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guide:compiling_octave [2011/12/05 14:43]
hamish [Configuration] 		guide:compiling_octave [2021/12/09 16:42] (current)
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-====== Compiling Octave from Source ======+====== Compiling Octave 3.4.3 from Source ======
  
-This guide is written as to try and help CHPC users who are struggling to compile the Octave version required for their codes. This guide is written for the Sun Tsessbe Cluster. The reader is advise to read through the INSTALL file located in the Octave Source they wish to install before proceeding with this guide.+This guide is written for the Sun Tsessbe Cluster. The reader is advise to read through the INSTALL file located in the Octave Source Folder before proceeding with this guide. Also it recommended to make use of temporary or scratch directory to do all the compilation in (i.e. ~/scratch or /tmp/$USER), as to save disk space in your home directory. This guide assumes GCC 4.6.2 has been installed in your home directory as  in [[guide:compiling_gcc|Compiling GCC from Source]]. Paste the following lines at the end of your ./bashrc file 
 +  export LD_LIBRARY_PATH=$HOME/lib:$LD_LIBRARY_PATH 
 +  export LD_LIBRARY_PATH=$HOME/lib64:$LD_LIBRARY_PATH 
 +  export PATH=$HOME/bin:$PATH 
 +  export LDFLAGS="-L$HOME/lib64 -L$HOME/lib" 
 +  export CPPFLAGS="-I$HOME/include -L$HOME/lib64 -L$HOME/lib" 
 +  export CXXFLAGS=$CPPFLAGS 
 +  export F77=gfortran
  
-Before you begin, make sure your bash environmental variable are set correctly, for [[quick:start#what_you_can_do|example ]]. Also it recommended that you make you use of temporary or scratch directory to do all the compilation in (i.e. ~/scratch or /tmp/$USER), as to save disk space in your home directory.+log out and in again,  
 +  $  gcc --version 
 +  gcc (GCC) 4.6.2 
 +  
  
-Also note that for this guide, all binary and libraries are installed home directory, i.e prefix=$HOME. My setup + 
-  $ export PATH=/opt/gridware/gcc-4.3/bin:$PATH +===== Prerequisites  ===== 
-  $ export LD_LIBRARY_PATH=/opt/gridware/gcc-4.3/lib/:$LD_LIBRARY_PATH + 
-  $ export LD_LIBRARY_PATH=/opt/gridware/gcc-4.3/lib64/:$LD_LIBRARY_PATH +Before you build Octave, you some libraries need to be built 
-  $ gcc --version + 
-    gcc (GCC) 4.3.4+=== LAPACK and BLAS === 
 + 
 +Download the LAPACK source and extract, setup make and build as follows, 
 +  $ cd ~/scratch 
 +  $ wget http://www.netlib.org/lapack/lapack-3.4.0.tgz 
 +  $ tar -xf lapack-3.4.0.tgz 
 +  $ cd lapack-3.4.0 
 +Setup make,   
 +  $ cp make.inc.example make.inc 
 +  $ emacs make.inc 
 +  # change  
 +  #  OPTS     = -O2  and, NOOPT    = -O0 
 +  # to 
 +  #  OPTS     = -O2 -fPIC and, NOOPT    = -O0 -fPIC 
 +  # save (crtl-x crtl-s) and exit (crtl-x ctrl-c) 
 +  $ make 
 +Make BLAS 
 +  $ cd BLAS/SRC 
 +  $ make 
 +Make LAPACK 
 +  $ cd ../../ 
 +  $ make 
 +Which should give you test results such as 
 +    -->   LAPACK TESTING SUMMARY  <-- 
 +  Processing LAPACK Testing output found in the TESTING direcory 
 +  SUMMARY              nb test run numerical error    other error   
 +  ================    =========== ================= ================   
 +  REAL              1070421 38 (0.004%) 0 (0.000%)  
 +  DOUBLE PRECISION 1052315 204 (0.019%) 0 (0.000%)  
 +  COMPLEX          508588 2 (0.000%) 0 (0.000%)  
 +  COMPLEX16          549510 24 (0.004%) 0 (0.000%)  
 +   
 +  --> ALL PRECISIONS 3180834 268 (0.008%) 0 (0.000%) 
 + 
 +For more information visit [[ http://www.netlib.org/lapack/lawn81/ | Quick Installation Guide for LAPACK on Unix Systems ]] 
 + 
 +=== PCRE - Perl Compatible Regular Expressions === 
 + 
 +From the [[http://www.pcre.org/|PCRE website]], follow the link source forge to download the appropriate source file. Extract, go into directory, make BUILD directory, enter build directory. ../configure with home prefix. make. make check. make install. If $HOME/lib is not in your LD_LIBRARY_PATH, add it via export or in your .bashrc file. 
 + 
 +=== FFTW  === 
 + 
 +Refer to [[guide:compiling_octave_3_2_4|Compiling Octave 3.2.4 from Source]] 
 + 
 +=== binutils and libtools (optional) ===  
 + 
 +binutils 
 +  $ wget http://www.mirrorservice.org/sites/ftp.gnu.org/gnu/binutils/binutils-2.22.tar.bz2 
 +  $ tar -xf binutils-2.22.tar.bz2 
 +  $ cd binutils-2.22 
 +  $ mkdir BUILD 
 +  $ cd BUILD 
 +  $ ../configure --prefix=$HOME 
 +  $ make 
 +  $ make -k check 
 +  # If all the tests are passed, install into you home directory 
 +  $ make install 
 + 
 +libtools 
 +  $ wget http://www.mirrorservice.org/sites/ftp.gnu.org/gnu/libtool/libtool-2.4.2.tar.gz 
 +  $ tar -xf libtool-2.4.2.tar.gz 
 +  $ cd libtool-2.4.2.tar.gz 
 +  $ mkdir BUILD 
 +  $ cd BUILD 
 +  $ ../configure --prefix=$HOME 
 +  $ make  
 +  $ make -k check 
 +  # If all the tests are passed, install into you home directory 
 +  $ make install 
 + 
 +If you have not already add the following line in your .bashrc file 
 +  export PATH=$HOME/bin:$PATH 
 +then logout and login again, you should see 
 +  $ ld -v 
 +  GNU ld (GNU Binutils) 2.22 
 + 
 + 
 +=== UMFPACK (optional) === 
 +"UMFPACK is a set of routines for solving unsymmetric sparse linear systems, Ax=b, using the Unsymmetric MultiFrontal method." [[http://www.cise.ufl.edu/research/sparse/umfpack/|UMFPACK]]. See [[http://matrixprogramming.com/2008/03/umfpack| Compiling UMFPACK]] 
 + 
 +  $#still to be done 
 + 
 + 
 +    
          
 ===== Download Source ===== ===== Download Source =====
  
-Since the ftp is blocked on the Tsessbe login node, i made use of http mirror to download octave.+Since the ftp is blocked on the Tsessbe login node, make use of an http mirror to download octave.
   $ cd ~/scratch    $ cd ~/scratch 
-  $ wget http://www.mirrorservice.org/sites/ftp.gnu.org/gnu/octave/octave-3.2.4.tar.bz2 +  $ wget http://www.mirrorservice.org/sites/ftp.gnu.org/gnu/octave/octave-3.4.3.tar.bz2 
-  $ tar -xf octave-3.2.4.tar.bz2+  $ tar -xf octave-3.4.3.tar.bz2
      
 ===== Configuration ===== ===== Configuration =====
  
-At the time this guide was written, the f77 compiler was broken [?]: +   $ cd ~/scratch/octave-3.4.3
-   $ f77 --help +
-   /usr/bin/dirname: missing operand +
-   Try `/usr/bin/dirname --help' for more information. +
-   NOTICE: Invoking /usr/bin/f90 -f77 -ftrap=%none --help +
-   /usr/bin/f77: line 43: /usr/bin/f90: No such file or directory +
-   /usr/bin/f77: line 43: exec: /usr/bin/f90: cannot execute: No such file or directory +
-    +
-So gfortran will be used in its place, +
-   $ cd ~/scratch/octave-3.2.4+
    $ mkdir BUILD    $ mkdir BUILD
    $ cd BUILD    $ cd BUILD
-   $ export F77=gfortran +   $ ../configure --prefix=$HOME --with-blas=$HOME/scratch/lapack-3.4.0/librefblas.a --with-lapack=$HOME/scratch/lapack-3.4.0/liblapack.a  --disable-docs  
-   $ ../configure --prefix=$HOME --without-fftw3 --without-fftw3f --without-umfpack +   $ cp ../AUTHORS ./ #this is a bug in the configuration script...
- +
-Options explained +
-  * --prefix=$HOME, configure for installation into home directory +
-  * --without-fftw3 --without-fftw3f, Use the included fftpack library for computing Fast Fourier Transforms instead of the fftw3 library. If this option is not chosen the following build was encounter : +
- +
-  /usr/bin/ld: /usr/local/lib/libfftw3f.a(apiplan.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC +
-  /usr/local/lib/libfftw3f.a: could not read symbols: Bad value +
-  +
-  * --without-umfpack (is the UMFPACK library available?) +
  
 After configuration is complete, alot of warning about missing librarys are given After configuration is complete, alot of warning about missing librarys are given
Line 55: Line 129:
   * g++: Internal error: Killed (program cc1plus)   * g++: Internal error: Killed (program cc1plus)
 wait a while and then make again, as the process was killed by the usage limiter which runs on the login node. If nessary try the approach shown in [[guide:compiling_gcc#compiling_gcc|Compiling GCC from Source]]. wait a while and then make again, as the process was killed by the usage limiter which runs on the login node. If nessary try the approach shown in [[guide:compiling_gcc#compiling_gcc|Compiling GCC from Source]].
 +
 +===== Check =====
 +
 +  $ make check
 +
 +notable failures are
 +  scripts/linear-algebra/onenormest.m .................... PASS    3/4    FAIL 1
 +  scripts/optimization/sqp.m ............................. ** On entry to DORGLQ parameter number  5 had an illegal value 
 +    PASS   16/17   FAIL 1
 +
 +Summary:
 +
 +  PASS   6829
 +  FAIL     11
 +
 +
 +===== Install =====
 +
 +  $ make install
 +  
 +Add the following to the end of your .bashrc file
 +
 +  # for Octave 3.4.3 installed in $HOME
 +  export LD_LIBRARY_PATH=$HOME/lib/octave/3.4.3:$LD_LIBRARY_PATH
 +  
 +Log in and out, then 
 +  $ octave --version
 +  GNU Octave, version 3.4.3
 +  Copyright (C) 2011 John W. Eaton and others.
  
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