AMBER Archive (2005)

Subject: RE: AMBER: New problem of parallel sander

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Jun 03 2005 - 11:53:55 CDT

Is sander in your path?
 
If you just type on the command line:
 
sander
 
what do you get?
 
All the best
Ross

  _____

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Zhang Bing
Sent: 02 June 2005 19:46
To: amber_at_scripps.edu
Subject: AMBER: New problem of parallel sander

Dear Prof. David A. Case:

 

Thanks a lot for your help. I got the test jobs passed by issuing the new
test command. However, when I tried my own works, it failed again:

 

[nnizb_at_nemo exe]$ mpirun -np 4 sander -O -i min.in -p cdk5.parm -c cdk5.crd
-o cdk.out -r cdk.rst

[0] MPI Abort by user Aborting program !

[0] Aborting program!

p0_3517: p4_error: : 1

Killed by signal 2.

Killed by signal 2.

Killed by signal 2.

 

I think it is something wrong with my command line. 'Coz I did see 4
processors running there simultaneously after I submitted test jobs by "make
test.sander". So now, I am wondering how you made your script for the
parallel sander and why you need a DO_PARALLEL environment variable first. I
tried to set such a variable before my "mpirun -np 4 sander -O -i 888.in -p
888.parm -c 888.crd -o 888.out -r 888.rst" command, it did not work. So
would you kindly show me the script or the command line for a parallel
sander? Any advice from you will be greatly appreciated.

 

Sincerely yours,

 

Zhang Bing

 

NUSNNI

 

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