On Wed, Sep 28, 2016, shahab shariati wrote:
>
> After using "mpirun -np 8 $AMBERHOME/bin/sander.MPI -O -i min.in -o min.out
> -p comp_sol.prmtop -c comp_sol.inpcrd -r min.rst -ref comp_sol.inpcrd -inf
> min_info",
> *** Process received signal ***
> Signal: Segmentation fault (11)
> Signal code: Address not mapped (1)
> Failing at address: 0x7f63add2b628
Usual sort of debugging:
(I'm assuming here that the serial and parallel sander tests are passing: that
is always the first thing to check.)
1. Look in the min.out file: that is where any error messages will reside;
Pay special attention to see if it looks like the job actually finished,
but just failed to print the final timings.
2. Run a test using sander, not sander.MPI -- will help decide where the
problem lies.
3. Run a test with pmemd rather than sander.
>
> Is Segmentation fault related to following lines in " saveamberparm LIG
> lig.prmtop lig.inpcrd "?
>
> 1-4: angle 33 62 duplicates bond ('triangular' bond) or angle ('square'
> bond)
No.
....dac
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Received on Wed Sep 28 2016 - 12:00:03 PDT
