Submitting Enroot jobs to LSF

Use the Enroot application profiles or queues to submit Enroot jobs to LSF.

1. Submit a job to an Enroot application profile or queue.
   • Use the bsub -app option to submit a job to an Enroot application profile (that is, an application profile with a specified value for the CONTAINER parameter).

     For example, if CONTAINER is defined in the enrootapp application profile, run the following command to submit a Enroot job:

     bsub -app enrootapp ./myjob.sh

   • Use the bsub -q option to submit a job to a Enroot queue (that is, a queue with a specified value for the CONTAINER parameter).

     For example, if CONTAINER is defined in the enrootq queue, run the following command to submit a Enroot job:

     bsub -q enrootq ./myjob.sh

   If you specify both the application profile and the queue in the same job submission, the CONTAINER and EXEC_DRIVER parameter settings in the application profile take precedence over the same parameter settings in the queue.

   For example, if you submit a job with the following command, the parameters in the enrootapp application profile override the corresponding parameters in the enrootq queue:

   bsub -app enrootapp -q enrootq ./myjob.sh

2. If users are allowed to specify image names for Enroot container jobs at job submission time (that is, if the $LSB_CONTAINER_IMAGE environment variable is used as the image name when specifying the image keyword), set the LSB_CONTAINER_IMAGE environment variable at job submission time to specify the Enroot image name.

   Specify a container image name (such as centos) at the job submission time by setting the LSB_CONTAINER_IMAGE environment using one of the following methods:

   • Specify the LSB_CONTAINER_IMAGE environment variable according to your shell environment. For example, to specify the Enroot image named centos, set the environment variable as follows:
     • In csh or tcsh:

       setenv LSB_CONTAINER_IMAGE centos

     • In sh, ksh, or bash:

       export LSB_CONTAINER_IMAGE=centos

   • Use the bsub -env option. For example, to specify the Enroot image named centos

     bsub -env LSB_CONTAINER_IMAGE=centos -app enrootapp a.out -in in.dat -out out.dat

   • Use an esub script to set the LSB_CONTAINER_IMAGE environment variable, then call the esub with the bsub command:
     For example, create an esub.enroot script in the $LSF_SERVERDIR directory with the following contents:

     #!/bin/sh
     exec 1>&2
     echo "LSB_CONTAINER_IMAGE=\"$1\"" >> $LSB_SUB_MODIFY_ENVFILE

     Submit a job to call the esub.enroot script by running the following command:

     bsub -a "docker(centos)" -app enrootapp a.out -in in.dat -out out.dat