AMBER Archive (2005)

Subject: Re: AMBER: What does a crash mean while running a md simulation?

From: shuli kang (mmv_at_whu.edu.cn)
Date: Mon Jan 24 2005 - 23:58:54 CST

Dear Ross,

Thanks for your help.I`m sorry I ignore the following message in the log
file :
Filesize limit exceeded

I find similar question has beed asked by MURAT CETINKAYA.My file system
is ext3, with 2TB file size limit.
Is there anyway to break through the 2GB limit if I don`t want to split
my job up into too many chunks?

Ross Walker wrote:

>Dear Shuli,
>
>
>
>>I`m running a long md simulation.So I divided the simulation into
>>several jobs.
>>One of the jobs suddenly stoped for something wrong.And the next job
>>started automaticly according to the .rst file produced before the
>>crash. No error or warning information appears in the log
>>file.And the
>>consequent job seems fine now.
>>What may be the reason for the crash ?Should I rerun the crashed job?
>>
>>
>
>This could be due to anything, without more information it is hard to tell.
>Are you running in a queuing environment (PBS?). If yes have you hit the
>time limit for your job? PBS will often kill a job with no error message if
>you exceed the maximum wallclock or cputime allowed. You might also faulty
>hardware, this could cause a job to crash with no error message.
>
>Secondly, if you ran the job just backgrounded in a shell, without nohup,
>closing that shell will kill the job.
>
>You also redirect standard error to a file so that the error message is not
>lost.
>
>E.g.
>
>Sander -O -i mdin -o mdout -p prmtop -c inpcrd >& logfile
>
>As for the new job starting immediately from the crashed job this is fine,
>except for the fact that it will have started from an earlier time in the
>simulation than you were expecting. Make sure you are aware of this and
>adjust your interpretation of the results as necessary.
>
>All the best
>Ross
>
>/\
>\/
>|\oss Walker
>
>| Department of Molecular Biology TPC15 |
>| The Scripps Research Institute |
>| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
>| http://www.rosswalker.co.uk/ | PGP Key available on request |
>
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