Re: r2390 - in /branches/c_modules/maths_fns: c_chi2.c exponential.c relax_fit.c relax_fit.h -- March 16, 2006 - 07:11

To try to fix the memory leak problem, I've added Py_DECREF() calls to
the 'func' and 'dfunc' functions to deallocate the memory used by the
parameter vector 'numpy_params'.  This function is part of the
Python/C API.  I've also added declarations for the pointer '*params'
used within those functions.  The main reason I made the pointers
'*values, *sd, *relax_times, *scaling_matrix' external was to make the
data persistent so that the values are set once during the setup and
then each 'func' call uses that data.  As for the layout of the
relax_fit.c code, I've simply followed the instructions in the
Python/C API found at http://docs.python.org/api/api.html.  I've
separated the chi2.c function, etc, so that these can be reused by
future C modules.  I can't currently test if the memory leak has been
fixed as the changes to the residue selection code is causing
problems.

Thank again for the help,

Edward


On 3/16/06, Edward d'Auvergne <edward.dauvergne@xxxxxxxxx> wrote:
> Thank you Gary for the help with the C code.  Your fixes have been
> merged into the main relax development line, they are much
> appreciated.  Apart from the memory leak, which I think is because I
> need to call the Numeric-Python C function Py_DECREF() more often, the
> code works beautifully.
>
> Thanks,
>
> Edward
>
>
> On 3/16/06, c.a.macraild@xxxxxxxxxxx <c.a.macraild@xxxxxxxxxxx> wrote:
> > Author: macraild
> > Date: Wed Mar 15 16:17:06 2006
> > New Revision: 2390
> >
> > URL: http://svn.gna.org/viewcvs/relax?rev=2390&view=rev
> > Log:
> > A fix for the -fPIC compilation bug (#5473). Some problems remain.
> >
> > Modified:
> >     branches/c_modules/maths_fns/c_chi2.c
> >     branches/c_modules/maths_fns/exponential.c
> >     branches/c_modules/maths_fns/relax_fit.c
> >     branches/c_modules/maths_fns/relax_fit.h
> >
> > Modified: branches/c_modules/maths_fns/c_chi2.c
> > URL: 
> > http://svn.gna.org/viewcvs/relax/branches/c_modules/maths_fns/c_chi2.c?rev=2390&r1=2389&r2=2390&view=diff
> > ==============================================================================
> > --- branches/c_modules/maths_fns/c_chi2.c (original)
> > +++ branches/c_modules/maths_fns/c_chi2.c Wed Mar 15 16:17:06 2006
> > @@ -20,15 +20,6 @@
> >
> >  #include <stdio.h>
> >  #include <math.h>
> > -
> > -/* This include must come first */
> > -#include <Python.h>
> > -
> > -/* The header for all functions which will be called */
> > -#include "relax_fit.h"
> > -
> > -/* The Numeric array object header file, must come second */
> > -#include <Numeric/arrayobject.h>
> >
> >  #define square(x) (x)*(x)
> >
> > @@ -53,15 +44,15 @@
> >         */
> >
> >      /* Declarations */
> > -    extern int *num_times;
> > -    extern PyArrayObject *values, *sd;
> > +    extern int num_times;
> > +    extern double *values, *sd;
> >      extern double back_calc[];
> >         int i;
> >         double chi2 = 0.0;
> >
> >      /* Loop over the time points and sum the chi-squared components */
> > -       for (i = 0; i < *num_times; ++i) {
> > -               chi2 = chi2 + square((*(double *)values->data[i] - 
> > back_calc[i]) / *(double *)sd->data[i]);
> > +       for (i = 0; i < num_times; ++i) {
> > +               chi2 = chi2 + square((values[i] - back_calc[i]) / sd[i]);
> >         }
> >
> >         return chi2;
> >
> > Modified: branches/c_modules/maths_fns/exponential.c
> > URL: 
> > http://svn.gna.org/viewcvs/relax/branches/c_modules/maths_fns/exponential.c?rev=2390&r1=2389&r2=2390&view=diff
> > ==============================================================================
> > --- branches/c_modules/maths_fns/exponential.c (original)
> > +++ branches/c_modules/maths_fns/exponential.c Wed Mar 15 16:17:06 2006
> > @@ -22,11 +22,11 @@
> >  /* This include must come first */
> >  #include <Python.h>
> >
> > +/* The Numeric array object header file, must come second */
> > +#include <Numeric/arrayobject.h>
> > +
> >  /* The header for all functions which will be called */
> >  #include "relax_fit.h"
> > -
> > -/* The Numeric array object header file, must come second */
> > -#include <Numeric/arrayobject.h>
> >
> >
> >
> > @@ -35,22 +35,23 @@
> >         */
> >
> >      /* Declarations */
> > -    extern int *num_times;
> > -    extern PyArrayObject *params, *relax_times;
> > +    extern int num_times;
> > +    extern double *params, *relax_times;
> >      extern double back_calc[];
> >      double Rx, I0;
> >      int i;
> >
> >
> >      /* Loop over the time points */
> > -    for (i = 0; i < *num_times; i++) {
> > +    /* for (i = 0; i < num_times; i++) { */
> > +    for (i = 0; i < num_times; i++) {
> >          /* Zero Rx value */
> >          if (params[0] == 0.0)
> >              back_calc[i] = 0.0;
> >
> >          /* Back calculate */
> >          else
> > -            back_calc[i] = (double *)params->data[1] * exp(-(double 
> > *)relax_times->data[i] * (double *)params->data[0]);
> > +            back_calc[i] = params[1] * exp(-relax_times[i] * params[0]);
> >
> >      }
> >  }
> >
> > Modified: branches/c_modules/maths_fns/relax_fit.c
> > URL: 
> > http://svn.gna.org/viewcvs/relax/branches/c_modules/maths_fns/relax_fit.c?rev=2390&r1=2389&r2=2390&view=diff
> > ==============================================================================
> > --- branches/c_modules/maths_fns/relax_fit.c (original)
> > +++ branches/c_modules/maths_fns/relax_fit.c Wed Mar 15 16:17:06 2006
> > @@ -21,58 +21,46 @@
> >  /* This include must come first */
> >  #include <Python.h>
> >
> > +/* The Numeric array object header file, must come second */
> > +#include <Numeric/arrayobject.h>
> > +
> >  /* The header for all functions which will be called */
> >  #include "relax_fit.h"
> > -
> > -/* The Numeric array object header file, must come second */
> > -#include <Numeric/arrayobject.h>
> >
> >
> >
> >  static PyObject *
> >  setup(PyObject *self, PyObject *args, PyObject *keywords) {
> > -    /* Debugging */
> > -    printf("Setting up\n");
> > -
> >      /* Python declarations */
> >      PyObject *values_arg, *sd_arg, *relax_times_arg, *scaling_matrix_arg;
> > -    extern PyArrayObject *values, *sd, *relax_times, *scaling_matrix;
> > +    PyArrayObject *numpy_values, *numpy_sd, *numpy_relax_times, 
> > *numpy_scaling_matrix;
> >
> >      /* Normal declarations */
> > -    extern double *relax_time_array;
> > -    extern int *num_params, *num_times;
> > +    extern double *values, *sd, *relax_times, *scaling_matrix;
> > +    extern double relax_time_array;
> > +    extern int num_params, num_times;
> >
> >      /* The keyword list */
> >      static char *keyword_list[] = {"num_params", "num_times", "values", 
> > "sd", "relax_times", "scaling_matrix", NULL};
> >
> > -
> >      /* Parse the function arguments */
> > -    if (!PyArg_ParseTupleAndKeywords(args, keywords, "iiOOOO", 
> > keyword_list, &num_params, &num_times, &values_arg, &sd, 
> > &relax_times_arg, &scaling_matrix_arg))
> > +    if (!PyArg_ParseTupleAndKeywords(args, keywords, "iiOOOO", 
> > keyword_list, &num_params, &num_times, &values_arg, &sd_arg, 
> > &relax_times_arg, &scaling_matrix_arg))
> >          return NULL;
> >
> > -    /* Debugging */
> > -    printf("Function args have been parsed\n");
> > +    /* Make the Numeric arrays contiguous */
> > +    numpy_values = (PyArrayObject *) 
> > PyArray_ContiguousFromObject(values_arg, PyArray_DOUBLE, 1, 1);
> > +    numpy_sd = (PyArrayObject *) PyArray_ContiguousFromObject(sd_arg, 
> > PyArray_DOUBLE, 1, 1);
> > +    numpy_relax_times = (PyArrayObject *) 
> > PyArray_ContiguousFromObject(relax_times_arg, PyArray_DOUBLE, 1, 1);
> > +    numpy_scaling_matrix = (PyArrayObject *) 
> > PyArray_ContiguousFromObject(scaling_matrix_arg, PyArray_DOUBLE, 2, 2);
> >
> > -    /* Make the Numeric arrays contiguous */
> > -    values = (PyArrayObject *) PyArray_ContiguousFromObject(values_arg, 
> > PyArray_DOUBLE, 1, 1);
> > -    sd = (PyArrayObject *) PyArray_ContiguousFromObject(sd_arg, 
> > PyArray_DOUBLE, 1, 1);
> > -    relax_times = (PyArrayObject *) 
> > PyArray_ContiguousFromObject(relax_times_arg, PyArray_DOUBLE, 1, 1);
> > -    scaling_matrix = (PyArrayObject *) 
> > PyArray_ContiguousFromObject(scaling_matrix_arg, PyArray_DOUBLE, 2, 2);
> > -
> > -    /* Debugging */
> > -    printf("Py_INCREF\n");
> > -
> > -    /* ??? */
> > -    Py_INCREF(Py_None);
> > -    Py_INCREF(values);
> > -    Py_INCREF(sd);
> > -    Py_INCREF(relax_times);
> > -    Py_INCREF(scaling_matrix);
> > -
> > -    /* Debugging */
> > -    printf("Finished setup\n");
> > +    /* Pointers to the Numeric arrays */
> > +    values = (double *) numpy_values->data;
> > +    sd = (double *) numpy_sd->data;
> > +    relax_times = (double *) numpy_relax_times->data;
> > +    scaling_matrix = (double *) numpy_scaling_matrix->data;
> >
> >      /* Return nothing */
> > +    Py_INCREF(Py_None);
> >      return Py_None;
> >  }
> >
> > @@ -85,13 +73,9 @@
> >       * calculated
> >       */
> >
> > -    /* Debugging */
> > -    printf("Inside func\n");
> > -
> >      /* Declarations */
> >      PyObject *arg1;
> > -    extern PyArrayObject *params;
> > -    extern double *params;
> > +    extern PyArrayObject *numpy_params;
> >      double chi2(void);
> >
> >
> > @@ -100,13 +84,13 @@
> >          return NULL;
> >
> >      /* Convert the Numeric array to be contiguous */
> > -    params = (PyArrayObject *) PyArray_ContiguousFromObject(arg1, 
> > PyArray_DOUBLE, 1, 1);
> > +    numpy_params = (PyArrayObject *) PyArray_ContiguousFromObject(arg1, 
> > PyArray_DOUBLE, 1, 1);
> > +
> > +    /* Pointers to the Numeric arrays */
> > +    params = (double *) numpy_params->data;
> >
> >      /* Back calculated the peak intensities */
> >      exponential();
> > -
> > -    /* ??? */
> > -    Py_INCREF(params);
> >
> >      /* Calculate and return the chi-squared value */
> >      return Py_BuildValue("f", chi2());
> > @@ -119,8 +103,7 @@
> >
> >      /* Declarations */
> >      PyObject *arg1;
> > -    extern PyArrayObject *params;
> > -    extern double *params;
> > +    extern PyArrayObject *numpy_params;
> >
> >      /* Temp Declarations */
> >      PyArrayObject *aaa_numpy;
> > @@ -133,7 +116,10 @@
> >          return NULL;
> >
> >      /* Convert the Numeric array to be contiguous */
> > -    params = (PyArrayObject *) PyArray_ContiguousFromObject(arg1, 
> > PyArray_DOUBLE, 1, 1);
> > +    numpy_params = (PyArrayObject *) PyArray_ContiguousFromObject(arg1, 
> > PyArray_DOUBLE, 1, 1);
> > +
> > +    /* Pointers to the Numeric arrays */
> > +    params = (double *) numpy_params->data;
> >
> >      /* Back calculated the peak intensities */
> >      exponential();
> > @@ -141,7 +127,8 @@
> >
> >      /* Test code (convert aaa to a Numeric array */
> >      /* aaa_numpy = (PyArrayObject *) PyArray_FromDimsAndData(1, 
> > num_params, PyArray_DOUBLE, aaa_pointer); */
> > -    aaa_numpy = (PyArrayObject *) PyArray_FromDims(1, (int *) 
> > *num_params, PyArray_DOUBLE);
> > +    aaa_numpy = (PyArrayObject *) PyArray_FromDims(1, &num_params, 
> > PyArray_DOUBLE);
> > +    aaa_pointer = (double *) aaa_numpy->data;
> >
> >      /* Fill the Numeric array */
> >      for (i = 0; i < 2; i++)
> > @@ -164,14 +151,14 @@
> >
> >      /* Declarations */
> >      extern double back_calc[];
> > -    extern int *num_times;
> > +    extern int num_times;
> >      int i;
> >
> > -    PyObject *back_calc_py = PyList_New(*num_times);
> > +    PyObject *back_calc_py = PyList_New(num_times);
> >      assert(PyList_Check(back_calc_py));
> >
> >      /* Copy the values out of the C array into the Python array */
> > -    for (i = 0; i < *num_times; i++)
> > +    for (i = 0; i < num_times; i++)
> >          PyList_SetItem(back_calc_py, i, Py_BuildValue("f", 
> > back_calc[i]));
> >
> >      /* Return the Numeric array */
> >
> > Modified: branches/c_modules/maths_fns/relax_fit.h
> > URL: 
> > http://svn.gna.org/viewcvs/relax/branches/c_modules/maths_fns/relax_fit.h?rev=2390&r1=2389&r2=2390&view=diff
> > ==============================================================================
> > --- branches/c_modules/maths_fns/relax_fit.h (original)
> > +++ branches/c_modules/maths_fns/relax_fit.h Wed Mar 15 16:17:06 2006
> > @@ -36,11 +36,16 @@
> >  /****************************************/
> >
> >  /* Variables sent to the setup function to be stored for later use */
> > -PyArrayObject *values, *sd, *relax_times, *scaling_matrix;
> > -int *num_params, *num_times;
> > +PyArrayObject *numpy_values, *numpy_sd, *numpy_relax_times, 
> > *numpy_scaling_matrix;
> > +int num_params, num_times;
> > +double *sd;
> >
> >  /* Variables sent to 'func', 'dfunc', and 'd2func' during optimisation */
> > -PyArrayObject *params;
> > +PyArrayObject *numpy_params;
> > +
> > +/* Pointers to contiguous PyArrayObjects */
> > +double *values, *sd, *relax_times, *scaling_matrix;
> > +double *params;
> >
> >  /* Variables used for storage during the function calls of optimisation 
> > */
> >  double back_calc[MAXTIMES];
> >
> >
> > _______________________________________________
> > Relax-commits mailing list
> > Relax-commits@xxxxxxx
> >
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