AMBER Archive (2003)

Subject: AMBER: AMBER7 & mpich : (no-attachment version)

From: takanori.kanazawa_at_pharma.novartis.com
Date: Sat Aug 02 2003 - 08:03:06 CDT

I'm resending the question I have just posted because I was suggested that
the attachment be removed
due to a potential virus infection.
(Thanks a lot, Dr. Simmerling)
-----------------------------------------------------------------------------------

Dear AMBER users,

I have a problem running parallel sander jobs on a linux cluster.

I have succesfully compiled, sander and other modules of AMBER7 using the
mpif77 compiler and
Machine.g77_mpich as the MACHINE file.
However, when I submit parallel sander jobs, such errors as shown below
occur.

------------------------------ start of log-file
-------------------------------------
clddc 44> ./Run.dhfr7_MPI
  Unit 5 Error on OPEN: gbin
[0] MPI Abort by user Aborting program !
[0] Aborting program!
p0_3504: p4_error: : 1

  Unit 5 Error on OPEN: gbin
[0] MPI Abort by user Aborting program !
[0] Aborting program!
p0_3505: p4_error: : 1

  Unit 5 Error on OPEN: gbin
[0] MPI Abort by user Aborting program !
[0] Aborting program!
p0_3506: p4_error: : 1
-----------------------------------------------------------------------------
It seems that [at least] one of 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.
-----------------------------------------------------------------------------
Killed
diffing mdout.dhfr.save with mdout
egrep: mdout: No such file or directory
possible FAILURE: check mdout.dif

------------------------------ end of log-file
-------------------------------------

This test job was taken from the one in the $AMBERHOME/test/dhfr.

I would appreciate it very much your any kind suggestion to solve the
problem.

Best regards,
Takanori Kanazawa

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