Re: Memory contents mysteriously changing

Mark <>
Fri, 22 Jan 2010 12:46:35 -0800 (PST)
Hi Victor,

Thanks for your response and for your questions. Just having someone
ask me questions helps me make progress in debugging.

T * data;

A pointer? A *naked* pointer? Why? Couldn't you use 'vector<T>' or
some other container?

Good point. I started out as a C programmer once upon a time and old
habits die hard. ;-)
I went ahead and changed it to a vector<T>.

Inside my write_to_file() method, I am invoking a library called SILO

<shrug> You shouldn't assume that we know anything about it.

I'm not assuming you do. Nor do I know much about it, really. It's
just a library that for me is essentially a black box.

So, here you pass 'data'. Has it been initialized, assigned to
anything? You don't show that part of your code. Memory management can
become tricky. Are you sure you're doing it right?

I agree, memory management is tricky and it is likely the source of my
problems. I'll post the rest of the code below. I apologize for not
posting more code in the first place... I have hundreds of lines of
code and I didn't want to overwhelm this forum with code. I tried to
pick "relevant" lines but clearly I should've included more. So since
you apparently don't mind reading my code, here is a larger sample
(but still a sample nonetheless)...

template <class T>
class Mesh3d {


        // constructors and initialization:

        ~Mesh3d() { }

        Mesh3d(float Xmin, float Xmax, float Ymin, float Ymax, float
Zmin, float Zmax, int Xres, int Yres, int Zres);
                        // creates a 3d mesh on a rectangular volume
with the appropriate maxes and mins as the boundaries
                        // of the volume; the resolution in each X, Y,
and Z direction is given by Xres, Yres, and Zres

        void zero(); // sets the value of every
grid point to 0
                                        // only call this if T is of
type float, int, etc

        // mesh properties:

        float xmin, xmax, ymin, ymax, zmin, zmax, xinc, yinc, zinc;
        int gridpoints;
        int xgridmax, ygridmax, zgridmax;


        void construct_mesh(float Xmin, float Xmax, float Ymin, float
Ymax, float Zmin, float Zmax, int Xres, int Yres, int Zres);
                        // helper function for the constructors

        // mesh data:

        vector<T> data;

template <class T>
Mesh3d<T>::Mesh3d(float Xmin, float Xmax, float Ymin, float Ymax,
float Zmin, float Zmax, int Xres, int Yres, int Zres)
        construct_mesh(Xmin, Xmax, Ymin, Ymax, Zmin, Zmax, Xres, Yres,

template <class T>
void Mesh3d<T>::construct_mesh(float Xmin, float Xmax, float Ymin,
float Ymax, float Zmin, float Zmax, int Xres, int Yres, int Zres)
        xmin = Xmin;
        xmax = Xmax;
        ymin = Ymin;
        ymax = Ymax;
        zmin = Zmin;
        zmax = Zmax;

        xgridmax = Xres;
        ygridmax = Yres;
        zgridmax = Zres;

        gridpoints = xgridmax * ygridmax * zgridmax;

        xinc = (xmax - xmin) / (xgridmax-1);
        yinc = (ymax - ymin) / (ygridmax-1);
        zinc = (zmax - zmin) / (zgridmax-1);

        xmax = xmin + (xgridmax-1)*xinc;
        ymax = ymin + (ygridmax-1)*yinc;
        zmax = zmin + (zgridmax-1)*zinc;


        // initialize data to all zeroes; for now I'm assuming that T
will be of type float

template <class T>
void Mesh3d<T>::zero()
        for(int i=0; i<gridpoints; i++)
                data[i] = 0;

template <class T>
void Mesh3d<T>::writesilo(string filename)
     // create the coordinate grid
     float * xcoords = new float[xgridmax];
     float * ycoords = new float[ygridmax];
     float * zcoords = new float[zgridmax];

     for(int i=0; i<xgridmax; i++) {
        xcoords[i] = itox(i);
     for(int i=0; i<ygridmax; i++) {
        ycoords[i] = jtoy(i);
     for(int i=0; i<zgridmax; i++) {
        zcoords[i] = ktoz(i);

     float * coordinates[3] = {xcoords, ycoords, zcoords};

     // open the output file
     DBfile * file = NULL;
     file = DBCreate(filename.c_str(), DB_CLOBBER, DB_LOCAL, NULL,

     // construct the quad mesh
     int ndims = 3;
     int dims[3] = {xgridmax, ygridmax, zgridmax};

     DBPutQuadmesh(file, "SPH_data", NULL, coordinates, dims, ndims,

     // collect the density data (later this will be more complicated
than a simple 1 to 1 assign)
     float density[gridpoints];
     for(int i=0; i<gridpoints; i++) density[i] = data[i];

     // write density data to the quad mesh
     DBPutQuadvar1(file, "density", "SPH_data", density, dims, ndims,


And the code that utilizes this Mesh3d class:

int main(int argc, char** argv) {

  if (argc < 5) {
        printf("Usage: %s <gadget_snapshot> xdim ydim zdim\n",argv
        return 0;

  snapshot *snap = new snapshot();


  vector<float> bb = snap->getBB();

  printf("Bounding box:\nMinima: x = %f, y = %f, z = %f\nMaxima: x =
%f, y = %f, z = %f\n",bb[0],bb[2],bb[4],bb[1],bb[3],bb[5]);

  int xdim = atoi(argv[2]);
  int ydim = atoi(argv[3]);
  int zdim = atoi(argv[4]);
  Mesh3d<float> * mesh = new Mesh3d<float>(bb[0], bb[1], bb[2], bb[3],
bb[4], bb[5], xdim, ydim, zdim);

  string fn("mesh.silo");
  if (snap->convert_to_mesh(mesh)) {


The mesh object above is populated with data during the
convert_to_mesh method. By using a debugger I see the data contained
in the mesh is what I want. Now I want to output that data to a file
using the SILO library, and that is done inside the writesilo()
method. Unfortunately, within the writesilo() method, the data in the
mesh object is being changed during the line that includes a call to
DBCreate(). I don't know why. Thanks for any insight.


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