[petsc-users] Error on INTEGER SIZE using DMDACreate3d

Mark Adams mfadams at lbl.gov
Tue Jul 21 09:58:32 CDT 2020 

This also looks like it could be some sort of library mismatch. You might
try deleting your architecture directory and start over. This PETSc's "make
realclean"

On Tue, Jul 21, 2020 at 10:45 AM Stefano Zampini <stefano.zampini at gmail.com>
wrote:

>
>
> On Jul 21, 2020, at 1:32 PM, Pierpaolo Minelli <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       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?
>
>
> These configure options compile hypre with 64bit indices support.
> It should work just fine. Can you run a very small case of your code to
> confirm?
>
>
> 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?
>
> Thanks in advance
>
> Pierpaolo
>
>
> Il giorno 27 mag 2020, alle ore 11:26, Stefano Zampini <
> 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> 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
>> [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
>> 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
>
>
>
>
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