Re: AMBER: Question on Amber7...

From: David A. Case <>
Date: Thu, 1 Apr 2004 17:33:30 -0800

On Thu, Apr 01, 2004, Pmartin wrote:

> I am working on Amber 7 and as I try to run an md simulation, i get this:
> 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

This looks like the same error reported by Anshul Awasthi on March 27 (check
the amber mail archives).

The first thing we need is confirmation that you have run the test suite
on this machine. That will help decide whether or not the failure is
specific to your problem (in particular, try the dhfr test case, for example).

If the standard test cases work, then try a non-parallel run with your inputs.
That will at least narrow things down. Some user that has this problem is
going to have to be willing to post their input files. This is the first time
in two years that this problem has come up, which only means that we are
unlikely to be able to help much with just a stack trace....


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            |
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Fri Apr 02 2004 - 02:53:00 PST
Custom Search