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Merge pull request #8182 from ttuegel/openblas

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Numerical computing overhaul
This commit is contained in:
Thomas Tuegel
2015-06-12 08:06:03 -05:00
parent cb6daa036b c02dd4a726
commit 2a2448bcb7
28 changed files with 346 additions and 845 deletions
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31
pkgs/development/libraries/qrupdate/default.nix
View File

@@ -1,29 +1,34 @@
{ stdenv
, fetchurl
, gfortran
, liblapack
, openblas
}:
stdenv.mkDerivation {
name = "qrupdate-1.1.2";
src = fetchurl {
url = mirror://sourceforge/qrupdate/qrupdate-1.1.2.tar.gz ;
sha256 = "024f601685phcm1pg8lhif3lpy5j9j0k6n0r46743g4fvh8wg8g2";
sha256 = "024f601685phcm1pg8lhif3lpy5j9j0k6n0r46743g4fvh8wg8g2";
};
configurePhase = ''
export PREFIX=$out
sed -i -e 's,^BLAS=.*,BLAS=-L${liblapack}/lib -L${liblapack.blas} -lcblas -lf77blas -latlas,' \
-e 's,^LAPACK=.*,LAPACK=-L${liblapack}/lib -llapack -lcblas -lf77blas -latlas,' \
Makeconf
'';
configurePhase =
''
export PREFIX=$out
sed -i -e 's,^BLAS=.*,BLAS=-L${openblas}/lib -lopenblas,' \
-e 's,^LAPACK=.*,LAPACK=-L${openblas}/lib -lopenblas,' \
Makeconf
''
+ stdenv.lib.optionalString openblas.blas64
''
sed -i Makeconf -e '/^FFLAGS=.*/ s/$/-fdefault-integer-8/'
'';
doCheck = true;
checkTarget = "test";
buildTarget = "lib";
buildFlags = [ "lib" "solib" ];
installTarget = "install-staticlib";
buildInputs = [ gfortran liblapack ];
installTargets = "install";
buildInputs = [ gfortran openblas ];
}

13
pkgs/development/libraries/science/math/arpack/default.nix
View File

@@ -1,4 +1,6 @@
{ stdenv, fetchurl, gfortran, atlasWithLapack }:
{ stdenv, fetchurl, gfortran, openblas }:
with stdenv.lib;
let
version = "3.2.0";
@@ -10,10 +12,15 @@ stdenv.mkDerivation {
sha256 = "1fwch6vipms1ispzg2djvbzv5wag36f1dmmr3xs3mbp6imfyhvff";
};
buildInputs = [ gfortran atlasWithLapack ];
buildInputs = [ gfortran openblas ];
# Auto-detection fails because gfortran brings in BLAS by default
configureFlags="--with-blas=-latlas --with-lapack=-latlas";
configureFlags = [
"--with-blas=-lopenblas"
"--with-lapack=-lopenblas"
];
FFLAGS = optional openblas.blas64 "-fdefault-integer-8";
meta = {
homepage = "http://forge.scilab.org/index.php/p/arpack-ng/";

9
pkgs/development/libraries/science/math/ipopt/default.nix
View File

@@ -1,4 +1,4 @@
{ stdenv, fetchurl, unzip, blas, liblapack, gfortran }:
{ stdenv, fetchurl, unzip, openblas, gfortran }:
stdenv.mkDerivation rec {
version = "3.12.3";
@@ -13,9 +13,14 @@ stdenv.mkDerivation rec {
export CXXDEFS="-DHAVE_RAND -DHAVE_CSTRING -DHAVE_CSTDIO"
'';
configureFlags = [
"--with-blas-lib=-lopenblas"
"--with-lapack-lib=-lopenblas"
];
nativeBuildInputs = [ unzip ];
buildInputs = [ gfortran blas liblapack ];
buildInputs = [ gfortran openblas ];
enableParallelBuilding = true;

37
pkgs/development/libraries/science/math/openblas/0.2.10.nix
View File

@@ -1,37 +0,0 @@
{ stdenv, fetchurl, gfortran, perl, liblapack, config }:
let local = config.openblas.preferLocalBuild or false;
localTarget = config.openblas.target or "";
in
stdenv.mkDerivation rec {
version = "0.2.10";
name = "openblas-${version}";
src = fetchurl {
url = "https://github.com/xianyi/OpenBLAS/tarball/v${version}";
sha256 = "06i0q4qnd5q5xljzrgvda0gjsczc6l2pl9hw6dn2qjpw38al73za";
name = "openblas-${version}.tar.gz";
};
preBuild = "cp ${liblapack.src} lapack-${liblapack.meta.version}.tgz";
buildInputs = [gfortran perl];
cpu = builtins.head (stdenv.lib.splitString "-" stdenv.system);
target = if local then localTarget else
if cpu == "i686" then "P2" else
if cpu == "x86_64" then "CORE2" else
# allow autodetect
"";
makeFlags = "${if target != "" then "TARGET=" else ""}${target} FC=gfortran CC=cc PREFIX=\"\$(out)\" INTERFACE64=1";
meta = with stdenv.lib; {
description = "Basic Linear Algebra Subprograms";
license = licenses.bsd3;
homepage = "https://github.com/xianyi/OpenBLAS";
platforms = [ "x86_64-linux" ];
maintainers = with maintainers; [ ttuegel ];
};
}

37
pkgs/development/libraries/science/math/openblas/0.2.2.nix
View File

@@ -1,37 +0,0 @@
{ stdenv, fetchurl, gfortran, perl, liblapack, config }:
let local = config.openblas.preferLocalBuild or false;
localTarget = config.openblas.target or "";
in
stdenv.mkDerivation rec {
version = "0.2.2";
name = "openblas-${version}";
src = fetchurl {
url = "https://github.com/xianyi/OpenBLAS/tarball/v${version}";
sha256 = "13kdx3knff5ajnmgn419g0dnh83plin07p7akwamr3v7z5qfrzqr";
name = "openblas-${version}.tar.gz";
};
preBuild = "cp ${liblapack.src} lapack-${liblapack.meta.version}.tgz";
buildInputs = [gfortran perl];
cpu = builtins.head (stdenv.lib.splitString "-" stdenv.system);
target = if local then localTarget else
if cpu == "i686" then "P2" else
if cpu == "x86_64" then "CORE2" else
# allow autodetect
"";
makeFlags = "${if target != "" then "TARGET=" else ""}${target} FC=gfortran CC=cc PREFIX=\"\$(out)\"";
meta = with stdenv.lib; {
description = "Basic Linear Algebra Subprograms";
license = licenses.bsd3;
homepage = "https://github.com/xianyi/OpenBLAS";
platforms = [ "x86_64-linux" ];
maintainers = with maintainers; [ ttuegel ];
};
}

20
pkgs/development/libraries/science/math/openblas/default.nix
View File

@@ -1,22 +1,24 @@
{ stdenv, fetchurl, gfortran, perl, liblapack, config, coreutils }:
{ stdenv, fetchurl, gfortran, perl, liblapack, config, coreutils
# Most packages depending on openblas expect integer width to match pointer width,
# but some expect to use 32-bit integers always (for compatibility with reference BLAS).
, blas64 ? null
}:
with stdenv.lib;
let local = config.openblas.preferLocalBuild or false;
binary =
{
i686-linux = "32";
{ i686-linux = "32";
x86_64-linux = "64";
x86_64-darwin = "64";
}."${stdenv.system}" or (throw "unsupported system: ${stdenv.system}");
genericFlags =
[
"DYNAMIC_ARCH=1"
[ "DYNAMIC_ARCH=1"
"NUM_THREADS=64"
"BINARY=${binary}"
];
localFlags = config.openblas.flags or
optionals (hasAttr "target" config.openblas) [ "TARGET=${config.openblas.target}" ];
blas64Orig = blas64;
in
stdenv.mkDerivation rec {
version = "0.2.14";
@@ -43,9 +45,13 @@ stdenv.mkDerivation rec {
# thus is not an explicit dependency.
"CC=${if stdenv.isDarwin then "clang" else "gcc"}"
''PREFIX="''$(out)"''
"INTERFACE64=1"
"BINARY=${binary}"
"USE_OPENMP=${if stdenv.isDarwin then "0" else "1"}"
"INTERFACE64=${if blas64 then "1" else "0"}"
];
blas64 = if blas64Orig != null then blas64Orig else hasPrefix "x86_64" stdenv.system;
meta = with stdenv.lib; {
description = "Basic Linear Algebra Subprograms";
license = licenses.bsd3;

36
pkgs/development/libraries/science/math/suitesparse/0001-disable-metis.patch
View File

@@ -1,36 +0,0 @@
From 456b26d0c9101adaa5876954baac0ca0e872dab6 Mon Sep 17 00:00:00 2001
From: Thomas Tuegel <ttuegel@gmail.com>
Date: Mon, 15 Dec 2014 10:18:01 -0600
Subject: [PATCH 1/3] disable metis
---
SuiteSparse_config/SuiteSparse_config.mk | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/SuiteSparse_config/SuiteSparse_config.mk b/SuiteSparse_config/SuiteSparse_config.mk
index ba2da23..e1514bf 100644
--- a/SuiteSparse_config/SuiteSparse_config.mk
+++ b/SuiteSparse_config/SuiteSparse_config.mk
@@ -212,8 +212,8 @@ XERBLA =
# 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
+# METIS_PATH = ../../metis-4.0
+# METIS = ../../metis-4.0/libmetis.a
#------------------------------------------------------------------------------
# UMFPACK configuration:
@@ -273,7 +273,7 @@ UMFPACK_CONFIG =
# -DNSUNPERF for Solaris only. If defined, do not use the Sun
# Performance Library
-CHOLMOD_CONFIG = $(GPU_CONFIG)
+CHOLMOD_CONFIG = $(GPU_CONFIG) -DNPARTITION
# uncomment this line to compile CHOLMOD without METIS:
# CHOLMOD_CONFIG = -DNPARTITION
--
2.1.3

27
pkgs/development/libraries/science/math/suitesparse/0002-set-install-dir.patch
View File

@@ -1,27 +0,0 @@
From e0fee492a315ce1ef8697b056af210beb1465334 Mon Sep 17 00:00:00 2001
From: Thomas Tuegel <ttuegel@gmail.com>
Date: Mon, 15 Dec 2014 10:18:12 -0600
Subject: [PATCH 2/3] set install dir
---
SuiteSparse_config/SuiteSparse_config.mk | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/SuiteSparse_config/SuiteSparse_config.mk b/SuiteSparse_config/SuiteSparse_config.mk
index e1514bf..f1046a6 100644
--- a/SuiteSparse_config/SuiteSparse_config.mk
+++ b/SuiteSparse_config/SuiteSparse_config.mk
@@ -95,8 +95,8 @@ F77LIB =
# LIB = -lm
# For "make install"
-INSTALL_LIB = /usr/local/lib
-INSTALL_INCLUDE = /usr/local/include
+INSTALL_LIB = @out@/lib
+INSTALL_INCLUDE = @out@/include
# Which version of MAKE you are using (default is "make")
# MAKE = make
--
2.1.3

27
pkgs/development/libraries/science/math/suitesparse/0003-blas-lapack-flags.patch
View File

@@ -1,27 +0,0 @@
From a99cca30cfd965683564ae024e8ecc615c61697a Mon Sep 17 00:00:00 2001
From: Thomas Tuegel <ttuegel@gmail.com>
Date: Mon, 15 Dec 2014 10:24:08 -0600
Subject: [PATCH 3/3] blas lapack flags
---
SuiteSparse_config/SuiteSparse_config.mk | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/SuiteSparse_config/SuiteSparse_config.mk b/SuiteSparse_config/SuiteSparse_config.mk
index f1046a6..1710162 100644
--- a/SuiteSparse_config/SuiteSparse_config.mk
+++ b/SuiteSparse_config/SuiteSparse_config.mk
@@ -119,8 +119,8 @@ INSTALL_INCLUDE = @out@/include
# naming the BLAS and LAPACK library (*.a or *.so) files.
# This is probably slow ... it might connect to the Standard Reference BLAS:
- BLAS = -lblas -lgfortran
- LAPACK = -llapack
+ BLAS = @blasFlags@
+ LAPACK = @lapackFlags@
# 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
--
2.1.3

34
pkgs/development/libraries/science/math/suitesparse/4.2.nix
View File

@@ -1,22 +1,44 @@
{ stdenv, fetchurl, blas, liblapack, gfortran } :
{ stdenv, fetchurl, gfortran, openblas }:
let
int_t = if openblas.blas64 then "int64_t" else "int32_t";
in
stdenv.mkDerivation rec {
version = "4.2.1";
name = "suitesparse-${version}";
src = fetchurl {
url = "http://www.cise.ufl.edu/research/sparse/SuiteSparse/SuiteSparse-${version}.tar.gz" ;
sha256 = "1ga69637x7kdkiy3w3lq9dvva7220bdangv2lch2wx1hpi83h0p8";
sha256 = "1ga69637x7kdkiy3w3lq9dvva7220bdangv2lch2wx1hpi83h0p8";
};
buildInputs = [blas liblapack gfortran] ;
patches = [./disable-metis.patch];
nativeBuildInputs = [ gfortran ];
buildInputs = [ openblas ];
preConfigure = ''
export PREFIX=$out
mkdir -p $out/lib
mkdir -p $out/include
sed -i "SuiteSparse_config/SuiteSparse_config.mk" \
-e 's/METIS .*$/METIS =/' \
-e 's/METIS_PATH .*$/METIS_PATH =/' \
-e '/CHOLMOD_CONFIG/ s/$/-DNPARTITION -DLONGBLAS=${int_t}/' \
-e '/UMFPACK_CONFIG/ s/$/-DLONGBLAS=${int_t}/'
'';
makeFlags = ''PREFIX=\"$(out)\" INSTALL_LIB=$(out)/lib INSTALL_INCLUDE=$(out)/include'';
makeFlags = [
"PREFIX=\"$(out)\""
"INSTALL_LIB=$(out)/lib"
"INSTALL_INCLUDE=$(out)/include"
"BLAS=-lopenblas"
"LAPACK="
];
NIX_CFLAGS = "-fPIC";
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 ];
};
}

452
pkgs/development/libraries/science/math/suitesparse/SuiteSparse_config.mk
View File

@@ -1,452 +0,0 @@
#===============================================================================
# SuiteSparse_config.mk: common configuration file for the SuiteSparse
#===============================================================================
# This file contains all configuration settings for all packages authored or
# 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

53
pkgs/development/libraries/science/math/suitesparse/default.nix
View File

@@ -1,34 +1,53 @@
{ stdenv, fetchurl, substituteAll
, atlasWithLapack, gfortran }:
{ stdenv, fetchurl, gfortran, openblas }:
let
name = "suitesparse-4.4.1";
version = "4.4.4";
name = "suitesparse-${version}";
int_t = if openblas.blas64 then "int64_t" else "int32_t";
in
stdenv.mkDerivation {
inherit name;
src = fetchurl {
url = "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.4.1.tar.gz";
sha256 = "0y8i6dizrr556xggpjyc7wijjv4jbizhssmjj4jv8n1s7zxy2z0n";
url = "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-${version}.tar.gz";
sha256 = "1zdn1y0ij6amj7smmcslkqgbqv9yy5cwmbyzqc9v6drzdzllgbpj";
};
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 $out/include
sed -i "SuiteSparse_config/SuiteSparse_config.mk" \
-e 's/METIS .*$/METIS =/' \
-e 's/METIS_PATH .*$/METIS_PATH =/' \
-e '/CHOLMOD_CONFIG/ s/$/-DNPARTITION -DLONGBLAS=${int_t}/' \
-e '/UMFPACK_CONFIG/ s/$/-DLONGBLAS=${int_t}/'
'';
makeFlags = [
"PREFIX=\"$(out)\""
"INSTALL_LIB=$(out)/lib"
"INSTALL_INCLUDE=$(out)/include"
"BLAS=-lopenblas"
"LAPACK="
];
NIX_CFLAGS = "-fPIC";
postInstall = ''
# Build and install shared library
(
cd "$(mktemp -d)"
for i in "$out"/lib/lib*.a; do
ar -x $i
done
gcc *.o --shared -o "$out/lib/libsuitesparse.so"
)
for i in umfpack cholmod amd camd colamd spqr; do
ln -s libsuitesparse.so "$out"/lib/lib$i.so;
done
# Install documentation
outdoc=$out/share/doc/${name}
mkdir -p $outdoc
@@ -47,7 +66,7 @@ stdenv.mkDerivation {
'';
nativeBuildInputs = [ gfortran ];
buildInputs = [ atlasWithLapack ];
buildInputs = [ openblas ];
meta = with stdenv.lib; {
homepage = http://faculty.cse.tamu.edu/davis/suitesparse.html;

18
pkgs/development/libraries/science/math/suitesparse/disable-metis.patch
View File

@@ -1,18 +0,0 @@
diff -Nrc SuiteSparse/UMFPACK/Demo/Makefile SuiteSparse-new/UMFPACK/Demo/Makefile
*** SuiteSparse/UMFPACK/Demo/Makefile 2009-11-11 21:09:45.000000000 +0100
--- SuiteSparse-new/UMFPACK/Demo/Makefile 2010-08-02 12:53:16.000000000 +0200
***************
*** 40,46 ****
../../CAMD/Lib/libcamd.a:
( cd ../../CAMD ; $(MAKE) library )
- $(METIS):
- ( cd $(METIS_PATH) && $(MAKE) )
UMFPACK = ../Lib/libumfpack.a ../../AMD/Lib/libamd.a \
--- 40,44 ----
../../CAMD/Lib/libcamd.a:
( cd ../../CAMD ; $(MAKE) library )
UMFPACK = ../Lib/libumfpack.a ../../AMD/Lib/libamd.a \

4
pkgs/development/libraries/utf8proc/default.nix
View File

@@ -11,9 +11,7 @@ stdenv.mkDerivation rec {
sha256 = "1ryjlcnpfm7fpkq6444ybi576hbnh2l0w7kjhbqady5lxwjyg3pf";
};
installPhase = ''
make install prefix=$out
'';
makeFlags = [ "prefix=$(out)" ];
meta = with stdenv.lib; {
description = "A clean C library for processing UTF-8 Unicode data";