Batch Jobs

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Important note: bwUniCluster is not in production mode yet.


Any kind of calculation on the compute nodes of bwUniCluster requires the user to define calculations as a sequence of commands or single command together with required run time, number of CPU cores and main memory and submit all, i.e., the batch job, to a resource and workload managing software. All bwHPC cluster, including bwUniCluster, have installed the workload managing software MOAB. Therefore any job submission by the user is to be executed by commands of the MOAB software. MOAB queues and runs user jobs based on fair sharing policies.


MOAB commands Brief explanation
msub submits a job and queues it in an input queue
checkjob displays detailed job state information
showq displays information about active, eligible, blocked, and/or recently completed jobs
showbf shows what resources are available for immediate use


1 Job Submission

Batch jobs are submitted using the command msub. The main purpose of the msub command is to specify the resources that are needed to run the job. msub will then queue the job into the input queue. The jobs are organized into different job classes. For each job class there are specific limits for the available resources (number of nodes, number of CPUs, maximum CPU time, maximum memory etc.).


1.1 msub Command

The syntax and use of msub can be displayed via:

$ man msub

msub options can be used from the command line or in your job script.


msub Options
Command line Script Purpose
-l resources #MSUB -l resources Defines the resources that are required by the job. See the description below for this important flag.
-N name #MSUB -N name Gives a user specified name to the job.
-I Declares the the job is to be run interactively.
-o filename #MSUB -o filename Defines the filename to be used for the standard output stream of the batch job. By default the file with defined filename is placed under your job submit directory. To place under a different location, expand filename by the relative or absolute path of destination.


1.1.1 msub -l resource_list

The -l option is one of the most important msub options. It is used to specify a number of resource requirements for your job. Multiple resource strings are separated by commas.


msub -l resource_list
resource Purpose
-l nodes=1
-l nodes=2:ppn=8
Number of nodes
Number of nodes and number of processes per node
-l walltime=600
-l walltime=1:30:00
Wall-clock time. Default units are seconds.
HH:MM:SS format is also accepted.
-l feature=tree
-l feature=blocking
-l feature=fat
For jobs that span over several nodes
For sequential jobs
For jobs that require up to 1 TB memory
-l pmem=1000mb Memory per process, allowed units are kb,mb,gb. Be aware that processes are either MPI tasks if running MPI parallel jobs or threads if running multithreaded jobs.


1.2 msub Examples

1.2.1 Serial Programs

To submit a serial job that runs the script job.sh and that requires 5000 MB of main memory and 3 hours of wall clock time

a) execute:

$ msub -N test -l nodes=1:ppn=1,walltime=3:00:00,pmem=5000mb   job.sh

or

b) add after the initial line of your script job.sh the lines:

#MSUB -l nodes=1:ppn=1
#MSUB -l walltime=3:00:00
#MSUB -l pmem=5000mb
#MSUB -N test

and execute the modified script without any msub command line options:

$ msub job.sh


Note, that msub command line options overrule script options.


1.2.1.1 Handling job script options and arguments

Job script options and arguments as followed:

./job.sh -n 10

can not be passed while using msub command since those will be interpreted as command line options of msub.


Solution A:

Submit a wrapper script, e.g. job_msub.sh:

msub job_msub.sh

which simply contains all your job script options and arguments. The script job_msub.sh would at least contain the following lines:

#!/bin/bash
./job_msub.sh -n 10


Solution B:

Add after the header of your BASH script job.sh the following lines:

## check if $SCRIPT_FLAGS is "set"
if [ -n "${SCRIPT_FLAGS}" ] ; then
   ## but if positional parameters are already present
   ## we are going to ignore $SCRIPT_FLAGS
   if [ -z "${*}"  ] ; then
      set -- ${SCRIPT_FLAGS}
   fi
fi

These lines modify your BASH script to read options and arguments from the environment variable $SCRIPT_FLAGS. Now submit your script job.sh as followed:

msub -v SCRIPT_FLAGS='-n 10' job.sh 


For advanced users: generalised version of solution B if job script arguments contain whitespaces.


1.2.2 Multithreaded Programs

Multithreaded programs operate faster than serial programs on CPUs with multiple cores. Moreover, multiple threads of one process share resources such as memory.

For multithreaded programs based on Open Multi-Processing (OpenMP) number of threads are defined by the environment variable OMP_NUM_THREADS. By default this variable is set to 1 (OMP_NUM_THREADS=1).

To submit a fourfold threaded program, omp_program, that requires 6000 MByte shared memory and total wall clock time of 3 hours

a) execute:

$ msub -v OMP_NUM_THREADS=4 -N test -l nodes=1:ppn=4,walltime=3:00:00,pmem=1500mb  omp_program

or

b) generate the script job_omp.sh containing the following the lines:

#!/bin/bash
#MSUB -l nodes=1:ppn=4
#MSUB -l walltime=3:00:00
#MSUB -l pmem=6000mb
#MSUB -N test

export OMP_NUM_THREADS=${MOAB_PROCCOUNT}
./omp_program

and execute the script job_omp.sh without any msub command line options:

$ msub job_omp.sh

1.2.3 MPI parallel Programs

Under construction.


1.2.4 Multithreaded + MPI parallel Programs

Under construction.


1.2.5 Interactive Jobs

Under construction.


2 Display Status of submitted Jobs

Under construction.


3 Environment Variables for Batch Jobs

Under construction.