Specifying Parallel Environment on Google Compute Engine using Elasticluster

Question

I recently created a Grid Engine cluster on Compute Engine using Elasticluster (http://googlegenomics.readthedocs.org/en/latest/use_cases/setup_gridengine_cluster_on_compute_engine/index.html).

I was wondering what is the appropriate command to run shared-memory multithreaded batch jobs on a cluster of Compute Engine virtual machine running Grid Engine.

In other words, what is the name (i.e. pe_name) of the Grid Engine parallel environment.

Let's say I want to run a job requesting 4 cpus on 1 node, what would be the right qsub command.

So far I tried the following command:

qsub -cwd -l h_vmem=800G -pe smp 6 run.sh Unable to run job: job rejected: the requested parallel environment "smp" does not exist.

qsub -cwd -l h_vmem=800G -pe omp 6 run.sh Unable to run job: job rejected: the requested parallel environment "omp" does not exist.

Thank you for your help!

Answer 1

I don't believe that Elasticluster's Ansible playbook includes a parallel environment. You can see the main configuration run on the master here:

https://github.com/gc3-uzh-ch/elasticluster/blob/master/elasticluster/providers/ansible-playbooks/roles/gridengine/tasks/master.yml

I believe you can simply connect to the master and issue the "add parallele environment" command:

$ qconf -ap smp

and write a configuration file like:

pe_name         smp
slots           9999
user_lists      NONE
xuser_lists     NONE
start_proc_args /bin/true
stop_proc_args  /bin/true
allocation_rule $fill_up
control_slaves  FALSE
job_is_first_task  FALSE
urgency_slots   min
accounting_summary FALSE

and then modify the queue configuration for all.q:

$ qconf -mq all.q

...
pe_list             make smp
...

I would also suggest filing an issue with Elasticluster here:

https://github.com/gc3-uzh-ch/elasticluster/issues

I would expect that someone has already done this in a fork of Elasticluster and may be able to provide a pull request to the master fork.

Hope that helps.

-Matt