Community
cancel
Showing results for 
Search instead for 
Did you mean: 
Jonathan_C_2
Beginner
51 Views

Strange sparse_matrix_checker() Error in MKL with Matlab MEX file

I am performing a simple test of a sparse matrix stores in CRS3 format with sparse_matrix_checker(). When I perform this test in the matrix_check.c MKL example code, it passes as expected. Also, I compiled the examples with GCC.

However, when I perform an identical check in a Matlab C++ MEX function (also compiled with GCC), I get a strange error that doesn't make sense. The matrix is identical to the one given in the MKL documentation at https://software.intel.com/en-us/node/471374. I am using zero-based indexing. Therefore, my row, column and value arrays are:

/* Matrix data. */
    MKL_INT n = 5;
    MKL_INT ia[6] = {0,3,5,8,11,13};
    MKL_INT ja[13] =
      {0,1,3,0,1,2,3,4,0,2,3,1,4};
    double a[13] =
      {1,-1,-3,-2,5,4,6,4,-4,2,7,8,-5};

BA54DCA8-3253-4EEA-8E8F-CA40CA13C022-imageId=6E57861E-B280-4A7B-AACB-06FC74ECFC79.gif

The parameters of my matrix check are:

    pt.n = n;
    pt.csr_ia = ia;
    pt.csr_ja = ja;
    pt.indexing         = MKL_ZERO_BASED;
    pt.matrix_structure = MKL_GENERAL_STRUCTURE;
    pt.print_style      = MKL_C_STYLE; 
    pt.message_level    = MKL_PRINT;

Again, when I run this check in matrix_check.c compiled from the examples, it passes. But when I compile this in a Matlab MEX, I get the error:

Matrix check result code: 21 (MKL_SPARSE_CHECKER_NON_MONOTONIC)
Matrix check details: (1, 0, 0)

However, this error doesn't make sense because ia[1] and ia[2] are not zero. Instead, they are 3 and 5. Thus, it seems there is some memory read error by the MKL library.

Note, I am compiling the MEX file with the following compiler options using G++ 4.9.2:

LDFLAGS=-m64 -I/opt/intel/compilers_and_libraries_2016.0.109/linux/mkl/include -L/opt/intel/mkl/lib/intel64 -lmkl_core -lmkl_intel_ilp64 -lmkl_gnu_thread myTest.cpp

Also, I verified that the matrix is in fact stored correctly by reading it out in the Matlab MEX file:

0: 	val: 1	cols: 0	rows: 0
1: 	val: -1	cols: 1	rows: 3
2: 	val: -3	cols: 3	rows: 5
3: 	val: -2	cols: 0	rows: 8
4: 	val: 5	cols: 1	rows: 11
5:			rows: 13
5: 	val: 4	cols: 2
6: 	val: 6	cols: 3
7: 	val: 4	cols: 4
8: 	val: -4	cols: 0
9: 	val: 2	cols: 2
10: 	val: 7	cols: 3
11: 	val: 8	cols: 1
12: 	val: -5	cols: 4

It seems to me that there is some issue caused by the way I am compiling this test that causes the MKL library to access memory differently than how it is being allocated. Does this make sense? Any thoughts or ideas for me to check?

0 Kudos
2 Replies
Ying_H_Intel
Employee
51 Views

Hi Jonathen,

I haven't test.  But a tiny issue about mkl_intel_lp64 and mkl_intel_ilp64.  Do you know the int  type in mex are 64bit or 32bit?

Anyway,   you may try  -L/opt/intel/mkl/lib/intel64 -lmkl_core -lmkl_intel_lp64 and see if it works?

or add -DMKL_ILP64 with mkl_intel_ilp64 in compile command line

Best Regards,

Ying

 

mecej4
Black Belt
51 Views

From what you have posted I cannot gather what the mex-function arguments are. In particular, are you defining the sparse matrix in Matlab and passing the matrix (and other arguments) to the mex-function? If so, where do you convert from the COO representation used in Matlab to the CSR representation used in MKL/Pardiso?

Can we see the source code for the mex-function? Which version of Matlab do you use?

Reply