User:Jonas Lindemann (LUNARC)/SweGrid runtime environments

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APPS/MATH/OCTAVE

Building Octave 3.2.4 (CentOS 5.x)

Download from ftp://ftp.gnu.org/gnu/octave

Required build packages:

  • glpk-devel
  • qrupdate-devel
  • hdf5-devel
  • fftw-devel
  • qhull-devel
  • curl-devel
  • arpack-devel
  • readline-devel
  • pcre-devel
  • gnuplot
  • suitesparse-devel
  • texinfo

Required runtime packages:

  • glpk
  • qrupdate
  • hdf5
  • fftw
  • qhull
  • curl
  • arpack
  • readline
  • pcre
  • gnuplot
  • suitesparse

Packages built from source:

GotoBLAS2 - BLAS/LAPACK http://www.tacc.utexas.edu/tacc-projects/gotoblas2/

Configuration script (conf_octave): 

#!/bin/sh

INSTALLDIR=/sw/pkg/octave/3.2.4
BLASLIB=/sw/pkg/gotoblas2/1.13/lib/libgoto2.a
LAPACKLIB=/sw/pkg/gotoblas2/1.13/lib/libgoto2.a
F77="gfortran"

./configure --prefix=$INSTALLDIR --with-blas=$BLASDIR --with-lapack=$LAPACKLIB --without-curl --disable-docs

Build octave: 

$ ./conf_octave
$ make

Test octave: 

$ make test

The imread test will fail as we haven't configured it.

Install octave: 

$ su
$ make install

Setting up runtime environment

The following runtime script can be used. Please replace with your own search paths: 

#!/bin/bash
#
# OCTAVE runtime environment script for Nordugrid ARC
#
# Runtime environment scripts are called (bash source)
#   from NorduGrid ARC with argument 0,1 or 2.
# First call with argument "0" is made before the the batch
#   job submission script is written.
# Second call is made with argument "1" just prior to execution of the
#   user specified executable.
# Third "clean-up" call is made with argument "2" after the user
#   specified executable has returned.
#
# author: Jonas Lindemann <jonas.lindemann@lunarc.lu.se>
#

case "$1" in
0 )
	# --- Called before job script creation ---
;;

1 )

	# --- Called before execution of job script on node ---
	
	# Setup octave home directory
	export OCTAVE_HOME=/sw/pkg/octave/3.2.4

	# include HMMer binaries in the path
	export PATH=$PATH:$OCTAVE_HOME/bin
;;
2 )
	# --- Called after job execution on node ---
;;
esac

copy the file under [RE-dir]/APPS/MATH/OCTAVE-3.2.4

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