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Jonathan_C_2

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10-28-2015
06:47 PM

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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};

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: 115: rows: 135: 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?**

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Ying_H_Intel

Employee

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10-29-2015
06:29 PM

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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

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10-29-2015
07:40 PM

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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?

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