[Bioclusters] interpro with MOSIX cluster

[Philip E Macmenamin]

I am posting this, in response to a question I myself posed to the forum, and to which I recieved no replies. It is from Emmanuel Quevillon, who is responsible for at least part (if not all) of the InterPRoScan project. 

I hope this might be of use to others. 

All the best,
Philip. 

##Mail follows:

Hi Philip, 

InterPRoScan is not supporting yet correctly all the queueing system. I am trying to rewrite 
everything to support the maximum of queueing systems.

So the alternative you can have is to relaunch the CONFIG.pl script to reinstall everything and and 
do not answer yes when the prompt is asking you if you want to use a queueing system.
After that, edit the file called CONFIG.pm, and for each applications you set, in the hash table 
called '%appl_queuecmd' at the bottom of the file, enter the queueing command you want to put in the 
front of the command line used to run BlastProDom for example.

See :

%appl_queuecmd = ("ScanRegExp" => "", ...

become %appl_queuecmd = ("ScanRegExp" => "nice -5 mosrun -l", ... and so on for the applications you 
set.

Thus, iprscan will concatenate the above command line to the command line used to  launch ScanRegExp.

I think the best thing to do is also to install iprscan on the master node of your cluster, and that 
the directory where is installed iprscan must be shared by all the different nodes of your cluster, 
e.g via NFS.

Hope this will help.

Let me know, it could be helpfull for my future implementations.

Regards


Emmanuel

> Hi, I am trying to install interpro on a MOSIX cluster. 
> 
> On the UNIX QUEUING question on the CONFIG.pl script I am not sure what to 
> put. If I were running a process on the machine I would normally enter:
> nice -5 mosrun -l my_job, or somthing similar. So I have entered "mosrun 
> queue_name mosrun -l command_line". However, it later asks me the queue name 
> for the various scans, and I do not know what queue name to give them. I have 
> tried things like '5', but this does not work.  
> 
> When I run the scan the std.err file gives the following message:
> 
> exec: No such file or directory
> exec: No such file or directory
> gmake[1]: *** [blprodom.out] Error 1
> gmake[1]: *** [coil.out] Error 1
> exec: No such file or directory
> exec: No such file or directory
> gmake[1]: *** [hmmpfam.out] Error 1
> gmake[1]: *** [fps.out] Error 1
> exec: No such file or directory
> exec: No such file or directory
> gmake[1]: *** [hmmsmart.out] Error 1
> gmake[1]: *** [hmmpir.out] Error 1
> exec: No such file or directory
> exec: No such file or directory
> gmake[1]: *** [scpr.out] Error 1
> gmake[1]: *** [prfs.out] Error 1
> exec: No such file or directory
> exec: No such file or directory
> gmake[1]: *** [seg.out] Error 1
> gmake[1]: *** [signalp.out] Error 1
> exec: No such file or directory
> exec: No such file or directory
> gmake[1]: *** [tigrfam.out] Error 1
> gmake[1]: *** [tmhmm.out] Error 1
> gmake[1]: Target `raw' not remade because of errors.
> gmake: *** [cnk_1/merged.raw] Error 2
> gmake: Target `raw' not remade because of errors.
> 
> However, if I choose no to use the UNIX QUEUING system question, and enter 
> the same answers to all other questions it will run interpro fine. The 
> problem is it runs it all on the one node. (Obviously). If I enter:
> 
> mosrun gmake raw -j1 -k 2> ERROR 1> OUT
> 
> Leaving mosix to do the load distrib, it does not distribute the load as it 
> should.