softwre

[Bard Ermentrout]

	F R E E    S I M U L A T I O N   S O F T W A R E

I thought perhaps that modellers etc might be interested to know of the 
availability of software for the analysis and simulation of dynamical and
probabilistic phenomena.  xpp is available free via anonymous ftp.  It solves
integro-differential equations, delay equations, iterative equations, all
combined with probabilistic models.  Postscript output is supported.
A variety of numerical methods are employed so that the user can
generally be sure that the solutions are accurate.  Examples are
connectionist type neural nets, biophysical models, models with
memory, and models of cells with random inputs or with random
transitions.  A graphical interface using X windows as well as
numerous plotting options are provided.  The requirements are a C
compiler and an OS capable of running X11.  The software has been
successfully compiled on DEC,HP,SUN,IBM,NEXT workstations as well as
on a PC running Linux.  Once it is compiled, no more compilation is
necessary as the program can read algebraic expressions and interpret
them in order to solve them.   The program has been used in various
guises for the last 5 years by a variety of mathematicians,
physicists, and biologists.  To get it follow the instructions below:

------------Installing XPP1.6--------------------------------

 XPP is pretty simple to install 
although you might have to add a line here and there
to the Makefile.  You can get it from 
            mthsn4.math.pitt.edu (130.49.12.1)
here is how:

   ftp 130.49.12.1
   cd /pub
   bin
   get xpp1.6.tar.Z
   quit
   uncompress xpp1.6.tar.Z
   tar xf xpp1.6.tar
   make -k

If you get errors in the compilation it is likely to be one
of the following:
1) gcc not found in which case you should edit the Makefile
   so that it says  CC= cc
2)  Cant find X include files.  Then edit the line that says
    CFLAGS= ....
    by adding  
            -I<pathname>
where <pathname> is where the include files are for X, e,g,
     -I/usr/X11/include
3) Cant find X libraries.  Then add a line
LDFLAGS= -L<pathname>
right after the CFLAGS= line where <pathname> is where to find the X11
libraries
then  change this line: 
$(CC) -o xpp $(OBJECTS) $(LIBS)
to this line
$(CC) -o xpp $(OBJECTS) $(LDFLAGS) $(LIBS)

That should do it!!

If it still doesnt compile, then you should ask your sysadmin about
the proper paths.  

Finally, some compilers have trouble with the GEAR algorithm if they
are optimized so you should remove the optimization flags i.e. replace
CFLAGS=  -O2 -I<your pathnames>
with
CFLAGS=   -I<your pathnames>

delete all the .o files and recompile

Good luck!
   Bard Ermentrout
   

  Send comments and bug reports to
     bard at mthbard.math.pitt.edu