AMBER Archive (2008)

Subject: AMBER: Problems in execution of Replica Exchange calculations Amber 9.0

From: rebeca_at_mmb.pcb.ub.es
Date: Thu Jan 24 2008 - 10:50:22 CST

Hello,
I am trying to do Replica Exchange Molecular dynamics using Amber 9.0 and I am
having problems in the execution.
I have read in the manual that with Amber 9 it is not neccesary to compile Amber
specifically for Replica Exchange, so I have used it only with the parallel
version.
My script for execution is (I am using only 2 replicas to set up the
calculations, then I will add more):

#! /bin/tcsh
# @ job_name = replica_exchange
# @ class = bsc_ls
# @ initialdir = /gpfs/projects/
# @ wall_clock_limit = 3:00:00
# @ output = test.out
# @ error = test.err
# @ total_tasks = 2
# @ queue

srun /gpfs/apps/AMBER/9/exe/sander.MPI -A -rem 1 -np 2 -ng 2 -groupfile
groupfile

I am getting errors in test.err such as:

[0] MPI Abort by user Aborting program !
[0] Aborting program!
[1] MPI Abort by user Aborting program !
[1] Aborting program!
srun: error: s01c5b04: task[0-1]: Exited with exit code 25

and in the test.out file I get:

  Running multisander version of sander amber9
     Total processors = 2
     Number of groups = 2

     Looping over processors:
        WorldRank is the global PE rank
        NodeID is the local PE rank in current group

        Group = 0
        WorldRank = 0
        NodeID = 0

        Group = 1
        WorldRank = 1
        NodeID = 0

The files rem.out.001 and rem.out.002 are created, but they are empty.

I have also tried adding

setenv DO_PARALLEL "srun -np 2"

or

setenv DO_PARALLEL "mpirun -np 2"

but it does not worked either.

Could anyone help me with the execution of Replica Exchange calculations,
please?

Thank you very much, in advance.

Rebeca García Fandiño
Parc Cientific de Barcelona
Barcelona (Spain)
rebeca_at_mmb.pcb.ub.es

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