AMBER Archive (2009)

Subject: RE: [AMBER] symbol lookup error

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Sep 01 2009 - 14:42:49 CDT

Hi Bala,

This is not an AMBER problem perse but a problem with your MPI
implementation or the way you are running it. Most likely the mpif90 script
used to compile the executable does not match the mpirun command you are
using. You need to check your paths. Check which compiler you used to
compile AMBER and what MPI_HOME was set to. Then when you run inside the
queuing system check that your environment and subsequent paths match what
you used during the compilation.

All the best
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of Bala subramanian
> Sent: Tuesday, September 01, 2009 1:44 AM
> To: AMBER Mailing List
> Subject: [AMBER] symbol lookup error
>
> Friends,
>
> We have installed amber9 in a SGI altix machine running with SUSE 10. I
> submitted the job with the following command. The job stops throwing an
> error message.
>
> mpirun -np 12 sander.MPI -O -i eq.in -c eq66.rst -p ALL.top -o
> eq67.out &
>
> I get the following error. Someone please write how i can resolve the
> mpd
> hosts problem.
>
> WARNING: Can't read mpd.hosts for list of hosts, start only on current
> sander.MPI: symbol lookup error: sander.MPI: undefined symbol:
> mpi_init_
> sander.MPI: symbol lookup error: sander.MPI: undefined symbol:
> mpi_init_
> sander.MPI: symbol lookup error: sander.MPI: undefined symbol:
> mpi_init_
> sander.MPI: symbol lookup error: sander.MPI: undefined symbol:
> mpi_init_
> sander.MPI: symbol lookup error: sander.MPI: undefined symbol:
> mpi_init_
> sander.MPI: symbol lookup error: sander.MPI: undefined symbol:
> mpi_init_
> sander.MPI: symbol lookup error: sander.MPI: undefined symbol:
> mpi_init_
> sander.MPI: symbol lookup error: sander.MPI: undefined symbol:
> mpi_init_
> sander.MPI: symbol lookup error: sander.MPI: undefined symbol:
> mpi_init_
> sander.MPI: symbol lookup error: sander.MPI: undefined symbol:
> mpi_init_
> sander.MPI: symbol lookup error: sander.MPI: undefined symbol:
> mpi_init_
> sander.MPI: symbol lookup error: sander.MPI: undefined symbol:
> mpi_init_
> Thanks in advance,
> Bala
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