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Help with MMPBSA.py.MPI
Answer
11/10/15 6:58 PM
All,

I am having problems with the MMPBSA.py.MPI python script to run normal mode analysis on my amber molecular dynamics trajectory. My batch files run fine in serial mode but fail when I try to use the .MPI implementation with this error message;

Traceback (most recent call last):
File "/opt/amber/bin/MMPBSA.py.MPI", line 51, in <module>
raise MMPBSA_Error('Could not import mpi4py package! Use serial version '
MMPBSA_mods.exceptions.MMPBSA_Error: Could not import mpi4py package! Use serial version or install mpi4py.

The same batch file runs fine if I call the serial version of the program.


Below is the actual script. Thoughts appreciated.

Nic out

#!/bin/bash
#SBATCH --job-name="nmode"
#SBATCH --output="nmode.out"
#SBATCH --partition=shared
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4
#SBATCH --export=ALL
#SBATCH -t 12:00:00


module load amber
module load openmpi_ib
module load mpi4py


cd $PWD


mpirun -np 4 $AMBERHOME/bin/MMPBSA.py.MPI -O -i nmode_mod.in\
-o nmode_6frames.dat\
-sp /home/csteussy/amber/mmpbsa/ref194na/complex-wat.top \
-srp /home/csteussy/amber/mmpbsa/ref194na/protein-wat.top \
-slp /home/csteussy/amber/mmpbsa/ref194na/ligand-wat.top \
-cp /home/csteussy/amber/mmpbsa/ref194na/complex.top \
-rp /home/csteussy/amber/mmpbsa/ref194na/protein.top \
-lp /home/csteussy/amber/mmpbsa/ref194na/ligand.top \
-y /home/csteussy/amber/mmpbsa/ref194na/complex_prodc.mdcrd.gz \
-yr /home/csteussy/amber/mmpbsa/ref194na/protein_prodc.mdcrd.gz \
-yl /home/csteussy/amber/mmpbsa/ref194na/ligand_prodc.mdcrd.gz