MATLAB Answers

With mxMalloc() and mxSetDoubles(), mex function crash matlab

166 views (last 30 days)
I try to build a mex interface for a C function r8mat_expm1() that calculates matrix exponential,
double *r8mat_expm1 ( int n, double a[] );
Where n is the dimension and a is the matrix.
My mex function my_expm.c is as follows,
void mexFunction(int nlhs,mxArray *plhs[], int nrhs, const mxArray *prhs[])
{
double *tmpResult;
double *inputMat;
int numRows;
numRows = mxGetM(prhs[0]);
inputMat = mxGetPr(prhs[0]);
tmpResult = mxMalloc(numRows*numRows*sizeof(*tmpResult));
tmpResult = r8mat_expm1(numRows, inputMat); // calculate matrix exponential
plhs[0] = mxCreateDoubleMatrix(numRows, numRows, mxREAL);
mxSetDoubles(plhs[0], tmpResult);
mxFree(tmpResult);
}
Which parse the input and call the computational routine r8mat_expm1().
After building on linux, I use
c=my_expm(2,[1,0;0,2]') % this is problematic, thanks Bruno Luong for pointing out
to run the compiled function. However, it just crashes matlab, and "Segmentation fault (core dumped) matlab" appears on linux terminal.
I suspect this is related to mxMalloc() and mxSetDoubles(). When I did not use these two functions, matlab will not crash. I chose to use mxSetDoubles() to fix an error, as suggested in this post.
I also tried another suggestion in that post, i.e. change r8mat_expm1() from
double *r8mat_expm1 ( int n, double a[] );
to
void r8mat_expm1 ( int n, double a[], doule output[] );
to avoid return all zeros error, but it still return all zeros.
So what is the problem behind this and how can I fix this crash error or get the right ouput instead of all zeros?
  3 Comments
Xingwang Yong
Xingwang Yong on 30 Dec 2020
The latter, but I want to do this in C language. I compiled it to see if it works by comparing its output to matlab built-in expm(). But later I found there is already a test case to demonstrate its effectiveness. So no need to compile it for comparison...

Sign in to comment.

Accepted Answer

James Tursa
James Tursa on 26 Dec 2020
Edited: James Tursa on 26 Dec 2020
You have memory leaks in your current code. E.g.,
tmpResult = mxMalloc(numRows*numRows*sizeof(*tmpResult)); // this memory gets leaked by the very next line
tmpResult = r8mat_expm1(numRows, inputMat); // leaks memory from the mxMalloc( ) call
plhs[0] = mxCreateDoubleMatrix(numRows, numRows, mxREAL); // this memory gets leaked by the very next line
mxSetDoubles(plhs[0], tmpResult); // leaks memory from the mxCreateDoubleMatrix( ) call
This leaked memory is bad but does not cause the crash.
It appears you attach native C/C++ allocated memory to an mxArray, and this will cause a crash. You can't mix native C/C++ allocated memory in an mxArray. All memory in an mxArray must come from MATLAB API memory allocation functions.
You really need to post some details about the r8mat_expm1( ) function for us to be sure about what the real problem is. But from your description it sounds like it allocates the memory for the result using native C/C++ routines (e.g., malloc or calloc) and then returns the pointer to that, which you then attach to an mxArray ... resulting in a crash. If this is true, then you will either need to change the function to use MATLAB API allocation functions, or copy the results. To copy the results you would do something like this:
#include <string.h> // for memcpy( )
#include <stdlib.h> // for free( )
double *tmpResult;
double *inputMat;
double *pr;
int numRows;
numRows = mxGetM(prhs[0]);
inputMat = mxGetDoubles(prhs[0]);
tmpResult = r8mat_expm1(numRows, inputMat); // calculate matrix exponential
plhs[0] = mxCreateDoubleMatrix(numRows, numRows, mxREAL);
pr = mxGetDoubles(plhs[0]);
memcpy(pr,tmpResult,numRows*numRows*sizeof(double));
free(tmpResult); // use free( ) for native C/C++ allocated memory
To avoid the data copy and use MATLAB API allocation functions, you would need to alter the source code of r8mat_expm1( ) and pass in the pointer instead of allocating memory inside the function. Then your mexFunction( ) code would look like this instead of the above:
double *inputMat;
double *pr;
int numRows;
numRows = mxGetM(prhs[0]);
inputMat = mxGetDoubles(prhs[0]);
plhs[0] = mxCreateDoubleMatrix(numRows, numRows, mxREAL);
pr = mxGetDoubles(plhs[0]);
r8mat_expm1(numRows, inputMat, pr); // calculate matrix exponential
And the signature for the r8mat_expm1( ) function would change to this:
void r8mat_expm1(int, double *, double *);
where the 3rd input argument is used inside r8mat_expm1( ) for the output, and no memory allocation is done inside this function.
Another way to do this is to change the malloc( ) and calloc( ) inside r8mat_expm1( ) to be mxMalloc( ) and mxCalloc( ) instead, and then attach that result to the mxArray. If you want I can post that code, but frankly it is more complicated than what I have posted above so I would see no practical reason to code it this way.
  18 Comments

Sign in to comment.

More Answers (2)

Bruno Luong
Bruno Luong on 26 Dec 2020
You must not call
mxFree(tmpResult);
Since the data is attached to the output.
  4 Comments
Xingwang Yong
Xingwang Yong on 26 Dec 2020
Yes, r8mat_expm1() called some other C sub-routines, which contains alloc() and free().
Do you have any idea how can I copy the output of 8mat_expm1(), which is double * , to the output of mex function?

Sign in to comment.


Bruno Luong
Bruno Luong on 26 Dec 2020
You seem to call
mxGetM(prhs[0])
To get dimensions of the first parameter of calling
c=my_expm(2,[1,0;0,2]')
which is 2 and not the 2x2 matrix.
Who knows what else. The mex code seem to have quality issue, which is not tolerable and resulting crash.
  7 Comments
Bruno Luong
Bruno Luong on 27 Dec 2020
Sorry, you are right I make a typo. Shoul read "The fact that you use mxMalloc before calling r8mat_expm1 "

Sign in to comment.

Community Treasure Hunt

Find the treasures in MATLAB Central and discover how the community can help you!

Start Hunting!