Getting_started_MAC_OS_X_N1SGE6_parallel

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  -  Bioclustersbioinformatics.org
https://bioinformatics.org/mailman/listinfo/bioclusters

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.sun
source.net (main site for the codebase)

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

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.

Regards,
Chris





On Jul 6, 2006, at 4:42 PM, francois.fauteux2mail.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  -  Bioclustersbioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters

_______________________________________________
Bioclusters maillist  -  Bioclustersbioinformatics.org
https://bioinformatics.org/mailman/listinfo/bioclusters