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diff --git a/docs/proj/blas-lapack.xml b/docs/proj/blas-lapack.xml deleted file mode 100644 index f4ef31cee..000000000 --- a/docs/proj/blas-lapack.xml +++ /dev/null @@ -1,492 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE guide SYSTEM "/dtd/guide.dtd"> - -<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.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>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=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/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> |