AMBER Archive (2007)

Subject: Re: AMBER: Help!! I cannot perform the ambpdb

From: WANG,YING (wangying_at_ufl.edu)
Date: Wed Feb 07 2007 - 15:23:16 CST

Hi, Mark,
Thanks very much!! The problem is solved.
Thanks again!!
Happy bird.................. :)

On Wed Feb 07 15:25:19 EST 2007, Mark Williamson
<Mark.Williamson_at_imperial.ac.uk> wrote:

> WANG,YING wrote:
>
>> | New format PARM file being parsed.
>> | Version = 1.000 Date = 02/06/07 Time = 11:40:55
>> mpirun: killing job...
>
> Dear Ying,
>
> I still do not understand why the mpirun related error message is
> here, yet you say you are not specifying it in your command line,
> hence it may be an issue with with the PBS queuing system.
> Perhaps, at the queuing level, every job command is being
> prefixed with mpirun? I do not know.
>
> A second thing to look at is that some queuing systems sometimes
> run in other directories that submitted. Hence use full paths in
> all files being operated on.
>
> Overall, I think the the problem lies somewhere with your
> cluster. As it has been mentioned, ambpdb is not designed to be
> run in parallel. I think you should talk to your cluster
> administrator since the I feel problem is in a realm over which
> we have no control or knowledge.
>
> regards,
>
> Mark
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