and FFTs.
</li>
<li>
<uri link="http://developer.intel.com/software/products/mkl/">MKL</uri>:
Intel® Math Kernel Library is a closed-source but free package for
non-commercial use containing BLAS (FORTRAN 77 and C), LAPACK optimized for
Intel® based architectures: x86, amd64 and ia64.
</li>
</ul>
<p>
Usually performance gain is noticeable mainly with BLAS, since LAPACK routines
depend on BLAS kernels.
</p>
</body>
</section>
<section>
<title>Compiling and linking with installed libraries</title>
<body>
<p>
We took great care to make sure that each package provides consistent pkg-config files.
Hence, compiling and linking with BLAS/LAPACK should be simple and straightforward:
</p>
<pre caption="Compiling and linking BLAS/LAPACK">
# <i>pkg-config --libs blas</i> <comment>(To link with FORTRAN 77 BLAS library)</comment>
# <i>pkg-config --cflags cblas</i> <comment>(To compile against C BLAS library)</comment>
# <i>pkg-config --libs cblas</i> <comment>(To link with C BLAS library)</comment>
# <i>pkg-config --libs lapack</i> <comment>(To link with FORTRAN 77 LAPACK library)</comment>
</pre>
<p>
<c>pkg-config</c> files are available for whichever implementation you select with <c>eselect</c>.
More information on using <c>pkg-config</c> can be obtained with <c>man pkg-config</c>.
</p>
</body>
</section>
<section>
<title>Choosing libraries</title>
<body>
<p>
You can easily switch BLAS, CBLAS and LAPACK implementations with
<c>eselect</c>. At this point, you probably have <c>eselect-blas</c>,
<c>eselect-cblas</c> and <c>eselect-lapack</c> installed. If you do not,
install them now! Using eselect, you can view which implementations of CBLAS
are available.
</p>
<pre caption="Viewing available implementations">
# <i>eselect cblas list</i>
Installed CBLAS for library directory lib64
[1] atlas
[2] atlas-threads
[3] gsl
[4] mkl-threads *
[5] reference
</pre>
<p>
The implementation marked with an asterisk (*) is the currently
selected implementation. To switch implementations, run:
</p>
<pre caption="Switching to the ATLAS implementation of LAPACK">
# <i>eselect lapack set atlas</i>
</pre>
<p>
To learn more about the <c>eselect</c> tool, visit the
<uri link="http://www.gentoo.org/proj/en/eselect/user-guide.xml">eselect guide</uri>
</p>
<p>
When selecting blas, cblas or lapack profiles try to avoid mixing
different implementations since we don't have any mechanism to enforce
reasonable profiles. However, here is a list of well performing
profile combinations that have been used successfully in the past:
</p>
<ul>
<li> Most CPUs:
<ul>
<li>blas,cblas: atlas (or atlas-threads with multi-processor)</li>
<li>lapack:atlas</li>
</ul>
</li>
<li> Most CPUs:
<ul>
<li>blas: goto </li>
<li>cblas,lapack: reference</li>
</ul>
</li>
<li> AMD based CPUs:
<ul>
<li>blas,lapack: acml-gfortran (or acml-gfortran-openmp with
multi-processors) </li>
<li>cblas: reference</li>
</ul>
</li>
<li> Intel based CPUs:
<ul>
<li>blas,cblas,lapack: mkl-threads</li>
</ul>
</li>
</ul>
</body>
</section>
<section>
<title>Choosing a compiler</title>
<body>
<p>
Most of the libraries can compile with both the GNU compiler collection and the
Intel® compilers on the x86, amd64 and ia64 architectures. By default, you are
probably using <c>gcc</c>. You can also compile the <c>*-reference</c> packages
with <c>ifort</c> and <c>icc</c>. To do this, you need to define the F77
environment variable and don't forget the FFLAGS.
</p>
<pre caption="Using non-GCC compilers">
# <i>F77=ifort FFLAGS="-O2 -mp" emerge blas-reference</i>
</pre>
<p>
Depending on your hardware, a small performance gain can be noticed thanks to
vectorization. The <c>-mp</c> flag maintains floating-point precision, since by
default ifort is pretty aggressive on floating point arithmetic, and we are
actually compiling a math package. Try <c>man ifort</c> to see additional flags
to fit your hardware.
</p>
<p>
Some of the implementations let you specify the Intel® C compiler as
well. Please beware that not all libraries compile with all
combinations. You should receive an error during the emerge in case you have
chosen an incompatible combination.
</p>
<p>
As usual for Gentoo, there are many combinations of USE flags and
compilers with which you could compile a package. Unfortunately
switching compilers between BLAS and LAPACK might not be always
compatible. For example:
</p>
<pre caption="Incompatible combinations">
# <i>F77=ifort FFLAGS="-O2 -mp" USE="openmp" emerge =acml-3.6.0-r1</i>
# <i>eselect blas set acml-ifort-openmp</i>
# <i>F77=gfortran FFLAGS="-O2" emerge lapack-reference</i>
</pre>
<p>
This will most likely break things or not even compile.
</p>
<p>
Try to be consistent in your choice. Stay with the GCC most of the time will
avoid you some trouble, unless you want to use the MKL, in which case the Intel®
C and FORTRAN compilers make a good combination.
</p>
</body>
</section>
<section>
<title>Documentation</title>
<body>
<p>
If you need BLAS or LAPACK to develop your own programs, the documentation
becomes pretty handy. Setting the USE="doc" flag for the corresponding BLAS or
LAPACK package will install man pages and quick reference sheets from the
<c>app-doc/blas-docs</c> and <c>app-doc/lapack-docs</c> packages. They are
standard and valid for all implementations. For optimized packages, the
USE="doc" flags will usually install extra doc in PDF or HTML format.
</p>
</body>
</section>
</chapter>
<chapter>
<title>For Developers</title>
<section>
<title>Providing new implementations</title>
<body>
<p>
The Portage tree contains many ebuilds that depend on the BLAS/CBLAS/LAPACK
libraries. As there is more than one possible implementation, the Gentoo
Scientific Project reorganized all the packages to provide <c>virtual/blas</c>,
<c>virtual/cblas</c>, and <c>virtual/lapack</c>. All ebuilds using BLAS should
depend on this virtual package, unless it is explicitly known to break with
different BLAS implementations.
</p>
<p>
To work with Gentoo's configuration tools
<c>app-admin/eselect-{blas,cblas,lapack}</c>, and the virtual, every ebuild that
installs a BLAS implementation must fulfill following requirements:
</p>
<ol>
<li>
The ebuild must install an eselect file for each profile it provides. The
libraries should link to the ones in <path>/usr/$(get_libdir)</path>
directories and the include files in <path>/usr/include</path>:
<ul>
<li>
<path>libblas.so[.0]</path> - Shared object for FORTRAN BLAS
applications
</li>
<li>
<path>libblas.a</path> - Static library for FORTRAN BLAS applications
</li>
<li>
<path>libcblas.so[.0]</path> - Shared object for C/C++ CBLAS applications
</li>
<li>
<path>libcblas.a</path> - Static library for C/C++ CBLAS applications
</li>
<li><path>cblas.h</path> - Include header for C/C++ applications</li>
<li>
<path>liblapack.so[.0]</path> - Shared object for FORTRAN LAPACK
applications
</li>
<li>
<path>liblapack.a</path> - Static library for FORTRAN LAPACK applications
</li>
</ul>
</li>
<li>
The ebuild must install a <path>blas.pc</path>, <path>cblas.pc</path> and/or
<path>lapack.pc</path> pkg-config file and therefore RDEPEND on
<c>dev-util/pkgconfig</c>. They should also be included in the eselect
files, and link to the <path>/usr/$(get_libdir)/pkgconfig</path> directory:
<ul>
<li><path>blas.pc</path> - BLAS pkg-config file</li>
<li><path>cblas.pc</path> - CBLAS pkg-config file</li>
<li><path>lapack.pc</path> - LAPACK pkg-config file</li>
</ul>
</li>
<li>Be included in the virtual package as a possible provider:
<ul>
<li><c>virtual/blas</c> - BLAS virtual package</li>
<li><c>virtual/cblas</c> - CBLAS virtual package</li>
<li><c>virtual/lapack</c> - LAPACK virtual package</li>
</ul>
</li>
</ol>
<p>
The easiest way of understanding all this is probably getting inspiration from
one of the available packages. Currently the Portage tree provide the following
virtuals:
</p>
<table>
<tr>
<th>Package name</th>
<th>virtual/blas</th>
<th>virtual/cblas</th>
<th>virtual/lapack</th>
</tr>
<tr>
<ti><c>sci-libs/acml</c></ti>
<ti>*</ti>
<ti></ti>
<ti>*</ti>
</tr>
<tr>
<ti><c>sci-libs/blas-atlas</c></ti>
<ti>*</ti>
<ti>*</ti>
<ti></ti>
</tr>
<tr>
<ti><c>sci-libs/blas-goto</c></ti>
<ti>*</ti>
<ti></ti>
<ti></ti>
</tr>
<tr>
<ti><c>sci-libs/blas-reference</c></ti>
<ti>*</ti>
<ti></ti>
<ti></ti>
</tr>
<tr>
<ti><c>sci-libs/cblas-reference</c></ti>
<ti></ti>
<ti>*</ti>
<ti></ti>
</tr>
<tr>
<ti><c>sci-libs/gsl</c></ti>
<ti></ti>
<ti>*</ti>
<ti></ti>
</tr>
<tr>
<ti><c>sci-libs/lapack-atlas</c></ti>
<ti></ti>
<ti></ti>
<ti>*</ti>
</tr>
<tr>
<ti><c>sci-libs/lapack-reference</c></ti>
<ti></ti>
<ti></ti>
<ti>*</ti>
</tr>
<tr>
<ti><c>sci-libs/mkl</c></ti>
<ti>*</ti>
<ti>*</ti>
<ti>*</ti>
</tr>
</table>
</body>
</section>
<section>
<title>Packages with BLAS/LAPACK dependencies</title>
<body>
<p>
Simply use <c>virtual/{blas,cblas,lapack}</c> as a [R]DEPEND. To build some
packages, you might need to use the pkg-config tool. If you are lucky, the
package uses autotools together with common BLAS and LAPACK M4 macros.In this
case, the configuration step becomes simple. For example:
</p>
<pre caption="Sample package configuration">
<keyword>econf</keyword> --with-blas="<var>$(pkg-config --libs blas)</var>"
</pre>
<impo>
Don't forget to add <c>dev-util/pkgconfig</c> in DEPEND.
</impo>
</body>
</section>
</chapter>
<chapter>
<title>In the near future</title>
<section>
<body>
<p>
We plan to include more standard BLAS, LAPACK libraries: BLAS 95, LAPACK 95,
Sparse BLAS, ScaLAPACK. If you feel inclined to write an ebuild for these, you
are more than welcomed to file it on our <uri
link="http://bugs.gentoo.org">Bugzilla</uri>.
</p>
</body>
</section>
</chapter>
</guide>
|
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