Re: AMBER: Unexpected stop of Sander run

From: David A. Case <>
Date: Mon, 23 May 2005 08:00:46 -0700

On Sun, May 22, 2005, Grzegorz Jezierski wrote:

> While trying to run Sander in short test simulations, I have encoutered
> strange errors which stopped the execution of a program. I used to work
> with AMBER package, and I think I checked all the options carefully this
> time, so probably the error is non-trivial.
> Here I tried several structures (peptides and nucleic acids), also with
> and without MPI, with Amber6 and Amber8, and on three different machines
> (#1, Opteron cluster; #'s 2 and 3, SGI).

Be sure to run the test cases that come with Amber. It's much easier to debug
a known problem (the test cases) than one that you have made up. If the test
cases pass, then you can try to slowly morph one of them into your problem,
until you find what it is that does not work.

First, make sure that you can run the test cases without MPI. Then, try to
run *your* programs without MPI. Next, be sure that you can run the test
cases that come with your MPI distribution; then try the Amber test cases with
MPI. Finally, you can try your problems with MPI.

....good luck....dac

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Received on Mon May 23 2005 - 16:53:00 PDT
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