Vulnerant omnes, ultima necat

Here is how I successfully installed the Perl module Parallel::MPI::Simple (v0.03) in a clustered environment with the mpich MPI implementation. There are other ways this could be achieved, but I present here what I’ve done.

Before proceeding, make sure the command « mpicc » is available on your system.

1. Installing Perl

On the system I have access to (and on which I have no root access), the installed version of Perl is 5.8.8, which is insufficient for my needs; notably, I need threads support. So I downloaded the 5.12.2 Perl sources and configured it for my system with:

sh Configure -Dusethreads -Dusemorebits -Dcc=icc -A ccflags='-fPIC' -Dprefix='/my_home/path' -de

then « make » (or preferably qmake with SGE), then « make install ».

2. Fixing CPAN

Don’t do the following if your cpan is working fine; however, if you get errors about file locks, here is a VERY dirty fix:

1. save the following into a file, say « CPAN.pm.patch »:

   --- CPAN.pm.orig        2010-10-23 11:52:01.000000000 -0400
   +++ CPAN.pm     2010-10-23 11:52:39.000000000 -0400
   @@ -504,6 +504,11 @@
   
    sub _flock {
    my($fh,$mode) = @_;
   +
   +#EM: Dirty hack
   +flock $fh, $mode;
   +return 1;
   +
    if ( $Config::Config{d_flock} || $Config::Config{d_fcntl_can_lock} ) {
    return flock $fh, $mode;
    } elsif (!$Have_warned->{"d_flock"}++) {

2. find your CPAN.pm file (mine is in $PREFIX/lib/perl5/5.12.2)
3. do:

   cp CPAN.pm.patch $PREFIX/lib/perl5/5.12.2/
   cd $PREFIX/lib/perl5/5.12.2
   patch <CPAN.pm.patch

4. If you have the file « $PREFIX/lib/perl5/5.12.2/CPAN/Config.pm », delete it.

3. Installing Parallel::MPI::Simple

1. Run « cpan » (procede with configuration if asked to).
2. Do:

   install Parallel::MPI::Simple

3. If you notice well, it won’t work, because compilation will fail at some point. So exit from cpan and go to « ~/.cpan/build », and there you should see a folder named something like « Parallel-MPI-Simple-0.03-xxxxxx ». Go in it, then edit the file « Makefile » and change the line « CC = cc » for « CC = mpicc », and change the line « LD = cc » for « LD = mpicc ».
4. Run « make », then « make install », and you’re done! 🙂