[GE users] parallel jobs submission help

Wheeler, Dr M.D. mdw10 at leicester.ac.uk
Sat Nov 27 18:24:45 GMT 2004


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One question,
what is SCRATCH in this context, is it the temporary directory for molpro??
 
Martyn

________________________________

From: Reuti [mailto:reuti at staff.uni-marburg.de]
Sent: Sat 27/11/2004 08:53
To: users at gridengine.sunsource.net
Subject: Re: [GE users] parallel jobs submission help



To complete the things to mention for an integration of parallel molpro:

There is a hardcoded "/usr/bin/rsh" in "g/tcgmsg/ipcv4.0/parallel.c". For Linux
you have to change it to:

#if defined(LINUX)
      (void) execvp("rsh",argv2);
#endif

Take care also to change "execv" to "execvp" in the statement above. When you
already compiled Molpro, there is no need to recompile it, but just use the new
compiled parallel command and copy it to your Molpro binary location, replacing
the already during "make" and "make install" copied one.

The script should contain the lines:

export PBS_NODEFILE=$TMPDIR/machines
export SCRATCH=$TMPDIR
molprop myinputfile

this way you don't have to specify any "-n" or "-N" for Molpro at all, the
information of the $PBS_NODEFILE is sufficient. If you want to check the
correct distribution of scratch files, I found that Molpro will delete them
immediately after opening, hence leaving them only open to the process having
an open file handle on it. But you can check this (e.g. on Linux/AIX) with
"lsof" (list open files).

Reuti

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