HPC/Submitting and Managing Jobs

Directories and Environment

First read: directory configuration.

Applications

We use the environment-modules package to manage user applications. This is similar to places like NERSC or PNNL. The basic CNM-specific user environment is configured automatically in /etc/profile.d/cnm.{sh,csh}.

For now the only applications are the Development tools.

Submitting jobs to Moab/Torque

 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.

Removing jobs

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

 qdel jobnumber

Example job file

• sample job file for Infiniband interconnect (recommended):

#!/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

PPN Tricks

Each Carbon node has 8 cores, and for many jobs users indeed request entire nodes by specififying ppn=8 in the job submission. However, you may need to request fewer cores, e.g. for the following reasons:

• your application is not parallelized
• your application has limited hardcoded parallelization, e.g. for 2 or 4 cores only
• your application runs multi-threaded but uses $PBS_NODEFILE to infer the number of processes to start
• your application runs busy service processes or service threads (e.g. NWChem)
• your application saturates a resource, e.g. memory bandwidth (some large VASP calculations)
• the node's memory is not sufficient to run processes on all cores.

Depending on the reason, the node should or should not be used by other jobs. In the past, the only way to achieve exclusive but undersubscribed node access was to request ppn=8 and then to thin out a copy of the nodefile before passing it to the application. To eliminate the need to edit the nodefile, use the -l naccesspolicy=… flag to differentiate between resources requested from PBS from those passed to the application.

Select an option from the following scenarios.

Shared vs. Exclusive Node Access

General node sharing

When a job requires only a few cores and a commensurate fraction of other resources, simply specify ppn as needed:

#PBS -l nodes=nnn:ppn=4

In this case, the remaining cores may be allocated to other jobs, which is the default policy:

#PBS -l naccesspolicy=SHARED

User-specific node sharing

To permit node sharing among your own jobs, specify a SINGLEUSER policy:

#PBS -l nodes=nnn:ppn=2
#PBS -l naccesspolicy=SINGLEUSER

Exclusive node access

When your job requires only a few cores but a disproportionate fraction of another resource on a node (such as most of its memory or a lot of I/O bandwidth), claim the entire node:

#PBS -l nodes=nnn:ppn=4
#PBS -l naccesspolicy=SINGLEJOB

PBS will reserve the entire node(s), but place each node name only ppn times in the $PBS_NODEFILE.

Different PPN by node

When your first MPI process (the "master" process) requires more memory than your other "worker" processes, give several nodes specifications, separated by a "+" character (which is unusal and born of historical necessity):

#PBS -l nodes=1:ppn=1+2:ppn=4
#PBS -l naccesspolicy=SINGLEJOB

For clarity, the nodes specification in this example reads as follows:

nodes = ( 1:ppn=1 ) + ( 2:ppn=4 )

This will request 3 node exclusively, but the first node will occur only once in the $PBS_NODEFILE, e.g.

n011
n012
n012
n012
n012
n034
n034
n034
n034

In all of the preceding scenarios the following applies:

• The $PBS_NODEFILE seen by the job script will always match ppn.
• For accounting, the job will be billed by the number of cores blocked from use by other users, i.e., ncores=ppn for shared nodes, and ncores=8 otherwise.

Multithreading (OpenMP)

When you wish to use multithreading, you must ensure that the total number of "busy" user threads and processes corresponds to the number of cores requested from PBS. Today, multithreading in applications and libraries is typically programmed using the OpenMP interface and the number of threads is controlled by the environment variable $OMP_NUM_THREADS. Select from the following scenarios.

OpenMP, single entire node

#PBS -l nodes=1:ppn=8
...
cd $PBS_O_WORKDIR
export OMP_NUM_THREADS=8
...

OpenMP, single node, possibly shared

choose the number of cores n such that 1 ≤ n ≤ 8:

#PBS -l nodes=1:ppn=n
...
cd $PBS_O_WORKDIR
export OMP_NUM_THREADS=`uniq -c $PBS_NODEFILE | awk '{print $1; exit}'`
...

Here, the default policy "SHARED" is in effect, and OMP_NUM_THREADS is set automatically by counting the number of times that the first node occurs in $PBS_NODEFILE. This will allow you to vary or override the nodes setting using "qsub -l nodes=…" without having to edit it twice in the job file.

OpenMP/MPI hybrid

Making efficient use of multithreading on multiple nodes which communicate over MPI is fairly involved and is subject to ongoing research. PBS requests are the same as in the preceding case (OpenMP only), but you must export OMP_NUM_THREADS to all MPI satellite nodes. Further, since $PBS_NODEFILE is typically used to identify remote nodes, you must thin out the file before using it as machinefile:

#!/bin/bash
#PBS -l nodes=nnn:ppn=8
...
MACHINEFILE=$PBS_NODEFILE
...
if [ multithreaded ]            # insert specific condition
then
    MACHINEFILE=machinefile
    sort -u $PBS_NODEFILE > $MACHINEFILE
fi
...
mpirun -x OMP_NUM_THREADS=`uniq -c $PBS_NODEFILE | awk '{print $1; exit}'` \
    -machinefile $MACHINEFILE \
    -np `wc -l < $MACHINEFILE` \
    …

The -x option is specific to OpenMPI; please consult the documentation to achieve the same behavior in other MPI implementations.

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.