AMBER Archive (2007)

Subject: Re: AMBER: Sander (Amber 9) crash on cortex

From: David A. Case (case_at_scripps.edu)
Date: Thu May 10 2007 - 14:55:16 CDT

On Thu, May 10, 2007, Evan Kelly wrote:

> I was recently met with the following error in the output file after
> a sander crash. The simulation I called for was an energy
> minimization at the force-field level of a small (148 residue)
> protein in a larger box of water (16000 water molecules). The crash
> occurred running in parallel on 4 cpus on an IBM 595 cluster. The
> error is found below:
>
> | Memory Use Allocated
> | Real 3301101
> | Hollerith 318114
> | Integer 1271200
> | Max Pairs 178595354
> ASSERTion 'ier == 0' failed in sander.f at line 223.

The error message means that the system failed to allocate the needed
memory. The pairlist is asking four roughly 800 MBytes of memory (200 million
4-byte integers). You might try to find out the maximum amount of memory
available per node on the IBM system. Maybe there is some software means to
increase it.

...good luck...dac

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