Difference: InstallNumpyScipy (3 vs. 4)

Revision 404 Jan 2011 - Main.BillRice

 
META TOPICPARENT name="CemITSystem"
Contents

Numpy and Scipy

Download files

  • AMD.tar.gz
  • CHOLMOD.tar.gz
  • UFconfig.tar.gz
  • UMFPACK.tar.gz
  • atlas3.8.3.tar.gz
  • lapack-3.1.1.tgz
  • fftw-3.2.1.tar.gz
  • numpy-1.0.4.tar.gz
  • scipy-0.6.0.tar.gz

Prepare for installation

  • do this as yourself (not root)
  • sudo chmod 777 /usr/local/src -- so that you can compile here
  • prepare a place to put the files: 
   mkdir -p local/lib
   mkdir local/include
  • it is important that gfortran is used to compile the fortran portions, so g777 must be removed from the path for the rest of the install 
   sudo mv /usr/bin/g77 /usr/bin/g77_TEMPORARY

compile lapack 

   cd /usr/local/src
   tar xvzf ~/lapack-3.1.1.tgz
   cd lapack-3.1.1/
   cp INSTALL/make.inc.gfortran make.inc
  • edit make.inc as follows: 
OPTS = -O2 -fPIC
NOOPT = -O0 -fPIC
  • compile: 
   cd src
   make
  • output file is /usr/local/src/lapack-3.1.1/lapack_LINUX.a

compile atlas

  • NOTE -- atlas will not compile if CPU throttling is turned on
    • to turn off, reboot, go to BIOS, and disable AMD POWERNOW
  • extract atlas 
   cd /usr/local/src
   tar xvzf ~/atlas3.8.3.tar.gz
   cd ATLAS
   mkdir ATLAS_X86-64
   cd ATLAS_X86-64
   ../configure -Fa alg -fPIC --with-netlib-lapack=/usr/local/src/lapack-3.1.1/lapack_LINUX.a
   make
   cd lib
   make shared     # for sequential libraries
   make ptshared   # for threaded libraries
   cp * /home/rice/local/lib/.
   cp ../include/* /home/rice/local/include/.

compile fftw3

  • extract and install (needs to be put into /usr/local/lib) 
   ./configure --enable-sse2 --enable-threads --with-combined-threads CFLAGS="-O3 -fomit-frame-pointer -fstrict-aliasing -ffast-math -pthread -fPIC -m64" FFLAGS="-g -O2 -fPIC -m64" CXXFLAGS="-g -O2 -fPIC -m64"
   make
   sudo make install

compile UMFPACK, AMD,CHOLMOD,UFconfig

  • these must all be done within one directory 
   cd /usr/local/src
   mkdir umf
   cd umf
   tar xvzf ~/AMD.tar.gz
   tar xvzf ~/CHOLMOD.tar.gz
   tar xvzf ~/UMFPACK.tar.gz
   tar xvzf ~/UFconfig.tar.gz
  • now need to edit config file so it compiles with right flags and uses newly-created blas and atlas libraries 
   cd UFconfig
  • edit UFconfig.mk to read as follows: 
CC = gcc
CFLAGS = -O3 -fexceptions -m64 -fPIC

F77 = gfortran
F77FLAGS = -O -m64 -fPIC

INSTALL_LIB = /home/rice/local/lib
INSTALL_INCLUDE = /home/rice/local/include

BLAS = -L/usr/lib64 -L/home/rice/local/lib -llapack -lf77blas -lcblas -latlas -lgfortran
LAPACK = -L/usr/lib64 -L/home/rice/local/lib -llapack -lf77blas -lcblas -latlas -lgfortran

METIS_PATH =
METIS =

CHOLMOD_CONFIG = -DNPARTITION
  • now compile and install 
   cd ../UMFPACK/
   make library
   make install
   cd ../AMD
   make install
   cd ../UFconfig
   cp UFconfig.h /home/rice/local/include/.
Added:
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>

compile numpy

  • extract 
   cd /usr/local/src
   tar xvzf ~/numpy-1.0.4.tar.gz
   cd numpy-1.0.4
   cp site.cfg.example site.cfg
  • edit newly-created site.cfg as follows (be sure to uncomment header lines): 
[DEFAULT]
library_dirs = /home/rice/local/lib
include_dirs = /home/rice/local/include

[blas_opt]
libraries = ptf77blas, ptcblas, atlas
#
[lapack_opt]
libraries = lapack, ptf77blas, ptcblas, atlas

[amd]
amd_libs = amd
#
[umfpack]
umfpack_libs = umfpack

[fftw]
libraries = fftw3
  • build and install 
   python setup.py build
   python setup.py install --prefix=/home/rice/local

scipy

  • extract, build and install 
   cd /usr/local/src
   tar xvzf ~/scipy
   cd scipy1.0.4
   python setup.py build
   python setup.py install --prefix = /home/rice/local

test

  • need to add local/lib to LD_LIBRARY_PATH, and also update PYTHONPATH 
   setenv LD_LIBRARY_PATH /home/rice/local/lib:$LD_LIBRARY_PATH
   setenv PYTHONPATH /home/rice/local/lib64/python2.4/site-packages/:$PYTHONPATH
<verbatim>
   * test numpy and scipy in python
<verbatim>
   python
   import numpy
   import scipy
</verbatim>


---++ finish install -- put in place so all can use
   * copy python packages to standard location
<verbatim>
   sudo cp -r /home/rice/local/lib64/python2.4/site-packages/numpy /usr/lib64/python2.4/site-packages/.
   sudo cp -r /home/rice/local/lib64/python2.4/site-packages/scipy /usr/lib64/python2.4/site-packages/.
</verbatim>
   * copy blas,lapack libraries to /usr/local/lib/lapack
<verbatim>
   sudo mkdir /usr/local/lib/lapack
   sudo cp /home/rice/local/lib/* /usr/local/lib/lapack/.
   sudo cp /home/rice/local/include/* /usr/local/include/.
</verbatim>
   * remember to add new library location to LD_LIBRARY_PATH in .cshrc:
<verbatim>
setenv LD_LIBRARY_PATH /usr/local/lib/lapack:$LD_LIBRARY_PATH
</verbatim>



</verbatim>
<nop>
 

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-- BillRice - 04 Jan 2011

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