Hello,
This looks like the Python version used for mvapich is now not working...
Does the serial version work? You should start with the serial version
making sure that works fine before moving on to the parallel one.
Good luck!
Jason
On Mon, Sep 27, 2010 at 2:00 PM, Anuradha Mittal
<anuradha.mittal.gmail.com>wrote:
> 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
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Sep 27 2010 - 12:30:05 PDT
