Batch Jobs - bwUniCluster Features

This article contains information on features of the batch job system only applicable on bwUniCluster.

Job Submission

msub Command

The bwUniCluster supports the following additional msub option(s):

bwUniCluster additional msub Options
Command line	Script	Purpose
-I		Declares the job is to be run interactively.

msub -l resource_list

No deviation or additional features to general batch job setting.

msub -q queues

Compute resources such as walltime, nodes and memory are restricted and must fit into queues. Since requested compute resources are NOT always automatically mapped to the correct queue class, you must add to your msub command the correct queue class. Details are:

msub -q queue
queue	node	default resources	minimum resources	maximum resources	node access policy
develop	thin	walltime=00:10:00,procs=1, pmem=4000mb	nodes=1	nodes=1:ppn=16, walltime=00:30:00	shared
singlenode	thin	walltime=00:30:01,procs=1, pmem=4000mb	nodes=1, walltime=00:30:01	nodes=1:ppn=16, walltime=3:00:00:00	shared
multinode	thin	walltime=00:10:00,procs=1, pmem=4000mb	nodes=2	nodes=16:ppn=16, walltime=2:00:00:00	singlejob
verylong	thin	walltime=3:00:00:01,procs=1, pmem=4000mb	nodes=1, walltime=3:00:00:01	nodes=1:ppn=16, walltime=6:00:00:00	shared
fat	fat	walltime=00:10:00,procs=1, pmem=32000mb	nodes=1	nodes=1:ppn=32, walltime=3:00:00:00	shared

Note that node access policy=singlejob means that, irrespected of the requested number of cores, node access is exclusive. Default resources of a queue class defines walltime, processes and memory if not explicitly given with msub command. Resource list acronyms walltime, procs, nodes and ppn are described here.

Queue class examples

• To run your batch job longer than 3 days, please use$ msub -q verylong.

• To run your batch job on one of the fat nodes, please use$ msub -q fat.

Environment Variables for Batch Jobs

The bwUniCluster expands the common set of MOAB environment variables by the following variable(s):

bwUniCluster specific MOAB variables
Environment variables	Description
MOAB_SUBMITDIR	Directory of job submission

Since the work load manager MOAB on bwUniCluster uses the resource manager SLURM, the following environment variables of SLURM are added to your environment once your job has started:

SLURM variables
Environment variables	Description
SLURM_JOB_CPUS_PER_NODE	Number of processes per node dedicated to the job
SLURM_JOB_NODELIST	List of nodes dedicated to the job
SLURM_JOB_NUM_NODES	Number of nodes dedicated to the job
SLURM_MEM_PER_NODE	Memory per node dedicated to the job
SLURM_NPROCS	Total number of processes dedicated to the job

Node Monitoring

By default nodes are not used exclusive anless they are requested with -l naccesspolicy=singlejob as described here.
If a Job runs exclusive on one node you may do a ssh login to that node. To get the nodes of your job need to read the environment variable SLURM_JOB_NODELIST, e.g.

 echo $SLURM_JOB_NODELIST > nodelist

Interactive Jobs

Interactive jobs on bwUniCluster must NOT run on the logins nodes, however resources for interactive jobs can be requested using msub. Considering a serial application with a graphical frontend that requires 5000 MByte of memory and limiting the interactive run to 2 hours execute the following:

$ msub  -I  -V  -l nodes=1:ppn=1 -l walltime=0:02:00:00

The option -V defines that all environment variables are exported to the compute node of the interactive session. After execution of this command DO NOT CLOSE your current terminal session but wait until the queueing system MOAB has granted you the requested resources on the compute system. Once granted you will be automatically logged on the dedicated resource. Now you have an interactive session with 1 core and 5000 MByte of memory on the compute system for 2 hours. Simply execute now your application:

$ cd to_path
$ ./application

Note that, once the walltime limit has been reached you will be automatically logged out of the compute system.

Chain Jobs

The CPU time requirements of many applications exceed the limits of the job classes. In those situations it is recommended to solve the problem by a job chain. A job chain is a sequence of jobs where each job automatically starts its successor.

#!/bin/bash ################################################## ## simple job run template for bwUniCluster ## ## to run chain jobs with MOAB ## ################################################## ## ## usage : ## msub -v myloop_counter=0 ./moab_chain_job.sh #MSUB -l nodes=1:ppn=1 #MSUB -l walltime=00:00:05 #MSUB -l pmem=50mb #MSUB -q develop #MSUB -N chain ## Defaults loop_max=10 cmd='sleep 2' ## Check if counter environment variable is set if [ -z "${myloop_counter}" ] ; then echo " ERROR: myloop_counter is undefined, stop chain job" exit 1 fi ## only continue if below loop_max if [ ${myloop_counter} -lt ${loop_max} ] ; then ## increase counter let myloop_counter+=1 ## print current Job number echo " Chain job iteration = ${myloop_counter}" ## Define your command cmd='sleep 2' echo " -> executing ${cmd}" ${cmd} if [ $? -eq 0 ] ; then ## continue only if last command was successful msub -v myloop_counter=${myloop_counter} ./moab_chain_job.sh else ## Terminate chain echo " ERROR: ${cmd} of chain job no. ${myloop_counter} terminated unexpectedly" exit 1 fi fi

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