/\
Hi, \/
|\oss, Thanks very much!! I delete the "mpirun" command in my
PBS script and directly input ambpdb... and then it works. So
happy!!
Sorry for all of you to suffer my stupid questions! Thanks very
much!!
\ /\ /
\/ \/ ang
On Wed Feb 07 10:21:13 EST 2007, Ross Walker
<ross.rosswalker.co.uk> wrote:
> Hi Wang,
>
>> mpirun: killing job...
>>
>> I del my job and run again but it didn't work. I log out and log
>> in the PBS systerm again but it didn't work too........... :(
>> Could you help me?.......... Sorry, really sorry to trouble
>> you....
>
> The only software in the Amber package that is parallel and needs
> mpirun is
> pmemd and sander.MPI (and it's derivatives). All other programs
> are serial
> and should NOT be run with mpirun. Ambpdb is a very simple
> program that
> should take seconds at most to run. Thus there is no point in
> submitting
> this via queuing system such as pbs unless it is part of some
> elaborate
> script. You can simply run it from the command line as:
>
> $AMBERHOME/exe/ambpdb -p prmtop < inpcrd > my.pdb
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of
> delivery, may not
> be read every day, and should not be used for urgent or sensitive
> issues.
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Feb 11 2007 - 06:07:11 PST
