[petsc-users] Strange efficiency in PETSc-dev using OpenMP
Barry Smith
bsmith at mcs.anl.gov
Sun Sep 22 16:24:33 CDT 2013
If you run the Openmp compiled version WITHOUT the
-threadcomm_nthreads 1
-threadcomm_type openmp
command line options is it still slow?
I want to understand if the MPI compile options triggering the much slower run.
Barry
On Sep 22, 2013, at 2:43 PM, Danyang Su <danyang.su at gmail.com> wrote:
> Hi Barry,
>
> Thanks, please find the answer bellow.
>
> On 22/09/2013 9:53 AM, Barry Smith wrote:
>> 1) # WARNING!!! #
>> # #
>> # This code was compiled with a debugging option, #
>> # To get timing results run ./configure #
>> # using --with-debugging=no, the performance will #
>> # be generally two or three times faster. #
>>
>> Never time without optimization, it can give very misleading information because different parts of the code speedup very differently when optimized
> With optimization, the problem still exists. See attached log, using 1 thread and 4 threads.
>> 2) Where are the 4 MPI processes being placed on your system? Are they being placed on 4 cores on the same CPU (as with the OpenMP run) or possibly on different CPUs?
> Yes, the system information are as follows
> OS: Windows 7 X64 Pro, CYGWIN
> Processor: Intel Xeon E5-2620 2.0GHz, 6cores/12threads
> Memory: 16GB
> Compiler: Intel Visual Fortran V13.1.
>> 3) Do you have any OpenMP pragmas in your code. Make a run where you take them all out
> For the current, I have no OpenMP pragmas in the code. The code is just the same as I used for PETSc MPI version and it works fine when using MPI.
>>
>> 4) Both runs are actually taking very little time in the solver;
>>
>> KSPSolve 1 1.0 9.2897e-002
>> KSPSolve 1 1.0 2.9056e-001
>>
>> How are you getting your matrix? From a file?
> Yes, the matrix are currently from the files. Should this be the problem? The timing is started after the reading matrix. And I didn't see the speedup for the solver, the runtime for kspsolve are almost the same.
>
> nthreads = 1, KSPSolve 1 1.0 6.2800e-002
>
> nthreads = 4, KSPSolve 1 1.0 5.5090e-002
>
> The main question is that the program is stuck in the following codes when run with openmp, but no problem when run with mpi.
>
> 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 testing codes has also been attached. I have removed some unnecessary codes, but some are still there.
>>
>> Barry
>>
>>
>> On Sep 21, 2013, at 11:06 PM, Danyang Su <danyang.su at gmail.com> 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>
>
> <log_openmp_petsc_dev_opt_1.log><log_openmp_petsc_dev_opt_4.log><ksp_inhm_test.F90>
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