Batch Jobs Moab
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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.
|-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|
|Number of nodes |
Number of nodes and number of processes per node
|Wall-clock time. Default units are seconds. |
HH:MM:SS format is also accepted.
|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 execute:
$ msub -N test -l nodes=1:ppn=1,walltime=3:00:00,pmem=5000mb job.sh
or add to the 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.
1.2.2 Multithreaded Programs
1.2.3 MPI parallel Programs
1.2.4 Multithreaded + MPI parallel Programs
1.2.5 Interactive Jobs
2 Display Status of submitted Jobs
3 Environment Variables for Batch Jobs