[GE users] Having problems setting up PEs

Margaret Doll Margaret_Doll at brown.edu
Thu Nov 13 22:18:25 GMT 2008


I am running sge-V6lu4-1 and rocks-sge-5.0-2

If I run my programs using

qsub -pe mpich 4 shll

where shll contains:

#!/bin/bash
#$ -o $HOME/works-1/Out
#$ -j y

/opt/openmpi/bin/mpirun -v -n 4 /home/mad/works-1/mad   ,

this works but the job is assigned to an arbitrary compute node.


I created a PE,  called chemistry.  My version of qmon does not have  
the option
of assigning the PE to a queue in the PE list setup page as shown on  
page 247
of the "Administration and User's Guide."  I, therefore, assigned an  
unique
machine  file to the startup shell.  See below.

When I run

qsub -pe chemistry 4 shll

my job is stuck in the pending bin with the following errors:

scheduling info:	queue instance "all.q at compute-0-1.local" dropped  
because it is
  				temporarily not available
			queue instance "all.q at compute-0-2.local" dropped because it is
  				temporarily not available
			queue instance "het at compute-0-32.local" dropped because it is
				full
			queue instance "het at compute-0-  ...
Error for job 17330:  11/13/2008 ...: exit_status of pe_start = 1
Error for job 17330:  11/13/2008 ...: exit_status of pe_start = 1


PE List

	chemistry	PE Name		chemistry
			Slots		16
			Users		chemistry
			Xusers		NONE
			Start Proc Args /opt/gridengine/mpi/startmpi.sh -unique /opt/ 
gridengine/mpi/chem-machinefile
			Stop Proc Args	/opt/gridengine/mpt/stopmpi.sh	
			Allocation Rule	$fill_up
			Urgency Slots	min

Contents of /opt/gridengine/mpi/chem-machinefile
	compute-0-10 7 mem8.q 8
	compute-0-11 7 mem8.q 8

Referenced PEs for all.q and mem16.q

	chemistry
	make
	mpi
	mpich


	mem16.q and all.q, both contain nodes compute-0-10 and compute-0-11.

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