歸去來兮，田園將蕪，胡不歸！: 2011

Sunday, December 18, 2011

Extend Numpy with ctypes

The idea is to write extend numpy with c. Thus, you can enjoy the performance of c and also employ any c only libs. Passing data between numpy and c with numpy arrays and c pointers.

PS: ctypes dose not recognize c++ symbols. Make sure to put your wrap function between extern "C" { and }

Here is the example.
We need 3 files.
C implimentation func.c;
Python wrapping func.py;
and Python calling interface test.py.

/*func.c*/
/* You can complie it with the following command*/
/* gcc -O2 -fPIC func.c -shared -o libfunc.so */
#ifdef __cplusplus
extern "C" {
#endif
int skew_symmetric_matrix(double *t, double *tx)
{
    tx[0] = 0;
    tx[1] = -t[2];
    tx[2] = t[1];
    tx[3] = t[2];
    tx[4] = 0;
    tx[5] = -t[0];
    tx[6] = -t[1];
    tx[7] = t[0];
    tx[8] = 0;
    return 0;
}
#ifdef __cplusplus
}
#endif

##Python wrapping file
##func.py

import numpy as np

import ctypes as ct

##load the s

_func = np.ctypeslib.load_library('libfunc', '.')

ndpointer = np.ctypeslib.ndpointer

array_double = ndpointer(dtype = ct.POINTER(ct.c_double), flags='CONTIGUOUS,ALIGNED')

##Specify the arg types the numpy arrays which have to be aligned continuously.

##Passing a[::2] directly might not work. Using a[::2].copy() instead.

##There also other arg types such as [array_double, ct.c_int, ct.c_double]

_func.skew_symmetric_matrix.argtypes = [array_double] * 2

##Define python wrapping funcion

##ctypes can only see pointers but no size or shape of your numpy array

def skew_symmetric_matrix(t):

if t.size != 3:

return None

tx = np.zeros((3, 3), dtype=np.double)

_func.skew_symmetric_matrix(t, tx)

return tx

##Python interface

##test.py

import scipy as sp, numpy as np

import func

t = np.array([1.0, 2.0, 3.0])

tx = func.skew_symmetric_matrix(t)

print (t)

print (tx)

Saturday, December 10, 2011

cblas of gotoblas2

According to
"http://shimingyoung.blogspot.com/2010/01/gotoblas-and-lapackwrapper.html"

Also edit the cblas.h by adding one line
#define blasint int
And edit the f2c.h by changing the line on the 10th line to
typedef int integer;

Otherwise, blasint is not defined while compiling.

Thursday, November 17, 2011

git remote

git pull ssh://usr@ip:port/~/path branch_name
git push ssh://usr@ip:port/~/path local_branch:remote_branch

Check disk usage

jdiskreport
There is another software visualize disk usage with squares, but I forget its name.

Sunday, October 30, 2011

linking libf2c.so and undefined reference to `MAIN__'

The problem is that f2c wants to link to the MAIN__ function which is

the "fortran main". Apparently it is just a dummy function call. And
the fix is quite simple:

Add "int  MAIN__( ) {  return 0; }" somewhere is the sources.

Or pass the option -u MAIN__ to the linker.

The attached patch correct the problem.