Re: [ccp4bb]: Batch quese submission using CCP4i/ARP

[Steve Litster <steve_litster@vpharm.com>]

Title:

I managed to get it work ( with a wee fiddle) if anyone is interested here's
how and the environment we use.

We are currently using LSF on a multinode linux system (56 x 2CPU 1U units).
 The queuing system is neccessary in our environment so we can automatically
start the jobs on a under utilized nodes. For Parallel jobs we are using
MPICH-over-ethernet and MPICH-over-myrinet.


ARP/wARP batch submission:

Environment variables/paths must be set for CCP4 and ARP/wARP in your .cshrc
(or whatever you use)

1.  Launch  CCP4i and specify your scratch location (in our case this has
to be a filesystem accessible to all nodes) 
2.  Launch ARP/wARP, add your values and choose Run Remote/Batch/Later- choose
Later when the second window pops up.
3.  You should find  #_arp_warp_def.com and a #_arp_warp.def files in your
scratch dir.
4.  From the command line you can then launch the job using LSF (or DQS,NQS
etc) you can type:  

                bsub 'ccp4ish -r #_arp_warp.def' 

This is also working with Buster, Sharp and CNX.

Cheers,

Steve


Paul Emsley wrote:
> ***  For details on how to be removed from this list visit the  ***
> ***          CCP4 home page http://www.ccp4.ac.uk         ***
>
> On Fri, 2002-10-25 at 22:02, Steve Litster wrote:
> > ***  For details on how to be removed from this list visit the  ***
> > ***          CCP4 home page http://www.ccp4.ac.uk         ***
> >
> > Has anyone used the CCP4i/ARP, remote/batch submission option in an LSF 
> > environment?
> >
> >   
>
> I thought that someone else may have answered this by now - seems not...
>
> Currently, there is no batch queueing system support in ccp4i (and
> AFAIK, ARP/wARP).  You can however, use remote job submission from these
> using rsh.  (Indeed ARP/wARP will try to parallelize the jobs).
>
> Some CCP4 developers expressed some reservations at using rsh as a long
> term solution (due to security reasons).  Instead ssh was suggested. 
> Howver, using ssh (it seems to me) lays considerable administrative
> burden on the user - perhaps too much.  
>
> AFAIK, there are no ccp4 programs/tasks that support parallelization -
> so there has not been any need for a batch system [*].  This may change
> in the future.  If you have practical acquaintance of batch systems,
> then some ccp4 developers may well be interested in your experiences.
>
> (Of course it goes without saying that MPI and PVM are not used)
>
> (Currently :)
>
> HTH, 
>
> Paul.
>
> [*] well, we used a batch system everyday when there were VAXes, but
> that is not what I mean here.

-- 
Steve Litster
Senior Systems Engineer
IS
Vertex Pharmaceuticals
617-444-6399