Hoffman2:Batch Mode

Back to all things Hoffman2

To use a batch job, you need to create a batch file with bash or tcsh. This find should have three parts:

Part 1: List all the resource you want to reserve for your job

Part 2: Load your modules, export the Unix environment that needed for your script to run

Part 3: Call your job script

Here are some batch file templates you can start with

Job Submission Templates

Please use these job submission template scripts to simplify job submission.

What's in the Part 1

The first part of the batch file should let the job scheduler know how much resource you want to reserve for your job

#!/bin/bash
#$ -cwd
# error = Merged with joblog
#$ -o joblog.$JOB_ID
#$ -j y
#$ -pe shared 2
#$ -l h_rt=8:00:00,h_data=4G
# Email address to notify
#$ -M $USER@mail
# Notify when
#$ -m bea

Here are what they mean:

#$ -cwd
Using the current directory for the job

#$ -o joblog.$JOB_ID

Write standard output to file joblog.$JOB_ID. $JOB_ID will be replaced by your job ID which is assigned once you submit your job.

#$ -j y

Merge error log with joblog.$JOB_ID

So you'll be able to find error output together with standard output of your job script in this joblog.$JOB_ID log file.

#$ -pe shared 2

Request 2 processor cores

#$ -l h_rt=8:00:00,h_data=4G

Use -l option to specify job running time length and reserve memory

h_rt=8:00:00 : reserve 8 hours for your job running time

h_data=4G: reserve 4G per-core (since -pe 2 is used above, it will reserve 2 core x 4G memory = 8G total memory)

#$ -M $USER@mail

Send notification email to your user email address

 #$ -m bea

Specify the timing of the notification email to be sent out:

• b - when the job begins
• e - when the job ends
• a - when the job is aborted (ends in an error state)