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| author |   Sébastien Fabbro <sebfabbro@gmail.com> | 2011-01-10 06:09:24 +0000 |
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| committer | Sébastien Fabbro <sebfabbro@gmail.com> | 2011-01-10 06:09:24 +0000 |
| commit | ba0f4cdfdf0316b728161ecd78f9fff5ee5ae623 (patch) | |
| tree | cdabd272cc62cb7f901a6a4961e97e4d7bd8dfd4 /docs | |
| parent | more removing (diff) | |
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diff --git a/docs/proj/#linalg.xml# b/docs/proj/#linalg.xml# deleted file mode 100644 index 3105039cc..000000000 --- a/docs/proj/#linalg.xml# +++ /dev/null @@ -1,551 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE guide SYSTEM "/dtd/guide.dtd"> -<!-- $Header: $ --> - -<guide link="/proj/en/science/linalg.xml"> -<title>Linear Algebra on Gentoo</title> - -<author title="Author"> - <mail link="bicatali@gentoo.org">Sébastien Fabbro</mail> -</author> - -<abstract> - This guide explains the use of linear algebra libraries and focus on - how to use the different implementations of BLAS and LAPACK available on Gentoo. -</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>2010-12-22</date> - -<chapter> -<title>Introduction</title> -<section> -<body> - -<p> - There are <uri link="http://en.wikipedia.org/wiki/List_of_numerical_libraries">many</uri> - performant numerical libraries available. - The Basic Linear Algebra Subprograms (BLAS) and the Linear Algebra PACKage (LAPACK) - are well designed linear algebra libraries developed by the - High Performance Computing (HPC) community. BLAS is an API of 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> - BLAS and LAPACK were originally written in FORTRAN 77. Since then, a - number of additional language wrappers have been developed for - languages like C, C++, FORTRAN 95, Java, Python, etc... - Netlib offers exact implementations of the APIs and they are called - "reference" libraries. There is also some parallel implementations - for -</p> - -<ul> -<li> - <uri link="http://www.netlib.org/blas/">BLAS</uri>: FORTRAN 77 and C - (CBLAS) implementations of BLAS -</li> -<li> - <uri link="http://www.netlib.org/lapack/">LAPACK</uri>: FORTRAN 77 and - C (LAPACKE) implementations of LAPACK -</li> -</ul> - -<p> - -</p> - -<ul> -<li> - <uri link="http://www.netlib.org/blacs/">BLACS</uri>: FORTRAN 77 and C - implementations of BLACS -</li> -<li> - <uri link="http://www.netlib.org/scalapack/">ScaLAPACK</uri>: FORTRAN 77 and - C implementations of PBLAS and ScaLAPACK -</li> -</ul> - -<p> - In addition, Gentoo provides a number of optimized implementations - of the above linear algebra libraries that will be described - below. You can switch between implementations with the - 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 - package: -</p> - -<pre caption="Installing"> -# <i>emerge lapack</i> -</pre> - -<p> - This will install both <><> and <><> the reference packages from - <uri>http://www.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>linear algebra libraries 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/tacc-projects/gotoblas2/">GotoBLAS</uri>: - Goto BLAS provides open-source, free for academic use, hand-coded - machine language, processor optimized versions of the FORTRAN 77 - and C BLAS routines. Still claims to be the fastest BLAS. - </li> - <li> - <uri link="http://developer.amd.com/cpu/libraries/acml/Pages/default.aspx">ACML</uri>: - AMD Core Math Library is a closed-source but free package containing BLAS (FORTRAN 77 - only) and LAPACK for x86 and x86_64 architectures, but also other math tools - such as statistical libraries and FFTs. - </li> - <li> - <uri link="http://software.intel.com/en-us/articles/intel-mkl/">MKL</uri>: - Intel® Math Kernel Library is a closed-source but free package for - non-commercial use on Linux systems containing implementations of all the linear - algebra libraries mentioned here. - </li> -</ul> - -<p> - Usually performance gain is noticeable mainly with BLAS, since LAPACK routines - depend on BLAS kernels. -</p> - -</body> -</section> - - -<section> -<title>Developping with the installed linear algebra libraries</title> -<body> - -<p> - We took great care to make sure that each package provides - consistent pkg-config files generated by us. - Compiling and linking becomes straightforward: -</p> - -<pre caption="Compiling and linking linear algebra libraries"> -# <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 scalapack</i> <comment>(To link with the ScaLAPACK library)</comment> -</pre> - -<p> - <c>pkg-config</c> files are available for all implementations and - various alternatives within implementations. The default names of - the implementations are: blas, cblas, lapack, lapacke, blacs and - scalapack, and they can be chosen with <c>eselect</c>. You can also always compile or link - with an library not selected for the - More information on using <c>pkg-config</c> can be obtained with <c>man pkg-config</c>. -</p> - -</body> -</section> -<section> -<title>Selecting libraries</title> -<body> - -<p> - You can switch BLAS, CBLAS and LAPACK implementations with - <c>eselect</c>. you can view which implementations of CBLAS - are available. -</p> - -<pre caption="Viewing available implementations of CBLAS"> -# <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 threaded ATLAS implementation of BLAS"> -# <i>eselect blas set atlas-threads</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 your linear algebra 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> performant on most CPUs: - <ul> - <li>blas, cblas: atlas (or atlas-threads with multi-processor)</li> - <li>lapack, lapacke: atlas</li> - </ul> - </li> - <li> performant on most CPUs: - <ul> - <li>blas, cblas: goto2 </li> - <li>lapack, lapacke: reference</li> - </ul> - </li> - <li> performant on AMD based CPUs: - <ul> - <li>blas, lapack: acml-gfortran (or acml-gfortran-openmp with - multi-processors) </li> - <li>cblas: reference</li> - </ul> - </li> - <li> performant on Intel based CPUs: - <ul> - <li>blas,cblas,lapack: mkl-threads</li> - </ul> - </li> -</ul> - -</body> -</section> - -<section> -<title>Choosing a compiler</title> -<body> - -<p> - All the above libraries have been tested with the GNU compiler - collections (gcc, gfortran). - There are many available C compilers and a few FORTRAN (ifort, - Open64) compilers on Gentoo and many other FORTRAN compilers outside - of Gentoo (). -</p> - -<pre caption="Installing BLAS with the Intel FORTRAN compiler"> -# <i>F77=ifort FFLAGS="-O2 -mp1" 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="Looking for trouble combinations"> -# <i>USE=ifort emerge acml</i> -# <i>eselect blas set acml-ifort-openmp</i> -# <i>FC=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 - 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 ebuild developers</title> -<section> - -<section> -<title>Packages with BLAS/LAPACK dependencies</title> -<body> - -<p> - You need two things: - set [R]DEPEND to <c>virtual/<imp></c>. To build some - packages, you m need to use the pkg-config tool. If you are lucky, the - package uses autotools together with the autoconf <>AX_BLAS and <>AX_LAPACK M4 - macros. In this case, the configuration step becomes simple. For example: -</p> - -<pre caption="Sample package configuration with autotools"> -<keyword>econf</keyword> --with-blas="<var>$(pkg-config --libs blas)</var>" -</pre> - -</body> -</section> - - - -<title>Providing new implementations</title> -<body> - -<p> - The Portage tree contains many ebuilds that depend on the - BLAS/CBLAS/LAPACK/BLACS/ScaLAPACK libraries. As there is more than - one possible implementation, the Gentoo Science Project - reorganized all the packages to provide <c>virtual</c>. All ebuilds using - should depend on this virtual package, unless it is explicitly - known to break with a specific implementation. -</p> - -<p> - To work with Gentoo's configuration tools - <c>app-admin/eselect-{blas,cblas,lapack}</c>, and the virtual, every ebuild that - installs a BLAS implementation must fulfill following requirements: -</p> - -<ol> -<li> - The ebuild must install an eselect file for each profile it provides. The - libraries should link to the ones in <path>/usr/$(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 - virtual packages: -</p> - -<table> -<tr> - <th>Package name</th> - <th>virtual/blas</th> - <th>virtual/cblas</th> - <th>virtual/lapack</th> - <th>virtual/lapacke</th> - <th>virtual/blacs</th> - <th>virtual/scalapack</th> -</tr> -<tr> - <ti><c>sci-libs/acml</c></ti> - <ti>*</ti> - <ti></ti> - <ti>*</ti> - <ti></ti> - <ti></ti> - <ti></ti> -</tr> -<tr> - <ti><c>sci-libs/atlas</c></ti> - <ti>*</ti> - <ti>*</ti> - <ti>*</ti> - <ti>*</ti> - <ti></ti> - <ti></ti> -</tr> -<tr> - <ti><c>sci-libs/gotoblas2</c></ti> - <ti>*</ti> - <ti>*</ti> - <ti></ti> - <ti></ti> - <ti></ti> - <ti></ti> -</tr> -<tr> - <ti><c>sci-libs/blas-reference</c></ti> - <ti>*</ti> - <ti></ti> - <ti></ti> - <ti></ti> - <ti></ti> - <ti></ti> -</tr> -<tr> - <ti><c>sci-libs/cblas-reference</c></ti> - <ti></ti> - <ti>*</ti> - <ti></ti> - <ti></ti> - <ti></ti> - <ti></ti> -</tr> -<tr> - <ti><c>sci-libs/gsl</c></ti> - <ti></ti> - <ti>*</ti> - <ti></ti> - <ti></ti> - <ti></ti> - <ti></ti> -</tr> -<tr> - <ti><c>sci-libs/lapack-reference</c></ti> - <ti></ti> - <ti></ti> - <ti>*</ti> - <ti></ti> - <ti></ti> - <ti></ti> -</tr> -<tr> - <ti><c>sci-libs/mkl</c></ti> - <ti>*</ti> - <ti>*</ti> - <ti>*</ti> - <ti>*</ti> - <ti>*</ti> - <ti>*</ti> -</tr> -</table> - -</body> -</section> - -</chapter> - -<chapter> -<title>Benchmarks</title> -<section> -<body> - -<p> - 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> |