Re: AMBER: Question on Amber7...

From: David A. Case <>
Date: Tue, 6 Apr 2004 17:25:37 -0700

On Tue, Apr 06, 2004, Pmartin wrote:

> Thanks for your help, i ran the general tests for the suite on xleap and
> sander, both worked with the exception of a rounding problem in sander,
> which is not a problem from what i have read in the user guide. i then
> tried running the single processor md run but it gave me this:
> Rohan 7# mpirun -np 1 ./sander -O -i moldyin -o yayout -p yaytop -c redo
> -r retry

> MPI: --------stack traceback-------
> PC: 0x5ddb100 MPI_SGI_stacktraceback in /usr/lib32/
> PC: 0x5e02a70 PMPI_Abort in /usr/lib32/
> PC: 0x5e32968 pmpi_abort_ in /usr/lib32/
> PC: 0x101064dc mexit in ./sander
> PC: 0x1008b874 compute_nfft in ./sander
> i am just learning the ropes of the program so i apologize if this question
> is stupid, but do you have any ideas as to what might be going wrong?

Let me see if I understand you situation. In an earlier email, you reported
essentially the same error, but with mpirun -np 2:

> >>Rohan 8# mpirun -np 2 ./sander -O -i moldyin -o finout -p yaytop -c redo
> >>-r retry
> >>MPI: Program ./sander, Rank 0, Process 1484 called
> >>MPI_Abort(<communicator>, 1)
> >>
> >>MPI: --------stack traceback-------
> >>PC: 0x5ddb100 MPI_SGI_stacktraceback in /usr/lib32/
> >>PC: 0x5e02a70 PMPI_Abort in /usr/lib32/
> >>PC: 0x5e32968 pmpi_abort_ in /usr/lib32/
> >>PC: 0x101064dc mexit in ./sander
> >>PC: 0x1008b874 compute_nfft in ./sander

My suggestion was to run the test suite, since in that way we could
distinguish between an installation problem (in which case the test suite
would fail), and a problem with your particular inputs.

You say that "I ran the general tests", but (specifically) did you run the
tests with both "mpirun -np 2" and "mpirun -np 1"? Assuming that you did
that, we would need to provide a description of how you created the "yaytop"
and "redo" files that you are using as input; you might as well send the files
themselves as well (along with moldyin). That way we can actually try to
reproduce the error you are getting. As I said, I've never seen this
particular problem before.


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
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Received on Wed Apr 07 2004 - 01:53:01 PDT
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