[GE users] Gaussian09 with Linda 8.2

reuti reuti at staff.uni-marburg.de
Tue Dec 15 11:31:06 GMT 2009


Am 15.12.2009 um 11:56 schrieb buudo:

> Thank you very much, you solved my problem very well, I ajusted the  
> script for our needs and it works!
> Do you reserve nodes for gaussian  exclusively ?

Nowadays: partly (by a PE smp with $pe_slots as allocation_rule).  
Most of the time we use 4 or 8 cores. In fact, with 8 cores per node  
we are no longer using Linda in a new cluster.


> If not, there is a problem of possible overloading the nodes,  
> because the Linda variable

In the past we used a) Linda only without shared memory. Simply  
because you are then stuck to get the same number of slots per Linda  
process. Although you could then get a distribution of 4+2+2 for 4  
Linda processes (times 2 by shared memory) we never used it. In  
another cluster used by several groups we often got a random  
distribution of slots, so it was not worth putting any special  
allocation rule there to create a combination of shared memory and  
Linda instances. Or we used b) only shared memory on one node.


> %NProcShared is not affecting the $NSLOTS.

$NSLOTS is the number of slots in total, so it can't be used for % 
nprocs, unless you are on one node and run without Linda.


> In a mixed environment with other parallel jobs it is not usable  
> and the allocation rule "4" or "6" can not work as $pe_slots.

I assume you refer to the fact that a fixed allocation rule is not  
reserving the slots multiple times, i.e. 2 times 4 with  
"allocation_rule 4" on a machine with 8 cores. It's an RFE to allow  
this:

http://gridengine.sunsource.net/issues/show_bug.cgi?id=2985

and the issue mentioned therein.


> In another thread I found the similar problem concerning mixed MPI/ 
> OpenMP jobs with a nice started_method for the queues from reuti:
> --------------
> #!/bin/sh
> export OMP_NUM_THREADS=$NSLOTS
> exec "$@"
> --------------
> Unfortunately I am not able to include the strage variable starting  
> with "%" in such a similar script. Does anyone know how to manage  
> this ?

It's used in my awk script to modify a copy of the inputfile without  
any problems.

-- Reuti


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