Using (popular) mexed c++ kdtree from fileexchange leads to Matlab system crashes.

I have matlab system errors i.e. total crashes, when I run the following kdtree implementation shared on fileexchange https://ch.mathworks.com/matlabcentral/fileexchange/21512-ataiya-kdtree ; Matlab crashes already for the there provided minimal kdtree_delete_demo.

In this demo

• two cpp files are mexed to provide two separate functions: kdtree_build and kdtree_delete;
• A c++ object is allocated via kdtree_build, and returned as a pointer to matlab
• The c++ object is deleted by a call to kdtree_delete, the pointer is provided as an argument.

When I run it:

• Mexing and creation works fine - apart of a few uninteresting c++ warnings nothing is reported in verbose mex mode.
• The crashes happen upon deletion
• With printouts I was able to pin down that the crash happens as soon as any member of the dereferenced pointer is accessed (namely tree->ndim()).

My question: Could memory persistancy be an issue for this library? As far as I can tell the kdtree library allocates memory in the standard c++ way (new/ ~) without doing any matlab related magic. It is strange that for many the library works fine. I have no experience with mexing, only with c++ and cannot judge if the library has issues or if this example not working means that something is fishy with my whole OS/compilers/system. (Windows 10, Matlab 2016b, Visual studio 2013 c++ professional)

Ps. I cannot easily switch to an alternative kdtree implementation, I try to run code which uses this implementation as 3rd party code, and I really would prefer not to start rewriting this code.

**Update****

Praise goes to Philip Borghesani who found the problem. As visual c++ longs have 4 Byte only, all occurences of long need to be replaced by intptr_t. This need to be done in the files:

• KDTree.h
• kdtree_ball_query.cpp
• kdtree_build.cpp
• kdtree_io_from_mat.cpp
• kdtree_k_neares_neighbors.cpp
• kdtree_nearest_neighbor.cpp
• kdtree_range_query.cpp

[James Tursa]

Have you contacted the author?

Answer 1

[Philip Borghesani]

After a quick look at the code I will guess it is not compatible with 64 bit windows. If the objects are allocated at memory addresses below 4gb it might work otherwise this code will cause a crash:

    static KDTree* retrieve_pointer(const mxArray* matptr){
        // retrieve pointer from the MX form
        double* pointer0 = mxGetPr(matptr);
        // check that I actually received something
        if( pointer0 == NULL )
            mexErrMsgTxt("varargin{1} must be a valid kdtree pointer\n");
        // convert it to "long" datatype (good for addresses)
        long pointer1 = (long) pointer0[0];
        // convert it to "KDTree"
        KDTree* tree = (KDTree*) pointer1;
        // check that I actually received something
        if( tree == NULL )
            mexErrMsgTxt("varargin{1} must be a valid kdtree pointer\n");
        if( tree->ndims() <= 0 )
            mexErrMsgTxt("the k-D tree must have k>0");
        return tree;
    }

The problem is that on win64 long can't store a pointer. It is possible that by changing this line to use size_t or intptr_t and fixing the corresponding code for creating the matptr the code will work but there are most likely other other problems.

Change:

         long pointer1 = (long) pointer0[0];

To

        intptr_t pointer1 = (intptr_t) pointer0[0];

[tep]

Thanks a lot for having a look! Now I feel a little bit stupid, because I also thought of the visual c++ oddity (or stupidity) of longs having 4 Byte only, and I thought I excluded it as the error source (I replaced longs by _int64 but intptr_t is a much better choice). As I wanted to document this behaviour with your proposed fix - it turns out it really fixes it -all the demos run! Who knows what I did wrong before.... I'll list all needed changes.

Thank you again and have a great day!

Answer 2

[Jnh Zhu]

我也遇到了类似的问题，matlab运行时kd树时一直提示错误使用 kdtree_nearest_neighbor

vararg{1} must be a [Nxk] matrix of N points in k dimensions。

非常感谢Philip Borghesani的建议，我将我代码中的long 替换成了 intptr_t便成功了。

Thank all of you again and have a nice day!

[FAN ZHANG]

你好，我在64位windows下使用kdtree时一直出现matlab crash，报错mex文件error，把long替换成intptr_t之后也还是这样（2017版本的kdtree看起来已经把long全部替换掉了），请问您是怎么解决的这个问题呢？可以交流一下吗？

[Jnh Zhu]

我调用的kdtree是比较早期的版本了，没替换之前出错语句就是上面说的，用long替换 intptr_t可以解决问题。但我是今年4月在做毕业设计时候才用得到这个的，我自己对这个了解也是不深，可能帮不了您。