Hi Jason,
So I've tried to run this system on stampede.tacc.texas.edu and I am getting an error when I run it in parallel, but it will run just fine in serial.
My input there is:
> module load python
> module load mpi4py
> module load amber
>
> ibrun python $AMBERHOME/bin/MMPBSA.py.MPI -O -i mmpbsa.in -sp solv_com.prmtop -cp complex.prmtop -rp receptor.prmtop -lp ligand.prmtop -y short.dcd
You may not be familiar with stampede, but the output is probably similar to other computer systems.
Here is the output:
> TACC: Starting up job 993330
> TACC: Setting up parallel environment for MVAPICH2+mpispawn.
> TACC: Starting parallel tasks...
> Running MMPBSA.MPI on 4 processors
> Reading command-line arguments and input files...
> Loading and checking parameter files for compatibility...
> mmpbsa_py_energy found! Using /opt/apps/intel13/mvapich2_1_9/amber/12.0/bin/mmpbsa_py_energy
> cpptraj found! Using /opt/apps/intel13/mvapich2_1_9/amber/12.0/bin/cpptraj
> Preparing trajectories for simulation...
> 8 frames were processed by cpptraj for use in calculation.
>
> Beginning PB calculations with /opt/apps/intel13/mvapich2_1_9/amber/12.0/bin/mmpbsa_py_energy
> calculating complex contribution...
> CalcError: /opt/apps/intel13/mvapich2_1_9/amber/12.0/bin/mmpbsa_py_energy failed with prmtop complex.prmtop!
>
>
> Error occured on rank 1.
> Exiting. All files have been retained.
> [cli_1]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1
> [c401-404.stampede.tacc.utexas.edu:mpispawn_0][child_handler] MPI process (rank: 1, pid: 46569) exited with status 1
> [c401-404.stampede.tacc.utexas.edu:mpispawn_0][readline] Unexpected End-Of-File on file descriptor 8. MPI process died?
> [c401-404.stampede.tacc.utexas.edu:mpispawn_0][mtpmi_processops] Error while reading PMI socket. MPI process died?
> TACC: MPI job exited with code: 1
>
> TACC: Shutdown complete. Exiting.
Any suggestions?
I've requested they update the code to include the latest code revisions (the current install is from May 2013), but I couldn't find anything that suggested that MMPBSA.py got updated for an error like this.
Best,
Jesper
On Jun 19, 2013, at 6:23 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
>
> On Jun 19, 2013, at 7:08 PM, "Sorensen, Jesper" <jesorensen.ucsd.edu> wrote:
>
>> I did try it now with a DCD and it does work.
>> I assumed that it wouldn't based on reading the manual and running MMPBSA.py --help, which sort of specified that is "has" to be an mdcrd.
>>
>
> Ah, I see. I will try to clarify this for later versions.
>
> Thanks!
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Thu Jun 20 2013 - 10:00:04 PDT
