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, mem=4000mb | nodes=1 | nodes=1:ppn=16, walltime=00:30:00 | shared |
| singlenode | thin | walltime=00:30:01,procs=1, mem=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, mem=4000mb | nodes=2 | nodes=16:ppn=16, walltime=2:00:00:00 | singlejob |
| verylong | thin | walltime=3:00:00:01,procs=1, mem=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, mem=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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