[AMBER] mmpbsa.py.mpi error

From: Anuradha Mittal <anuradha.mittal.gmail.com>
Date: Mon, 27 Sep 2010 12:05:08 -0500

Hi,

I get the following error when I run the MMPBSA.py.MPI

Traceback (most recent call last):
  File "/u/ac/amitta2/amber11/bin/MMPBSA.py.MPI", line 380, in <module>
    print >> sys.stdout, 'MMPBSA.py.MPI being run on {0}
processors'.format(mpi_size)
AttributeError: 'str' object has no attribute 'format'


The job script looks like this:
#!/bin/tcsh
#PBS -l walltime=00:30:00
#PBS -q normal
# Run on 64 cores
#PBS -l nodes=1:ppn=3
#PBS -V
#PBS -N testjob
#PBS -A TG-MCB090168

mvapich2-start-mpd
setenv NP `wc -l ${PBS_NODEFILE} | cut -d'/' -f1`
setenv PYTHONPATH /u/ac/amitta2/lib/python/
setenv AMBERHOME ~/amber11
setenv MV2_SRQ_SIZE 4000
cd /cfs/scratch/users/amitta2/fabh
mpirun -machinefile ${PBS_NODEFILE} -np ${NP} $AMBERHOME/bin/MMPBSA.py.MPI
-O -i mmpbsa_per_res_decomp.in -o final_results_mmpbsa.dat -sp
com_solvated.top -cp com.top -rp rec.top -lp lig.top -y md13.x
mpdallexit



When I compiled mmpbsa.py.mpi I got the following:

/bin/bash setup.sh
Python version 2 detected. No file conversion necessary.
'import site' failed; use -v for traceback
/bin/cp MMPBSA.py.MPI *pyc /u/ac/amitta2/amber11/bin


I have Python-2.5.2 and mvapich2-1.2-intel-ofed-1.2.5.5.

Thanks
Anu
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Received on Mon Sep 27 2010 - 10:30:03 PDT