Dear Bill
[user3.mcuserver ~]$ locate libmpi_f90.so.0
/usr/lib64/compat-openmpi/lib/libmpi_f90.so.0
/usr/lib64/compat-openmpi/lib/libmpi_f90.so.0.0.1
/usr/lib64/compat-openmpi-psm/lib/libmpi_f90.so.0
/usr/lib64/compat-openmpi-psm/lib/libmpi_f90.so.0.0.1
/usr/local/amber11/AmberTools/src/openmpi-1.4.5/build/ompi/mpi/f90/.libs/libmpi_f90.so.0
/usr/local/amber11/AmberTools/src/openmpi-1.4.5/build/ompi/mpi/f90/.libs/libmpi_f90.so.0.1.0
/usr/local/amber11/AmberTools/src/openmpi-1.4.5/build/ompi/mpi/f90/.libs/libmpi_f90.so.0.1.0T
/usr/local/lib/libmpi_f90.so.0
/usr/local/lib/libmpi_f90.so.0.1.0
However my library is also found in
/usr/lib64/openmpi/lib
but even if i change this path to
setenv LD_LIBRARY_PATH /usr/lib64/compat-openmpi/lib/
set path = ($path $LD_LIBRARY_PATH)
it is showing same error
On Wed, Sep 14, 2016 at 12:09 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> I have no MPI experience, but can you run other MPI jobs on that machine
> or those machines? Does
>
> $ locate libmpi_f90.so.0
>
> show the presence of the file? Does /usr/lib64/openmpi/lib have that
> file or anything else indicating a successful install in it?
>
> Also on the PATH, should it be $AMBERHOME/bin ?
>
> Bill
>
>
> On 9/13/16 11:00 PM, Pooja Kesari wrote:
> > Dear All,
> > I have a query regarding amber installation
> > My amber folder is located in
> > /usr/bin/amber11/
> >
> > in my tcshrc file i have defined the path
> >
> > setenv AMBERHOME "/usr/local/amber11"
> > set PATH=($path $AMBERHOME)
> > setenv LD_LIBRARY_PATH "/usr/lib64/openmpi/lib"
> > set path = ($path $LD_LIBRARY_PATH)
> >
> > 1. now if i run a job it says
> > *mpirun -np 60 sander.MPI -O -i prod.in <http://prod.in> -o
> > prod_complex-solv.out -p complex-solv.prmtop -c protein_solv-equil.rst -r
> > protein_solv-prod.rst -x prod.mdcrd -ref protein_solv-equil.rst *
> > ------------------------------------------------------------
> --------------
> > mpirun was unable to launch the specified application as it could not
> find
> > an executable:
> > Executable: sander.MPI
> > while attempting to start process rank 0.
> >
> > 2. If i defined the path of sander mpi it says
> > *mpirun -np 60 /usr/local/amber11/bin/sander.MPI -O -i prod.in
> > <http://prod.in> -o prod_complex-solv.out -p complex-solv.prmtop -c
> > protein_solv-equil.rst -r protein_solv-prod.rst -x prod.mdcrd -ref
> > protein_solv-equil.rst *
> > /usr/local/amber11/bin/sander.MPI: error while loading shared libraries:
> > libmpi_f90.so.0: cannot open shared object file: No such file or
> directory
> > /usr/local/amber11/bin/sander.MPI: error while loading shared libraries:
> > libmpi_f90.so.0: cannot open shared object file: No such file or
> directory
> > /usr/local/amber11/bin/sander.MPI: error while loading shared libraries:
> > libmpi_f90.so.0: cannot open shared object file: No such file or
> directory
> > /usr/local/amber11/bin/sander.MPI: error while loading shared libraries:
> > libmpi_f90.so.0: cannot open shared object file: No such file or
> directory
> > /usr/local/amber11/bin/sander.MPI: error while loading shared libraries:
> > libmpi_f90.so.0: cannot open shared object file: No such file or
> directory
> >
> > Please help
> >
> >
> >
> > _______________________________________________
> > 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
>
--
Thanks & Regards,
Pooja Kesari
Research Scholar
Department Of Biotechnology
Indian Institute of Technology Roorkee
INDIA
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Received on Wed Sep 14 2016 - 00:30:02 PDT
