Click here for zip file containing all the above *.m and *.txt files. Place all files in Matlab working directory.
Here are the two ODEs and the three PDEs we examine. Here also are some good online materials for three of the functions we use:
The instructions below are unfortunately obsolete and require updating. Please visit this UChicago webpage for the interim (running jobs with SLURM).
We give a sample batch job submission on the cluster based
on small portions of parts 1 & 6.
Log into odyssey.fas.harvard.edu and upload the Matlab code
Then issue two commands at the UNIX prompt:
module load hpc/matlab bsub -q short_serial matlab -nodisplay -nojvm -nosplash -r test16 -logfile output_test16.txtThe suffix ".m" is omitted from "test16.m" in this command.
All text output goes to "output_test16.txt", but graphics output is less convenient.
It is not possible to insert multiple figures in a PDF file. You can save one graph to PDF at a time via the "print -dpdf" command within Matlab.
You can, however, insert multiple graphs in a PS file via the "print -dpsc" command using the -append option. Of course, the PS file can then be converted to PDF.
In the Matlab code, we also had no choice but to replace "uiimport" by "importdata" (an error message arose about Java not being available on the cluster). The syntax for "importdata" is slightly different from "uiimport".
Here is general information on running pre-installed software packages in batch on Odyssey.
To run Matlab interactively on the cluster, issue two commands at the UNIX prompt:
module load hpc/matlab bsub -Is -n 1 -q interact matlabTo exit Matlab, type exit at the Matlab prompt.
If you wish to display graphic results on the screen, you need to have X-windows server software and enable X11 tunneling in your ssh client, e.g., Cygwin/X, XMing or X-Win32.
Here is general information on interactive use of Odyssey (i.e., not submitting jobs).