The first example works, because sander does not use the MPI libraries,
the second fails because it appears they are not loaded and sander.MPI
needs them. To fix this, you should also load the openmpi module in
addition to the amber module, which can be accomplished by something
similar to:
module load openmpi/gcc/1.6.2_rocks
In any case, better contact your sysadmin for the exact procedure, since
we cannot possibly know how the environment is setup and how amber was
compiled on your cluster. Seems like it could be the rocks cluster distro,
so with some luck the above command might even work.
Best,
------------------------------------------------------
Dr. Matej Repic
Ecole Polytechnique Fédérale de Lausanne
Laboratory of Computational Chemistry and Biochemistry
SB - ISIC LCBC
BCH 4108
CH - 1015 Lausanne
------------------------------------------------------
On 10/1/15, 10:34, "Atila Petrosian" <atila.petrosian.gmail.com> wrote:
>Dear amber users,
>
>I am using ambertools 14 to do MD simulation on Rocks Compute Node.
>
>I did minimization step without any problem using:
>
>$AMBERHOME/bin/sander -O -i min.in -o min.out -p comp_sol.prmtop -c
>comp_sol.inpcrd -r min.rst -ref comp_sol.inpcrd -inf min_info
>
>But, when I use following commands:
>
>mpirun -np 12 $AMBERHOME/bin/sander.MPI -O -i min.in -o min.out -p
>comp_sol.prmtop -c comp_sol.inpcrd -r min.rst -ref comp_sol.inpcrd -inf
>min_info
>
>I encountered with
>
>/share/apps/amber/amber14/bin/sander.MPI: error while loading shared
>libraries: libmpi_cxx.so.1: cannot open shared object file: No such file
>or
>directory
>
>What is the reason of this problem and how to resolve that?
>
>Any help will highly appreciated.
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Received on Thu Oct 01 2015 - 02:30:03 PDT
