Merge pull request #5484 from ttuegel/linear-algebra
Version bump some linear algebra packages
This commit is contained in:
Thomas Tuegel
commit
09435f05d4
@ -1,31 +1,26 @@
|
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{ stdenv, fetchurl, gfortran, openblas }:
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{ stdenv, fetchurl, gfortran, atlasWithLapack }:
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let version = "3.1.5";
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let
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version = "3.2.0";
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in
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stdenv.mkDerivation {
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name = "arpack-${version}";
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src = fetchurl {
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url = "http://forge.scilab.org/index.php/p/arpack-ng/downloads/get/arpack-ng_${version}.tar.gz";
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sha256 = "05fmg4m0yri47rzgsl2mnr1qbzrs7qyd557p3v9wwxxw0rwcwsd2";
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url = "https://github.com/opencollab/arpack-ng/archive/${version}.tar.gz";
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sha256 = "1fwch6vipms1ispzg2djvbzv5wag36f1dmmr3xs3mbp6imfyhvff";
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};
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buildInputs = [ gfortran ];
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propagatedBuildInputs = [ openblas ];
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preConfigure = ''
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substituteInPlace arpack.pc.in \
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--replace "@BLAS_LIBS@" "-L${openblas}/lib @BLAS_LIBS@"
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'';
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buildInputs = [ gfortran atlasWithLapack ];
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# Auto-detection fails because gfortran brings in BLAS by default
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configureFlags="--with-blas=-lopenblas --with-lapack=-lopenblas";
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configureFlags="--with-blas=-latlas --with-lapack=-latlas";
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meta = {
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homepage = "http://forge.scilab.org/index.php/p/arpack-ng/";
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description = "A collection of Fortran77 subroutines to solve large scale eigenvalue problems";
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# Looks like OpenBLAS is not that easy to build
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# there is a sgemm_itcopy undefined reference on 32-bit, for example
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platforms = ["x86_64-linux"];
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description = ''
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A collection of Fortran77 subroutines to solve large scale eigenvalue
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problems.
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'';
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license = stdenv.lib.licenses.bsd3;
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maintainers = [ stdenv.lib.maintainers.ttuegel ];
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};
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@ -1,5 +1,8 @@
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{ stdenv, fetchurl, gfortran, tolerateCpuTimingInaccuracy ? true, shared ? false
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, cpuConfig ? if stdenv.isi686 then "-b 32 -A 18 -V 1" else "-b 64 -A 31 -V 384"
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, cpuConfig ? if stdenv.isi686 then "-b 32 -A 12 -V 1" else "-b 64 -A 14 -V 384"
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, cacheEdge ? "262144"
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, threads ? "0"
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, liblapack, withLapack
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}:
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# Atlas detects the CPU and optimizes its build accordingly. This is great when
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@ -9,31 +12,44 @@
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# cannot execute.
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#
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# To avoid these issues, the build is configured using the 'cpuConfig'
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# parameter as follows:
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# parameter. Upstream recommends these defaults for distributions:
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#
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# | x86 CPU | x86_64 CPU |
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# |---------------------------------------------+------------------------|
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# | -b 32 | -b 64 |
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# | -A 18 (Pentium II) | -A 31 (Athlon K7) |
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# | -V 1 (No SIMD: Pentium II doesn't have SSE) | -V 384 (SSE1 and SSE2) |
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# | -A 12 (x86x87) | -A 14 (x86SSE2) |
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# | -V 1 (No SIMD) | -V 384 (SSE1 and SSE2) |
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#
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# Users who want to compile a highly optimized version of ATLAS that's suitable
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# for their local machine can override these settings accordingly.
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# These defaults should give consistent performance across machines.
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# Performance will be substantially lower than an optimized build, but a build
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# optimized for one machine will give even worse performance on others. If you
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# are a serious user of Atlas (e.g., you write code that uses it) you should
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# compile an optimized version for each of your machines.
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#
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# The parameter 'cacheEdge' sets the L2 cache per core (in bytes). Setting this
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# parameter reduces build time because some tests to detect the L2 cache size
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# will not be run. It will also reduce impurity; different build nodes on Hydra
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# may have different L2 cache sizes, but fixing the L2 cache size should
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# account for that. This also makes the performance of binary substitutes more
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# consistent.
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#
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# The -V flags can change with each release as new instruction sets are added
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# because upstream thinks it's a good idea to add entries at the start of an
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# enum, rather than the end. If the build suddenly fails with messages about
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# missing instruction sets, you may need to poke around in the source a bit.
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#
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# Upstream recommends the x86x87/x86SSE2 architectures for generic x86/x86_64
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# for distribution builds. Additionally, we set 'cacheEdge' to reduce impurity.
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# Otherwise, the cache parameters will be detected by timing which will be
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# highly variable on Hydra.
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let
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inherit (stdenv.lib) optional optionalString;
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version = "3.10.2";
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optionalString = stdenv.lib.optionalString;
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optional = stdenv.lib.optional;
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in
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stdenv.mkDerivation {
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name = "atlas-${version}";
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name = "atlas-${version}" + optionalString withLapack "-with-lapack";
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src = fetchurl {
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url = "mirror://sourceforge/math-atlas/atlas${version}.tar.bz2";
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@ -50,27 +66,53 @@ stdenv.mkDerivation {
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patches = optional tolerateCpuTimingInaccuracy ./disable-timing-accuracy-check.patch;
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# Configure outside of the source directory.
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preConfigure = '' mkdir build; cd build; configureScript=../configure; '';
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preConfigure = ''
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mkdir build
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cd build
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configureScript=../configure
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'';
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# * -fPIC is passed even in non-shared builds so that the ATLAS code can be
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# used to inside of shared libraries, like Octave does.
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#
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# * -t 0 disables use of multi-threading. It's not quite clear what the
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# consequences of that setting are and whether it's necessary or not.
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configureFlags = "-Fa alg -fPIC -t 0 ${cpuConfig}" + optionalString shared " --shared";
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configureFlags = [
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"-Fa alg"
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"-fPIC"
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"-t ${threads}"
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cpuConfig
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] ++ optional shared "--shared"
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++ optional withLapack "--with-netlib-lapack-tarfile=${liblapack.src}";
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postConfigure = ''
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if [[ -n "${cacheEdge}" ]]; then
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echo '#define CacheEdge ${cacheEdge}' >> include/atlas_cacheedge.h
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echo '#define CacheEdge ${cacheEdge}' >> include/atlas_tcacheedge.h
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fi
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'';
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doCheck = true;
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postInstall = ''
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# Avoid name collision with the real lapack (ATLAS only builds a partial
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# lapack unless withLapack = true).
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if ${if withLapack then "false" else "true"}; then
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mv $out/lib/liblapack.a $out/lib/liblapack_atlas.a
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fi
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'';
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meta = {
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homepage = "http://math-atlas.sourceforge.net/";
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description = "Automatically Tuned Linear Algebra Software (ATLAS)";
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license = stdenv.lib.licenses.bsd3;
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longDescription = ''
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The ATLAS (Automatically Tuned Linear Algebra Software) project is an ongoing
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research effort focusing on applying empirical techniques in order to provide
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portable performance. At present, it provides C and Fortran77 interfaces to a
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portably efficient BLAS implementation, as well as a few routines from LAPACK.
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The ATLAS (Automatically Tuned Linear Algebra Software) project is an
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ongoing research effort focusing on applying empirical techniques in
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order to provide portable performance. At present, it provides C and
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Fortran77 interfaces to a portably efficient BLAS implementation, as well
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as a few routines from LAPACK.
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'';
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maintainers = with stdenv.lib.maintainers; [ ttuegel ];
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@ -4,12 +4,12 @@ let local = config.openblas.preferLocalBuild or false;
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localTarget = config.openblas.target or "";
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in
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stdenv.mkDerivation rec {
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version = "0.2.11";
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version = "0.2.13";
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name = "openblas-${version}";
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src = fetchurl {
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url = "https://github.com/xianyi/OpenBLAS/tarball/v${version}";
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sha256 = "1va4yhzgj2chcj6kaxgfbzirajp1zgvkic61959aka2xq2c5igms";
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sha256 = "1asg5mix13ipxgj5h2yj2p0r8km1di5jbcjkn5gmhb37nx7qfv6k";
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name = "openblas-${version}.tar.gz";
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};
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@ -0,0 +1,36 @@
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From 456b26d0c9101adaa5876954baac0ca0e872dab6 Mon Sep 17 00:00:00 2001
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From: Thomas Tuegel <ttuegel@gmail.com>
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Date: Mon, 15 Dec 2014 10:18:01 -0600
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Subject: [PATCH 1/3] disable metis
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---
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SuiteSparse_config/SuiteSparse_config.mk | 6 +++---
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1 file changed, 3 insertions(+), 3 deletions(-)
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diff --git a/SuiteSparse_config/SuiteSparse_config.mk b/SuiteSparse_config/SuiteSparse_config.mk
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index ba2da23..e1514bf 100644
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--- a/SuiteSparse_config/SuiteSparse_config.mk
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+++ b/SuiteSparse_config/SuiteSparse_config.mk
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@@ -212,8 +212,8 @@ XERBLA =
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# The path is relative to where it is used, in CHOLMOD/Lib, CHOLMOD/MATLAB, etc.
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# You may wish to use an absolute path. METIS is optional. Compile
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# CHOLMOD with -DNPARTITION if you do not wish to use METIS.
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-METIS_PATH = ../../metis-4.0
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-METIS = ../../metis-4.0/libmetis.a
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+# METIS_PATH = ../../metis-4.0
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+# METIS = ../../metis-4.0/libmetis.a
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#------------------------------------------------------------------------------
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# UMFPACK configuration:
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@@ -273,7 +273,7 @@ UMFPACK_CONFIG =
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# -DNSUNPERF for Solaris only. If defined, do not use the Sun
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# Performance Library
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-CHOLMOD_CONFIG = $(GPU_CONFIG)
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+CHOLMOD_CONFIG = $(GPU_CONFIG) -DNPARTITION
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# uncomment this line to compile CHOLMOD without METIS:
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# CHOLMOD_CONFIG = -DNPARTITION
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--
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2.1.3
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@ -0,0 +1,27 @@
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From e0fee492a315ce1ef8697b056af210beb1465334 Mon Sep 17 00:00:00 2001
|
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From: Thomas Tuegel <ttuegel@gmail.com>
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Date: Mon, 15 Dec 2014 10:18:12 -0600
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Subject: [PATCH 2/3] set install dir
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|
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---
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SuiteSparse_config/SuiteSparse_config.mk | 4 ++--
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1 file changed, 2 insertions(+), 2 deletions(-)
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diff --git a/SuiteSparse_config/SuiteSparse_config.mk b/SuiteSparse_config/SuiteSparse_config.mk
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index e1514bf..f1046a6 100644
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--- a/SuiteSparse_config/SuiteSparse_config.mk
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+++ b/SuiteSparse_config/SuiteSparse_config.mk
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@@ -95,8 +95,8 @@ F77LIB =
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# LIB = -lm
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# For "make install"
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-INSTALL_LIB = /usr/local/lib
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-INSTALL_INCLUDE = /usr/local/include
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+INSTALL_LIB = @out@/lib
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+INSTALL_INCLUDE = @out@/include
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# Which version of MAKE you are using (default is "make")
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# MAKE = make
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--
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2.1.3
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|
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@ -0,0 +1,27 @@
|
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From a99cca30cfd965683564ae024e8ecc615c61697a Mon Sep 17 00:00:00 2001
|
||||
From: Thomas Tuegel <ttuegel@gmail.com>
|
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Date: Mon, 15 Dec 2014 10:24:08 -0600
|
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Subject: [PATCH 3/3] blas lapack flags
|
||||
|
||||
---
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SuiteSparse_config/SuiteSparse_config.mk | 4 ++--
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1 file changed, 2 insertions(+), 2 deletions(-)
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diff --git a/SuiteSparse_config/SuiteSparse_config.mk b/SuiteSparse_config/SuiteSparse_config.mk
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index f1046a6..1710162 100644
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--- a/SuiteSparse_config/SuiteSparse_config.mk
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+++ b/SuiteSparse_config/SuiteSparse_config.mk
|
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@@ -119,8 +119,8 @@ INSTALL_INCLUDE = @out@/include
|
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# naming the BLAS and LAPACK library (*.a or *.so) files.
|
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|
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# This is probably slow ... it might connect to the Standard Reference BLAS:
|
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- BLAS = -lblas -lgfortran
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- LAPACK = -llapack
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+ BLAS = @blasFlags@
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+ LAPACK = @lapackFlags@
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|
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# MKL
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# BLAS = -Wl,--start-group $(MKLROOT)/lib/intel64/libmkl_intel_lp64.a $(MKLROOT)/lib/intel64/libmkl_core.a $(MKLROOT)/lib/intel64/libmkl_intel_thread.a -Wl,--end-group -lpthread -lm
|
||||
--
|
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2.1.3
|
||||
|
||||
@ -0,0 +1,452 @@
|
||||
#===============================================================================
|
||||
# SuiteSparse_config.mk: common configuration file for the SuiteSparse
|
||||
#===============================================================================
|
||||
|
||||
# This file contains all configuration settings for all packages authored or
|
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# co-authored by Tim Davis:
|
||||
#
|
||||
# Package Version Description
|
||||
# ------- ------- -----------
|
||||
# AMD 1.2 or later approximate minimum degree ordering
|
||||
# COLAMD 2.4 or later column approximate minimum degree ordering
|
||||
# CCOLAMD 1.0 or later constrained column approximate minimum degree ordering
|
||||
# CAMD any constrained approximate minimum degree ordering
|
||||
# UMFPACK 4.5 or later sparse LU factorization, with the BLAS
|
||||
# CHOLMOD any sparse Cholesky factorization, update/downdate
|
||||
# KLU 0.8 or later sparse LU factorization, BLAS-free
|
||||
# BTF 0.8 or later permutation to block triangular form
|
||||
# LDL 1.2 or later concise sparse LDL'
|
||||
# CXSparse any extended version of CSparse (int/long, real/complex)
|
||||
# SuiteSparseQR any sparse QR factorization
|
||||
# RBio 2.0 or later read/write sparse matrices in Rutherford-Boeing format
|
||||
#
|
||||
# By design, this file is NOT included in the CSparse makefile.
|
||||
# That package is fully stand-alone. CSparse is primarily for teaching;
|
||||
# production code should use CXSparse.
|
||||
#
|
||||
# The SuiteSparse_config directory and the above packages should all appear in
|
||||
# a single directory, in order for the Makefile's within each package to find
|
||||
# this file.
|
||||
#
|
||||
# To enable an option of the form "# OPTION = ...", edit this file and
|
||||
# delete the "#" in the first column of the option you wish to use.
|
||||
#
|
||||
# The use of METIS 4.0.1 is optional. To exclude METIS, you must compile with
|
||||
# CHOLMOD_CONFIG set to -DNPARTITION. See below for details. However, if you
|
||||
# do not have a metis-4.0 directory inside the SuiteSparse directory, the
|
||||
# */Makefile's that optionally rely on METIS will automatically detect this
|
||||
# and compile without METIS.
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
# Generic configuration
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
# Using standard definitions from the make environment, typically:
|
||||
#
|
||||
# CC cc C compiler
|
||||
# CXX g++ C++ compiler
|
||||
# CFLAGS [ ] flags for C and C++ compiler
|
||||
# CPPFLAGS [ ] flags for C and C++ compiler
|
||||
# TARGET_ARCH [ ] target architecture
|
||||
# FFLAGS [ ] flags for Fortran compiler
|
||||
# RM rm -f delete a file
|
||||
# AR ar create a static *.a library archive
|
||||
# ARFLAGS rv flags for ar
|
||||
# MAKE make make itself (sometimes called gmake)
|
||||
#
|
||||
# You can redefine them here, but by default they are used from the
|
||||
# default make environment.
|
||||
|
||||
# To use OpenMP add -openmp to the CFLAGS
|
||||
# If OpenMP is used, it is recommended to define CHOLMOD_OMP_NUM_THREADS
|
||||
# as the number of cores per socket on the machine being used to maximize
|
||||
# memory performance
|
||||
CFLAGS =
|
||||
# CFLAGS = -g
|
||||
# for the icc compiler and OpenMP:
|
||||
# CFLAGS = -openmp
|
||||
|
||||
# C and C++ compiler flags. The first three are standard for *.c and *.cpp
|
||||
# Add -DNTIMER if you do use any timing routines (otherwise -lrt is required).
|
||||
# CF = $(CFLAGS) $(CPPFLAGS) $(TARGET_ARCH) -O3 -fexceptions -fPIC -DNTIMER
|
||||
CF = $(CFLAGS) $(CPPFLAGS) $(TARGET_ARCH) -O3 -fexceptions -fPIC
|
||||
# for the MKL BLAS:
|
||||
# CF = $(CFLAGS) $(CPPFLAGS) $(TARGET_ARCH) -O3 -fexceptions -fPIC -I$(MKLROOT)/include -D_GNU_SOURCE
|
||||
# with no optimization:
|
||||
# CF = $(CFLAGS) $(CPPFLAGS) $(TARGET_ARCH) -fexceptions -fPIC
|
||||
|
||||
# ranlib, and ar, for generating libraries. If you don't need ranlib,
|
||||
# just change it to RANLAB = echo
|
||||
RANLIB = ranlib
|
||||
ARCHIVE = $(AR) $(ARFLAGS)
|
||||
|
||||
# copy and delete a file
|
||||
CP = cp -f
|
||||
MV = mv -f
|
||||
|
||||
# Fortran compiler (not required for 'make' or 'make library')
|
||||
F77 = gfortran
|
||||
F77FLAGS = $(FFLAGS) -O
|
||||
F77LIB =
|
||||
|
||||
# C and Fortran libraries. Remove -lrt if you don't have it.
|
||||
LIB = -lm -lrt
|
||||
# Using the following requires CF = ... -DNTIMER on POSIX C systems.
|
||||
# LIB = -lm
|
||||
|
||||
# For "make install"
|
||||
INSTALL_LIB = @out@/lib
|
||||
INSTALL_INCLUDE = @out@/include
|
||||
|
||||
# Which version of MAKE you are using (default is "make")
|
||||
# MAKE = make
|
||||
# MAKE = gmake
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
# BLAS and LAPACK configuration:
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
# UMFPACK and CHOLMOD both require the BLAS. CHOLMOD also requires LAPACK.
|
||||
# See Kazushige Goto's BLAS at http://www.cs.utexas.edu/users/flame/goto/ or
|
||||
# http://www.tacc.utexas.edu/~kgoto/ for the best BLAS to use with CHOLMOD.
|
||||
# LAPACK is at http://www.netlib.org/lapack/ . You can use the standard
|
||||
# Fortran LAPACK along with Goto's BLAS to obtain very good performance.
|
||||
# CHOLMOD gets a peak numeric factorization rate of 3.6 Gflops on a 3.2 GHz
|
||||
# Pentium 4 (512K cache, 4GB main memory) with the Goto BLAS, and 6 Gflops
|
||||
# on a 2.5Ghz dual-core AMD Opteron.
|
||||
|
||||
# These settings will probably not work, since there is no fixed convention for
|
||||
# naming the BLAS and LAPACK library (*.a or *.so) files.
|
||||
|
||||
# This is probably slow ... it might connect to the Standard Reference BLAS:
|
||||
BLAS = -lf77blas -latlas -lcblas -lgfortran
|
||||
LAPACK = -llapack -latlas -lcblas
|
||||
|
||||
# MKL
|
||||
# BLAS = -Wl,--start-group $(MKLROOT)/lib/intel64/libmkl_intel_lp64.a $(MKLROOT)/lib/intel64/libmkl_core.a $(MKLROOT)/lib/intel64/libmkl_intel_thread.a -Wl,--end-group -lpthread -lm
|
||||
# LAPACK =
|
||||
|
||||
# ACML
|
||||
# BLAS = -lacml -lgfortran
|
||||
# LAPACK =
|
||||
|
||||
# OpenBLAS
|
||||
# BLAS = -lopenblas
|
||||
# LAPACK =
|
||||
|
||||
# NOTE: this next option for the "Goto BLAS" has nothing to do with a "goto"
|
||||
# statement. Rather, the Goto BLAS is written by Dr. Kazushige Goto.
|
||||
# Using the Goto BLAS:
|
||||
# BLAS = -lgoto -lgfortran -lgfortranbegin
|
||||
# BLAS = -lgoto2 -lgfortran -lgfortranbegin -lpthread
|
||||
|
||||
# Using non-optimized versions:
|
||||
# BLAS = -lblas_plain -lgfortran -lgfortranbegin
|
||||
# LAPACK = -llapack_plain
|
||||
|
||||
# BLAS = -lblas_plain -lgfortran -lgfortranbegin
|
||||
# LAPACK = -llapack
|
||||
|
||||
# The BLAS might not contain xerbla, an error-handling routine for LAPACK and
|
||||
# the BLAS. Also, the standard xerbla requires the Fortran I/O library, and
|
||||
# stops the application program if an error occurs. A C version of xerbla
|
||||
# distributed with this software (SuiteSparse_config/xerbla/libcerbla.a)
|
||||
# includes a Fortran-callable xerbla routine that prints nothing and does not
|
||||
# stop the application program. This is optional.
|
||||
|
||||
# XERBLA = ../../SuiteSparse_config/xerbla/libcerbla.a
|
||||
|
||||
# If you wish to use the XERBLA in LAPACK and/or the BLAS instead,
|
||||
# use this option:
|
||||
XERBLA =
|
||||
|
||||
# If you wish to use the Fortran SuiteSparse_config/xerbla/xerbla.f instead,
|
||||
# use this:
|
||||
|
||||
# XERBLA = ../../SuiteSparse_config/xerbla/libxerbla.a
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
# GPU configuration for CHOLMOD and SPQR
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
# no cuda
|
||||
CUDA_ROOT =
|
||||
GPU_BLAS_PATH =
|
||||
GPU_CONFIG =
|
||||
CUDA_PATH =
|
||||
CUDART_LIB =
|
||||
CUBLAS_LIB =
|
||||
CUDA_INC_PATH =
|
||||
NV20 =
|
||||
NV30 =
|
||||
NV35 =
|
||||
NVCC = echo
|
||||
NVCCFLAGS =
|
||||
|
||||
# with cuda for CHOLMOD
|
||||
# CUDA_ROOT = /usr/local/cuda
|
||||
# GPU_BLAS_PATH = $(CUDA_ROOT)
|
||||
# with 4 cores (default):
|
||||
# GPU_CONFIG = -I$(CUDA_ROOT)/include -DGPU_BLAS
|
||||
# with 10 cores:
|
||||
# GPU_CONFIG = -I$(CUDA_ROOT)/include -DGPU_BLAS -DCHOLMOD_OMP_NUM_THREADS=10
|
||||
# CUDA_PATH = $(CUDA_ROOT)
|
||||
# CUDART_LIB = $(CUDA_ROOT)/lib64/libcudart.so
|
||||
# CUBLAS_LIB = $(CUDA_ROOT)/lib64/libcublas.so
|
||||
# CUDA_INC_PATH = $(CUDA_ROOT)/include/
|
||||
# NV20 = -arch=sm_20 -Xcompiler -fPIC
|
||||
# NV30 = -arch=sm_30 -Xcompiler -fPIC
|
||||
# NV35 = -arch=sm_35 -Xcompiler -fPIC
|
||||
# NVCC = $(CUDA_ROOT)/bin/nvcc
|
||||
# NVCCFLAGS = $(NV20) -O3 -gencode=arch=compute_20,code=sm_20 -gencode=arch=compute_30,code=sm_30 -gencode=arch=compute_35,code=sm_35
|
||||
|
||||
# was NVCC = $(CUDA_ROOT)/bin/nvcc $(NV35) $(NV30) $(NV20)
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
# METIS, optionally used by CHOLMOD
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
# If you do not have METIS, or do not wish to use it in CHOLMOD, you must
|
||||
# compile CHOLMOD with the -DNPARTITION flag.
|
||||
|
||||
# The path is relative to where it is used, in CHOLMOD/Lib, CHOLMOD/MATLAB, etc.
|
||||
# You may wish to use an absolute path. METIS is optional. Compile
|
||||
# CHOLMOD with -DNPARTITION if you do not wish to use METIS.
|
||||
# METIS_PATH = ../../metis-4.0
|
||||
# METIS = ../../metis-4.0/libmetis.a
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
# UMFPACK configuration:
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
# Configuration flags for UMFPACK. See UMFPACK/Source/umf_config.h for details.
|
||||
#
|
||||
# -DNBLAS do not use the BLAS. UMFPACK will be very slow.
|
||||
# -D'LONGBLAS=long' or -DLONGBLAS='long long' defines the integers used by
|
||||
# LAPACK and the BLAS (defaults to 'int')
|
||||
# -DNSUNPERF do not use the Sun Perf. Library (default is use it on Solaris)
|
||||
# -DNRECIPROCAL do not multiply by the reciprocal
|
||||
# -DNO_DIVIDE_BY_ZERO do not divide by zero
|
||||
# -DNCHOLMOD do not use CHOLMOD as a ordering method. If -DNCHOLMOD is
|
||||
# included in UMFPACK_CONFIG, then UMFPACK does not rely on
|
||||
# CHOLMOD, CAMD, CCOLAMD, COLAMD, and METIS.
|
||||
|
||||
UMFPACK_CONFIG =
|
||||
|
||||
# uncomment this line to compile UMFPACK without CHOLMOD:
|
||||
# UMFPACK_CONFIG = -DNCHOLMOD
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
# CHOLMOD configuration
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
# CHOLMOD Library Modules, which appear in libcholmod.a:
|
||||
# Core requires: none
|
||||
# Check requires: Core
|
||||
# Cholesky requires: Core, AMD, COLAMD. optional: Partition, Supernodal
|
||||
# MatrixOps requires: Core
|
||||
# Modify requires: Core
|
||||
# Partition requires: Core, CCOLAMD, METIS. optional: Cholesky
|
||||
# Supernodal requires: Core, BLAS, LAPACK
|
||||
#
|
||||
# CHOLMOD test/demo Modules (all are GNU GPL, do not appear in libcholmod.a):
|
||||
# Tcov requires: Core, Check, Cholesky, MatrixOps, Modify, Supernodal
|
||||
# optional: Partition
|
||||
# Valgrind same as Tcov
|
||||
# Demo requires: Core, Check, Cholesky, MatrixOps, Supernodal
|
||||
# optional: Partition
|
||||
#
|
||||
# Configuration flags:
|
||||
# -DNCHECK do not include the Check module. License GNU LGPL
|
||||
# -DNCHOLESKY do not include the Cholesky module. License GNU LGPL
|
||||
# -DNPARTITION do not include the Partition module. License GNU LGPL
|
||||
# also do not include METIS.
|
||||
# -DNCAMD do not use CAMD, etc from Partition module. GNU LGPL
|
||||
# -DNGPL do not include any GNU GPL Modules in the CHOLMOD library:
|
||||
# -DNMATRIXOPS do not include the MatrixOps module. License GNU GPL
|
||||
# -DNMODIFY do not include the Modify module. License GNU GPL
|
||||
# -DNSUPERNODAL do not include the Supernodal module. License GNU GPL
|
||||
#
|
||||
# -DNPRINT do not print anything.
|
||||
# -D'LONGBLAS=long' or -DLONGBLAS='long long' defines the integers used by
|
||||
# LAPACK and the BLAS (defaults to 'int')
|
||||
# -DNSUNPERF for Solaris only. If defined, do not use the Sun
|
||||
# Performance Library
|
||||
|
||||
CHOLMOD_CONFIG = $(GPU_CONFIG) -DNPARTITION
|
||||
|
||||
# uncomment this line to compile CHOLMOD without METIS:
|
||||
# CHOLMOD_CONFIG = -DNPARTITION
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
# SuiteSparseQR configuration:
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
# The SuiteSparseQR library can be compiled with the following options:
|
||||
#
|
||||
# -DNPARTITION do not include the CHOLMOD partition module
|
||||
# -DNEXPERT do not include the functions in SuiteSparseQR_expert.cpp
|
||||
# -DHAVE_TBB enable the use of Intel's Threading Building Blocks (TBB)
|
||||
|
||||
# default, without timing, without TBB:
|
||||
SPQR_CONFIG = $(GPU_CONFIG)
|
||||
# with TBB:
|
||||
# SPQR_CONFIG = -DHAVE_TBB
|
||||
|
||||
# This is needed for IBM AIX: (but not for and C codes, just C++)
|
||||
# SPQR_CONFIG = -DBLAS_NO_UNDERSCORE
|
||||
|
||||
# with TBB, you must select this:
|
||||
# TBB = -ltbb
|
||||
# without TBB:
|
||||
TBB =
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
# code formatting
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
# Use "grep" only, if you do not have "indent"
|
||||
# PRETTY = grep -v "^\#"
|
||||
# PRETTY = grep -v "^\#" | indent -bl -nce -ss -bli0 -i4 -sob -l120
|
||||
PRETTY = grep -v "^\#" | indent -bl -nce -bli0 -i4 -sob -l120
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
# Linux
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
# Using default compilers:
|
||||
# CC = gcc
|
||||
# CF = $(CFLAGS) -O3 -fexceptions
|
||||
|
||||
# alternatives:
|
||||
# CF = $(CFLAGS) -g -fexceptions \
|
||||
# -Wall -W -Wshadow -Wmissing-prototypes -Wstrict-prototypes \
|
||||
# -Wredundant-decls -Wnested-externs -Wdisabled-optimization -ansi \
|
||||
# -funit-at-a-time
|
||||
# CF = $(CFLAGS) -O3 -fexceptions \
|
||||
# -Wall -W -Werror -Wshadow -Wmissing-prototypes -Wstrict-prototypes \
|
||||
# -Wredundant-decls -Wnested-externs -Wdisabled-optimization -ansi
|
||||
# CF = $(CFLAGS) -O3 -fexceptions -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE
|
||||
# CF = $(CFLAGS) -O3
|
||||
# CF = $(CFLAGS) -O3 -g -fexceptions
|
||||
# CF = $(CFLAGS) -g -fexceptions \
|
||||
# -Wall -W -Wshadow \
|
||||
# -Wredundant-decls -Wdisabled-optimization -ansi
|
||||
|
||||
# consider:
|
||||
# -fforce-addr -fmove-all-movables -freduce-all-givs -ftsp-ordering
|
||||
# -frename-registers -ffast-math -funroll-loops
|
||||
|
||||
# Using the Goto BLAS:
|
||||
# BLAS = -lgoto -lfrtbegin -lg2c $(XERBLA) -lpthread
|
||||
|
||||
# Using Intel's icc and ifort compilers:
|
||||
# (does not work for mexFunctions unless you add a mexopts.sh file)
|
||||
# F77 = ifort
|
||||
# CC = icc
|
||||
# CF = $(CFLAGS) -O3 -xN -vec_report=0
|
||||
# CF = $(CFLAGS) -g
|
||||
|
||||
# 64bit:
|
||||
# F77FLAGS = -O -m64
|
||||
# CF = $(CFLAGS) -O3 -fexceptions -m64
|
||||
# BLAS = -lgoto64 -lfrtbegin -lg2c -lpthread $(XERBLA)
|
||||
# LAPACK = -llapack64
|
||||
|
||||
# SUSE Linux 10.1, AMD Opteron, with GOTO Blas
|
||||
# F77 = gfortran
|
||||
# BLAS = -lgoto_opteron64 -lgfortran
|
||||
|
||||
# SUSE Linux 10.1, Intel Pentium, with GOTO Blas
|
||||
# F77 = gfortran
|
||||
# BLAS = -lgoto -lgfortran
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
# Mac
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
# As recommended by macports, http://suitesparse.darwinports.com/
|
||||
# I've tested them myself on Mac OSX 10.6.1 and 10.6.8 (Snow Leopard),
|
||||
# on my MacBook Air, and they work fine.
|
||||
|
||||
# F77 = gfortran
|
||||
# CF = $(CFLAGS) -O3 -fno-common -fexceptions -DNTIMER
|
||||
# BLAS = -framework Accelerate
|
||||
# LAPACK = -framework Accelerate
|
||||
# LIB = -lm
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
# Solaris
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
# 32-bit
|
||||
# CF = $(CFLAGS) -KPIC -dalign -xc99=%none -Xc -xlibmieee -xO5 -xlibmil -m32
|
||||
|
||||
# 64-bit
|
||||
# CF = $(CFLAGS) -fast -KPIC -xc99=%none -xlibmieee -xlibmil -m64 -Xc
|
||||
|
||||
# FFLAGS = -fast -KPIC -dalign -xlibmil -m64
|
||||
|
||||
# The Sun Performance Library includes both LAPACK and the BLAS:
|
||||
# BLAS = -xlic_lib=sunperf
|
||||
# LAPACK =
|
||||
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
# Compaq Alpha
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
# 64-bit mode only
|
||||
# CF = $(CFLAGS) -O2 -std1
|
||||
# BLAS = -ldxml
|
||||
# LAPACK =
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
# IBM RS 6000
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
# BLAS = -lessl
|
||||
# LAPACK =
|
||||
|
||||
# 32-bit mode:
|
||||
# CF = $(CFLAGS) -O4 -qipa -qmaxmem=16384 -qproto
|
||||
# F77FLAGS = -O4 -qipa -qmaxmem=16384
|
||||
|
||||
# 64-bit mode:
|
||||
# CF = $(CFLAGS) -O4 -qipa -qmaxmem=16384 -q64 -qproto
|
||||
# F77FLAGS = -O4 -qipa -qmaxmem=16384 -q64
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
# SGI IRIX
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
# BLAS = -lscsl
|
||||
# LAPACK =
|
||||
|
||||
# 32-bit mode
|
||||
# CF = $(CFLAGS) -O
|
||||
|
||||
# 64-bit mode (32 bit int's and 64-bit long's):
|
||||
# CF = $(CFLAGS) -64
|
||||
# F77FLAGS = -64
|
||||
|
||||
# SGI doesn't have ranlib
|
||||
# RANLIB = echo
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
# AMD Opteron (64 bit)
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
# BLAS = -lgoto_opteron64 -lg2c
|
||||
# LAPACK = -llapack_opteron64
|
||||
|
||||
# SUSE Linux 10.1, AMD Opteron
|
||||
# F77 = gfortran
|
||||
# BLAS = -lgoto_opteron64 -lgfortran
|
||||
# LAPACK = -llapack_opteron64
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
# remove object files and profile output
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
CLEAN = *.o *.obj *.ln *.bb *.bbg *.da *.tcov *.gcov gmon.out *.bak *.d *.gcda *.gcno
|
||||
@ -0,0 +1,58 @@
|
||||
{ stdenv, fetchurl, substituteAll
|
||||
, atlasWithLapack, gfortran }:
|
||||
|
||||
let
|
||||
name = "suitesparse-4.4.1";
|
||||
in
|
||||
stdenv.mkDerivation {
|
||||
inherit name;
|
||||
|
||||
src = fetchurl {
|
||||
url = "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.4.1.tar.gz";
|
||||
sha256 = "0y8i6dizrr556xggpjyc7wijjv4jbizhssmjj4jv8n1s7zxy2z0n";
|
||||
};
|
||||
|
||||
patches = [
|
||||
./0001-disable-metis.patch
|
||||
./0002-set-install-dir.patch
|
||||
(substituteAll {
|
||||
src = ./0003-blas-lapack-flags.patch;
|
||||
blasFlags = "-lf77blas -latlas -lcblas -lgfortran";
|
||||
lapackFlags= "-llapack -latlas -lcblas";
|
||||
})
|
||||
];
|
||||
|
||||
preConfigure = ''
|
||||
substituteAllInPlace SuiteSparse_config/SuiteSparse_config.mk
|
||||
mkdir -p $out/lib
|
||||
mkdir -p $out/include
|
||||
'';
|
||||
|
||||
postInstall = ''
|
||||
# Install documentation
|
||||
outdoc=$out/share/doc/${name}
|
||||
mkdir -p $outdoc
|
||||
cp -r AMD/Doc $outdoc/amd
|
||||
cp -r BTF/Doc $outdoc/bft
|
||||
cp -r CAMD/Doc $outdoc/camd
|
||||
cp -r CCOLAMD/Doc $outdoc/ccolamd
|
||||
cp -r CHOLMOD/Doc $outdoc/cholmod
|
||||
cp -r COLAMD/Doc $outdoc/colamd
|
||||
cp -r CXSparse/Doc $outdoc/cxsparse
|
||||
cp -r KLU/Doc $outdoc/klu
|
||||
cp -r LDL/Doc $outdoc/ldl
|
||||
cp -r RBio/Doc $outdoc/rbio
|
||||
cp -r SPQR/Doc $outdoc/spqr
|
||||
cp -r UMFPACK/Doc $outdoc/umfpack
|
||||
'';
|
||||
|
||||
nativeBuildInputs = [ gfortran ];
|
||||
buildInputs = [ atlasWithLapack ];
|
||||
|
||||
meta = with stdenv.lib; {
|
||||
homepage = http://faculty.cse.tamu.edu/davis/suitesparse.html;
|
||||
description = "A suite of sparse matrix algorithms";
|
||||
license = with licenses; [ bsd2 gpl2Plus lgpl21Plus ];
|
||||
maintainers = with maintainers; [ ttuegel ];
|
||||
};
|
||||
}
|
||||
@ -3499,13 +3499,14 @@ let
|
||||
liblapack = liblapack.override {shared = true;};
|
||||
llvm = llvm_33;
|
||||
openblas = openblas_0_2_2;
|
||||
suitesparse = suitesparse_4_2;
|
||||
};
|
||||
|
||||
julia033 = let
|
||||
liblapack = liblapack_3_5_0.override {shared = true;};
|
||||
in callPackage ../development/compilers/julia/0.3.3.nix {
|
||||
inherit liblapack;
|
||||
suitesparse = suitesparse.override {
|
||||
suitesparse = suitesparse_4_2.override {
|
||||
inherit liblapack;
|
||||
};
|
||||
llvm = llvm_33;
|
||||
@ -6981,8 +6982,6 @@ let
|
||||
|
||||
suil = callPackage ../development/libraries/audio/suil { };
|
||||
|
||||
suitesparse = callPackage ../development/libraries/suitesparse { };
|
||||
|
||||
sutils = callPackage ../tools/misc/sutils { };
|
||||
|
||||
sword = callPackage ../development/libraries/sword { };
|
||||
@ -12174,8 +12173,12 @@ let
|
||||
# great feature, but it's of limited use with pre-built binaries
|
||||
# coming from a central build farm.
|
||||
tolerateCpuTimingInaccuracy = true;
|
||||
liblapack = liblapack_3_5_0;
|
||||
withLapack = false;
|
||||
};
|
||||
|
||||
atlasWithLapack = atlas.override { withLapack = true; };
|
||||
|
||||
blas = callPackage ../development/libraries/science/math/blas { };
|
||||
|
||||
content = builderDefsPackage ../applications/science/math/content {
|
||||
@ -12207,6 +12210,9 @@ let
|
||||
|
||||
sage = callPackage ../applications/science/math/sage { };
|
||||
|
||||
suitesparse_4_2 = callPackage ../development/libraries/science/math/suitesparse/4.2.nix { };
|
||||
suitesparse_4_4_1 = callPackage ../development/libraries/science/math/suitesparse {};
|
||||
|
||||
ipopt = callPackage ../development/libraries/science/math/ipopt { };
|
||||
|
||||
### SCIENCE/MOLECULAR-DYNAMICS
|
||||
|
||||
Loading…
Reference in New Issue
Block a user