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
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Received on Tue Jun 01 2010 - 11:00:04 PDT
