[MUMmerGPU-devel] MUMmer GPU Segmentation fault and a few fixes

[Jaakan S. <jaa...@gm...>]

I did read through the thread "Re: [MUMmerGPU-devel] MUMmer GPU build error"

that did help me. I'm also at the point were CPU using the -C switch
works and Segmentation faults without it.
I have access to NV GPU+RHEL5 x64 server, if you need me to send you
the gdb/debuged output


I might have done a few more changes to get this to run on RHEL5 x64,
I can tar.gz my current source for this with my changes if anyone
needs to look at all of the changes.

I hope I can help.

--Jaakan

Here are some changes I made to fix the following warnings on 64bit
linux and don't forget to add " #include <stdint.h> "
"warning: conversion from pointer to smaller integer"
 this " * timer = (unsigned int) ptr " should be "  * timer = (uintptr_t) ptr"

"warning: cast to pointer from integer of different size"

basicly "unsigned int ptr" needs to be "uintptr_t ptr"



mummergpu.cu
...

#include <stdint.h>
// includes, kernels
#include "common.cu"
#include "mummergpu.h"
#include "mummergpu_kernel.cu"

#define ulong4 uint32_t

....

// Timer management
struct Timer_t
{
  struct timeval start_m;
  struct timeval end_m;
};

void createTimer(unsigned int * timer)
{
  unsigned int * ptr = (unsigned int *) malloc(sizeof(struct Timer_t));
  memset(ptr, 0, sizeof(struct Timer_t));

   // * timer = (unsigned int) ptr;
   * timer = (uintptr_t) ptr;
}

// void startTimer(unsigned int ptr)
void startTimer(uintptr_t ptr)
{
  gettimeofday(&(((struct Timer_t *)ptr)->start_m), NULL);
}

// void stopTimer(unsigned int ptr)
void stopTimer(uintptr_t ptr)
{
  gettimeofday(&(((struct Timer_t *)ptr)->end_m), NULL);
}

//float getTimerValue(unsigned int ptr)
float getTimerValue(uintptr_t ptr)
{
  Timer_t * timer = (Timer_t*) ptr;

  if (timer == NULL)
  {
    fprintf(stderr, "Uninitialized timer!!!\n");
    return 0.0;
  }

  if (timer->end_m.tv_sec == 0) { stopTimer(ptr); }

  return  (float) (1000.0 * (timer->end_m.tv_sec - timer->start_m.tv_sec)
                + (0.001 *  (timer->end_m.tv_usec - timer->start_m.tv_usec)));
}

//void deleteTimer(unsigned int ptr)
void deleteTimer(uintptr_t ptr)
{
  free((Timer_t *)ptr);
}

....

I changed    " ulong4 data " to " unsigned int data " in the following.

common.cu
....

#ifndef COMMON_CU__
#define COMMON_CU__ 1
// Children are labeled as ACGT$
const int basecount = 5;

// Note: max pixel size is 16 bytes

const unsigned char DNA_A = 'A';
const unsigned char DNA_C = 'B';
const unsigned char DNA_G = 'C';
const unsigned char DNA_T = 'D';
const unsigned char DNA_S = 'E';

// 4 bytes
struct TextureAddress
{
  union
  {
    unsigned int data;

    struct
    {
	  unsigned short x;
      unsigned short y;
    };
  };
};

// Store the start, end coordinate of node, and $link in 1 pixel
struct PixelOfNode
{
  union
  {
    // ulong4 data;
	unsigned int data;
    struct
    {
      int start;
      int end;
      TextureAddress childD;
      TextureAddress suffix;
    };
  };
};

// Store the ACGT links in 1 pixel
struct PixelOfChildren
{
  union
  {
    // ulong4 data;
	unsigned int data;
	TextureAddress children[4];
  };
};

#define FORWARD   0x0000
#define REVERSE   0x8000
#define FRMASK    0x8000
#define FRUMASK   0x7FFF


#endif