[petsc-users] Error on INTEGER SIZE using DMDACreate3d
Pierpaolo Minelli
pierpaolo.minelli at cnr.it
Tue Jul 21 11:06:52 CDT 2020
> Il giorno 21 lug 2020, alle ore 16:56, Mark Adams <mfadams at lbl.gov> ha scritto:
>
>
>
> On Tue, Jul 21, 2020 at 9:46 AM Matthew Knepley <knepley at gmail.com <mailto:knepley at gmail.com>> wrote:
> On Tue, Jul 21, 2020 at 9:35 AM Pierpaolo Minelli <pierpaolo.minelli at cnr.it <mailto:pierpaolo.minelli at cnr.it>> wrote:
> Thanks for your reply.
> As I wrote before, I use these settings:
>
> -dm_mat_type hypre -pc_type hypre -pc_hypre_type boomeramg -pc_hypre_boomeramg_relax_type_all SOR/Jacobi -pc_hypre_boomeramg_coarsen_type PMIS -pc_hypre_boomeramg_interp_type FF1 -ksp_type richardson
>
> Is there a way to emulate this features also with GAMG?
>
> Smoothers: You have complete control here
>
> -mg_levels_pc_type sor (the default is Chebyshev which you could also try)
>
> And you set the KSP type. You have -ksp_type richardson above but that is not used for Hypre. It is for GAMG. Chebyshev is a ksp type (-ksp_type chebyshev).
>
> Hypre is very good on Poisson. THe grid complexity (cost per iteration) can be high but the convergence rate will be better than GAMG.
>
> But, you should be able to get hypre to work.
Yes it is very good for Poisson, and on a smaller case, at the beginning of my code development, I have tried Hypre, ML, and GAMG (without adding more options I have to admit) and hypre was faster without losing in precision and accurateness of results (I have checked them with -ksp_monitor_true_residual).
I left -kps_type Richardson instead of default gmres only because from residuals it seems more accurate.
So first, i will try again to see if hypre (with integer 64bit) is able to work on a smaller case as suggested by Stefano.
Then I will investigate GAMG options and I will give you a feedback.
The problem is that I need 64bit integers because of my problem size so I have to follow both path, but I hope that I will be able to continue to use hypre.
Thanks
Pierpaolo
>
>
> Coarsening: This is much different in agglomeration AMG. There is a discussion here:
>
> https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/PC/PCGAMGSetThreshold.html <https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/PC/PCGAMGSetThreshold.html>
> https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/PC/PCGAMGSetSquareGraph.html <https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/PC/PCGAMGSetSquareGraph.html>
>
> Interpolation: This is built-in for agglomeration AMG.
>
> It would be better to use only native Petsc implementations, but these settings, up to single precision indexing for integers, gave me optimal performances.
> For this reason I asked also, if it was possible to configure hypre (inside Petsc) with 64bit integers.
>
> Yes. That happened when you reconfigured for 64 bits. You may have encountered a Hypre bug.
>
> Thanks,
>
> Matt
>
> Pierpaolo
>
>
>> Il giorno 21 lug 2020, alle ore 13:36, Dave May <dave.mayhem23 at gmail.com <mailto:dave.mayhem23 at gmail.com>> ha scritto:
>>
>>
>>
>> On Tue, 21 Jul 2020 at 12:32, Pierpaolo Minelli <pierpaolo.minelli at cnr.it <mailto:pierpaolo.minelli at cnr.it>> wrote:
>> Hi,
>>
>> I have asked to compile a Petsc Version updated and with 64bit indices.
>> Now I have Version 3.13.3 and these are the configure options used:
>>
>> #!/bin/python
>> if __name__ == '__main__':
>> import sys
>> import os
>> sys.path.insert(0, os.path.abspath('config'))
>> import configure
>> configure_options = [
>> '--CC=mpiicc',
>> '--CXX=mpiicpc',
>> '--download-hypre',
>> '--download-metis',
>> '--download-mumps=yes',
>> '--download-parmetis',
>> '--download-scalapack',
>> '--download-superlu_dist',
>> '--known-64-bit-blas-indices',
>> '--prefix=/cineca/prod/opt/libraries/petsc/3.13.3_int64/intelmpi--2018--binary',
>> '--with-64-bit-indices=1',
>> '--with-blaslapack-dir=/cineca/prod/opt/compilers/intel/pe-xe-2018/binary/mkl',
>> '--with-cmake-dir=/cineca/prod/opt/tools/cmake/3.12.0/none',
>> '--with-debugging=0',
>> '--with-fortran-interfaces=1',
>> '--with-fortran=1',
>> 'FC=mpiifort',
>> 'PETSC_ARCH=arch-linux2-c-opt',
>> ]
>> configure.petsc_configure(configure_options)
>>
>> Now, I receive an error on hypre:
>>
>> forrtl: error (78): process killed (SIGTERM)
>> Image PC Routine Line Source
>> libHYPRE-2.18.2.s 00002B33CF465D3F for__signal_handl Unknown Unknown
>> libpthread-2.17.s 00002B33D5BFD370 Unknown Unknown Unknown
>> libpthread-2.17.s 00002B33D5BF96D3 pthread_cond_wait Unknown Unknown
>> libiomp5.so 00002B33DBA14E07 Unknown Unknown Unknown
>> libiomp5.so 00002B33DB98810C Unknown Unknown Unknown
>> libiomp5.so 00002B33DB990578 Unknown Unknown Unknown
>> libiomp5.so 00002B33DB9D9659 Unknown Unknown Unknown
>> libiomp5.so 00002B33DB9D8C39 Unknown Unknown Unknown
>> libiomp5.so 00002B33DB993BCE __kmpc_fork_call Unknown Unknown
>> PIC_3D 00000000004071C0 Unknown Unknown Unknown
>> PIC_3D 0000000000490299 Unknown Unknown Unknown
>> PIC_3D 0000000000492C17 Unknown Unknown Unknown
>> PIC_3D 000000000040562E Unknown Unknown Unknown
>> libc-2.17.so <http://libc-2.17.so/> 00002B33DC5BEB35 __libc_start_main Unknown Unknown
>> PIC_3D 0000000000405539 Unknown Unknown Unknown
>>
>> Is it possible that I need to ask also to compile hypre with an option for 64bit indices?
>> Is it possible to instruct this inside Petsc configure?
>> Alternatively, is it possible to use a different multigrid PC inside PETSc that accept 64bit indices?
>>
>> You can use
>> -pc_type gamg
>> All native PETSc implementations support 64bit indices.
>>
>>
>> Thanks in advance
>>
>> Pierpaolo
>>
>>
>>> Il giorno 27 mag 2020, alle ore 11:26, Stefano Zampini <stefano.zampini at gmail.com <mailto:stefano.zampini at gmail.com>> ha scritto:
>>>
>>> You need a version of PETSc compiled with 64bit indices, since the message indicates the number of dofs in this case is larger the INT_MAX
>>> 2501×3401×1601 = 13617947501
>>>
>>> I also suggest you upgrade to a newer version, 3.8.3 is quite old as the error message reports
>>>
>>> Il giorno mer 27 mag 2020 alle ore 11:50 Pierpaolo Minelli <pierpaolo.minelli at cnr.it <mailto:pierpaolo.minelli at cnr.it>> ha scritto:
>>> Hi,
>>>
>>> I am trying to solve a Poisson equation on this grid:
>>>
>>> Nx = 2501
>>> Ny = 3401
>>> Nz = 1601
>>>
>>> I received this error:
>>>
>>> [0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
>>> [0]PETSC ERROR: Overflow in integer operation: http://www.mcs.anl.gov/petsc/documentation/faq.html#64-bit-indices <http://www.mcs.anl.gov/petsc/documentation/faq.html#64-bit-indices>
>>> [0]PETSC ERROR: Mesh of 2501 by 3401 by 1 (dof) is too large for 32 bit indices
>>> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html <http://www.mcs.anl.gov/petsc/documentation/faq.html> for trouble shooting.
>>> [0]PETSC ERROR: Petsc Release Version 3.8.3, Dec, 09, 2017
>>> [0]PETSC ERROR: /marconi_scratch/userexternal/pminelli/PIC3D/2500_3400_1600/./PIC_3D on a arch-linux2-c-opt named r129c09s02 by pminelli Tu
>>> e May 26 20:16:34 2020
>>> [0]PETSC ERROR: Configure options --prefix=/cineca/prod/opt/libraries/petsc/3.8.3/intelmpi--2018--binary CC=mpiicc FC=mpiifort CXX=mpiicpc
>>> F77=mpiifort F90=mpiifort --with-debugging=0 --with-blaslapack-dir=/cineca/prod/opt/compilers/intel/pe-xe-2018/binary/mkl --with-fortran=1
>>> --with-fortran-interfaces=1 --with-cmake-dir=/cineca/prod/opt/tools/cmake/3.5.2/none --with-mpi-dir=/cineca/prod/opt/compilers/intel/pe-xe-
>>> 2018/binary/impi/2018.4.274 --download-scalapack --download-mumps=yes --download-hypre --download-superlu_dist --download-parmetis --downlo
>>> ad-metis
>>> [0]PETSC ERROR: #1 DMSetUp_DA_3D() line 218 in /marconi/prod/build/libraries/petsc/3.8.3/intelmpi--2018--binary/BA_WORK/petsc-3.8.3/src/dm/
>>> impls/da/da3.c
>>> [0]PETSC ERROR: #2 DMSetUp_DA() line 25 in /marconi/prod/build/libraries/petsc/3.8.3/intelmpi--2018--binary/BA_WORK/petsc-3.8.3/src/dm/impl
>>> s/da/dareg.c
>>> [0]PETSC ERROR: #3 DMSetUp() line 720 in /marconi/prod/build/libraries/petsc/3.8.3/intelmpi--2018--binary/BA_WORK/petsc-3.8.3/src/dm/interf
>>> ace/dm.c
>>> forrtl: error (76): Abort trap signal
>>>
>>>
>>> I am on an HPC facility and after I loaded PETSC module, I have seen that it is configured with INTEGER size = 32
>>>
>>> I solve my problem with these options and it works perfectly with smaller grids:
>>>
>>> -dm_mat_type hypre -pc_type hypre -pc_hypre_type boomeramg -pc_hypre_boomeramg_relax_type_all SOR/Jacobi -pc_hypre_boomeramg_coarsen_type PMIS -pc_hypre_boomeramg_interp_type FF1 -ksp_type richardson
>>>
>>> Is it possible to overcome this if I ask them to install a version with INTEGER SIZE = 64?
>>> Alternatively, is it possible to overcome this using intel compiler options?
>>>
>>> Thanks in advance
>>>
>>> Pierpaolo Minelli
>>>
>>>
>>> --
>>> Stefano
>
>
>
> --
> 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
>
> https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
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