Did you try with serial version MMPBSA.py (not MMPBSA.py.MPI)?
Hai
On Wed, Jun 1, 2016 at 2:34 PM, Kalenkiewicz, Andrew (NIH/NICHD) [F] <
andrew.kalenkiewicz.nih.gov> wrote:
> Still have not been able to solve this issue - any of the MMPBSA
> developers have any idea what is going on, or have ideas for other ways I
> can troubleshoot this?
>
> Thanks,
>
> Andrew Kalenkiewicz
> Postbaccalaureate Technical IRTA
> National Institutes of Health
> andrew.kalenkiewicz.nih.gov
> 734-709-0355
>
> ________________________________________
> From: Kalenkiewicz, Andrew (NIH/NICHD) [F]
> Sent: Monday, May 23, 2016 5:33 PM
> To: jason.swails.gmail.com
> Cc: AMBER Mailing List
> Subject: Re: [AMBER] MMPBSA.py issue with complex prmtop file
>
> Hi Jason,
>
> Thanks for your response. There are no errors in
> _MMPBSA_complex_gb.mdout.127 as far as I can tell. I did as you suggested
> and switched to one CPU and got 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...
> 10 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...
> calculating ligand contribution...
>
> Beginning PB calculations with /usr/local/apps/amber/amber14/bin/sander
> calculating complex 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
> LtTub_colchicine_complex.prmtop!
>
>
> Exiting. All files have been retained.
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 0 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.
> --------------------------------------------------------------------------
> -------------------------------------------------------
> Primary job terminated normally, but 1 process returned
> a non-zero exit code.. Per user-direction, the job has been aborted.
> -------------------------------------------------------
> --------------------------------------------------------------------------
> mpirun detected that one or more processes exited with non-zero status,
> thus causing
> the job to be terminated. The first process to do so was:
>
> Process name: [[40463,1],0]
> Exit code: 1
> --------------------------------------------------------------------------
>
> I checked the last few lines of tail -25 _MMPBSA_complex_pb.mdout.0, and
> it looks like it's crashing just before it's supposed to report total
> surface charge:
>
> Atom 13822 ( 899) : -899 0
> Atom 13823 ( 899) : -899 0
> Atom 13824 ( 899) : -899 0
> Atom 13825 ( 899) : -899 0
> Atom 13826 ( 899) : -899 0
> Atom 13827 ( 899) : -899 0
> | INFO: Old style inpcrd file read
>
>
>
> --------------------------------------------------------------------------------
> 3. ATOMIC COORDINATES AND VELOCITIES
>
> --------------------------------------------------------------------------------
>
> Cpptraj Generated Restart
> begin time read from input coords = 100.000 ps
>
> Number of triangulated 3-point waters found: 0
>
>
> --------------------------------------------------------------------------------
> 4. RESULTS
>
> --------------------------------------------------------------------------------
>
> POST-PROCESSING OF TRAJECTORY ENERGIES
> Cpptraj Generated trajectory
> minimizing coord set # 1
>
> I.e. _MMPBSA_complex_pb.mdout.0 cuts off right here. The only difference
> with this job is the input trajectory has fewer frames and it was run on
> one core. Given this result, along with the fact that
> _MMPBSA_complex_gb.mdout.127 (from my previous job) doesn't appear to have
> errors, I would guess the problem has to do with the PB stage (though it
> seems odd the error shows up in the GB stage for the 128 core job). The &pb
> namelist for my input file has istrng=0.100, inp=1, radiopt=0; setting inp
> and radiopt is required to avoid the error mentioned in this thread<
> http://archive.ambermd.org/201303/0551.html>. However, in this case there
> seems to be another complication causing the surface charge calculation to
> crash. The manual says for PB simulations with inp=1, use_sav should be
> zero. However, the default value is 1 and it's not possible to set use_sav
> within the &pb namelist for mmpbsa. In any case, the manual says the theory
> supports use_sav=1 (which specifies that molecular volume be used to
> calculate cavity free energy as opposed to SASA). Any suggestions on where
> to go from here?
>
> Andrew Kalenkiewicz
> Postbaccalaureate Technical IRTA
> National Institutes of Health
> andrew.kalenkiewicz.nih.gov
> 734-709-0355
>
> ________________________________________
> From: Jason Swails [jason.swails.gmail.com]
> Sent: Monday, May 23, 2016 8:53 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] MMPBSA.py issue with complex prmtop file
>
> 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 Wed Jun 01 2016 - 12:00:03 PDT
