AMBER Archive (2006)

Subject: RE: AMBER: amber9

From: Ross Walker (
Date: Fri Jul 14 2006 - 17:37:19 CDT

Hi Piotr,

> sander.MPI: error while loading shared libraries:
> cannot open shared object file: No such file or directory
> This fortran library is located in my case in /opt/intel_fc_80/lib
> and my environment is properly setup for recognizing the path
> to this directory.
> (maybe the program tries to load it from /usr/local/bin/lib?)
> (this is excerpt from env:
> LD_LIBRARY_PATH=/usr/local/lib:/opt/intel_fc_80/lib)

Are you certain every node has the libraries installed in the same place and
all are correctly setting up LD_LIBRARY_PATH? When running shared library
executables in parallel all of the nodes need to have access to the library
and all need to have the path setup correctly.

I typically get around this on large clusters by copying the whole of
intel_fc_80/lib to ~/lib and then edit my .cshrc files to add ~/lib to my
LD_LIBRARY_PATH and my PATH (just to be sure). Then I make sure that the job
submission system is setup so that it correctly sources my cshrc file on
every node before doing the mpirun command.

You might also want to try and see if you can compile statically (may or may
not work depending on your mpi installation.)

Note, also check to see if mpirun -np 1 works - I.e. 1 thread run on the
node you are physically logged into.

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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