Dear Ross
Yes I have two machines on which I have installed AMBER.
On one machine it installed perfectly and is working fine whereas on other
machine with same procedure of installation it is showing some error.
On Wed, Sep 14, 2016 at 1:57 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> Are you running on multiple machines that may not have the libs in the
> same place? I'd expect the error msgs to say so, so I doubt it. I am out
> of ideas. The one thing you could blindly try is using $AMBERHOME/bin in
> your path, but I doubt that would solve it.
>
> Bill
>
>
> On 9/14/16 12:12 AM, Pooja Kesari wrote:
> > Dear Bill
> > [user3.mcuserver ~]$ 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
> >>
> >
> >
>
>
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>
--
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 - 22:00:02 PDT
