AMBER Archive (2009)

Subject: RE: [AMBER] sander error

From: Ross Walker (
Date: Mon Jun 08 2009 - 20:41:06 CDT

Hi John,

> I am trying to run sander remotely through a ssh connection. I get an
> error message (below) and sander doesn't run:
> sander: relocation error: sander: undefined symbol: ___svm1__acos2
> What does this mean? How do I address the problem?

This generally means that the executable was not built statically and
instead dynamically links to libraries. Then since the executable was built
either the compiler version in you environment (defined by your
LD_LIBRARY_PATH) and/or the version of MKL you are using has changed.

The solution is to modify your environment to make sure it is setup to use
the original version of the compiler, MPI and MKL libraries against which
AMBER was built (difficult if some 'upgraded' the machine for you) or
rebuild AMBER using the new environment.

You can avoid this problem in future by building statically (provide -static
flag to ./configure_amber) although some MPI implementations have issues
with this but generally if you can you should always build statically.

Good luck,

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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