[petsc-users] Strange efficiency in PETSc-dev using OpenMP

[Shri]

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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