AMBER Archive (2005)

Subject: AMBER: New problem of parallel sander

From: Zhang Bing (nnizb_at_nus.edu.sg)
Date: Thu Jun 02 2005 - 21:46:13 CDT

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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