UniTree and Batch Jobs

• How can I access UniTree from a batch script?
• Is there a sample batch script with UniTree commands?
• The sample batch script assumes that files are already on UniTree. How do I move my files there?
• I'm running a very small program that is already in my home directory. How do I change the sample batch script to use it?
• My standard output and standard error files are not on UniTree. Where are they?
• I'm having trouble with the msscmd commands in my batch script. How do I figure out what's happening?

How can I access UniTree from a batch script?

On NCSA production machines, the msscmd utility is available to access UniTree from a batch script. The syntax of the command is:

 msscmd  ftp-commands  

where ftp-commands is either an ftp command (e.g., ls, put, get, mkdir) or a list of ftp commands separated by commas. Some examples:

• msscmd cd cfdjob, get file3
• msscmd "cd cfdjob, mget file*"
• msscmd mkdir job25, cd job25, put job25.tar

Be sure to include quotes when using wildcards.

Is there a sample batch script with UniTree commands?

Sample batch scripts are available on NCSA HPC machines in the following locations:
• /usr/local/doc/lsf/ on the Xeon Cluster (tungsten)
• /usr/local/doc/batch_scripts (abe)
• Sample Batch Script on the IA-64 Linux Cluster (mercury)

The sample batch script assumes that files are already on UniTree. How do I move my files there?

Prior to the job running, you'll need to move the files to UniTree. You can use mssftp to do it interactively. Or you can use msscmd commands to create the directory and move the files there. For example, go to the directory that contains the files, then:

   msscmd "mkdir testdir"

   msscmd "cd testdir, put myexe"
   or 
   msscmd "cd testdir, mput *"  

See the online documentation for more information.

I'm running a very small program that is already in my home directory. How do I change the sample batch script to use it?

Here are the lines to change:
• Remove the msscmd get line and the chmod line.
• Replace them with a standard cp command, like:

        cp ~/testdir/myexe .
        

• Don't forget to copy any output files at the end of the job as well. They'll need to be copied from the scratch directory to UniTree or your home directory (assuming they fit within your home directory quota).

My standard output and standard error files are not on UniTree. Where are they?

The standard output and standard error from the batch job should be in the directory from which you submitted the job. So, an msscmd command from the scratch directory like:

  msscmd "cd test1, mput *.dat testjob.out testjob.err"  

will not find testjob.out and testjob.err in that directory. In the case of PBS, those files won't appear until after the job is done. So, if you want to have those files on UniTree, manually copy them after the job is done.

I'm having trouble with the msscmd commands in my batch script. How do I figure out what's happening?

Here are some things to try:
• You can run the msscmd commands interactively in a scratch directory.
• You can add "ls -l" statements after msscmd get commands or before the msscmd put commands so you can see what's in the directory.