[gmx-users] mpirun on lam again

Erik Lindahl lindahl at stanford.edu
Tue Apr 16 19:18:52 CEST 2002

Y U Sasidhar wrote:

>I hope at least my syntax is correct; Pl let me know how I should
>correct this.
>mpirun -v -c 16  -s n0 mdrun_mpi -- -v -s full.tpr -e full.edr -o
>full.trr -
>c after_full.gro -g full.log >& full.job &
>results in:
>5146 mdrun_mpi running on n0 (o)
>3245 mdrun_mpi running on n1
>mdrun_mpi: error while loading shared libraries: libmd_mpi.so.2: cannot
> shared object file: No such file or directory
>2909 mdrun_mpi running on n2
>2905 mdrun_mpi running on n3

You're probably using the RPM version of Gromacs. This is compiled with 
shared libraries to save space (or the download would be 75 Mb). "Shared 
libraries" means the mdrun_mpi file only contains a small amount of 
code, and as soon as it calls one of the routines in the library the 
system loads these routines from libmd_mpi.so or libgmx_mpi.so (i.e. the 
common routines are not duplicated).

For this to work, the system must know where to find the *.so files. By 
default, it looks in the place where it was installed, i.e. 
/usr/local/lib, but you can also tell the system to look for them in any 
other directory by adding that directory to the environment variable 

The simplest solution is probably to make sure gromacs is available on 
all the nodes; either by installing it on every one of them, or by 
mounting /usr/local/ from a server.

If this is inconvenient for some reason, you can of course also compile 
the code yourself - in that case the default will be static (i.e. 
non-shared) libraries.



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