[petsc-users] Error on INTEGER SIZE using DMDACreate3d

Tue Jul 21 06:32:13 CDT 2020

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?
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 <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

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