-cwd

Start job in directory from which it was submitted.

If this is not specified, the home directory will be the starting directory of the job.

-S <shell>

Use designated shell to execute the job script

Obligatory, since the standard first line #! <shell> is ignored due to a change in the SGE configuration. The entry used for the -S switch must be consistent with the shell dialect used in the batch script.

-M <mail_addr>

User's e-mail address.

Obligatory so LRZ can contact you in case of problems. Batch requests which do not specify an e-mail address will not be processed.

-m [a|b|e]

Batch system sends e-mail when [aborting|starting|ending] job.

-N <req_name>

Name of batch request. Default is name of the script.

8 characters at most will be retained.

-o <filename>

write standard output to specified file.

LRZ recommends specifying the full path name. Default value is job_name.ojob_id, where job_name is the name of the job specified via the -N parameter, and job_id its identification number.

Note that under SGE it is possible to use one of the following pseudo-environment variables as part of the full name specification:

These are replaced by the run-time contents of the actual environment variables. Other environment variables are not supported via this mechanism.

-e <filename>

-j y

write standard error to the same file as standard output

Any -e specification is ignored.

-v var1[=val1][,var2[=val2],...]

exports designated environment variables into SGE job

If only the name of a variable is specified, the existing value is used in the SGE script at run time. For more than one variable, a comma-separated list must be specified. Example:
-v PATH,MYVAR=xxyy,LD_LIBRARY_PATH.
Please use with care: It is probably better to write an environment module and load that in the script.

-V

exports all presently defined environment variables into SGE job.

Beware: This setting should not be used on the LRZ HPC systems since it interferes destructively with the module based configuration environment.

Job Control, Limits and Resource Requirements

-hard

All the following requirements must be fulfilled for the job to be initiated.

This is in fact the default, so you actually only need this to invalidate a previous -soft option.

-soft

after fulfillment of all -hard requirements the job is processed within the queue fulfilling as many -soft specifications as possible.

This means that at runtime not all requirements specified as -soft may be fulfilled. Hence the user's program must be able to cope with this situation.

-h

batch request is kept in User Hold (meaning it is queued but not initiated)

With qalter -hU <job_id> you can remove the user hold from your job.

-l h_rt=x:y:z

specify hard limit for job run time as x hours y minutes z seconds. All three fields must be provided.

The maximum run time value imposed by LRZ cannot be exceeded using this option.

-l mf=<memory>

explicit memory requirement (mf abbreviates mem_free)

Note that contradictory requirements (e. g., a low-memory queue and a high explicit memory requirement) will result in a non-initiating job. The "mf" setting replaces the "vf" setting, which could lead to swapping and consequent performance degradation since "vf" ("virtual_free") refers to free virtual memory, whereas "mf" refers to physical memory.

Examples:

-l mf=1200M specifies 1200 * 1024 * 1024 Bytes
-l mf=1200m specifies 1200 * 1000 * 1000 Bytes
-l mf=700000K specifies 700000 * 1024 Bytes
-l mf=700000k specifies 700000 * 1000 Bytes

-r y[es]|n[o]

Identifies the ability of a job to be rerun or not. If the value of -r is 'yes', the job will be rerun if the job was
aborted without leaving a consistent exit state. (This is typically the case if the node on which the job is running
crashes). If -r is 'no', the job will not be rerun under any circumstances.

Default is 'yes'.

-q <queue_name>

batch request targets a specific queue (mapped to a specific node)

Note that qstat -f gives you a table the first column of which gives the queue names. It is also possible to specify multiple queue names in a comma-separated list. The job then runs on the first queue becoming available. This option is deprecated for normal batch jobs; it should be only used for specific purposes (e.g., for qrsh to the Altix)

-pe <par_env> <num_cpus>

Specification of a parallel environment and the number of CPU's. The latter must be given as a fixed value.

Not supported any more at the LRZ SGE installation. Please submit a SLURM job if you need to do parallel processing.

-t n[:m[:s]]

submits an array job: n, m and s are integers with n, m and s > 0.

An array job means that in fact a number of jobs are run; each job is characterized by a value of $SGE_TASK_ID (available inside the script) which runs between n and m with a step size of s. If only n is specified, $SGE_TASK_ID takes the value n and only one task is performed.