Installing Scipy and PyNIO on a Bare Cluster with the Intel Compiler

2 years ago I had the task of running a python-program using scipy on our university cluster, using the Intel Compiler. I needed all those (as well as PyNIO and some other stuff) for running TM5 with the python shell on the HC3 of KIT.

This proved to be quite a bit more challenging than I had expected - but it was very interesting, too (and there I learned the basics of GNU autotools which still help me a lot).

But no one should have to go to the same effort with as little guidance as I had, so I decided to publish the script and the patches I created for installing everything we needed.1

The script worked 2 years ago, so you might have to fix some bits. I won’t promise that this contains everything you need to run the script - or that it won’t be broken when you install it. Actually I won’t promise anything at all, except that if the stuff here had been available 2 years ago, that could have saved me about 2 months of time (each of the patches here required quite some tracking of problems, experimenting and fixing, until it provided basic functionality - but actually I enjoyed doing that - I learned a lot - I just don’t want to be forced to do it again). Still, this stuff contains quite some hacks - even a few ugly ones. But it worked.

2 libraries and programs which get installed (=requirements)

This script requires and installs quite a few libraries. I retrieved most of the following tarballs from my Gentoo distfiles dir after installing the programs locally. I uploaded them to draketo.de/dateien/scipy-pynio-deps. These files are included there:

satexputils.so also needs interpolatelevels.F90 which I think that I am not allowed to share, so you’re on your own there. Guess why I do not like using non-free (or not-guaranteed-to-be-free) software.

3 Known Bugs

3.1 HDF autotools patch throws away some CFLAGS

The hdf autotools patch only retrieves the last CFLAG instead of all:

export CC='gcc-4.8.1 -Wall -Werror'                                                          
echo $CC | grep \ - | sed 's/.* -/-/'                                                                     
-Werror

If you have the regexp-foo to fix that, please improve the patch! But without perl (otherwise we’d have to install perl, too).

3.2 SciPy inline-C via weaver does not work

Udo Grabowski, the maintainer of our institutes sun-cluster somehow managed to get that working on OpenIndiana with the Sun-Compiler, but since I did not need it, I did not dig deeper to see whether I could adapt his solutions to the intel-compiler.

5 Implementation

This is the full install script I used to install all necessary dependencies.

#!/bin/bash

# Untar

for i in *.tar* *.tgz; do
  tar xvf $i || exit
done

# Install

PREFIX=/home/ws/babenhau/
PYPREFIX=/home/ws/babenhau/python/

# Blas

cd BLAS
cp ../blas-make.inc make.inc || exit
#make -j9 clean
F77=ifort make -j9 || exit
#make -j9 install --prefix=$PREFIX
# OR for Intel compiler:
ifort -fPIC -FI -w90 -w95 -cm -O3 -xHost -unroll -c *.f || exit
#Continue below irrespective of compiler:
ar r libfblas.a *.o || exit
ranlib libfblas.a || exit
cd ..
ln -s BLAS blas

## Lapack

cd lapack-3.3.1
ln -s ../blas
# this has a hardcoded absolute path to blas in it: replace is with the appropriate one for you.
cp ../lapack-make.inc make.inc || exit
make -j9 clean  || exit
make -j9
make -j9 || exit
cp lapack_LINUX.a libflapack.a || exit
#make -j9 install --prefix=$PREFIX
cd ..

# C interface

patch -p0 < lapacke-ifort.diff

cd lapacke
# patch for lapack 3.3.1 and blas
for i in gnu inc intel ; do 
    sed -i s/lapack-3\.2\.1\\/lapack\.a/lapack-3\.3\.1\\/lapack_LINUX.a/ make.$i; 
    sed -i s/lapack-3\.2\.1\\/blas\.a/blas\\/blas_LINUX.a/ make.$i; 
done

make -j9 clean || exit
#make -j9
LINKER=ifort LDFLAGS=-nofor-main make -j9 # || exit
#LINKER=ifort LDFLAGS=-nofor-main make -j9 install
cd ..

## ATLAS

cd ATLAS
cp ../Make.Linux_HC3 . || exit
echo "ATLAS needs manual intervention. Run make by hand first."
#echo "just say yes. It makes some stuff we need later."
#make
#mv bin/Linux_UNKNOWNSSE2_8 bin/Linux_HC3
#for i in bin/Linux_HC3/*; do sed -i s/UNKNOWNSSE2_8/HC3/ $i ; done
#rm bin/Linux_HC3/Make.inc
#cd bin/Linux_HC3/
#ln -s ../../Make.Linux_HC3 Make.inc
#cd -

make -j9 install arch=Linux_HC3 || exit
cd lib
for i in Linux_HC3/* ; do ln -s $i ; done
cd ../bin
for i in Linux_HC3/* ; do ln -s $i ; done
cd ../include
for i in Linux_HC3/* ; do ln -s $i ; done
cd ..
cd ..

# Numpy and SciPy with intel compilers

# Read this: http://marklodato.github.com/2009/08/30/numpy-scipy-and-intel.html

# patching

patch -p0 < SuiteSparse.diff  || exit
patch -p0 < SuiteSparse-umfpack.diff  || exit

rm numpy
ln -s numpy-*.*.*/ numpy
patch -p0 < numpy-icc.diff  || exit
patch -p0 < numpy-icpc.diff || exit
patch -p0 <<EOF
--- numpy/numpy/distutils/fcompiler/intel.py      2009-03-29 07:24:21.000000000 -0400
+++ numpy/numpy/distutils/fcompiler/intel.py  2009-08-06 23:08:59.000000000 -0400
@@ -47,6 +47,7 @@
     module_include_switch = '-I'

     def get_flags(self):
+        return ['-fPIC', '-cm']
         v = self.get_version()
         if v >= '10.0':
             # Use -fPIC instead of -KPIC.
@@ -63,6 +64,7 @@
         return ['-O3','-unroll']

     def get_flags_arch(self):
+        return ['-xHost']
         v = self.get_version()
         opt = []
         if cpu.has_fdiv_bug():
EOF
# include -fPIC in the fcompiler.
sed -i "s/w90/w90\", \"-fPIC/" numpy/numpy/distutils/fcompiler/intel.py
# and more of that
patch -p0 < numpy-ifort.diff

rm scipy
ln -s scipy-*.*.*/ scipy

patch -p0 < scipy-qhull-icc.diff || exit
patch -p0 < scipy-qhull-icc2.diff || exit

# # unnecessary!
# patch -p0 <<EOF
# --- scipy/scipy/special/cephes/const.c    2009-08-07 01:56:43.000000000 -0400
# +++ scipy/scipy/special/cephes/const.c        2009-08-07 01:57:08.000000000 -0400
# @@ -91,12 +91,12 @@
# double THPIO4 =  2.35619449019234492885;       /* 3*pi/4 */
# double TWOOPI =  6.36619772367581343075535E-1; /* 2/pi */
# #ifdef INFINITIES
# -double INFINITY = 1.0/0.0;  /* 99e999; */
# +double INFINITY = __builtin_inff();
# #else
# double INFINITY =  1.79769313486231570815E308;    /* 2**1024*(1-MACHEP) */
# #endif
# #ifdef NANS
# -double NAN = 1.0/0.0 - 1.0/0.0;
# +double NAN = __builtin_nanf("");
# #else
# double NAN = 0.0;
# #endif
# EOF


# building

# TODO: try again later

cd SuiteSparse

make -j9 -C AMD || exit
make -j9 -C UMFPACK || exit

cd ..

# TODO: build numpy again and make sure it has blas and lapack (and ATLAS?)

cd numpy
python setup.py -v build_src config --compiler=intel build_clib \
    --compiler=intel build_ext --compiler=intel || exit
python setup.py install --prefix=$PYPREFIX || exit
cd ..

# scons and numscons
cd scons-2.0.1
python setup.py -v install --prefix=/home/ws/babenhau/python/ || exit
cd ..

git clone git://github.com/cournape/numscons.git
cd numscons 
python setup.py -v install --prefix=/home/ws/babenhau/python/  || exit
cd ..

# adapt /home/ws/babenhau/python/lib/python2.7/site-packages/numpy/distutils/fcompiler/intel.py by hand to include fPIC for intelem

cd scipy

PYTHONPATH=/home/ws/babenhau/python//lib/scons-2.0.1/ ATLAS=../ATLAS/ \
    LAPACK=../lapack-3.3.1/libflapack.a LAPACK_SRC=../lapack-3.3.1 BLAS=../BLAS/libfblas.a \
    F77=ifort f77_opt=ifort python setup.py -v config --compiler=intel --fcompiler=intelem build_clib \
    --compiler=intel --fcompiler=intelem build_ext --compiler=intel --fcompiler=intelem \
    -I../SuiteSparse/UFconfig # no exit, because we do the linking by hand later on.

# one file is C++ :(
icpc -fPIC -I/home/ws/babenhau/python/include/python2.7 -I/home/ws/babenhau/python/lib/python2.7/site-packages/numpy/core/include -I/home/ws/babenhau/python/lib/python2.7/site-packages/numpy/core/include -c scipy/spatial/qhull/src/user.c -o build/temp.linux-x86_64-2.7/scipy/spatial/qhull/src/user.o || exit

# linking by hand

# for x in csr csc coo bsr dia; do
#    icpc -xHost -O3 -fPIC -shared \
#        build/temp.linux-x86_64-2.7/scipy/sparse/sparsetools/${x}_wrap.o \
#        -o build/lib.linux-x86_64-2.7/scipy/sparse/sparsetools/_${x}.so || exit
# done
#icpc -xHost -O3 -fPIC -openmp -shared \
#   build/temp.linux-x86_64-2.7/scipy/interpolate/src/_interpolate.o \
#   -o build/lib.linux-x86_64-2.7/scipy/interpolate/_interpolate.so || exit

# build again with the C++ file already compiled

PYTHONPATH=/home/ws/babenhau/python//lib/scons-2.0.1/ ATLAS=../ATLAS/ \
    LAPACK=../lapack-3.3.1/libflapack.a LAPACK_SRC=../lapack-3.3.1 BLAS=../BLAS/libfblas.a \
    F77=ifort f77_opt=ifort python setup.py config --compiler=intel --fcompiler=intelem build_clib \
    --compiler=intel --fcompiler=intelem build_ext --compiler=intel --fcompiler=intelem \
    -I../SuiteSparse/UFconfig || exit

# make sure we have cephes
cd scipy/special
PYTHONPATH=/home/ws/babenhau/python//lib/scons-2.0.1/ ATLAS=../../../ATLAS/ \
    LAPACK=../../../lapack-3.3.1/libflapack.a LAPACK_SRC=../lapack-3.3.1 BLAS=../../../BLAS/libfblas.a \
    F77=ifort f77_opt=ifort python setup.py -v config --compiler=intel --fcompiler=intelem build_clib \
    --compiler=intel --fcompiler=intelem build_ext --compiler=intel --fcompiler=intelem \
    -I../../../SuiteSparse/UFconfig
cd ../..

# install
PYTHONPATH=/home/ws/babenhau/python//lib/scons-2.0.1/ ATLAS=../ATLAS/ \
    LAPACK=../lapack-3.3.1/libflapack.a LAPACK_SRC=../lapack-3.3.1 BLAS=../BLAS/libfblas.a \
    F77=ifort f77_opt=ifort python setup.py config --compiler=intel --fcompiler=intelem build_clib \
    --compiler=intel --fcompiler=intelem install --prefix=$PYPREFIX || exit

cd ..

# PyNIO

# netcdf-4

patch -p0 < netcdf-patch1.diff || exit
patch -p0 < netcdf-patch2.diff || exit

cd netcdf-4.1.3

CPPFLAGS="-I/home/ws/babenhau/libbutz/hdf5-1.8.7/include -I/home/ws/babenhau/include" LDFLAGS="-L/home/ws/babenhau/libbutz/hdf5-1.8.7/lib/ -L/home/ws/babenhau/lib -lsz -L/home/ws/babenhau/libbutz/szip-2.1/lib -L/opt/intel/Compiler/11.1/080/lib/intel64/libifcore.a -lifcore" ./configure --prefix=/home/ws/babenhau/ --enable-netcdf-4 --enable-shared || exit

make -j9; make check install -j9 || exit

cd ..

# NetCDF4
cd netCDF4-0.9.7
HAS_SZIP=1 SZIP_PREFIX=/home/ws/babenhau/libbutz/szip-2.1/ HAS_HDF5=1 HDF5_DIR=/home/ws/babenhau/libbutz/hdf5-1.8.7 HDF5_PREFIX=/home/ws/babenhau/libbutz/hdf5-1.8.7 HDF5_includedir=/home/ws/babenhau/libbutz/hdf5-1.8.7/include HDF5_libdir=/home/ws/babenhau/libbutz/hdf5-1.8.7/lib HAS_NETCDF4=1 NETCDF4_PREFIX=/home/ws/babenhau/ python setup.py build_ext --compiler="intel" --fcompiler="intel -fPIC" install --prefix $PYPREFIX
cd ..

# parallel netcdf and hdf5: ~/libbutz/

patch -p0 < pynio-fix-no-grib.diff || exit

cd PyNIO-1.4.1
HAS_SZIP=1 SZIP_PREFIX=/home/ws/babenhau/libbutz/szip-2.1/ HAS_HDF5=1 HDF5_DIR=/home/ws/babenhau/libbutz/hdf5-1.8.7 HDF5_PREFIX=/home/ws/babenhau/libbutz/hdf5-1.8.7 HDF5_includedir=/home/ws/babenhau/libbutz/hdf5-1.8.7/include HDF5_libdir=/home/ws/babenhau/libbutz/hdf5-1.8.7/lib HAS_NETCDF4=1 NETCDF4_PREFIX=/home/ws/babenhau/ python setup.py install --prefix=$PYPREFIX || exit
# TODO: Make sure that the install goes to /home/ws/.., not home/ws/...
cd ..

# satexp_utils.so

f2py -c -m satexp_utils --f77exec=ifort --f90exec=ifort interpolate_levels.F90 || exit

## pyhdf

# recompile hdf with fPIC - grr!
cd hdf-4*/
# Fix configure for compilers with - in the name.
patch -p0 < ../hdf-fix-configure.ac.diff
autoconf
FFLAGS="-ip -O3 -xHost -fPIC -r8" CFLAGS="-ip -O3 -xHost -fPIC" CXXFLAGS="$CFLAGS -I/usr/include/rpc  -DBIG_LONGS -DSWAP" F77=ifort ./configure --prefix=/home/ws/babenhau/ --disable-netcdf --with-szlib=/home/ws/babenhau/libbutz/szip-2.1 # --with-zlib=/home/ws/babenhau/libbutz/zlib-1.2.5 --with-jpeg=/home/ws/babenhau/libbutz/jpeg-8c
# finds zlib and jpeg due to LD_LIBRARY_PATH (hack but works…)
make
make install
cd ..

# build pyhdf
cd pyhdf-0.8.3/
INCLUDE_DIRS="/home/ws/babenhau/include:/home/ws/babenhau/libbutz/szip-2.1/include" LIBRARY_DIRS="/home/ws/babenhau/lib:/home/ws/babenhau/libbutz/szip-2.1/lib" python setup.py build -c intel --fcompiler ifort install --prefix=/home/ws/babenhau/python 
cd ..

## matplotlib

cd matplotlib-1.1.0
patch -p0 < ../matplotlib-add-icc-support.diff
python setup.py build -c intel install --prefix=/home/ws/babenhau/python
cd ..

# GEOS → http://download.osgeo.org/geos/geos-3.3.2.tar.bz2

cd geos*/ 
./configure --prefix=/home/ws/babenhau/
make
make check
make install 
cd ..

# basemap

easy_install --prefix /home/ws/babenhau/python basemap
# fails but should now have all dependencies.

cd basemap-*/

python setup.py build -c intel install --prefix=/home/ws/babenhau/python

cd ..

6 Appendix

6.1 All patches inline

To ease usage and upstreaming of my fixes, I include all the patches below, so you can find them directly in this text instead of having to browse external textfiles.

6.1.1 SuiteSparse-umfpack.diff

--- SuiteSparse/UMFPACK/Lib/GNUmakefile 2009-11-11 21:09:54.000000000 +0100
+++ SuiteSparse/UMFPACK/Lib/GNUmakefile 2011-09-09 14:18:57.000000000 +0200
@@ -9,7 +9,7 @@
 C = $(CC) $(CFLAGS) $(UMFPACK_CONFIG) \
     -I../Include -I../Source -I../../AMD/Include -I../../UFconfig \
     -I../../CCOLAMD/Include -I../../CAMD/Include -I../../CHOLMOD/Include \
-    -I../../metis-4.0/Lib -I../../COLAMD/Include
+    -I../../COLAMD/Include

 #-------------------------------------------------------------------------------
 # source files

6.1.2 SuiteSparse.diff

--- SuiteSparse/UFconfig/UFconfig.mk    2011-09-09 13:14:03.000000000 +0200
+++ SuiteSparse/UFconfig/UFconfig.mk    2011-09-09 13:15:03.000000000 +0200
@@ -33,11 +33,11 @@
 # C compiler and compiler flags:  These will normally not give you optimal
 # performance.  You should select the optimization parameters that are best
 # for your system.  On Linux, use "CFLAGS = -O3 -fexceptions" for example.
-CC = cc
-CFLAGS = -O3 -fexceptions
+CC = icc
+CFLAGS = -O3 -xHost -fPIC -openmp -vec_report=0

 # C++ compiler (also uses CFLAGS)
-CPLUSPLUS = g++
+CPLUSPLUS = icpc

 # ranlib, and ar, for generating libraries
 RANLIB = ranlib
@@ -49,8 +49,8 @@
 MV = mv -f

 # Fortran compiler (not normally required)
-F77 = f77
-F77FLAGS = -O
+F77 = ifort
+F77FLAGS = -O3 -xHost
 F77LIB =

 # C and Fortran libraries
@@ -132,13 +132,13 @@
 # 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

 # If you use CHOLMOD_CONFIG = -DNPARTITION then you must use the following
 # options:
-# METIS_PATH =
-# METIS =
+METIS_PATH =
+METIS =

 #------------------------------------------------------------------------------
 # UMFPACK configuration:
@@ -194,7 +194,7 @@
 # -DNSUNPERF       for Solaris only.  If defined, do not use the Sun
 #          Performance Library

-CHOLMOD_CONFIG =
+CHOLMOD_CONFIG = -DNPARTITION

 #------------------------------------------------------------------------------
 # SuiteSparseQR configuration:

6.1.3 hdf-fix-configure.ac.diff (fixes a bug but still contains another known bug - see Known Bugs!)

--- configure.ac    2012-03-01 15:00:28.000000000 +0100
+++ configure.ac    2012-03-01 15:00:40.000000000 +0100
@@ -815,7 +815,7 @@
 dnl Report anything stripped as a flag in CFLAGS and 
 dnl only the compiler in CC_VERSION.
 CC_NOFLAGS=`echo $CC | sed 's/ -.*//'`
-CFLAGS_TO_ADD=`echo $CC | grep - | sed 's/.* -/-/'`
+CFLAGS_TO_ADD=`echo $CC | grep \ - | sed 's/.* -/-/'`
 if test -n $CFLAGS_TO_ADD; then
   CFLAGS="$CFLAGS_TO_ADD$CFLAGS"
 fi

6.1.4 lapacke-ifort.diff

--- lapacke/make.intel.old  2011-10-05 13:24:14.000000000 +0200
+++ lapacke/make.intel  2011-10-05 16:17:00.000000000 +0200
@@ -56,7 +56,7 @@
 # Ensure that the libraries have the same data model (LP64/ILP64).
 #
 LAPACKE = lapacke.a
-LIBS = ../../../lapack-3.3.1/lapack_LINUX.a ../../../blas/blas_LINUX.a -lm
+LIBS = /opt/intel/Compiler/11.1/080/lib/intel64/libifcore.a ../../../lapack-3.2.1/lapack.a ../../../lapack-3.2.1/blas.a -lm -ifcore
 #
 #  The archiver and the flag(s) to use when building archive (library)
 #  If your system has no ranlib, set RANLIB = echo.

6.1.5 matplotlib-add-icc-support.diff

diff -r 38c2a32c56ae matplotlib-1.1.0/setup.py
--- a/matplotlib-1.1.0/setup.py Fri Mar 02 12:29:47 2012 +0100
+++ b/matplotlib-1.1.0/setup.py Fri Mar 02 12:30:39 2012 +0100
@@ -31,6 +31,13 @@
 if major==2 and minor1<4 or major<2:
     raise SystemExit("""matplotlib requires Python 2.4 or later.""")

+if "intel" in sys.argv or "icc" in sys.argv:
+    try: # make it compile with the intel compiler
+        from numpy.distutils import intelccompiler
+    except ImportError:
+        print "Compiling with the intel compiler requires numpy."
+        raise
+
 import glob
 from distutils.core import setup
 from setupext import build_agg, build_gtkagg, build_tkagg,\

6.1.6 netcdf-patch1.diff

--- netcdf-4.1.3/fortran/ncfortran.h    2011-07-01 01:22:22.000000000 +0200
+++ netcdf-4.1.3/fortran/ncfortran.h    2011-09-14 14:56:03.000000000 +0200
@@ -658,7 +658,7 @@
  * The following is for f2c-support only.
  */

-#if defined(f2cFortran) && !defined(pgiFortran) && !defined(gFortran)
+#if defined(f2cFortran) && !defined(pgiFortran) && !defined(gFortran) &&!defined(__INTEL_COMPILER)

 /*
  * The f2c(1) utility on BSD/OS and Linux systems adds an additional

6.1.7 netcdf-patch2.diff

--- netcdf-4.1.3/nf_test/fortlib.c  2011-09-14 14:58:47.000000000 +0200
+++ netcdf-4.1.3/nf_test/fortlib.c  2011-09-14 14:58:38.000000000 +0200
@@ -14,7 +14,7 @@
 #include "../fortran/ncfortran.h"


-#if defined(f2cFortran) && !defined(pgiFortran) && !defined(gFortran)
+#if defined(f2cFortran) && !defined(pgiFortran) && !defined(gFortran) &&!defined(__INTEL_COMPILER)
 /*
  * The f2c(1) utility on BSD/OS and Linux systems adds an additional
  * underscore suffix (besides the usual one) to global names that have

6.1.8 numpy-icc.diff

--- numpy/numpy/distutils/intelccompiler.py 2011-09-08 14:14:03.000000000 +0200
+++ numpy/numpy/distutils/intelccompiler.py 2011-09-08 14:20:37.000000000 +0200
@@ -30,11 +30,11 @@
     """ A modified Intel x86_64 compiler compatible with a 64bit gcc built Python.
     """
     compiler_type = 'intelem'
-    cc_exe = 'icc -m64 -fPIC'
+    cc_exe = 'icc -m64 -fPIC -xHost -O3'
     cc_args = "-fPIC"
     def __init__ (self, verbose=0, dry_run=0, force=0):
         UnixCCompiler.__init__ (self, verbose,dry_run, force)
-        self.cc_exe = 'icc -m64 -fPIC'
+        self.cc_exe = 'icc -m64 -fPIC -xHost -O3'
         compiler = self.cc_exe
         self.set_executables(compiler=compiler,
                              compiler_so=compiler,

6.1.9 numpy-icpc.diff

--- numpy-1.6.1/numpy/distutils/intelccompiler.py   2011-10-06 16:55:12.000000000 +0200
+++ numpy-1.6.1/numpy/distutils/intelccompiler.py   2011-10-10 10:26:14.000000000 +0200
@@ -10,11 +10,13 @@
     def __init__ (self, verbose=0, dry_run=0, force=0):
         UnixCCompiler.__init__ (self, verbose,dry_run, force)
         self.cc_exe = 'icc -fPIC'
+   self.cxx_exe = 'icpc -fPIC'
         compiler = self.cc_exe
+   compiler_cxx = self.cxx_exe
         self.set_executables(compiler=compiler,
                              compiler_so=compiler,
-                             compiler_cxx=compiler,
-                             linker_exe=compiler,
+                             compiler_cxx=compiler_cxx,
+                             linker_exe=compiler_cxx,
                              linker_so=compiler + ' -shared')

 class IntelItaniumCCompiler(IntelCCompiler):

6.1.10 numpy-ifort.diff

--- numpy-1.6.1/numpy/distutils/fcompiler/intel.py.old  2011-10-10 17:52:34.000000000 +0200
+++ numpy-1.6.1/numpy/distutils/fcompiler/intel.py  2011-10-10 17:53:51.000000000 +0200
@@ -32,7 +32,7 @@
     executables = {
         'version_cmd'  : None,          # set by update_executables
         'compiler_f77' : [None, "-72", "-w90", "-fPIC", "-w95"],
-        'compiler_f90' : [None],
+        'compiler_f90' : [None, "-fPIC"],
         'compiler_fix' : [None, "-FI"],
         'linker_so'    : ["<F90>", "-shared"],
         'archiver'     : ["ar", "-cr"],
@@ -129,7 +129,7 @@
         'version_cmd'  : None,
         'compiler_f77' : [None, "-FI", "-w90", "-fPIC", "-w95"],
         'compiler_fix' : [None, "-FI"],
-        'compiler_f90' : [None],
+        'compiler_f90' : [None, "-fPIC"],
         'linker_so'    : ['<F90>', "-shared"],
         'archiver'     : ["ar", "-cr"],
         'ranlib'       : ["ranlib"]
@@ -148,7 +148,7 @@
         'version_cmd'  : None,
         'compiler_f77' : [None, "-FI", "-w90", "-fPIC", "-w95"],
         'compiler_fix' : [None, "-FI"],
-        'compiler_f90' : [None],
+        'compiler_f90' : [None, "-fPIC"],
         'linker_so'    : ['<F90>', "-shared"],
         'archiver'     : ["ar", "-cr"],
         'ranlib'       : ["ranlib"]
@@ -180,7 +180,7 @@
         'version_cmd'  : None,
         'compiler_f77' : [None,"-FI","-w90", "-fPIC","-w95"],
         'compiler_fix' : [None,"-FI","-4L72","-w"],
-        'compiler_f90' : [None],
+        'compiler_f90' : [None, "-fPIC"],
         'linker_so'    : ['<F90>', "-shared"],
         'archiver'     : [ar_exe, "/verbose", "/OUT:"],
         'ranlib'       : None
@@ -232,7 +232,7 @@
         'version_cmd'  : None,
         'compiler_f77' : [None,"-FI","-w90", "-fPIC","-w95"],
         'compiler_fix' : [None,"-FI","-4L72","-w"],
-        'compiler_f90' : [None],
+        'compiler_f90' : [None, "-fPIC"],
         'linker_so'    : ['<F90>',"-shared"],
         'archiver'     : [ar_exe, "/verbose", "/OUT:"],
         'ranlib'       : None

6.1.11 pynio-fix-no-grib.diff

--- PyNIO-1.4.1/Nio.py  2011-09-14 16:00:13.000000000 +0200
+++ PyNIO-1.4.1/Nio.py  2011-09-14 16:00:18.000000000 +0200
@@ -98,7 +98,7 @@
         if ncarg_dir == None or not os.path.exists(ncarg_dir) \
           or not os.path.exists(os.path.join(ncarg_dir,"lib","ncarg")):
             if not __formats__['grib2']:
-                return None
+                return "" # "", because an env variable has to be a string.
             else:
                 print "No path found to PyNIO/ncarg data directory and no usable NCARG installation found"
                 sys.exit()

6.1.12 scipy-qhull-icc.diff

--- scipy/scipy/spatial/qhull/src/qhull_a.h 2011-02-27 11:57:03.000000000 +0100
+++ scipy/scipy/spatial/qhull/src/qhull_a.h 2011-09-09 15:42:12.000000000 +0200
@@ -102,13 +102,13 @@
 #elif defined(__MWERKS__) && defined(__INTEL__)
 #   define QHULL_OS_WIN
 #endif
-#if defined(__INTEL_COMPILER) && !defined(QHULL_OS_WIN)
-template <typename T>
-inline void qhullUnused(T &x) { (void)x; }
-#  define QHULL_UNUSED(x) qhullUnused(x);
-#else
+/*#if defined(__INTEL_COMPILER) && !defined(QHULL_OS_WIN)*/
+/*template <typename T>*/
+/*inline void qhullUnused(T &x) { (void)x; }*/
+/*#  define QHULL_UNUSED(x) qhullUnused(x);*/
+/*#else*/
 #  define QHULL_UNUSED(x) (void)x;
-#endif
+*/#endif*/

 /***** -libqhull.c prototypes (alphabetical after qhull) ********************/

6.1.13 scipy-qhull-icc2.diff

--- scipy/scipy/spatial/qhull/src/qhull_a.h 2011-09-09 15:43:54.000000000 +0200
+++ scipy/scipy/spatial/qhull/src/qhull_a.h 2011-09-09 15:45:17.000000000 +0200
@@ -102,13 +102,7 @@
 #elif defined(__MWERKS__) && defined(__INTEL__)
 #   define QHULL_OS_WIN
 #endif
-/*#if defined(__INTEL_COMPILER) && !defined(QHULL_OS_WIN)*/
-/*template <typename T>*/
-/*inline void qhullUnused(T &x) { (void)x; }*/
-/*#  define QHULL_UNUSED(x) qhullUnused(x);*/
-/*#else*/
 #  define QHULL_UNUSED(x) (void)x;
-*/#endif*/

 /***** -libqhull.c prototypes (alphabetical after qhull) ********************/

6.1.14 scipy-spatial-lifcore.diff

--- scipy-0.9.0/scipy/spatial/setup.py  2011-10-10 17:11:23.000000000 +0200
+++ scipy-0.9.0/scipy/spatial/setup.py  2011-10-10 17:11:09.000000000 +0200
@@ -22,6 +22,8 @@
                                      get_numpy_include_dirs()],
                        # XXX: GCC dependency!
                        #extra_compiler_args=['-fno-strict-aliasing'],
+                       # XXX intel compiler dependency
+                       extra_compiler_args=['-lifcore'],
                        )

     lapack = dict(get_info('lapack_opt'))

7 Summary

I hope this helps someone out there saving some time - or even better: improving the upstream projects. At least it should be a nice reference for all who need to get scipy working on not-quite-supported architectures.

Happy Hacking!

Footnotes:

1

: Actually I already wanted to publish that script more than a year ago, but time flies and there’s always stuff to do. But at least I now managed to get it done.

Author: Arne Babenhauserheide

Created: 2013-09-26 Do

Emacs 24.3.1 (Org mode 8.0.2)

Validate XHTML 1.0

AnhangGröße
2013-09-26-Do-installing-scipy-and-matplotlib-on-a-bare-cluster-with-the-intel-compiler.org29.2 KB

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