On Fri, May 20, 2016 at 6:23 PM, Kalenkiewicz, Andrew (NIH/NICHD) [F] <
andrew.kalenkiewicz.nih.gov> wrote:
> Dear Amber Users,
>
> I'm trying to run MMPBSA.py with residue decomposition, but the job keeps
> failing with the following output:
>
> Loading and checking parameter files for compatibility...
> sander found! Using /usr/local/apps/amber/amber14/bin/sander
> cpptraj found! Using /usr/local/apps/amber/amber14/bin/cpptraj
> Preparing trajectories for simulation...
> 1000 frames were processed by cpptraj for use in calculation.
>
> Running calculations on normal system...
>
> Beginning GB calculations with /usr/local/apps/amber/amber14/bin/sander
> calculating complex contribution...
> calculating receptor contribution...
> File "/usr/local/apps/amber/amber14/bin/MMPBSA.py.MPI", line 104, in
> <module>
> app.run_mmpbsa()
> File
> "/usr/local/apps/amber/amber14/lib/python2.6/site-packages/MMPBSA_mods/main.py",
> line 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File
> "/usr/local/apps/amber/amber14/lib/python2.6/site-packages/MMPBSA_mods/calculation.py",
> line 82, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File
> "/usr/local/apps/amber/amber14/lib/python2.6/site-packages/MMPBSA_mods/calculation.py",
> line 431, in run
> self.prmtop) + '\n\t'.join(error_list) + '\n')
> CalcError: /usr/local/apps/amber/amber14/bin/sander failed with prmtop
> complex.prmtop!
>
>
> Error occured on rank 127.
> Exiting. All files have been retained.
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 127 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
> File "/usr/local/apps/amber/amber14/bin/MMPBSA.py.MPI", line 104, in
> <module>
> app.run_mmpbsa()
> File
> "/usr/local/apps/amber/amber14/lib/python2.6/site-packages/MMPBSA_mods/main.py",
> line 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File
> "/usr/local/apps/amber/amber14/lib/python2.6/site-packages/MMPBSA_mods/calculation.py",
> line 82, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File
> "/usr/local/apps/amber/amber14/lib/python2.6/site-packages/MMPBSA_mods/calculation.py",
> line 431, in run
> self.prmtop) + '\n\t'.join(error_list) + '\n')
> CalcError: /usr/local/apps/amber/amber14/bin/sander failed with prmtop
> complex.prmtop!
>
>
> Error occured on rank 125.
> Exiting. All files have been retained.
> [cn0935:52965] 1 more process has sent help message help-mpi-api.txt /
> mpi-abort
> [cn0935:52965] Set MCA parameter "orte_base_help_aggregate" to 0 to see
> all help / error messages
>
> My complex, receptor, and ligand files were generated with ante-MMPBSA.py
> and look fine as far as I can tell. I double checked the strip_mask and
> other likely problems. What other reasons could there be for this error
> message?
>
​Check the _MMPBSA_complex_gb.mdout.127 file for any error messages that
have been printed (this is where the real error message is contained --
MMPBSA.py doesn't know what went wrong, it only knows that something did go
wrong).
That said, 128 a *lot* of threads for an MMPBSA.py job. I would suggest
switching to 1 CPU with only a couple frames to make debugging easier.
HTH,
Jason
--
Jason M. Swails
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Received on Mon May 23 2016 - 06:00:04 PDT
