Skip to main content

Dynamical systems simulation in python

Trying out PyDSTools [webpage, download]
These guys look professional - they have a test suite that you can run to check everything out.
Issues:
  1. You need to put a file called PyDSTool.pth [read this]
    Play close attention to the trick about subdirectories - you have to repeat it for each level, not just the root level. I have my install in c:\programs\PyDSTool and my file has
    C:\\
    C:\\Programs\\
    C:\\Programs\\PyDSTool\\
  2. I have scipy version 0.6.0 but PyDSTool doesn't detect that properly. I commented out the relevant lines in PyDSTool's root __init__.py
    #if vernums[1] != 5:
    # raise RuntimeError("SciPy v0.5.1 or above is required")
    and it continued with the tests.
Things seem to work OK, only one thing was declared broken:
PyCont: appears to be broken on your system

But, there were periodic errors of the nature:

***** Testing script impfn_test.py ****************************

Gnuplot not available
------- Examples of implicit function as variable
1D example: a half-circle using newton's method (secant method for estimating de
rivative)
Change sign of 'y' initial condition to solve for other half-circle
Gen defined? => False
traj1 = testimp.compute('traj1')
Error in supplied functional specification code
Traceback (most recent call last):
File "impfn_test.py", line 54, in
traj1 = testimp.compute('traj1')
File "C:\Programs\PyDSTool\Generator\ImplicitFnGen.py", line 294, in compute
exec tempspec[0] in globals()
File "string", line 1
def _specfn_imptest_316e-006(ds, t, x, parsinps):
^
SyntaxError: invalid syntax

***** Testing passed on test file impfn_test.py

Which I can't understand
Labels:

Comments

  1. AnonymousApril 30, 2008 at 8:23 PM

    Hi -- that's an odd platform specific problem you have with time.clock(). The easy fix is to change the return line in the function PyDSTool.common.timestamp to be the following:

    return c.replace(".","").replace("-","")[:tdigits+1]

    (obviously without the newline that this comment box forces on me!)

    ReplyDelete

Post a Comment

Popular posts from this blog

A note on Python's __exit__() and errors

Python's context managers are a very neat way of handling code that needs a teardown once you are done. Python objects have do have a destructor method ( __del__ ) called right before the last instance of the object is about to be destroyed. You can do a teardown there. However there is a lot of fine print to the __del__ method. A cleaner way of doing tear-downs is through Python's context manager , manifested as the with keyword. class CrushMe: def __init__(self): self.f = open('test.txt', 'w') def foo(self, a, b): self.f.write(str(a - b)) def __enter__(self): return self def __exit__(self, exc_type, exc_val, exc_tb): self.f.close() return True with CrushMe() as c: c.foo(2, 3) One thing that is important, and that got me just now, is error handling. I made the mistake of ignoring all those 'junk' arguments ( exc_type, exc_val, exc_tb ). I just skimmed the docs and what popped out is that you need to return True or...
Post a Comment
Read more

Remove field code from Word document

e.g. before submitting a MS, or hand manipulating some formatting because Word does things (like cross-references) so half-assed [from here ] Select all the text (CTRL-A) Press Ctrl+Shift+F9 Editing to remove anonymous comments that only contain thanks. I really appreciate the thanks, but it makes it harder to find comments that carry pertinent information. I'm also going to try and paste informative comments in the body of the post to make them easier to find.
24 comments
Read more

h5py and multiprocessing

The HDF5 format has been working awesome for me, but I ran into danger when I started to mix it with multiprocessing. It was the worst kind of danger: the intermittent error. Here are the dangers/issues in order of escalation (TL;DR is use a generator to feed data from your file into the child processes as they spawn. It's the easiest way. Read on for harder ways.) An h5py file handle can't be pickled and therefore can't be passed as an argument using pool.map() If you set the handle as a global and access it from the child processes you run the risk of racing which leads to corrupted reads. My personal runin was that my code sometimes ran fine but sometimes would complain that there are NaNs or Infinity in the data. This wasted some time tracking down. Other people have had this kind of problem [ 1 ]. Same problem if you pass the filename and have the different processes open individual instances of the file separately. The hard way to solve this problem is to sw...
Post a Comment
Read more