Platform LSF Administration Guide Version 6.2

Handling Input and Output Files
Administering Platform LSF
418
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 419
◆ “Passing Arguments on the Command Line” on page 420
Preparing 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. 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