[Bioclusters] Getting_started_MAC_OS_X_N1SGE6_parallel

Chris Dagdigian dag at sonsorol.org
Thu Jul 6 19:17:45 EDT 2006

Hi François,

First off, what assembly program are you trying to run on your  
cluster? Are you sure it is even capable of running in parallel  
across many machines? Most people I know doing assembly are doing it  
within a single large SMP system because shared memory is easier/ 
faster and (I think...) there is a relative lack of "true parallel"  
assembly algorithms.

Here are some official grid engine helpful URLs:

- http://gridengine.sunsource.net (main site for the codebase)

- http://docs.sun.com/app/docs/coll/1017.3  (official documentation  

I also run a site at http://gridengine.info but that may not be  
helpful until you are at least up and running.

Some specific suggestions for you and your current setup:

(1) Ignore the 'qmon' GUI. You won't be using it anyway with your  
assembler and it just gets in the way of the more flexible command  
line programs. Stick with the unix binaries like "qstat", "qrsh" and  
"qsub".   You won't be able to use SGE to its fullest unless you are  
comfortable with the command line programs

(2) Send us (or me) the output of the command "qstat -f" when run on  
your system. It may explain why you could not run the simple.sh  
example job.

(3) Learn where your spool logs are, they will be invaluable in  
debugging failures. The default location is something along the lines  
of $SGE_ROOT/<cell>/spool/ -- in particular you want to look at the  
last few lines of "qmaster/messages", "qmaster/schedd/messages" and  
any messages files belonging to exec hosts that are not behaving.


On Jul 6, 2006, at 4:42 PM, francois.fauteux2 at mail.mcgill.ca wrote:

> Hi;
> I am totally new to grid computing. I recently tried to run some  
> sequence assembly process on a G5 (8Gb RAM) but the process did  
> require more memory.
> I installed N1SGE6 on 3 MACs G5 under 10.4.7 (connected trough a  
> router) (alltogheter 13Gb RAM) and I would like to run the assembly  
> process in parallel trough the cluster hoping that memory resources  
> would be sufficient for the process to complete.
> I would appreciate hints as to "for-dummies-fast-how-to" configure  
> the cluster / submit the job properly.
> I installed master and hosts with defaults settings. First try with  
> examples/simple.sh returns (w. qmon):
> No free slots for interactive job!
> while 5 PCUs are available.
> Any hint as to how to properly configure the cluster/project/queues/ 
> parallel environments; or to use qsub with usefull options -for a  
> fast getting started- would be greatly appreciated; thanks.
> François
> _______________________________________________
> Bioclusters maillist  -  Bioclusters at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters

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