Re: [AMBER] error in parallel md run

From: Jason Swails <>
Date: Thu, 25 Mar 2010 22:54:26 -0700


On Thu, Mar 25, 2010 at 10:43 PM, Nicee <> wrote:
> Hello all,
> I have installed amber10 along with tools successfully both in serial and
> parallel. The tests for serial and parallel were also successfully over. But
> when I am running the process in parallel with nohup command and following as
> input:
> /home/nicee/amber10/bin/mpirun -np 8 sander.MPI -O -i -o
> model_noref_3g5a_md1.out -p model_noref_3g5a.prmtop -c
> model_noref_3g5a_min22.restrt -r model_noref_3g5a_md1.restrt -ref
> model_noref_3g5a.inpcrd -x model_noref_3g5a_md1.mdcrd
> the process is ending up and the nohup.out file is showing following error:
> sander.MPI: error while loading shared libraries: cannot open
> shared object file: No such file or directory
> It seems that [at least] one of the processes that was started with
> mpirun did not invoke MPI_INIT before quitting (it is possible that
> more than one process did not invoke MPI_INIT -- mpirun was only
> notified of the first one, which was on node n0).
> mpirun can *only* be used with MPI programs (i.e., programs that
> invoke MPI_INIT and MPI_FINALIZE).  You can use the "lamexec" program
> to run non-MPI programs over the lambooted nodes.
> I had tried to locate the file and added its path to the path in
> .bash_profile file but even then i am getting the same error. Kindly help.
> Thanking you.

This file should be located in $MPI_HOME/lib, whatever MPI_HOME was
set to when you compiled amber. If the machine you're trying to run
on has multiple MPI implementations it is critical that you add that belongs to the MPI used to compile amber to the
appropriate path (for example, our university HPC cluster has multiple
MPI implementations installed with a utility designed to set up our
environment according to our selection so it is quite organized and we
avoid these errors).

That being said, the path you want to add this library to is actually

export LD_LIBRARY_PATH=$MPI_HOME/lib\:$LD_LIBRARY_PATH # for bash/sh

setenv LD_LIBRARY_PATH "$MPI_HOME/lib\:$LD_LIBRARY_PATH" # for csh variants

Good luck,

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Thu Mar 25 2010 - 23:00:04 PDT
Custom Search