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/libmpi.so
> PC: 0x5e02a70 PMPI_Abort in /usr/lib32/libmpi.so
> PC: 0x5e32968 pmpi_abort_ in /usr/lib32/libmpi.so
> 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/libmpi.so
> >>PC: 0x5e02a70 PMPI_Abort in /usr/lib32/libmpi.so
> >>PC: 0x5e32968 pmpi_abort_ in /usr/lib32/libmpi.so
> >>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.
....thanks...dac
--
==================================================================
David A. Case | e-mail: case.scripps.edu
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 | http://www.scripps.edu/case
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Received on Wed Apr 07 2004 - 01:53:01 PDT
