AMBER Archive (2006)

Subject: Re: AMBER: Compiling Amber8 with Sun HPC ClusterTools 5 Software

From: David A. Case (
Date: Sat Dec 23 2006 - 20:58:29 CST

On Fri, Dec 22, 2006, Muhammad Naim Mohmad Rouyan wrote:
> I have been attempting to compile a parallel version of amber 8 (Sun HPC
> ClusterTools 5) on a Sun Fire V1280 running on Solaris 9 using sparc as my
> compiler. The serial version compiles with no problems but when i attempt
> to compile the parallel version I don't know which one parallel flag to
> use. I'm trying to use mpi native flag and the compilation is succeed but
> when running a test run with make test.sender it get an error like this:
> .
> cd tgtmd/change_target.ntr; ./Run.tgtmd
> SANDER: Targeted MD with changing target and restraints
> Fatal error, aborting.
> Must have more residues than processors!
> Must have more residues than processors!

You don't say how many processors you asked for. Some of the tests (like this
one) have a limit, but don't correctly check to see if the limit is exceeded.

Try commenting out this line of the Makefile and running the tests again; or,
run a test with a small number of threads (say 2 or 4).

...good luck...dac

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