Tromso

Added functionality to choose which queue to submit to, along with other minor edits and bug fixes.

Rosa Helikopter

First Official Release

Convert all make options to lowercase flags, remove some that aren't applicable to this use case.

All rmake options are upper case (* marks arguments):

• -C Print only the changes to make flags (a subset of -H).
• -D Recon; do everything but submit qsub jobs.
• -H Print a help message and exit.
• -M Debug; print arguments to make call. (No qsub submission.)
• -N * Set job name; if not set, it will be set to target, then a random name.
• -O Save output/error files to qout-$user/ and qerr-$user.
• -P Append <date>_<time> to the jobid.
• -S * Run qsub on these subjects only; if not set, run on all.
• -T * Set the target for make. Will accept multiple space-separated targets, if the argument is quoted.

Calling rmake

Invoking rmake is simple. For example, to make the target sleep for everyone, call it with the -T flag.

rmake -T sleep

rmake can be called without the -T flag, in which case the default target will be the first target in the makefile within each subject directory.

You can also pass multiple targets to rmake, for example. Take care to quote them. Targets will be combined into the job name with a comma.

rmake -T "sleep1 sleep2"

The name of this job will be something like s99.sleep1,sleep2.

If you don't want your jobs to stop, you can pass that command to make like so (option can occur in any order):

rmake -k -T sleep

You can also call rmake only on a subset of the subjects with -S. If -S is not set, the default behavior is to work on them all.

Select subjects like so:

rmake -T sleep -S "subj1 subj2"

Note the argument to -S has to be quoted (if there is more than one). rmake will perform a small sanity check if it thinks you have misquote the argument to -S, but will attempt to run.

You can also use a regex. For example, to select only subjects beginning with 100-:

rmake -T sleep -S "100???"

Note that the regex must be quoted as well, as it is expanded by the shell before being sent to rmake.

Output

Each qsub job results in the creation of two files, named name.[e,o]ID, where name is the name you gave the job, and ID is a numerical ID qsub assigned it.

The files with e in the name contain the output of STDERR if the job had been executed normally, o files, STDOUT.

These files may be removed if you are satisfied with how your job executed.

Contact

Trevor McAllister-Day -- [email protected]