[Insight-users] about multithreading in ITK (Andriy Fedorov)

[Bill Lorensen]

I think -fopenmp is a compiler flag, not a linker flag.

Try changing CMAKE_C_FLAGS instead of CMAKE_EXE_LINKER_FLAGS

Bill

2009/1/22 Kaveh Kohan <kaveh.kohan at yahoo.com>:
> Thank you Andriy for your reply.
>
> Actually my problem is way simpler than that. I want to multiply matrices
> (ordinary matrix-matrix multiplication and element-wise multiplication) but
> my algorithm involves iterative and large matrix multiplication. I tried to
> exploit multi-threading by openmp (not openmpi). I googled it and find this
> simple code for multi-threaded matrix-matrix multiplication:
>
> from: https://computing.llnl.gov/tutorials/openMP/samples/C/omp_mm.c
> /******************************************************************************
> * FILE: omp_mm.c
> * DESCRIPTION:
> *   OpenMp Example - Matrix Multiply - C Version
> *   Demonstrates a matrix multiply using OpenMP. Threads share row
> iterations
> *   according to a predefined chunk size.
> * AUTHOR: Blaise Barney
> * LAST REVISED: 06/28/05
> ******************************************************************************/
> #include <omp.h>
> #include <stdio.h>
> #include <stdlib.h>
>
> #define NRA 62                 /* number of rows in matrix A */
> #define NCA 15                 /* number of columns in matrix A */
> #define NCB 7                  /* number of columns in matrix B */
>
> int main (int argc, char *argv[])
> {
> int    tid, nthreads, i, j, k, chunk;
> double    a[NRA][NCA],           /* matrix A to be multiplied */
>     b[NCA][NCB],           /* matrix B to be multiplied */
>     c[NRA][NCB];           /* result matrix C */
>
> chunk = 10;                    /* set loop iteration chunk size */
>
> /*** Spawn a parallel region explicitly scoping all variables ***/
> #pragma omp parallel shared(a,b,c,nthreads,chunk) private(tid,i,j,k)
>   {
>   tid = omp_get_thread_num();
>   if (tid == 0)
>     {
>     nthreads = omp_get_num_threads();
>     printf("Starting matrix multiple example with %d threads\n",nthreads);
>     printf("Initializing matrices...\n");
>     }
>   /*** Initialize matrices ***/
>   #pragma omp for schedule (static, chunk)
>   for (i=0; i<NRA; i++)
>     for (j=0; j<NCA; j++)
>       a[i][j]= i+j;
>   #pragma omp for schedule (static, chunk)
>   for (i=0; i<NCA; i++)
>     for (j=0; j<NCB; j++)
>       b[i][j]= i*j;
>   #pragma omp for schedule (static, chunk)
>   for (i=0; i<NRA; i++)
>     for (j=0; j<NCB; j++)
>       c[i][j]= 0;
>
>   /*** Do matrix multiply sharing iterations on outer loop ***/
>   /*** Display who does which iterations for demonstration purposes ***/
>   printf("Thread %d starting matrix multiply...\n",tid);
>   #pragma omp for schedule (static, chunk)
>   for (i=0; i<NRA; i++)
>     {
>     printf("Thread=%d did row=%d\n",tid,i);
>     for(j=0; j<NCB; j++)
>       for (k=0; k<NCA; k++)
>         c[i][j] += a[i][k] * b[k][j];
>     }
>   }   /*** End of parallel region ***/
>
> /*** Print results ***/
> printf("******************************************************\n");
> printf("Result Matrix:\n");
> for (i=0; i<NRA; i++)
>   {
>   for (j=0; j<NCB; j++)
>     printf("%6.2f   ", c[i][j]);
>   printf("\n");
>   }
> printf("******************************************************\n");
> printf ("Done.\n");
>
> }
>
>
> it compiles and works perfectly when I type:
>>> g++  omp_mm.c  -o omp_mm -fopenmp
>
> but when I add following lines to my CMakefile:
> SET(CurrentExe "omp_mm")
> ADD_EXECUTABLE(${CurrentExe} omp_mm.c ${SRCS} ${HDRS})
> TARGET_LINK_LIBRARIES(${CurrentExe} ${Libraries})
>
> and change :
> CMAKE_EXE_LINKER_FLAGS : -fopenmp
>
> here is what I get in compilation time:
> /home/kaveh/Src/ITKNMF/Source/omp_mm.c: In function 'main':
> /home/kaveh/Src/ITKNMF/Source/omp_mm..c:28: warning: ignoring #pragma omp
> parallel
> /home/kaveh/Src/ITKNMF/Source/omp_mm.c:38: warning: ignoring #pragma omp for
> /home/kaveh/Src/ITKNMF/Source/omp_mm.c:42: warning: ignoring #pragma omp for
> /home/kaveh/Src/ITKNMF/Source/omp_mm.c:46: warning: ignoring #pragma omp for
> /home/kaveh/Src/ITKNMF/Source/omp_mm.c:54: warning: ignoring #pragma omp for
> /home/kaveh/Src/ITKNMF/Source/omp_mm.c:76: warning: control reaches end of
> non-void function
>
> and no matter how I change the enviroment variable of $OMP_NUM_THREADS, it
> always lunches one thread. Unlike when I compile it with command line
> (without cmake), in which it works perfectly!!!!
>
> Now, I am confused!! There should be something wrong with cmake but how can
> I fix it?
>
> Second question is, ITK uses LAPACK and LAPACK is multithreaded (corret me
> if I am wrong). If yes how can I set number of threads for matrix
> multiplication?
>
> Regards,
> Kaveh
>
> Kaveh,
>
> You can look at PETSc for parallel linear algebra routines:
> http://www.mcs.anl.gov/petsc/petsc-as/.
>
> In the past I used PETSc in conjunction with ITK code. You have to be
> careful to make sure that both PETSc and ITK are compiled with the
> same mpicc/mpicxx/mpiCC compiler.
>
> Hope this helps
>
> Andriy Fedorov
>
>
>
>> Date: Wed, 21 Jan 2009 09:01:08 -0800 (PST)
>> From: Kaveh Kohan <kaveh.kohan at yahoo.com>
>> Subject: [Insight-users] about multithreading in ITK
>> To: insight-users at itk.org
>> Message-ID: <352748.10256.qm at web59915.mail.ac4.yahoo.com>
>> Content-Type: text/plain; charset="us-ascii"
>>
>> Hello All,
>>
>> I have a general question about multi-threading in ITK and I would be
>> thankful if anybody
>> answer:
>>
>> As far as I know, ITK uses vnl for linear albera operation but it is not
>> multithreaded (Please correct me if I am wrong). While many complicated
>> algorithm are already multithreaded in ITK, was there any technical reason
>> that
>> linear algebra operation (like matrix-matrix multiplication, solving
>> linear
>> system, LU, ....) is not multithreaded? Perhaps it didn't have priority.
>>
>> I would be appreciated if you tell what is the best way to implement
>> efficient,
>> multithread linear algebra operation. In case it is not a good idea to use
>> ITK
>> API for multithreading of such operation, is there any third party
>> multithreaded
>> libray for linear algebra operation that I can link to ITK.
>>
>>
>> Regards,
>> Kaveh
>>
>>
>>
>>
>
>
>
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