[BioBrew Users] Trouble running mpiBlast

Soumyadeep nandi soumyadeep_nandi at yahoo.com
Fri Mar 12 11:48:12 EST 2004

> Did you have to rebuild HMMER, or were you able to
> use it with pvm as  
> it was in BioBrew?

The pvm we were using in production mode was
HMMER-2.3.2 compiled with the intel compiler. We
eventually reloaded pvm 3.4.4 on the cluster from the
tar file we used in the production environment (a
loosely knit cluster of workstations in a computer
lab), and loaded the 2.3.2 version of HMMER which
works fine. The HMMER supplied (2.2g) somehow did not
work but we didn't bother troubleshooting it...

On another track -
the lam seems to have a version conflict: lam-6.5.6-4
is installed and runs with small test jobs. The
lam-mpi version in the /opt directory (and that shows
up with rpm -qa ) is lam-mpi-7.0.3-1> Is this a
problem? None of the gromacs mpi executables are
present and when we tried installing them they give an
execution error with a broken pipe. The lamboot with
the /opt/lam-mpi doesn't start. 


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