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| -rw-r--r-- | docs/proj/#linalg.xml# | 551 | ||||
| -rw-r--r-- | sci-libs/shogun/Manifest | 4 | ||||
| -rw-r--r-- | sci-libs/shogun/files/shogun-0.9.3-lapack.patch | 18 | ||||
| -rw-r--r-- | sci-libs/shogun/metadata.xml | 22 | ||||
| -rw-r--r-- | sci-libs/shogun/shogun-0.9.3.ebuild | 64 |
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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> diff --git a/sci-libs/shogun/Manifest b/sci-libs/shogun/Manifest deleted file mode 100644 index a8c260cf2..000000000 --- a/sci-libs/shogun/Manifest +++ /dev/null @@ -1,4 +0,0 @@ -AUX shogun-0.9.3-lapack.patch 583 RMD160 e1e70f045fa448601e8f43b6a7603030981dbf97 SHA1 abef54b23c9041ef65faa7e0324e89fed52749c4 SHA256 b86cbcb4f0003754393c6e55f501b0721d3479ee6bed48c876f1ee564b9a2825 -DIST shogun-0.9.3.tar.bz2 2853271 RMD160 9638a6b747a1177b048720b8999c60f33c7df5ef SHA1 d559dff3e11f777a23f00278d78d259ad896b829 SHA256 597d08155c7eff894dfae64dff8d4b37a5aba1da4a87b335881bddcb1a587526 -EBUILD shogun-0.9.3.ebuild 1625 RMD160 79dfc02d159c84b6cfcd749150779979e8273cdc SHA1 17df8f64dbe4270ead4158f54a6928fa05095a76 SHA256 42e0e74ebf89cff12b1c461264067ccf32350abd63899404add950aa8d290968 -MISC metadata.xml 1297 RMD160 dcc89a39c7d7a60ae5c128b8778cd314646e1417 SHA1 9ffe75693797b1eeb466223d6332cd589b32c624 SHA256 84677e9d55cab8bed4c8d99fdb917a6a31d21904526f20b95137716e6fed63e0 diff --git a/sci-libs/shogun/files/shogun-0.9.3-lapack.patch b/sci-libs/shogun/files/shogun-0.9.3-lapack.patch deleted file mode 100644 index 32e41aa1d..000000000 --- a/sci-libs/shogun/files/shogun-0.9.3-lapack.patch +++ /dev/null @@ -1,18 +0,0 @@ ---- src/configure.orig 2010-06-01 19:49:30.000000000 +0100 -+++ src/configure 2010-06-01 19:52:05.000000000 +0100 -@@ -2421,13 +2421,13 @@ - } - EOF - echocheck "AMD ACML support" -- if cc_check -lacml -lcblas -lgfortran -+ if cc_check $(pkg-config --libs cblas lapack) - then - echores "yes" - HAVE_ACML='#define HAVE_ACML 1' - HAVE_LAPACK='#define HAVE_LAPACK 1' - DEFINES="$DEFINES -DHAVE_ACML -DHAVE_LAPACK" -- LINKFLAGS="$LINKFLAGS -lacml -lcblas -lgfortran" -+ LINKFLAGS="$LINKFLAGS $(pkg-config --libs cblas lapack)" - else - echores "no" - diff --git a/sci-libs/shogun/metadata.xml b/sci-libs/shogun/metadata.xml deleted file mode 100644 index b5cdff054..000000000 --- a/sci-libs/shogun/metadata.xml +++ /dev/null @@ -1,22 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> -<herd>sci</herd> -<longdescription> - SHOGUN is a new machine learning toolbox with focus on large scale kernel - methods and especially on Support Vector Machines (SVM) with focus to - bioinformatics. It provides a generic SVM object interfacing to several - different SVM implementations. Each of the SVMs can be combined with a variety - of the many kernels implemented. It can deal with weighted linear combination - of a number of sub-kernels, each of which not necessarily working on the same - domain, where an optimal sub-kernel weighting can be learned using Multiple - Kernel Learning. Apart from SVM 2-class classification and regression - problems, a number of linear methods like Linear Discriminant Analysis (LDA), - Linear Programming Machine (LPM), (Kernel) Perceptrons and also algorithms to - train hidden markov models are implemented. The input feature-objects can be - dense, sparse or strings and of type int/short/double/char and can be - converted into different feature types. Chains of preprocessors (e.g. - substracting the mean) can be attached to each feature object allowing for - on-the-fly pre-processing. -</longdescription> -</pkgmetadata> diff --git a/sci-libs/shogun/shogun-0.9.3.ebuild b/sci-libs/shogun/shogun-0.9.3.ebuild deleted file mode 100644 index 321959d93..000000000 --- a/sci-libs/shogun/shogun-0.9.3.ebuild +++ /dev/null @@ -1,64 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=2 - -inherit eutils toolchain-funcs - -DESCRIPTION="Large Scale Machine Learning Toolbox" -HOMEPAGE="http://www.shogun-toolbox.org/" -SRC_URI="http://shogun-toolbox.org/archives/shogun/releases/${PV:0:3}/sources/${P}.tar.bz2" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -IUSE="boost bz2 cplex doc glpk gzip hdf5 lapack lpsolve lzma lzo octave python R readline threads" - -RDEPEND="virtual/lapack - bzip2? ( app-arch/bzip2 ) - cplex? ( sci-mathematics/cplex-bin ) - glpk? ( sci-mathematics/glpk ) - gzip? ( app-arch/gzip ) - hdf5? ( sci-libs/hdf5 ) - glpk? ( sci-mathematics/lpsolve ) - lzma? ( app-arch/xz-utils ) - lzo? ( dev-libs/lzo ) - octave? ( sci-mathematics/octave ) - python? ( dev-python/numpy ) - R? ( dev-lang/R ) - readline? ( sys-libs/readline )" - -DEPEND="${RDEPEND} - dev-libs/boost - dev-util/pkgconfig - doc? ( app-doc/doxygen )" - -S="${WORKDIR}/${P}/src" - -src_configure() { - # not an autotools configure (based on mplayer one) - # disable svmlight based on debian comment - ./configure \ - --cc=$(tc-getCC) \ - --cxx=$(tc-getCXX) \ - --prefix=/usr \ - --datadir=/usr/share/${PN} \ - --mandir=/usr/share/man \ - --confdir=/etc \ - --libdir=/usr/$(get_libdir) \ - --disable-cpudetection \ - --disable-svm-light \ - $(use_enable doc doxygen) \ - $(use_enable boost boost-serialization) \ - $(use_enable glpk) \ - $(use_enable hdf5) \ - $(use_enable lapack) \ - $(use_enable readline) \ - $(use_enable threads hmm-parallel) -} - -src_install() { - emake DESTDIR="${D}" install || die "emake install failed" -} |