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 - 12:00:02 PDT
