Problem using DSS

[Max_T_]

Hi!

I'm taking my first steps at MKL and after installation and linking libraries (I have Ubuntu 12.04, 64-bit) I tried to modify the direct solver dss_sym_c.c so that I could solve my sparse symmetric system which is stored in a binary file (1 based index). I changed CSR system but after that an unclassifiable error uccured at the "reorder step" of the program. What can be the reason of it?

Here's the code:

#include<stdio.h>
#include<stdlib.h>
#include<math.h>
#include "mkl_dss.h"
#include "mkl_types.h"

MKL_INT
main ()
{
  MKL_INT i;
  _MKL_DSS_HANDLE_t handle;
  _INTEGER_t error;
  _CHARACTER_t statIn[] = "determinant";
  _DOUBLE_PRECISION_t statOut[5];
  MKL_INT opt = MKL_DSS_DEFAULTS;
  MKL_INT sym = MKL_DSS_SYMMETRIC;
  MKL_INT type = MKL_DSS_POSITIVE_DEFINITE;
  MKL_INT nRows;
  MKL_INT nCols;
  MKL_INT nNonZeros;
  MKL_INT nRhs;
  _INTEGER_t *rowIndex;
  _INTEGER_t *columns;
  _DOUBLE_PRECISION_t *values;
  _DOUBLE_PRECISION_t *rhs;
  _DOUBLE_PRECISION_t *solValues;

  FILE *In;
  MKL_INT n, nz;
  MKL_INT *I = NULL, *J = NULL;
  _DOUBLE_PRECISION_t *val = NULL, *sol = NULL, *RHS = NULL;

  if ( ( In = fopen ("matr_rhs_binary", "rb" ) ) == NULL ) {
    fprintf (stderr, "Error opening file\n");		
    return (-1);
  }

  fread ( &n, sizeof(MKL_INT), 1, In );
  printf ("n = %d\n", n);	

  fread ( &nz, sizeof(MKL_INT), 1, In );
  printf ("nz = %d\n", nz);

  I = (MKL_INT *) malloc ( sizeof (I[0]) * (n + 1));                             // csr row pointers for matrix A
  J = (MKL_INT *) malloc ( sizeof (J[0]) * nz);                                  // csr column indices for matrix A
  val = (_DOUBLE_PRECISION_t *) malloc ( sizeof (val[0]) * nz);                  // csr values for matrix A	
  sol = (_DOUBLE_PRECISION_t *) malloc ( sizeof (sol[0]) * n);
  RHS = (_DOUBLE_PRECISION_t *) malloc ( sizeof (RHS[0]) * n);

  for (i = 0; i < n + 1; i++)
    fread ( &(I), sizeof(I[0]), 1, In );
  for (i = 0; i < nz; i++)
    fread ( &(val), sizeof(val[0]), 1, In );
  for (i = 0; i < nz; i++)
    fread ( &(J), sizeof(J[0]), 1, In );
  for (i = 0; i < n; i++)
    fread ( &(RHS), sizeof(RHS[0]), 1, In);	
	
  fclose (In);

  nRows = n;
  nCols = n;
  nNonZeros = nz;
  nRhs = n;

  rowIndex = (_INTEGER_t *) malloc ( sizeof (rowIndex[0]) * (nRows + 1) );
  columns = (_INTEGER_t *) malloc ( sizeof (columns[0]) * nNonZeros );
  values = (_DOUBLE_PRECISION_t *) malloc ( sizeof (values[0]) * nNonZeros );
  rhs = (_DOUBLE_PRECISION_t *) malloc ( sizeof (rhs[0]) * nCols );
  solValues = (_DOUBLE_PRECISION_t *) malloc ( sizeof (solValues[0]) * nCols );

  for (i = 0; i < n; i++) {
    rowIndex = I;
    rhs = RHS;
  }
  for (i = 0; i < nz; i++) {
    columns = J;
    values = val;
  }

  error = dss_create (handle, opt);
  if (error != MKL_DSS_SUCCESS)
    goto printError;

  error = dss_define_structure (handle, sym, rowIndex, nRows, nCols,
				columns, nNonZeros);
  if (error != MKL_DSS_SUCCESS)
    goto printError;

  error = dss_reorder (handle, opt, 0);
  if (error != MKL_DSS_SUCCESS)
    goto printError;

  error = dss_factor_real (handle, type, values);
  if (error != MKL_DSS_SUCCESS)
    goto printError;

  error = dss_solve_real (handle, opt, rhs, nRhs, solValues);
  if (error != MKL_DSS_SUCCESS)
    goto printError;
printf ("check\n");

  if (nRows < nNonZeros)
    {
      error = dss_statistics (handle, opt, statIn, statOut);
      if (error != MKL_DSS_SUCCESS)
	goto printError;

      printf (" determinant power is %g \n", statOut[0]);
      printf (" determinant base is %g \n", statOut[1]);
      printf (" Determinant is %g \n", (pow (10.0, statOut[0])) * statOut[1]);
    }

  error = dss_delete (handle, opt);
  if (error != MKL_DSS_SUCCESS)
    goto printError;

  printf (" Solution array: ");
  for (i = 0; i < nCols; i++)
    printf (" %g", solValues);
  printf ("\n");
  exit (0);
printError:
  printf ("Solver returned error code %d\n", error);
  exit (1);
}

And another question: When I compile pardiso_sym_c.c, several errors occur: undefined references to functions like atan2, sin, cos, log10, etc though I compile with an -lm option. Is it because of:

/usr/bin/ld: skipping incompatible /opt/intel/composer_xe_2013_sp1.0.080/mkl/lib/ia32/libmkl_intel_thread.so when searching for -lmkl_intel_thread
/usr/bin/ld: skipping incompatible /opt/intel/composer_xe_2013_sp1.0.080/mkl/lib/ia32/libmkl_intel_thread.a when searching for -lmkl_intel_thread

/usr/bin/ld: skipping incompatible /opt/intel/composer_xe_2013_sp1.0.080/mkl/lib/ia32/libmkl_core.so when searching for -lmkl_core
/usr/bin/ld: skipping incompatible /opt/intel/composer_xe_2013_sp1.0.080/mkl/lib/ia32/libmkl_core.a when searching for -lmkl_core

How can I fix it?

Thanks! Any help is appreciated!

[Gennady_F_Intel]

- check if you fill the input matrix be the right way in accordance with CSR. DSS interface dosn't provide  Matrix Checker functionality. see Pardiso ipatm(27).

- how did you link the example? please check with MKL Linker Adviser how to do that.  Here is the link to LA: http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor

[Max_T_]

Thanks for your quick response!

To link the example I do the following steps:

export MKLROOT=/opt/intel/mkl
export MKLPATH=$MKLROOT/lib/intel64
export MKLINCLUDE=$MKLROOT/include
source $MKLROOT/bin/mklvars.sh intel 64

Then according to my specification:

g++ pardiso_sym_c.c -o pardiso -L$MKLPATH -I$MKLINCLUDE -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -ldl

It gives:

/opt/intel/mkl/lib/intel64/libmkl_core.so: undefined reference to `logf'
/opt/intel/mkl/lib/intel64/libmkl_core.so: undefined reference to `atan2'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `sin'
/opt/intel/mkl/lib/intel64/libmkl_core.so: undefined reference to `fabs'
/opt/intel/mkl/lib/intel64/libmkl_core.so: undefined reference to `exp'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `cos'
/opt/intel/mkl/lib/intel64/libmkl_core.so: undefined reference to `sqrt'
/opt/intel/mkl/lib/intel64/libmkl_intel_lp64.so: undefined reference to `log'
/opt/intel/mkl/lib/intel64/libmkl_core.so: undefined reference to `pow'
/opt/intel/mkl/lib/intel64/libmkl_core.so: undefined reference to `log10'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `floor'
/opt/intel/mkl/lib/intel64/libmkl_core.so: undefined reference to `ceil'
/opt/intel/mkl/lib/intel64/libmkl_core.so: undefined reference to `expf'

Link advisor aslo suggests this option:

 -DMKL_ILP64 -m64 -I$(MKLROOT)/include

But it doesn't solve the problem.

Is it possible to use iparm(27) in this program? Or should I compile pardiso_sym_c.c first and try my system there?

[mecej4]

Does the reported 

source $MKLROOT/bin/mklvars.sh intel 64

contain just a typographical error, the real command being 

source $MKLROOT/bin/mklvars.sh intel64

?

[Max_T_]

Thanks, but it's really just a misprint in my post, of course I used

source $MKLROOT/bin/mklvars.sh intel64

This is strange: usually errors concerning 'logf', 'sin', 'cos', etc appear when -lm is missed. So this problem remains unsolved, but the error which occured during reordering was fixed: I didn't pass the last element to rowIndex, and now it works until dss_solve_real. Here memory crashes:

https://software.intel.com/en-us/forums/topic/509259