AMBER Archive (2009)

Subject: Re: [AMBER] error in executing sander.MPI in amber9

From: Atro Tossavainen (atro.tossavainen+amber_at_helsinki.fi)
Date: Thu Feb 05 2009 - 05:08:59 CST

> sander.MPI -O -i MD-betaMalto-lyoHIGH.in -p maltose_lyoHIGH.top -c betaMalto-lyoHIGH-MD18-run0700.rst_100000 -o betaMalto-lyoHIGH-MD18-run0700.out -x betaMalto-lyoHIGH-MD18-run0700.traj -r betaMalto-lyoHIGH-MD18-run0800.rst
>
> sander.MPI: error while loading shared libraries: libmkl_lapack.so: cannot open shared object file: No such file or directory

You have failed to compile AMBER with the linker flag -rpath pointing
to all the right directories. This can be circumvented at run time by
including the necessary directories in LD_LIBRARY_PATH. The path that
you posted does not seem to include your MKL directory, which would be
a strong candidate for the cause of the problem you reported.

I don't know about Altix systems specifically, but in general you should
not be able to run the MPI versions of the programs without "mpirun" of
some sort. If the program starts at all (when you've adjusted the LD_
LIBRARY_PATH), you should expect to see something like this:

% .../bin.sgi_65/pmemd.MPI
mpirun must be used to launch all MPI applications
% 

-- 
Atro Tossavainen (Mr.)               / The Institute of Biotechnology at
Systems Analyst, Techno-Amish &     / the University of Helsinki, Finland,
+358-9-19158939  UNIX Dinosaur     / employs me, but my opinions are my own.
< URL : http : / / www . helsinki . fi / %7E atossava / > NO FILE ATTACHMENTS

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