Re: [MUMmer-help] MUMmer patch for dynamic memory allocation.

[Adam Phillippy <aphillippy@gmail.com>]

Hi Charles,
I tested the patch you forwarded and it was nonfunctional. It attempted to construct a two-dimensional array "D" of dimensions (M+1 x N+1) like so:

   D_buf  = (int  *) calloc ( (M+1)*(N+1), sizeof(int) ) ;
   D  = &D_buf ;

This compiles, but doesn't work. There is no way to allocate a 2D matrix dynamically by only using malloc. To do the proper pointer arithmetic the D[row][col] operators used later in this source need to know at least one dimension of the matrix. This is known for static arrays, but not for dynamic arrays. The patch you forwarded always leads to a memory access error.

I implemented my own patch that handles the 2D pointer arithmetic in a small wrapper class. This new version is tested and dynamically allocates the memory, so it should fit your needs. You can find the new version of the "annotate.cc" file here:

http://mummer.cvs.sourceforge.net/viewvc/mummer/MUMmer/src/tigr/annotate.cc?revision=1.3&view=markup

This is included in a new MUMmer release (v3.22) I cut last week.

Best,
-Adam

On Sun, Aug 2, 2009 at 12:07 AM, Charles Plessy <plessy@debian.org> wrote:

Le Thu, Jul 30, 2009 at 03:25:53PM -0400, Adam Phillippy a écrit :

>    This patch looks fine. I saw it awhile back, but it got lost in the
>    shuffle and was never applied.  I'm on vacation right now, but I'll apply
>    it to our distribution when I return.

Thank you very much. In the meantime, an improved version was prepared by Boyd
Stephen Smith Jr. I updated our subversion repository accordingly, and you can
retreive it with the following link:

http://svn.debian.org/wsvn/debian-med/trunk/packages/mummer/trunk/debian/patches/01sm_src_tigr.diff

The difference with the previous patch is the following:

   int  Errors, Tmp;
   long int  i, j, Ct;

-   assert ( D_buf  = (int  *) calloc ( (M+1)*(N+1), sizeof(int) ) ) ;
+   assert ( SIZE_MAX / (M+1) >= (N+1) ) ;
+   D_buf  = (int  *) calloc ( (M+1)*(N+1), sizeof(int) ) ;
+   assert ( D_buf ) ;
   D  = &D_buf ;
-   assert ( Op_buf = (char *) calloc ( (M+1)*(N+1), sizeof(char) ) ) ;
+   Op_buf = (char *) calloc ( (M+1)*(N+1), sizeof(char) ) ;
+   assert ( Op_buf ) ;
   Op = &Op_buf ;
-   assert ( Show_A = (char *) calloc ( 2*(M+1) , sizeof(char) ) ) ;
-   assert ( Show_B = (char *) calloc ( 2*(N+1) , sizeof(char) ) ) ;
+
+   assert ( SIZE_MAX >> 1 >= (M+1) ) ;
+   Show_A = (char *) calloc ( 2*(M+1) , sizeof(char) ) ;
+   assert ( Show_A ) ;
+   Show_B = (char *) calloc ( 2*(N+1) , sizeof(char) ) ;
+   assert ( Show_B ) ;

   D [0] [0] = 0;
   Op [0] [0] = 'a';

Have a nice vacation !

--

Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan