HPC/Submitting and Managing Jobs

User environment

We use the environment-modules package to manage user applications. Learn more at HPC/Software/Environment.

See also: directory configuration.

Submitting and managing jobs

 qsub [-A accountname] [options] jobfile

For details on options:

 man qsub
 qsub --help

More details are at the Torque Manual, in particular the qsub man page.

The single main queue is batch and need not be specified. All job routing decisions are handled by the scheduler. In particular, short jobs are accommodated by a daily reserved node and by backfill scheduling, i.e. "waving forward" while a big job waits for full resources to become available.

Debug queue

For testing job processing and your job environment, use qsub -q debug or #PBS -q debug. The queue accepts jobs under the following conditions

nodes <= 2
ppn <= 4
walltime <= 1:00:00

Checking job status

Use the command qstat (from PBS) or showq (from Moab):

qstat [-u $USER]

showq [-u $USER]

regular output

qstat -a

showq -n

alternate format (showing job names)

Getting extra information

qstat -n [-1] jobnum

Show nodes where a job runs.

qstat -f [jobnum] [-1]

Full information such as submit arguments and run directories. The "-1" option disables wrapping for long output lines.

checkjob [-v] jobnum

Get extended jobs status information – useful to diagnose problems with "stuck" jobs.

Changing jobs after submission

You can use qalter to modify the attributes of a job before it starts. Specify the attributes to be modified on the command line. All others will not be changed. If any of the specified attributes cannot be modified for any reason, none of that job's attributes will be modified.

qalter [-l resource] […] jobnumber
qalter -A accountspec jobnumber

You cannot modify the job script itself after submission. You will have to remove and resubmit the job. For exceptional situations, contact me (stern) to arrange for a manual intervention.

Removing jobs

To retract a queued job or terminate an already running job:

 qdel jobnumber

Example job file

Here is a sample job script for an MPI application in the default user environment (OpenMPI over Infiniband interconnect):

#!/bin/bash

##  Basics: Number of nodes, processors per node (ppn), and walltime (hhh:mm:ss)
#PBS -l nodes=5:ppn=8
#PBS -l walltime=0:10:00
#PBS -N job_name
#PBS -A account

## File names for stdout and stderr.  If not set here, the defaults
## are <JOBNAME>.o<JOBNUM> and <JOBNAME>.e<JOBNUM>
#PBS -o job.out
#PBS -e job.err

## send mail at begin, end, abort, or never (b, e, a, n)
#PBS -m ea

# change into the directory where qsub will be executed
cd $PBS_O_WORKDIR

# count allocated cores
nprocs=$(wc -l < $PBS_NODEFILE)

# start MPI job over default interconnect
mpirun -machinefile $PBS_NODEFILE -np $nprocs \
        programname

• If your program reads from files or takes options and/or arguments, use and adjust one of the following forms

mpirun -machinefile $PBS_NODEFILE -np $nprocs \
       programname  < run.in

 

mpirun -machinefile $PBS_NODEFILE -np $nprocs \
       programname  -options arguments < run.in

 

mpirun -machinefile $PBS_NODEFILE -np $nprocs \
       programname < run.in > run.out 2> run.err

In this form, anything after programname is optional. If you use specific redirections for stdout or stderr as shown (>, 2>), the job-global files job.out, job.err declared earlier will remain empty or only contain output from your shell startup files (which should really be silent), and the rest of your job script.

• Infiniband (OpenIB) is the default (and fast) interconnect mechanism for MPI jobs. This is configured through the environment variable $OMPI_MCA_btl.
• To select ethernet transport (e.g. for embarrasingly parallel jobs), specify an -mca option:

mpirun -machinefile $PBS_NODEFILE -np $NPROCS \
	-mca btl self,tcp \
        programname

The account parameter

The parameter for option -A account is in most cases the CNM proposal, specified as follows:

cnm123

(3 digits) for proposals below 1000

cnm01234

(5 digits, 0-padded) for proposals from 1000 onwards.

user

(the actual string "user", not your user name) for a limited personal startup allocation

staff

for discretionary access by staff.

You can check your account balance in hours as follows:

mybalance -h
gbalance -u $USER -h

Advanced node selection

The PBS resource -l nodes=… can be refined further to:

• Select specific node hardware generations
• Control shared vs. exclusive node access
• Vary PPN within the job
• Accommodate multithreading (OpenMP).

See HPC/Submitting Jobs/Advanced node selection for these topics.

Interactive node access

• You can use ssh to interactively access any compute node on which a job of yours is running. As soon as a node no longer runs at least one of your jobs, your ssh session to that node will be terminated.