How to copy the environment variables in cluster system using qsub?

I use the SUN's SGE to submit my jobs into a cluster system. The problem is how to let the computing machine find the environment variables in the host machine, or how to config the qsub script to make the computing machine load the environment variables in host machine? The following is an script example, but it will say some errors, such as libraries not found:

    #!/bin/bash
    #
    #$ -V
    #$ -cwd
    #$ -j y
    #$ -o /home/user/jobs_log/$JOB_ID.out
    #$ -e /home/user/jobs_log/$JOB_ID.err
    #$ -S /bin/bash
    #

    echo "Starting job: $SGE_TASK_ID"

    # Modify this to use the path to matlab for your system
    /home/user/Matlab/bin/matlab -nojvm -nodisplay -r matlab_job 

    echo "Done with job: $SGE_TASK_ID"

Solution

The technique you are using (adding a -V) should work. One possibility since you are specifying the shell with -S is that grid engine is configured to launch /bin/bash as a login shell and your profile scripts are stomping all over the environment you are trying to pass to the job.

Try using qstat -xml -j on the job while it is queued/running to see what environment variables grid engine is trying to pass to the job.

Try adding an env command to the script to see what variables are set.

Try adding shopt -q login_shell;echo $? in the script to tell you if it is being run as a login shell.

To list out shells that are configured as login shells in grid engine try:

SGE_SINGLE_LINE=true qconf -sconf|grep ^login_shells