[petsc-users] Strange efficiency in PETSc-dev using OpenMP
Danyang Su
danyang.su at gmail.com
Mon Sep 23 14:01:29 CDT 2013
Hi Barry,
Sorry I forgot the message in the previous email. It is still slow when
run without the "-threadcomm_type openmp -threadcomm_nthreads 1"
Thanks,
Danyang
On 23/09/2013 11:43 AM, Barry Smith wrote:
> 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 <danyang.su at gmail.com> 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 <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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