Re: [AMBER] GPU related issues

From: Ross Walker <>
Date: Fri, 19 Nov 2010 09:23:48 -0800

Hi Ye,

> I have applied all the patches to AMBER 11 on my GPU machine, which has 4
> C2050 cards. But sometimes the jobs still fail. AMBER 11 is compiled with

Can you just confirm specifically up to what patch number you applied. Just
to be sure you have ALL of the latest patches.

> In the first job, the system has 12157 atoms only, and the simulation is
> NPT ensemble. If cut is set to 8A, this job runs fine. But if cut is set
to 10, it
> dies with a lot of NaN in energy terms and coordinates.

Can you confirm that you can run this simulation on the CPU with cut=10
without issue?
> In the second job, the system has 34116 atoms. The serial cuda run is OK.
> in parallel CUDA run, it dies with error message "max pairlist cutoff must
> less than unit cell max sphere radius". However, cut is set to 8A, and the
> distance between the protein and cell boundary is set to 10A.

This occurs when the system blows up, however why it blows up is the issue.

> Can anyone help me out?

Can you please send you input files so we can try to reproduce this.



|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
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| Tel: +1 858 822 0854 | EMail:- |

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Received on Fri Nov 19 2010 - 09:30:02 PST
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