The following are some things to look out for if you are having problems submitting jobs to the cluster. If you run qstat and you see the status code Eqw next to your job, then you should check the list below to see if you have any related problems.
If you edit text files in Windows and then transfer them to usher or enigma for use on the cluster, you may run into problems when using the Sun Grid Engine (i.e. qsub). For example, you may find that your R script works fine when you run R CMD BATCH but does not work when you submit a job to the cluster using qsub.
It is possible that the text file you created on Windows has CRLF (carriage return, line feed) line terminators and the Sun Grid Engine does not like text files with CRLF line terminators. There is a simple way to solve this problem. If you have a file called mycommands.R, then on usher just run
dos2unix mycommands.R
Your file will be converted to have LF (line feed) endings. Now try submitting the job to the cluster. If that doesn't work, then you've got other problems.
It's probably a good idea to run dos2unix on all files that you create on Windows and then transfer to Unix.
We've had some problems with executing scripts that do not contain a final new line at the very end of the file. This problem can be solve easily by opening the file in a text editor, going to the last line of the file and typing the [ENTER] or [RETURN] key so that there is a blank line at the end.
On Unix in general, you should avoid having spaces in the name of a file. Consider using underscores ('_') or hyphens ('-') instead.
If your job requires a lot of memory, you need to submit it to one of the large memory nodes. For information about how to do this, see the cluster usage page. If your job requires more memory than is available on the node (including swap space), then it may be killed without warning.
PLEASE monitor the usage of your job before submitting it to the cluster. On Unix you can monitor your job via top. In R, you can see how much memory you're using with the gc() function.