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
>>
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 14 2016 - 01:30:03 PDT
