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 <[email protected]> wrote:
On Jul 21, 2020, at 1:32 PM, Pierpaolo Minelli <[email protected]> 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 < [email protected]> 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 < [email protected]> 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