[SciPy-user] (no subject)
Adrián López
alopez at imim.es
Fri Feb 24 06:20:37 EST 2006
Very strange ... If I change just that single line as you said, it
runs correctly !!! THANKS!!! How did you know the problem was on that
line?
And also, another interesting thing, that maybe is easier to explain.
The code I posted, with the line corrected as you suggested gives me
this output
[alopez at thymus tmp]$ tail new/repressilator.out
99.91 0.0 106.561968929 12.8532193268 0.657464014072
120.022734481 10.2873375884 0.690593561295
99.92 0.0 107.232334762 12.7255621105 0.659198461945
120.585673723 10.1851132999 0.695453697878
99.93 0.0 107.897250845 12.5991702799 0.661090230937
121.140028167 10.0839043882 0.7005127881
99.94 0.0 108.556560119 12.4740313944 0.66314142979
121.685624094 9.98370079793 0.705774044541
99.95 0.0 109.210104618 12.3501331324 0.665354223171
122.222286288 9.88449257258 0.711240755997
99.96 0.0 109.857725438 12.2274632897 0.667730832672
122.749838018 9.78626985374 0.716916288878
99.97 0.0 110.499262751 12.1060097788 0.670273537691
123.268101064 9.6890228799 0.722804088444
99.98 0.0 111.134555765 11.985760628 0.672984676503
123.776895697 9.59274198564 0.728907680303
99.99 0.0 111.763442835 11.8667039806 0.67586664717
124.276040954 9.49741760048 0.735230671778
100.0 0.0 112.385761359 11.7488280938 0.678921908743
124.76535447 9.40304024813 0.741776753543
and the same code using Numeric instead of numpy, an extra line:
[alopez at thymus tmp]$ tail old/repressilator.out
99.92 0.0 107.232334762 12.7255621105 0.659198461945
120.585673723 10.1851132999 0.695453697878
99.93 0.0 107.897250845 12.5991702799 0.661090230937
121.140028167 10.0839043882 0.7005127881
99.94 0.0 108.556560119 12.4740313944 0.66314142979
121.685624094 9.98370079793 0.705774044541
99.95 0.0 109.210104618 12.3501331324 0.665354223171
122.222286288 9.88449257258 0.711240755997
99.96 0.0 109.857725438 12.2274632897 0.667730832672
122.749838018 9.78626985374 0.716916288878
99.97 0.0 110.499262751 12.1060097788 0.670273537691
123.268101064 9.6890228799 0.722804088444
99.98 0.0 111.134555765 11.985760628 0.672984676503
123.776895697 9.59274198564 0.728907680303
99.99 0.0 111.763442835 11.8667039806 0.67586664717
124.276040954 9.49741760048 0.735230671778
100.0 0.0 112.385761359 11.7488280938 0.678921908743
124.76535447 9.40304024813 0.741776753543
100.01 0.0 113.001347666 11.6321213375 0.682152982467
125.244652321 9.30960054565 0.74854970128
Why?
Finally I've tried the tool you pointed me. I run it importing numpy
and with *the* line changed as you said. The output is here:
[alopez at thymus new]$ gdb
GNU gdb Red Hat Linux (6.0post-0.20040223.19rh)
Copyright 2004 Free Software Foundation, Inc.
GDB is free software, covered by the GNU General Public License, and
you are
welcome to change it and/or distribute copies of it under certain
conditions.
Type "show copying" to see the conditions.
There is absolutely no warranty for GDB. Type "show warranty" for
details.
This GDB was configured as "i386-redhat-linux-gnu".
(gdb) file /home/alopez/software/bin/python
Reading symbols from /home/alopez/software/bin/python...done.
Using host libthread_db library "/lib/tls/libthread_db.so.1".
(gdb) run
Starting program: /home/alopez/software/bin/python
[Thread debugging using libthread_db enabled]
[New Thread -1208276480 (LWP 8532)]
Python 2.4.2 (#1, Feb 22 2006, 17:29:56)
[GCC 3.3.3 20040412 (Red Hat Linux 3.3.3-7)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> execfile('file.py')
message 1
message2
>>>
seems correct, doesn't it?
Thanks again and I'll report strange behavior as these ones if I
experience them,
--
Adrián López García de Lomana, Graduate Student
Computational Biochemistry and Biophysics Lab
Research Group on Biomedical Informatics (GRIB) - IMIM / UPF
c/ Dr. Aiguader, 80; 08003 Barcelona (Spain)
http://diana.imim.es
On Feb 24, 2006, at 10:51 AM, Travis Oliphant wrote:
> Adrián López wrote:
>
>> from numpy import *
>>
>> from scipy.integrate import odeint
>>
>> def func(x, t, *args):
>>
>> xdot = [0.0, 5.0, 0.0, 15.0, 0.0, 0.0, 0.0]
>>
>> xdot[0] = 0
>>
>> xdot[1] = - (x[1] * beta) + x[4] * beta
>>
>> xdot[2] = - (x[2] * beta) + x[5] * beta
>>
>> xdot[3] = + x[6] * beta - (x[3] * beta)
>>
>>
> Try changing this line to
>
> x[6] * beta - x[3] * beta
>
> I was getting a strange error from it that has me perplexed. Perhaps
> an un-handled exception is causing the segfault.
>
> It's hard to say.
>
> If you have gdb installed you can really help out by running under gdb
> so that when it segfaults we find out where...
>
> Here's how...
>
> gdb
> file /usr/bin/python (or whever Python is installed).
> run
> execfile('file.py')
>
>
> -Travis
>
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> SciPy-user at scipy.net
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