Pegasus Job Scheduling with LSF¶
Pegasus currently uses the LSF resource manager to schedule all compute resources. LSF (load sharing facility) supports over 1500 users and over 200,000 simultaneous job submissions. Jobs are submitted to queues, the software categories we define in the scheduler to organize work more efficiently. LSF distributes jobs submitted by users to our over 340 compute nodes according to queue, user priority, and available resources. You can monitor your job status, queue position, and progress using LSF commands.
Reserve an appropriate amount of resources through LSF for your jobs.
Jobs with insufficient resource allocations interfere with cluster performance and the IDSC account responsible for those jobs may be suspended (Policies).
Stage data for running jobs exclusively in the
/scratch file system, which is optimized for fast data access.
Any files used as input for your jobs must first be transferred to /scratch. See Pegasus Resource Allocations for more information. The /nethome file system is optimized for mass data storage and is therefore slower-access.
Using /nethome while running jobs degrades the performance of the entire system and the IDSC account responsible may be suspended*** (Policies).
Do not background processes with the
& operator in LSF.
These spawned processes cannot be killed with bkill after the parent is gone.
Using the & operator while running jobs degrades the performance of the entire system and the IDSC account responsible may be suspended (Policies).
LSF Batch Jobs¶
Batch jobs are self-contained programs that require no intervention to run. Batch jobs are defined by resource requirements such as how many cores, how much memory, and how much time they need to complete. These requirements can be submitted via command line flags or a script file. Detailed information about LSF commands and example script files can be found later in this guide.
Create a job scriptfile
Include your project ID
-P, a job name
-J, the information LSF needs to allocate resources to your job, and names for your output and error files.
scriptfile #BSUB -J test #BSUB -q general #BSUB -P myproject #BSUB -o %J.out ...
Submit your job to the appropriate project and queue with
bsub < scriptfile
Upon submission, the project is returned along with a
jobIDand the queue name.
[username@pegasus ~]$ bsub < scriptfile Job is submitted to <my_project> project. Job <6021006> is submitted to queue <general>.
Monitor your jobs with
Flags can be used to specify a single job or another user’s jobs.
[username@pegasus ~]$ bjobs JOBID USER STAT QUEUE FROM_HOST EXEC_HOST JOB_NAME SUBMIT_TIME 4225 usernam RUN general m1 16*n060 testjob Mar 2 11:53
Examine job output files
Once your job has completed, view output information.
[username@pegasus ~]$ cat test.out Sender: LSF System <email@example.com> Subject: Job 6021006: <test> in cluster <mk2> Done Job <test> was submitted from host <login4.pegasus.edu> by user <username> in cluster <mk2>. Job was executed on host(s) <8*n069>, in queue <general>, as user <username> in cluster <mk2>. ...