Help with MMPBSA.py.MPI Calvin Steussy https://conferences.xsede.org/c/message_boards/find_message?p_l_id=&messageId=1089700 2015-11-10T18:58:37Z 2015-11-10T18:57:54Z

All,<br /><br />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;<br /><br />Traceback (most recent call last):<br /> File &#034;/opt/amber/bin/MMPBSA.py.MPI&#034;, line 51, in &lt;module&gt;<br /> raise MMPBSA_Error(&#039;Could not import mpi4py package! Use serial version &#039;<br />MMPBSA_mods.exceptions.MMPBSA_Error: Could not import mpi4py package! Use serial version or install mpi4py.<br /><br />The same batch file runs fine if I call the serial version of the program.<br /><br /><br />Below is the actual script. Thoughts appreciated.<br /><br />Nic out<br /><br />#!/bin/bash<br />#SBATCH --job-name=&#034;nmode&#034;<br />#SBATCH --output=&#034;nmode.out&#034;<br />#SBATCH --partition=shared<br />#SBATCH --nodes=1<br />#SBATCH --ntasks-per-node=4<br />#SBATCH --export=ALL<br />#SBATCH -t 12:00:00<br /><br /><br />module load amber<br />module load openmpi_ib<br />module load mpi4py<br /><br /><br />cd $PWD<br /><br /><br />mpirun -np 4 $AMBERHOME/bin/MMPBSA.py.MPI -O -i nmode_mod.in\<br /> -o nmode_6frames.dat\<br /> -sp /home/csteussy/amber/mmpbsa/ref194na/complex-wat.top \<br /> -srp /home/csteussy/amber/mmpbsa/ref194na/protein-wat.top \<br /> -slp /home/csteussy/amber/mmpbsa/ref194na/ligand-wat.top \<br /> -cp /home/csteussy/amber/mmpbsa/ref194na/complex.top \<br /> -rp /home/csteussy/amber/mmpbsa/ref194na/protein.top \<br /> -lp /home/csteussy/amber/mmpbsa/ref194na/ligand.top \<br /> -y /home/csteussy/amber/mmpbsa/ref194na/complex_prodc.mdcrd.gz \<br /> -yr /home/csteussy/amber/mmpbsa/ref194na/protein_prodc.mdcrd.gz \<br /> -yl /home/csteussy/amber/mmpbsa/ref194na/ligand_prodc.mdcrd.gz

Calvin Steussy 2015-11-10T18:57:54Z