When you use the script in interactive mode, you can press the Return key to accept default values. Default values are specified in the prompts inside square brackets, and appear at the end of the prompt.
To use the
condor_submit_util script in interactive mode:
Type the following at the command prompt in your Condor working directory:
*** No arguments specified, defaulting to interactive mode...
*** Entering interactive mode.
*** Press return to use default value.
*** Some options allow the use of '--' to unset the value.
The script first prompts you to define the executable program that you choose to submit for batch processing, and then requests the list of arguments to provide to that executable:
Enter executable to submit [/usr/bin/R]: <executable name>
Enter arguments to /usr/bin/R [--no-save --vanilla]: <arguments>
The default argument
--no-savespecifies not to save the R workspace at exit. The default argument
--vanillainstructs R to not read any user or site profiles or restored data at start up and to not save data files at exit.
If you do not have any arguments to apply to your executable, then type -- to supply no arguments.
Next, the script prompts you to provide a name or pattern for the input, output, log, and error files for this Condor cluster submission. You can include a relative path in these entries, if you choose:
Enter input file base [in]: <input path and file name or pattern>
Enter output file base [out]: <output path and file name or pattern>
Enter log file base [log]: <log path and file name or pattern>
Enter error file base [error]: <error path and file name or pattern>
Note, if using the batch example the input file is bootstrap.R
After specifying the files, the script prompts you to define the number of iterations that you choose to execute your program for processing:
Enter number of iterations : <integer>
The system creates the submit file for this batch process using your responses to script prompts.
An example submit file is shown here. To view the contents of your submit file, include the option
-v(verbose) when you launch the
*** creating submit file '<login account name>-<date-time>.submit'
Universe = vanilla
Executable = /usr/bin/R
Arguments = --no-save --vanilla
when_to_transfer_output = ON_EXIT_OR_EVICT
transfer_output_files = <output file>
input = <input file>
output = <output file>
error = <error file>
Log = <log file>
If you use the verbose option, the script prompts you to confirm that the submit file is correct. To continue, press Return or type y.
Condor checks the submit file for errors, creates the
ClassAdobject for your submission, and adds that object to the end of the queue for processing. The script lists messages that report this progress in your terminal window, and includes the cluster number assigned to the batch process. For example:
Is this correct? (Enter y or n) [yes]: y
] submitting job to condor...
] removing submit file '<login account name>-<date-time>'
*** Job successfully submitted to cluster <cluster ID>.
Finally, the script prompts whether you choose to receive email when execution of your batch processing is complete. Press Return or type y to receive email, or type n to not send email and exit the script.
If you choose to receive email, before exiting, the script prompts you to enter the email address to which you choose to send the notification. The default email address for notification is your email account on the server on which you launched the script. For example:
Would you like to be notified when your jobs complete? (Enter y or n)
Please enter your email address [<your email account on this server>]:
*** creating watch file '/nfs/fs1/projects/condor_watch/<Condor machine>.<batch cluster>.<your email>'
View your job queue to ensure that your batch processing begins execution successfully.
See for complete details about checking the queue. An example is:
-- Submitter: vnc.hmdc.harvard.edu : <10.0.0.47:60603> : vnc.hmdc.harvard.edu
IDOWNER SUBMITTED RUN_TIME STPRISIZECMD
9.0arose10/4 11:02 0+00:00:00 R 0 9.8 dwarves.pl
9.1arose10/4 11:02 0+00:00:00 R0 9.8 dwarves.pl
9.2arose10/4 11:02 0+00:00:00 I 0 9.8 dwarves.pl
9.3arose10/4 11:02 0+00:00:00 R 0 9.8 dwarves.pl
4 jobs; 1 idle, 3 running, 0 held