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Batch Systems. In a number of scientific computing environments, multiple users must share a compute resource: research clusters supercomputing centers On multi-user HPC clusters, the batch system is a key component for aggregating compute nodes into a single, sharable computing resource

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batch systems
Batch Systems
  • In a number of scientific computing environments, multiple users must share a compute resource:
    • research clusters
    • supercomputing centers
  • On multi-user HPC clusters, the batch system is a key component for aggregating compute nodes into a single, sharable computing resource
  • The batch system becomes the “nerve center” for coordinating the use of resources and controlling the state of the system in a way that must be “fair” to its users
  • As current and future expert users of large-scale compute resources, you need to be familiar with the basics of a batch system
batch systems2
Batch Systems
  • The core functionality of all batch systems are essentially the same, regardless of the size or specific configuration of the compute hardware:
    • Multiple Job Queues:
      • queues provide an orderly environment for managing a large number of jobs
      • queues are defined with a variety of limits for maximum run times, memory usage, and processor counts; they are often assigned different priority levels as well
      • may be interactive or non-interactive
    • Job Control:
      • submission of individual jobs to do some work (eg. serial, or parallel HPC applications)
      • simple monitoring and manipulation of individual jobs, and collection of resource usage statistics (e.g., memory usage, CPU usage, and elapsed wall-clock time per job)
    • Job Scheduling
      • policy which decides priority between individual user jobs
      • allocates resources to scheduled jobs
batch systems3
Batch Systems
  • Job Scheduling Policies:
    • the scheduler must decide how to prioritize all the jobs on the system and allocate necessary resources for each job (processors, memory, file-systems, etc)
    • scheduling process can be easy or non-trivial depending on the size and desired functionality
      • first in, first out (FIFO)scheduling: jobs are simply scheduled in the order in which they are submitted
      • political scheduling: enables some users to have more priority than others
      • fairshare scheduling, scheduler ensures users have equal access over time
    • Additional features may also impact scheduling order:
      • advanced reservations - resources can be reserved in advance for a particular user or job
      • backfill -can be combined with any of the scheduling paradigms to allow smaller jobs to run while waiting for enough resources to become available for larger jobs
        • back-fill of smaller jobs helps maximize the overall resource utilization
        • back-fill can be your friend for small duration jobs
batch systems4
Batch Systems
  • Common batch systems you may encounter in scientific computing:
    • Platform LSF
    • PBS
    • Loadleveler (IBM)
    • SGE
  • All have similar functionality but different syntax
  • Reasonably straight forward to convert your job scripts from one system to another
  • Above all include specific batch system directives which can be placed in a shell script to request certain resources (processors, queues, etc).
  • We will focus on LSF primarily since it is the system running on Lonestar
batch submission process





Batch Submission Process


Compute Nodes




bsub < job





Queue: Job Script waits for resources on Server

Master: Compute Node that executes the job

script, launches ALL MPI processes

Launch: ssh to each compute node to start

executable (e.g. a.out)

ibrun ./a.out

mpirun –np # ./a.out

lsf batch system
LSF Batch System
  • Lonestar uses Platform LSF for both the batch queuing system and scheduling mechanism (provides similar functionality to PBS, but requires different commands for job submission and monitoring)
  • LSF includes global fairshare, a mechanism for ensuring no one user monopolizes the computing resources
  • Batch jobs are submitted on the front end and are subsequently executed on compute nodes as resources become available
  • Order of job execution depends on a variety of parameters:
    • Submission Time
    • Queue Priority: some queues have higher priorities than others
    • Backfill Opportunities: small jobs may be back-filled while waiting for bigger jobs to complete
    • Fairshare Priority: users who have recently used a lot of compute resources will have a lower priority than those who are submitting new jobs
    • Advanced Reservations: jobs my be blocked in order to accommodate advanced reservations (for example, during maintenance windows)
    • Number of Actively Scheduled Jobs: there are limits on the maximum number of concurrent processors used by each user
lonestar queue definitions8
Lonestar Queue Definitions
  • Additional Queue Limits
    • In the normal and high queues, only a maximum of 512 processes can be used at one time. Jobs requiring more processors are deferred for possible scheduling until running jobs complete. For example, a single user can have the following job combinations eligible for scheduling:
      • Run 2 jobs requiring 256 procs
      • Run 4 jobs requiring 128 procs each
      • Run 8 jobs requiring 64 procs each
      • Run 16 jobs requiring 32 procs each
    • A maximum of 25 queued jobs per user is allowed at one time
lsf fairshare
LSF Fairshare
  • A global fairshare mechanism is implemented on Lonestar to provide fair access to its substantial compute resources
  • Fairshare computes a dynamic priority for each user and uses this priority in making scheduling decisions
  • Dynamic priority is based on the following criteria
    • Number of shares assigned
    • Resources used by jobs belonging to the user:
      • Number of job slots reserved
      • Run time of running jobs
      • Cumulative actual CPU time (not normalized), adjusted so that recently used CPU time is weighted more heavily than CPU time used in the distant past
lsf fairshare10


LSF Fairshare
  • bhpart: Command to see current fairshare priority. For example:

lslogin1--> bhpart -r


HOSTS: all

SHARE_INFO_FOR: GlobalPartition/


avijit 1 0.333 0 0 0.0 0

chona 1 0.333 0 0 0.0 0

ewalker 1 0.333 0 0 0.0 0

minyard 1 0.333 0 0 0.0 0

phaa406 1 0.333 0 0 0.0 0

bbarth 1 0.333 0 0 0.0 0

milfeld 1 0.333 0 0 2.9 0

karl 1 0.077 0 0 51203.4 0

vmcalo 1 0.000 320 0 2816754.8 7194752

commonly used lsf commands
Commonly Used LSF Commands

Note: most of these commands support a “-l” argument for long listings. For example: bhist –l <jobID> will give a detailed history of a specific job. Consult the man pages for each of these commands for more information.

lsf batch system12
LSF Batch System
  • LSF Defined Environment Variables:
lsf batch system13
LSF Batch System
  • Comparison of LSF, PBS and Loadleveler commands that provide similar functionality
batch system concerns
Batch System Concerns
  • Submission (need to know)
    • Required Resources
    • Run-time Environment
    • Directory of Submission
    • Directory of Execution
    • Files for stdout/stderr Return
    • Email Notification
  • Job Monitoring
  • Job Deletion
    • Queued Jobs
    • Running Jobs
lsf basic mpi job script

Job name

Stdout Output file name (%J = jobID)

Stderr Output file name

Submission queue

Your Project Name

Max Run Time (15 minutes)

Echo pertinent environment info

LSF: Basic MPI Job Script

Total number of processes


#BSUB -n 32

#BSUB -J hello

#BSUB -o %J.out

#BSUB -e %J.err

#BSUB -q normal

#BSUB -P A-ccsc

#BSUB -W 0:15

echo "Master Host = "`hostname`


echo "PWD_DIR: "`pwd`

ibrun ./hello

Execution command

Parallel application manager and mpirun wrapper script


lsf extended mpi job script

Job name

Stdout Output file name (%J = jobID)

Stderr Output file name

Submission queue

Your Project Name

Max Run Time (15 minutes)

LSF: Extended MPI Job Script

Total number of processes


#BSUB -n 32

#BSUB -J hello

#BSUB -o %J.out

#BSUB -e %J.err

#BSUB -q normal

#BSUB -P A-ccsc

#BSUB -W 0:15

#BSUB -w ‘ended(1123)'

#BSUB -u



echo "Master Host = "`hostname`


ibrun ./hello

Dependency on Job <1123>

Email address

Email when job begins execution

Email job report informationupon completion

lsf job script submission
LSF: Job Script Submission
  • When submitting jobs to LSF using a job script, a redirection is required for bsub to read the commands. Consider the following script:lslogin1> cat job.script#!/bin/csh#BSUB -n 32#BSUB -J hello#BSUB -o %J.out#BSUB -e %J.err#BSUB -q normal#BSUB -W 0:15echo "Master Host = "`hostname`echo "LSF_SUBMIT_DIR: $LS_SUBCWD“echo "PWD_DIR: "`pwd`ibrun ./hello
  • To submit the job:lslogin1% bsub < job

Re-direction is required!

lsf interactive execution
LSF: Interactive Execution
  • Several ways to run interactively
    • Submit entire command to bsub directly:> bsub –q development -I -n 2 -W 0:15 ibrun ./helloYour job is being routed to the development queueJob <11822> is submitted to queue <development>.<<Waiting for dispatch ...>><<Starting on compute-1-0>> Hello, world! --> Process # 0 of 2 is alive. ->compute-1-0 --> Process # 1 of 2 is alive. ->compute-1-0
    • Submit using normal job script and include additional -I directive:> bsub -I < job.script
batch script suggestions
Batch Script Suggestions
  • Echo issuing commands
    • (“set -x” and “set echo” for ksh and csh).
  • Avoid absolute pathnames
    • Use relative path names or environment variables ($HOME, $WORK)
  • Abort job when a critical command fails.
  • Print environment
    • Include the "env" command if your batch job doesn't execute the same as in an interactive execution.
  • Use “./” prefix for executing commands in the current directory
    • The dot means to look for commands in the present working directory. Not all systems include "." in your $PATH variable. (usage: ./a.out).
  • Track your CPU time
lsf job monitoring showq utility
LSF Job Monitoring (showq utility)

lslogin1% showq

ACTIVE JOBS--------------------


11318 1024_90_96x6 vmcalo Running 64 18:09:19 Fri Jan 9 10:43:53

11352 naf phaa406 Running 16 17:51:15 Fri Jan 9 10:25:49

11357 24N phaa406 Running 16 18:19:12 Fri Jan 9 10:53:46

23 Active jobs 504 of 556 Processors Active (90.65%)

IDLE JOBS----------------------


11169 poroe8 xgai Idle 128 10:00:00 Thu Jan 8 10:17:06

11645 meshconv019 bbarth Idle 16 24:00:00 Fri Jan 9 16:24:183 Idle jobs

BLOCKED JOBS-------------------


11319 1024_90_96x6 vmcalo Deferred 64 24:00:00 Thu Jan 8 18:09:11

11320 1024_90_96x6 vmcalo Deferred 64 24:00:00 Thu Jan 8 18:09:11

17 Blocked jobs

Total Jobs: 43 Active Jobs: 23 Idle Jobs: 3 Blocked Jobs: 17

lsf job monitoring bjobs command
LSF Job Monitoring (bjobs command)

lslogin1% bjobs


11635 bbarth RUN normal lonestar 2*compute-8 *shconv009 Jan 9 16:24








11640 bbarth RUN normal lonestar 2*compute-3 *shconv014 Jan 9 16:24








11657 bbarth PEND normal lonestar *shconv028 Jan 9 16:38

11658 bbarth PEND normal lonestar *shconv029 Jan 9 16:38

11662 bbarth PEND normal lonestar *shconv033 Jan 9 16:38

11663 bbarth PEND normal lonestar *shconv034 Jan 9 16:38

11667 bbarth PEND normal lonestar *shconv038 Jan 9 16:38

11668 bbarth PEND normal lonestar *shconv039 Jan 9 16:38

Note: Use “bjobs -u all” to see jobs from all users.

lsf job monitoring lsuser utility
LSF Job Monitoring (lsuser utility)

lslogin1$ lsuser -u vap


547741 normal vap vap_hd_sh_p96 14 Tue Jun 7 10:37:01 2005


compute-11-11 2.0 2.0 1.4 4.9P/s 1840M 2038M 24320M

compute-8-3 2.0 2.0 2.0 1.9P/s 1839M 2041M 23712M

compute-7-23 2.0 2.0 1.9 2.3P/s 1838M 2038M 24752M

compute-3-19 2.0 2.0 2.0 2.6P/s 1847M 2041M 23216M

compute-14-19 2.0 2.0 2.0 2.1P/s 1851M 2040M 24752M

compute-3-21 2.0 2.0 1.7 2.0P/s 1845M 2038M 24432M

compute-13-11 2.0 2.0 1.5 1.8P/s 1841M 2040M 24752M

lsf job manipulation monitoring
LSF Job Manipulation/Monitoring
  • To kill a running or queued job (takes ~30 seconds to complete):bkill <jobID> bkill -r <jobID> (Use when bkill alone won’t delete the job)
  • To suspend a queued job:bstop <jobId>
  • To resume a suspended job:bresume <jobID>
  • To see more information on why a job is pending:bjobs –p <jobID>
  • To see a historical summary of a job:bhist <jobID>lslogin1> bhist 11821Summary of time in seconds spent in various states:JOBID USER JOB_NAME PEND PSUSP RUN USUSP SSUSP UNKWN TOTAL11821 karl hello 131 0 127 0 0 0 258