Computer Software for Math 430 and Math 635
Analytical and Computational Neuroscience
For assignments and projects, we will be using the program
XPP-AUT, a differential equation solving package developed by G. Bard Ermentrout.
XPP is installed on all AFS machines and can be run directly from an AFS
machine or can be run remotely. To run XPP-AUT directly on an AFS
machine, simply enter ``xpp file.ode'' at the prompt where file.ode
is an ascii file containing your differential equations (see assignment
handouts or Online Tutorial). When running, XPP creates a number
of different windows that rely on a Xwindows manager. This requires
that specific steps are taken when running it remotely, especially from
a MS-Windows PC (see instructions below).
There is also a MS-Windows version of XPP called WinPP
that you can download here
along with its documentation. There are some differences between
WinPP and XPP but all assignments can be completed equally well using either
program.
Resources for XPP:
Instructions for running XPP remotely
from an AFS machine:
-
1. If running from a LINUX or UNIX
machine, enter ``xhost +'' in the window you plan to run XPP.
Skip to #3.
-
2. If running from an MS-Windows PC,
you must have the software Xwindows Terminal
Emulator for Windows 9x and NT (download it
here).
The PCs in the PC Lab should have this program. Start the emulator
running.
-
3. Login to an AFS machine. Check
the load on the machine by entering ``w''. If the load on
the machine is heavy (load average numbers > 3), then running XPP will
be slow. Logout of that AFS machine and login to another AFS machine
with a lighter load. Below is an example output from the command
``w'' on a machine with a low load:
fischer-41 vbooth>: w
11:42am up 6:01,
4 users, load average: 0.04, 0.06, 0.07
User tty
login@ idle JCPU PCPU what
yp2
console 11:32am 10
2 1 dtwm
pt
pts/6 10:46am
53 2
-csh
pt
pts/7 10:35am
42
-csh
vbooth pts/4
11:42am
w
fischer-42 vbooth>:
-
4. Enter ``who''. Find your login
name in the output list. In parentheses after your login id is the
identifier of your local machine. Enter ``setenv DISPLAY xxx:0''
where xxx is your local machine identifier followed by ``:'' (colon)
and then ``0'' (zero). Below is an example output from the command
``who'':
fischer-42 vbooth>: who
yp2
console Sep 6 11:32 (:0)
pt
pts/6 Sep 6 10:46 (ptnt.njit.edu)
pt
pts/7 Sep 6 10:35 (ptnt.njit.edu)
vbooth
pts/4 Sep 6 11:42 (spike.njit.edu)
fischer-43 vbooth>:
-
5. You are now ready to run XPP by
entering ``xpp file.ode'' where file.ode is an ascii file
containing your differential equations (see Online Tutorial or assignment
handouts). Note: this may not work if
you are accessing the AFS machine via a local internet provider.