Python Sundials
From charlesreid1
This page details my installation procedure for the python-sundials library: https://code.google.com/p/python-sundials/
Contents
Installation
Mac OS X
The usual setup.py installation procedure was followed, although I had to make several modifications to the source code and the compile line to get it working (see the #Errors section below). The final command that I used to build the library was:
sudo CFLAGS='-I/Users/charlesreid/pkg/sundials/std/include -L/Users/charlesreid/pkg/sundials/std/lib' LDFLAGS="$CFLAGS" python setup.py build
Errors
NVECTOR.pxi: Taking Address of Non-Lvalue
On my first attempt to install python-sundials, I got this error:
sundials/NVECTOR.pxi:41:37: Taking address of non-lvalue
Here is the full error context:
$ python setup.py build
running build
running build_ext
cythoning sundials/sundials.pyx to sundials/sundials.c
Error compiling Cython file:
------------------------------------------------------------
...
buffer.obj = self
buffer.len = self.getsize() * sizeof(double)
buffer.readonly = 0
buffer.format = <char*>"d"
buffer.ndim = 1
buffer.shape = <Py_ssize_t *>&self.__shape
^
------------------------------------------------------------
sundials/NVECTOR.pxi:41:37: Taking address of non-lvalue
warning: sundials/KINSOL.pxi:183:39: Not all members given for struct 'kinsol_userdata'
warning: sundials/KINSOL.pxi:183:39: Not all members given for struct 'kinsol_userdata'
building 'sundials' extension
creating build
creating build/temp.macosx-10.8-intel-2.7
creating build/temp.macosx-10.8-intel-2.7/sundials
clang -fno-strict-aliasing -fno-common -dynamic -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -mno-fused-madd -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -Isundials -Isundials/include -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c sundials/sundials.c -o build/temp.macosx-10.8-intel-2.7/sundials/sundials.o
clang: warning: argument unused during compilation: '-mno-fused-madd'
sundials/sundials.c:1:2: error: #error Do not use this file, it is the result of a failed Cython compilation.
#error Do not use this file, it is the result of a failed Cython compilation.
^
1 error generated.
Traceback
:error: command 'clang' failed with exit status 1
I was able to resolve this issue by modifying the source code of NVECTOR.pxi. I changed this line (the line the error referred to):
buffer.shape = <Py_ssize_t *>&self.__shape
to this line:
buffer.shape = <Py_ssize_t *>self.__shape
removing the ampersand &.
Header Files Not Found
If you run into an error about header files not being found, like this one:
$ python setup.py build
running build
running build_ext
cythoning sundials/sundials.pyx to sundials/sundials.c
warning: sundials/KINSOL.pxi:183:39: Not all members given for struct 'kinsol_userdata'
warning: sundials/KINSOL.pxi:183:39: Not all members given for struct 'kinsol_userdata'
building 'sundials' extension
clang -fno-strict-aliasing -fno-common -dynamic -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -mno-fused-madd -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -Isundials -Isundials/include -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c sundials/sundials.c -o build/temp.macosx-10.8-intel-2.7/sundials/sundials.o
clang: warning: argument unused during compilation: '-mno-fused-madd'
sundials/sundials.c:313:10: fatal error: 'sundials/sundials_types.h' file not found
#include "sundials/sundials_types.h"
^
1 error generated.
Traceback
:error: command 'clang' failed with exit status 1
then you probably installed Sundials to a non-standard location. To instruct setup.py to use the Sundials libraries in a non-standard location, use the CFLAGS environment variable when calling setup.py:
CFLAGS="-L/Users/charlesreid/pkg/sundails/std/lib -I/Users/charlesreid/pkg/sundials/std/include" python setup.py build
Linker Command Failed: Library Not Found For lsundials_cvode
Once I fixed the pxi file, and instructed setup.py to use a C compiler command that would point to my non-standard sundials library install locations, I saw an error with the linker:
creating build/lib.macosx-10.8-intel-2.7 clang -bundle -undefined dynamic_lookup -Wl,-F. -arch i386 -arch x86_64 build/temp.macosx-10.8-intel-2.7/sundials/sundials.o -Lsundials -lsundials_cvode -lsundials_ida -lsundials_kinsol -lsundials_nvecserial -o build/lib.macosx-10.8-intel-2.7/sundials.so ld: library not found for -lsundials_cvode clang: error: linker command failed with exit code 1 (use -v to see invocation) Traceback :error: command 'clang' failed with exit status 1 Press enter to continue
This was easily solved by doing the same thing with the LDFLAGS variable as was done with the CFLAGS variable:
CFLAGS="-L/Users/charlesreid/pkg/sundails/std/lib -I/Users/charlesreid/pkg/sundials/std/include" LDFLAGS="$CFLAGS" python setup.py build
Must Be Compiled On Windows 32 Platform
creating 'dist/python-sundials-0.5.zip' and adding 'python-sundials-0.5' to it adding 'python-sundials-0.5/COPYING.txt' adding 'python-sundials-0.5/MANIFEST.in' adding 'python-sundials-0.5/PKG-INFO' adding 'python-sundials-0.5/README.txt' adding 'python-sundials-0.5/setup.py' adding 'python-sundials-0.5/sundials/CVODE.pxi' adding 'python-sundials-0.5/sundials/IDA.pxi' adding 'python-sundials-0.5/sundials/KINSOL.pxi' adding 'python-sundials-0.5/sundials/Makefile_embedded' adding 'python-sundials-0.5/sundials/NVECTOR.pxi' adding 'python-sundials-0.5/sundials/sundials.c' adding 'python-sundials-0.5/sundials/sundials.pxd' adding 'python-sundials-0.5/sundials/SundialsLib.pxd' adding 'python-sundials-0.5/sundials/test_cv_ball.py' adding 'python-sundials-0.5/sundials/test_cv_simple.py' adding 'python-sundials-0.5/sundials/test_cvRoberts_dns.py' adding 'python-sundials-0.5/sundials/test_embedded.pyx' adding 'python-sundials-0.5/sundials/test_idaRoberts_dns.py' adding 'python-sundials-0.5/sundials/test_kinsol.py' removing 'python-sundials-0.5' (and everything under it) running bdist_wininst Traceback :error: distribution contains extensions and/or C libraries; must be compiled on a Windows 32 platform
This was resolved by manually editing setup.py and removing the following line:
sys.argv.append('bdist_wininst')
Usage
Test Problem
The main python-sundials website gives a test problem:
import array
import numpy as np
from sundials import *
class Ball:
TINY = 1e-16
def __init__(self, e = 0.7, g = 9.81):
self.e = e
self.g = g
def f(self, t, y, sw):
if sw[0]:
return [0., 0.]
else:
return [-self.g, y[0]]
def rootf(self, t, y, sw):
return [y[1] + Ball.TINY]
def solve(self, plot = True):
t0 = 0
y0 = array.array('d', [0.,1.])
solver = CVodeSolver(RHS = self.f, ROOT = self.rootf, SW = [False],
abstol = 1.0e-6, reltol = 1.0e-6)
solver.init(t0,y0)
dt = .01
iter = solver.iter(t0, dt)
tres = array.array('d', [t0])
hres = array.array('d', [y0[1]])
while True:
try:
t, y = next(iter)
tres.append(t)
hres.append(y[1])
except CVodeRootException, info:
if abs(info.y[0]) < 0.01:
solver.SW[0] = True
tres.append(info.t)
hres.append(0.)
solver.init(info.t, [-self.e*info.y[0], 0.])
if t > 3.0:
break
if plot:
import matplotlib
import pylab
pylab.plot(tres,hres, linewidth=1.0)
pylab.xlabel('time (s)')
pylab.ylabel('height (m)')
pylab.title('Bouncing ball demo')
pylab.grid(True)
pylab.show()
else:
return tres, hres
ball = Ball()
ball.solve()