Did you try using the lib in the amber tree?
Bill
On 9/14/16 9:47 PM, Pooja Kesari wrote:
> 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
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>>>>> http://lists.ambermd.org/mailman/listinfo/amber
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>>>>
>>>
>>
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>
>
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Received on Wed Sep 14 2016 - 23:30:02 PDT
