python - Ctypes segmentation fault -

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so i'm trying speedup python script loading data files , storing in array. realized if repeat procedure around 1020 times don't ask me why arrive @ segmentation fault. code loading data is:

import os,sys import numpy np import pandas pd import ctypes ct  version = 0.1  try:     path = os.path.join(os.path.dirname(os.path.realpath(__file__)), "_vec") except nameerror:     path = "./_im7"  if not(sys.platform in ('win32', 'cygwin')):     path += '.so.'+str(version)     libfunctions = ct.cdll.loadlibrary(path) else:     libfunctions = ct.cdll.loadlibrary(path)  libfunctions.readvec.restype = ct.c_void_p libfunctions.readvec.argtypes = [ct.c_char_p, np.ctypeslib.ndpointer(ct.c_float), \     ct.c_int,ct.c_int,ct.c_int]   def readvecct(filename,nx,ny,nz):     # supposing moment naming scheme piv__vxy.case piv__vxy.geo not changes should     # not case appropriate changes have made corresponding file      # ctypes     data_temp = np.zeros((2*ny*nx,1),dtype=np.dtype('f4'))     libfunctions.readvec(ct.c_char_p(filename),data_temp,ct.c_int(nx), ct.c_int(ny),ct.c_int(3))      # w value     if (nz)>1:         return data_temp[:nx*ny].reshape(ny, nx), data_temp[nx*ny:2*nx*ny].reshape(ny, nx), data_temp[2*nx*ny:].reshape(ny, nx)     else:             return data_temp[:nx*ny].reshape(ny, nx), data_temp[nx*ny:].reshape(ny, nx)

the underlying c function:

#include <stdio.h>   void readvec(const char *fname, float *data,  int nx, int ny,int skiprows) {     //void cfun(const double * indata, int rowcount, int colcount, double * outdata) {     int i,j,check;     size_t length;     file *file;     char buffer[1024];     char *buffer_ptr = &buffer[0];     //puts("here go!");      file = fopen(fname, "r");     //printf("nx: %d ny: %d skiprows: %d \n",nx,ny,skiprows);     //printf("filename %s \n",fname);     (i=0;i<=skiprows;i++){     check=getline(&buffer_ptr,&length,file);     //printf("buffer: %s \n",buffer);     if (check==-1){         puts("error");     }     }      (i = 0; < ny; i++) {     (j=0;j<nx;j++){         check=fscanf(file,"%f",&data[i*nx+j]);         //printf("data %s\n",buffer);         if (check==-1){         puts("error");         }     }     }      (i = 0; < ny; i++) {     (j=0;j<nx;j++){         check=fscanf(file,"%f",&data[ny*nx+i*nx+j]);         if (check==-1){         puts("error");         }     }     }      //fclose(file);     //puts("done!"); }

and simple test produces error:

import time import numpy np import libvec.libvec vec import matplotlib.pyplot plt   tmp_geo = '/mnt/shared/projects/morphing/users/jschelle/raw_treated_201509/res_u_8-ms-dp-4-mmce_sma_0-mm-mcf_0-hz/u_8-ms-dp-4-mmce_sma_0-mm-mcf_0-hz_20150824_seq_01/paraview/piv__vxy.geo' tmp_file = '/mnt/shared/projects/morphing/users/jschelle/raw_treated_201509/res_u_8-ms-dp-4-mmce_sma_0-mm-mcf_0-hz/u_8-ms-dp-4-mmce_sma_0-mm-mcf_0-hz_20150824_seq_01/paraview/piv__vxy_01019.vec' tmp_case = '/mnt/shared/projects/morphing/users/jschelle/raw_treated_201509/res_u_8-ms-dp-4-mmce_sma_0-mm-mcf_0-hz/u_8-ms-dp-4-mmce_sma_0-mm-mcf_0-hz_20150824_seq_01/paraview/piv__vxy.case'  x,y,z = vec.readgeo(tmp_geo) nx = len(x) ny = len(y) nz = len(z) iterations = 1100  start_time = time.time()  in range(iterations):     u,v = vec.readvecct(tmp_file,nx,ny,nz);  print("ctypes --- %f seconds ---" % ((time.time() - start_time)/iterations))

now when number of iterations 1000 no problem occurs @ 1100 segmentation fault. imagine has sth memory management don't know how fix or start! appreciated.

thx lot in advance

j

turns out:

fclose(file)

was commented not directly lead error @ same time leads segfault after n iterations

thank everyone!


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