APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)

From: Bin He (binhe_at_hustunique.com)
Date: Thu Nov 13 2014 - 01:53:42 CST

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Hi,

I recompiled the namd, and got the version of mpi-smp-cuda version.

source code:NAMD_2.10b1_Source.tar.gz
compiler: intel icc (ICC) 14.0.0 20130728
mpi:Intel(R) MPI Library for Linux* OS, Version 4.1 Update 1 Build 20130522
OS:RHEL 6.2

When I run;

mpirun -ppn 1 -hosts node335,node334 -IB ./namd2 +ppn 8 +devices 0,1
 ../workload/f1atpase2000/f1atpase.namd

There will be lots of error like:

 ERROR: Atom 321692 velocity is 1191.13 -3428.88 10552 (limit is 11000,
atom 210 of 219 on patch 1249 pe 4)

ERROR: Atoms moving too fast; simulation has become unstable (152 atoms on
patch 1249 pe 4).
When I run;

mpirun -ppn 1 -hosts node335,node334 -IB ./namd2 +ppn 16 +devices 0,1
 ../workload/f1atpase2000/f1atpase.namd

It will exit with "APPLICATION TERMINATED WITH THE EXIT STRING:
Segmentation fault (signal 11)".

So what is wrong?

Thanks

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Bin He
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• Next message: Fotis Baltoumas: "Simulation of a membrane protein with large extracellular domains"
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• Reply: Jim Phillips: "Re: APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)"
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