Just to expand upon what Jason has already said, something like:
LD_LIBRARY_PATH=/opt/cluster/mpi/openmpi-1.3.3_intel
should probably be:
LD_LIBRARY_PATH=/opt/cluster/mpi/openmpi-1.3.3_intel/lib
On Tue, Jun 1, 2010 at 1:30 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Tue, Jun 1, 2010 at 12:18 PM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
>>
>> Hello all
>>
>> I am installing amber10 in paralllel using openmpi and ifort,openmpi is
>> located in
>>
>> opt/cluster/mpi/openmpi-1.3.3_intel.
>>
>> My bash_profile file is:
>>
>> AMBERHOME=/home/sangita/amber10; export AMBERHOME
>> MPI_HOME=/opt/cluster/mpi/openmpi-1.3.3_intel; export MPI_HOME
>>
>> LD_LIBRARY_PATH=/opt/cluster/mpi/openmpi-1.3.3_intel:$LD_LIBRARY_PATH:/opt/intel/fc/9.1.043/lib/libsvml.so
>> ; export LD_LIBRARY_PATH
>>
>
> My mistake, I forgot that libsvml was part of the intel compilers. Intel
> provides scripts that automatically set LD_LIBRARY_PATH properly for your
> intel compilers, so all you need to do is invoke that script. I'm not sure
> if it's the same for intel version 9 compilers, but for version 10 and later
> you can do this via the following:
>
> source /opt/intel/fc/9.1.043/bin/ifortvars.sh
>
> You may need to add your architecture at the end (i.e. intel64 or intel32 or
> something).
>
> As a note about your LD_LIBRARY_PATH definition -- it should only contain
> folders, not files (so the folder containing the file libsvml.so, not the
> libsvml.so file itself).
>
> Good luck!
> Jason
>
>
>> PATH=$PATH:$HOME/bin:$AMBERHOME/exe:/opt/cluster/mpi/openmpi-1.3.3_intel
>>
>>
>> when I am compiling, it giving the following error:
>>
>> [sangita.master1 src]$ make parallel
>> > Starting installation of Amber10 (parallel) at Mon May 31 22:55:09 IST
>> > 2010.
>> > cd sander; make parallel
>> > make[1]: Entering directory `/home/sangita/amber10/src/sander'
>> > ./checkparconf
>> > cpp -traditional -I/opt/cluster/mpi/openmpi-1.3.3_intel/include -P
>> > -DBINTRAJ
>> > -DMPI constants.f > _constants.f
>> > /opt/cluster/mpi/openmpi-1.3.3_intel/bin/mpif90 -c -w95 -vec_report0
>> -mp1
>> > -ip
>> > -O3 -axWP -FR -o constants.o _constants.f
>> > /opt/cluster/mpi/openmpi-1.3.3_intel/bin/mpif90: error while loading
>> shared
>> > libraries: libsvml.so: cannot open shared object file: No such file or
>> > directory
>> > make[1]: *** [constants.o] Error 127
>> > make[1]: Leaving directory `/home/sangita/amber10/src/sander'
>> > make: *** [parallel] Error 2
>>
>>
>> But when my bash_profile file is:
>>
>> AMBERHOME=/home/sangita/amber10; export AMBERHOME
>> MPI_HOME=/opt/cluster/mpi/openmpi-1.3.3_intel; export MPI_HOME
>>
>> LD_LIBRARY_PATH=$MPI_HOME/lib:/opt/cluster/mpi/openmpi-1.3.3_intel:$LD_LIBRARY_PATH:/opt/intel/fc/9.1.043/lib/libsvml.so
>> ; export LD_LIBRARY_PATH
>>
>>
>> PATH=$PATH:$HOME/bin:$AMBERHOME/exe:$MPI_HOME/bin:/opt/cluster/mpi/openmpi-1.3.3_intel
>>
>>
>> export PATH
>>
>> Its compiling the amber10.
>> Why it is so? While I have already set the MPI_HOME environment.
>>
>> Can anybody explain it?
>>
>>
>>
>>
>> With regard
>> Sangita Kachhap
>> JRF
>> BIC,IMTECH
>> CHANDIGARH
>>
>> _______________________________________________
>> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe
Postdoctoral Associate
SAS - Chemistry & Chemical Biology
610 Taylor Road
Piscataway, NJ 08854
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Received on Tue Jun 01 2010 - 11:00:06 PDT
