[BioBrew Users] Trouble running mpiBlast

Glen Otero gotero at linuxprophet.com
Fri Mar 12 15:09:41 EST 2004

On Mar 12, 2004, at 8:48 AM, Soumyadeep nandi wrote:

>> 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.

What flags did you use to compile HMMER with the Intel compiler? We'll 
be offering the Intel compilers and tools in our distro soon.
> 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.

We're looking into this.

Thanks for the info!


> Regards,
> Soumyadeep
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Glen Otero, Ph.D.
Linux Prophet

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