[gmx-users] mdrun hangs on nodes of P655+ aix 5.2

[Erik Lindahl]

Hi,

I'm certainly seeing lots of differences between 1.5 and 1.5.4.1 when  
I run diff in my cvs tree.

However, I think we made the 3.3.1 release after march 9, in which  
case it is included there.

Cheers,

Erik

On Aug 5, 2006, at 12:05 AM, Dongsheng Zhang wrote:

> Dear Erik,
>
> I had the same problem as Arthur Roberts. So I downloaded your new
> version of gmx_system_xdr.h and gmx_system_xdr.c from
> http://bugzilla.gromacs.org/show_bug.cgi?id=55
>
> Before I recompile gromacs, I checked the difference between your new
> version and the old one. The result is as follows:
>
> diff gmx_system_xdr.c gmx_system_xdr-n.c
> 2c2
> <  * $Id: gmx_system_xdr.c,v 1.5.4.1 2006/03/09 08:12:16 lindahl Exp $
> ---
>>  * $Id: gmx_system_xdr.c,v 1.5 2004/01/23 17:23:13 lindahl Exp $
>
>  diff gmx_system_xdr.h gmx_system_xdr-n.h
> 2c2
> <  * $Id: gmx_system_xdr.h,v 1.3.4.1 2006/03/09 08:12:09 lindahl Exp $
> ---
>>  * $Id: gmx_system_xdr.h,v 1.3 2003/11/17 21:50:40 spoel Exp $
>
> Both differences are in documentation. I am confused how your
> modification can solve the problem.
>
> I had the same problem and posted in the mailing list before (
> http://www.gromacs.org/pipermail/gmx-users/2006-June/022493.html ) I
> also found Jason O'Young had asked the similar question at
> http://www.gromacs.org/pipermail/gmx-users/2006-May/021605.html
>
> I think this problem sounds common, could you please investigate  
> what's
> wrong? Thank you very much for your help!
>
> By the way, I can continue the simulation by tpbconv, but hangs soon
> without any error message. The "top" command shows the programs is
> running, but no more output data.
>
>
> All the best!
>
> Dongsheng
>
>
> On Mon, 2006-07-31 at 08:36 +0200, Erik Lindahl wrote:
>> Hi,
>>
>> It _might_ be solved by the fix attachment at
>>
>> http://bugzilla.gromacs.org/show_bug.cgi?id=55
>>
>> (also in CVS)
>>
>> Cheers,
>>
>> Erik
>>
>> On Jul 31, 2006, at 8:11 AM, Arthur Roberts wrote:
>>
>>> Hi, all,
>>>
>>> I am trying to run Gromacs on a P655+ with Aix 5.2.
>>> Initially, mdrun appears to work, but always hangs.
>>> Eventually, I get timed out from the supercomputer
>>> with no data to show for it.  Below is a link
>>> detailing the problem:
>>>
>>> http://cetus.mchem.washington.edu/pub/supercomputer/Mdrun-hangs-
>>> without-showing-steps.html
>>>
>>> I appreciate your input.  Your previous suggestions
>>> have been very helpful.
>>>
>>> Best wishes,
>>> Art
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