You did not answer my question from yesterday: If you run the Openmp compiled version WITHOUT the
-threadcomm_nthreads 1 -threadcomm_type openmp command line options is it still slow? On Sep 23, 2013, at 1:33 PM, Danyang Su <[email protected]> wrote: > Hi Shri, > > It seems that the problem does not result from the affinities setting for > threads. I have tried several settings, the threads are set to different > cores, but there is no improvement. > > Here is the information of package, core and thread maps > > OMP: Info #204: KMP_AFFINITY: decoding x2APIC ids. > OMP: Info #202: KMP_AFFINITY: Affinity capable, using global cpuid leaf 11 > info > OMP: Info #154: KMP_AFFINITY: Initial OS proc set respected: > {0,1,2,3,4,5,6,7,8,9,10,11} > OMP: Info #156: KMP_AFFINITY: 12 available OS procs > OMP: Info #157: KMP_AFFINITY: Uniform topology > OMP: Info #179: KMP_AFFINITY: 1 packages x 6 cores/pkg x 2 threads/core (6 > total cores) > OMP: Info #206: KMP_AFFINITY: OS proc to physical thread map: > OMP: Info #171: KMP_AFFINITY: OS proc 0 maps to package 0 core 0 thread 0 > OMP: Info #171: KMP_AFFINITY: OS proc 1 maps to package 0 core 0 thread 1 > OMP: Info #171: KMP_AFFINITY: OS proc 2 maps to package 0 core 1 thread 0 > OMP: Info #171: KMP_AFFINITY: OS proc 3 maps to package 0 core 1 thread 1 > OMP: Info #171: KMP_AFFINITY: OS proc 4 maps to package 0 core 2 thread 0 > OMP: Info #171: KMP_AFFINITY: OS proc 5 maps to package 0 core 2 thread 1 > OMP: Info #171: KMP_AFFINITY: OS proc 6 maps to package 0 core 3 thread 0 > OMP: Info #171: KMP_AFFINITY: OS proc 7 maps to package 0 core 3 thread 1 > OMP: Info #171: KMP_AFFINITY: OS proc 8 maps to package 0 core 4 thread 0 > OMP: Info #171: KMP_AFFINITY: OS proc 9 maps to package 0 core 4 thread 1 > OMP: Info #171: KMP_AFFINITY: OS proc 10 maps to package 0 core 5 thread 0 > OMP: Info #171: KMP_AFFINITY: OS proc 11 maps to package 0 core 5 thread 1 > OMP: Info #144: KMP_AFFINITY: Threads may migrate across 1 innermost levels > of machine > > > And here is the internal thread bounding with different kmp_affinity settings: > > 1. KMP_AFFINITY=verbose,granularity=thread,compact > > OMP: Info #147: KMP_AFFINITY: Internal thread 0 bound to OS proc set {0} > OMP: Info #147: KMP_AFFINITY: Internal thread 1 bound to OS proc set {1} > OMP: Info #147: KMP_AFFINITY: Internal thread 2 bound to OS proc set {2} > OMP: Info #147: KMP_AFFINITY: Internal thread 3 bound to OS proc set {3} > > 2. KMP_AFFINITY=verbose,granularity=fine,compact > > OMP: Info #147: KMP_AFFINITY: Internal thread 0 bound to OS proc set {0} > OMP: Info #147: KMP_AFFINITY: Internal thread 1 bound to OS proc set {1} > OMP: Info #147: KMP_AFFINITY: Internal thread 2 bound to OS proc set {2} > OMP: Info #147: KMP_AFFINITY: Internal thread 3 bound to OS proc set {3} > > 3. KMP_AFFINITY=verbose,granularity=fine,compact,1,0 > > OMP: Info #147: KMP_AFFINITY: Internal thread 0 bound to OS proc set {0} > OMP: Info #147: KMP_AFFINITY: Internal thread 1 bound to OS proc set {2} > OMP: Info #147: KMP_AFFINITY: Internal thread 2 bound to OS proc set {4} > OMP: Info #147: KMP_AFFINITY: Internal thread 3 bound to OS proc set {6} > > 4. KMP_AFFINITY=verbose,scatter > > OMP: Info #147: KMP_AFFINITY: Internal thread 0 bound to OS proc set {0,1} > OMP: Info #147: KMP_AFFINITY: Internal thread 1 bound to OS proc set {2,3} > OMP: Info #147: KMP_AFFINITY: Internal thread 2 bound to OS proc set {4,5} > OMP: Info #147: KMP_AFFINITY: Internal thread 3 bound to OS proc set {6,7} > > 5. KMP_AFFINITY=verbose,compact (For this setting, two threads are assigned > to the same core) > > OMP: Info #147: KMP_AFFINITY: Internal thread 0 bound to OS proc set {0,1} > OMP: Info #147: KMP_AFFINITY: Internal thread 1 bound to OS proc set {0,1} > OMP: Info #147: KMP_AFFINITY: Internal thread 2 bound to OS proc set {2,3} > OMP: Info #147: KMP_AFFINITY: Internal thread 3 bound to OS proc set {2,3} > > 6. KMP_AFFINITY=verbose,granularity=core,compact (For this setting, two > threads are assigned to the same core) > > OMP: Info #147: KMP_AFFINITY: Internal thread 0 bound to OS proc set {0,1} > OMP: Info #147: KMP_AFFINITY: Internal thread 1 bound to OS proc set {0,1} > OMP: Info #147: KMP_AFFINITY: Internal thread 2 bound to OS proc set {2,3} > OMP: Info #147: KMP_AFFINITY: Internal thread 3 bound to OS proc set {2,3} > > The first 4 settings can assign threads to a distinct core, but the problem > is not solved. > > Thanks, > > Danyang > > > > On 22/09/2013 8:00 PM, Shri wrote: >> I think this is definitely an issue with setting the affinities for threads, >> i.e., the assignment of threads to cores. Ideally each thread should be >> assigned to a distinct core but in your case all the 4 threads are getting >> pinned to the same core resulting in such a massive slowdown. Unfortunately, >> the thread affinities for OpenMP are set through environment variables. For >> Intel's OpenMP one needs to define the thread affinities through the >> environment variable KMP_AFFINITY. See this document here >> http://software.intel.com/sites/products/documentation/studio/composer/en-us/2011Update/compiler_c/optaps/common/optaps_openmp_thread_affinity.htm. >> Try setting the affinities via KMP_AFFINITY and let us know if it works. >> >> Shri >> On Sep 21, 2013, at 11:06 PM, Danyang Su wrote: >> >>> Hi Shri, >>> >>> Thanks for your info. It can work with the option -threadcomm_type openmp. >>> But another problem arises, as described as follows. >>> >>> The sparse matrix is 53760*53760 with 1067392 non-zero entries. If the >>> codes is compiled using PETSc-3.4.2, it works fine, the equations can be >>> solved quickly and I can see the speedup. But if the code is compiled using >>> PETSc-dev with OpenMP option, it takes a long time in solving the equations >>> and I cannot see any speedup when more processors are used. >>> >>> For PETSc-3.4.2, run by "mpiexec -n 4 ksp_inhm_d -log_summary >>> log_mpi4_petsc3.4.2.log", the iteration and runtime are: >>> Iterations 6 time_assembly 0.4137E-01 time_ksp 0.9296E-01 >>> >>> For PETSc-dev, run by "mpiexec -n 1 ksp_inhm_d -threadcomm_type openmp >>> -threadcomm_nthreads 4 -log_summary log_openmp_petsc_dev.log", the >>> iteration and runtime are: >>> Iterations 6 time_assembly 0.3595E+03 time_ksp 0.2907E+00 >>> >>> Most of the time 'time_assembly 0.3595E+03' is spent on the following codes >>> do i = istart, iend - 1 >>> ii = ia_in(i+1) >>> jj = ia_in(i+2) >>> call MatSetValues(a, ione, i, jj-ii, ja_in(ii:jj-1)-1, >>> a_in(ii:jj-1), Insert_Values, ierr) >>> end do >>> >>> The log files for both PETSc-3.4.2 and PETSc-dev are attached. >>> >>> Is there anything wrong with my codes or with running option? The above >>> codes works fine when using MPICH. >>> >>> Thanks and regards, >>> >>> Danyang >>> >>> On 21/09/2013 2:09 PM, Shri wrote: >>>> There are three thread communicator types in PETSc. The default is "no >>>> thread" which is basically a non-threaded version. The other two types are >>>> "openmp" and "pthread". If you want to use OpenMP then use the option >>>> -threadcomm_type openmp. >>>> >>>> Shri >>>> >>>> On Sep 21, 2013, at 3:46 PM, Danyang Su <[email protected]> wrote: >>>> >>>>> Hi Barry, >>>>> >>>>> Thanks for the quick reply. >>>>> >>>>> After changing >>>>> #if defined(PETSC_HAVE_PTHREADCLASSES) || defined (PETSC_HAVE_OPENMP) >>>>> to >>>>> #if defined(PETSC_HAVE_PTHREADCLASSES) >>>>> and comment out >>>>> #elif defined(PETSC_HAVE_OPENMP) >>>>> PETSC_EXTERN PetscStack *petscstack; >>>>> >>>>> It can be compiled and validated with "make test". >>>>> >>>>> But I still have questions on running the examples. After rebuild the >>>>> codes (e.g., ksp_ex2f.f), I can run it with "mpiexec -n 1 ksp_ex2f", or >>>>> "mpiexec -n 4 ksp_ex2f", or "mpiexec -n 1 ksp_ex2f -threadcomm_nthreads >>>>> 1", but if I run it with "mpiexec -n 1 ksp_ex2f -threadcomm_nthreads 4", >>>>> there will be a lot of error information (attached). >>>>> >>>>> The codes is not modified and there is no OpenMP routines in it. For the >>>>> current development in my project, I want to keep the OpenMP codes in >>>>> calculating matrix values, but want to solve it with PETSc (OpenMP). Is >>>>> it possible? >>>>> >>>>> Thanks and regards, >>>>> >>>>> Danyang >>>>> >>>>> >>>>> >>>>> On 21/09/2013 7:26 AM, Barry Smith wrote: >>>>>> Danyang, >>>>>> >>>>>> I don't think the || defined (PETSC_HAVE_OPENMP) belongs in the >>>>>> code below. >>>>>> >>>>>> /* Linux functions CPU_SET and others don't work if sched.h is not >>>>>> included before >>>>>> including pthread.h. Also, these functions are active only if either >>>>>> _GNU_SOURCE >>>>>> or __USE_GNU is not set (see /usr/include/sched.h and >>>>>> /usr/include/features.h), hence >>>>>> set these first. >>>>>> */ >>>>>> #if defined(PETSC_HAVE_PTHREADCLASSES) || defined (PETSC_HAVE_OPENMP) >>>>>> >>>>>> Edit include/petscerror.h and locate these lines and remove that part >>>>>> and then rerun make all. Let us know if it works or not. >>>>>> >>>>>> Barry >>>>>> >>>>>> i.e. replace >>>>>> >>>>>> #if defined(PETSC_HAVE_PTHREADCLASSES) || defined (PETSC_HAVE_OPENMP) >>>>>> >>>>>> with >>>>>> >>>>>> #if defined(PETSC_HAVE_PTHREADCLASSES) >>>>>> >>>>>> On Sep 21, 2013, at 6:53 AM, Matthew Knepley >>>>>> <[email protected]> >>>>>> wrote: >>>>>> >>>>>> >>>>>>> On Sat, Sep 21, 2013 at 12:18 AM, Danyang Su <[email protected]> >>>>>>> wrote: >>>>>>> Hi All, >>>>>>> >>>>>>> I got error information in compiling petsc-dev with openmp in cygwin. >>>>>>> Before, I have successfully compiled petsc-3.4.2 and it works fine. >>>>>>> The log files have been attached. >>>>>>> >>>>>>> The OpenMP configure test is wrong. It clearly fails to find pthread.h, >>>>>>> but the test passes. Then in petscerror.h >>>>>>> we guard pthread.h using PETSC_HAVE_OPENMP. Can someone who knows >>>>>>> OpenMP fix this? >>>>>>> >>>>>>> Matt >>>>>>> >>>>>>> Thanks, >>>>>>> >>>>>>> Danyang >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> What most experimenters take for granted before they begin their >>>>>>> experiments is infinitely more interesting than any results to which >>>>>>> their experiments lead. >>>>>>> -- Norbert Wiener >>>>>>> >>>>> >>>>> <error.txt> >>> >>> <log_mpi4_petsc3.4.2.log><log_openmp_petsc_dev.log> >> >
