[Dock-fans] mpirun problem

Scott Brozell sbrozell at scripps.edu
Fri Jul 27 09:32:19 PDT 2007


On Fri, 27 Jul 2007, Voronkov Andrew wrote:

> how can I solve this problem?
> I've prepared this machinefile under Linux but still have the problems.
> PS I haven't found the answer  in archives.
> [voronkov at qsar21 Flexible]$ mpirun -machinefile machinefile -np 6 /data/soft/dock5/bin/dock5mpi -i anchor_and_grow.in -o anchor_and_grow.out
> Cannot read machinefile.
> Looked for files with extension LINUX in
> directory /usr/local/mpich-pgi/share .

First, I recommend that you upgrade to Dock 6.1.
Second, this looks like a system administration problem - contact them.
What is in /usr/local/mpich-pgi/share ?
Does this exist: /usr/local/mpich-pgi/share/machinefile ?
Does this exist: /usr/local/mpich-pgi/share/machinefile.LINUX ?
Where is your machine file ?
Sometimes it needs to be in one's home directory or in a
filesystem that is mounted on all nodes.
What happens with mpirun -np 1 /data/... ?
Can you rsh between nodes ?

Good luck,

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