Thanks! I re-compiled using pything 2.6.5. Now I get this:
'import site' failed; use -v for traceback
Traceback (most recent call last):
File "/usr/local/mvapich2-1.2-intel-ofed-1.2.5.5/bin/mpdboot", line 52, in
<module>
import re
ImportError: No module named re
'import site' failed; use -v for traceback
Traceback (most recent call last):
File "/usr/local/mvapich2-1.2-intel-ofed-1.2.5.5/bin/mpdtrace", line 19,
in <module>
import sys, os, signal
ImportError: No module named os
'import site' failed; use -v for traceback
Traceback (most recent call last):
File "/usr/local/mvapich2-1.2-intel-ofed-1.2.5.5/bin/mpirun", line 79, in
<module>
import sys, os, socket, re
ImportError: No module named os
'import site' failed; use -v for traceback
Traceback (most recent call last):
File "/usr/local/mvapich2-1.2-intel-ofed-1.2.5.5/bin/mpdallexit", line 18,
in <module>
import sys, os
ImportError: No module named os
On Mon, Sep 27, 2010 at 12:42 PM, Bill Miller III <brmilleriii.gmail.com>wrote:
> You will need Python 2.6 or higher to use MMPBSA.py and MMPBSA.py.MPI. The
> 'format' command in python was implemented in Python 2.6. Thus, you will
> have to upgrade your python version before this command will work.
>
> Good luck!
>
> -Bill
>
> On Mon, Sep 27, 2010 at 1:05 PM, Anuradha Mittal
> <anuradha.mittal.gmail.com>wrote:
>
> > 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Sep 27 2010 - 11:30:04 PDT
