LSF Version 7.3 - Administering Platform LSF

Administering Platform LSF 491
Job Arrays
By default, the maximum number of jobs in a job array is 1000, which means the
maximum size of a job array can never exceed 1000 jobs.
1 To make a change to the maximum job array value, set
MAX_JOB_ARRAY_SIZE in
lsb.params to any positive integer between 1
and 2147483646. The maximum number of jobs in a job array cannot exceed
the value set by MAX_JOB_ARRAY_SIZE.
Handling Input and Output Files
LSF provides methods for coordinating individual input and output files for the
multiple jobs created when submitting a job array. These methods require your
input files to be prepared uniformly. To accommodate an executable that uses
standard input and standard output, LSF provides runtime variables (%I and %J)
that are expanded at runtime. To accommodate an executable that reads command
line arguments, LSF provides an environment variable (LSB_JOBINDEX) that is set
in the execution environment.
Methods
◆ Redirecting Standard Input and Output on page 491
◆ Passing Arguments on the Command Line on page 492
Prepare input files
LSF needs all the input files for the jobs in your job array to be located in the same
directory. By default LSF assumes the current working directory (CWD); the
directory from where
bsub was issued.
1 To override CWD, specify an absolute path when submitting the job array.
Each file name consists of two parts, a consistent name string and a variable
integer that corresponds directly to an array index. For example, the following
file names are valid input file names for a job array. They are made up of the
consistent name
input and integers that correspond to job array indices from
1 to 1000:
input.1, input.2, input.3, ..., input.1000
Redirecting Standard Input and Output
The variables %I and %J are used as substitution strings to support file redirection
for jobs submitted from a job array. At execution time, %I is expanded to provide
the job array index value of the current job, and %J is expanded at to provide the job
ID of the job array.