[petsc-users] Strange efficiency in PETSc-dev using OpenMP
Shri
abhyshr at mcs.anl.gov
Sun Sep 22 22:00:52 CDT 2013
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 <danyang.su at gmail.com> 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 <petsc-maint at mcs.anl.gov> wrote:
>>>>
>>>>> On Sat, Sep 21, 2013 at 12:18 AM, Danyang Su <danyang.su at gmail.com> 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>
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