AMBER Archive (2003)

Subject: AMBER: Problem with MPI_Finalize

From: Thomas.Fox_at_bc.boehringer-ingelheim.com
Date: Tue Nov 18 2003 - 08:10:02 CST

Hi -

looking through the archives, I didnt find anything helpful, so Im reporting
my own observations:

I have compiled sander (amber7) on an SGI O3000 with IRIX64 6.5, and MPI
3.2.0.7, with MIPS Pro 7.3.1.2m.
Running a MD simulation of a protein on this machine, everything goes fine
and my MD
calculation runs through smoothly...however, we just got a new machine
(O3000 with IRIX 6.5, and MPI 4.3 MPT 1.8,
but no compiler on it) and running my sander executable on it, I get
basically identical results, my simulation runs
through to the end, but now I get the following error message

MPI: Program /home/foxt/amber7/exe_mpi/sander, Rank 0, Process 6182
received signal SIGSEGV(11)

MPI: --------stack traceback-------

sh: dbx: not found

MPI: -----stack traceback ends-----
MPI: Program /home/foxt/amber7/exe_mpi/sander, Rank 0, Process 6182:
Dumping core on signal SIGSEGV(11) into directory
/home/foxt/PROJECTS/LIE_FXA/LIE_RUNS/RUNS_RST
MPI: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize()
MPI: aborting job
MPI: Received signal 11

The output stops before the final timing information ("5. TIMINGS") - but
this could be a buffering issue...
minimizations are no problem, just MD calculations.

To be honest, this behavior is more an annoyance, as I dont get the timing
information and a lot of garbage
in my log-files (and, yes, lots of core dumps that I have to remove), but
still...I have looked through the code
but couldnt find anything obvious, but this is probalbly as Im not familiar
enough with MPI...

Any idea/suggestion ?

Th.

Dr. Thomas Fox
Dept. Lead Discovery - Computer Aided Molecular Design
K91-00-10
Boehringer Ingelheim Pharma GmbH & Co KG
88397 Biberach, Germany
thomas.fox_at_bc.boehringer-ingelheim.com

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