[petsc-users] Problem with large grid size

Thu Nov 29 21:00:14 CST 2018

> On Nov 29, 2018, at 8:55 PM, Fazlul Huq <huq2090 at gmail.com> wrote:
> 
> So, if I try to run the same code in a super computer then I can run with even larger matrix?

   Within reason. But every time you increase n by 10 it will require more than 100 times as much memory so even on the biggest machine you are limited in how large a problem you can run.

    Barry

> 
> Thanks.
> 
> Sincerely,
> Huq
> 
> On Thu, Nov 29, 2018 at 8:54 PM Fazlul Huq <huq2090 at gmail.com> wrote:
> Sorry! I made mistake in running the code.
> 
> It's actually working now until matrix size of 9999999!
> 
> But when I try to extend to one order more it give me error message:
> **************************************************************************************************************************
> Out of memory trying to allocate 799999992 bytes
> [0]PETSC ERROR: ------------------------------------------------------------------------
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
> [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
> [0]PETSC ERROR: likely location of problem given in stack below
> [0]PETSC ERROR: ---------------------  Stack Frames ------------------------------------
> [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
> [0]PETSC ERROR:       INSTEAD the line number of the start of the function
> [0]PETSC ERROR:       is given.
> [0]PETSC ERROR: [0] HYPRE_SetupXXX line 322 /home/huq2090/petsc-3.10.2/src/ksp/pc/impls/hypre/hypre.c
> [0]PETSC ERROR: [0] PCSetUp_HYPRE line 138 /home/huq2090/petsc-3.10.2/src/ksp/pc/impls/hypre/hypre.c
> [0]PETSC ERROR: [0] PCSetUp line 894 /home/huq2090/petsc-3.10.2/src/ksp/pc/interface/precon.c
> [0]PETSC ERROR: [0] KSPSetUp line 304 /home/huq2090/petsc-3.10.2/src/ksp/ksp/interface/itfunc.c
> [0]PETSC ERROR: [0] KSPSolve line 678 /home/huq2090/petsc-3.10.2/src/ksp/ksp/interface/itfunc.c
> [0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
> [0]PETSC ERROR: Signal received
> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
> [0]PETSC ERROR: Petsc Release Version 3.10.2, Oct, 09, 2018 
> [0]PETSC ERROR: ./poisson_m on a arch-linux2-c-debug named huq2090-XPS-15-9570 by huq2090 Thu Nov 29 20:47:50 2018
> [0]PETSC ERROR: Configure options --download-hypre --download-mpich --with-64-bit-indices
> [0]PETSC ERROR: #1 User provided function() line 0 in  unknown file
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
> [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=59
> :
> system msg for write_line failure : Bad file descriptor
> **************************************************************************************************************************************
> 
> I am using dell xps laptop with 32 GB RAM, Intel 8th generation core i7 processor. 
> Since the RAM is 32 GB, is there any way to allocate even higher order problem in my machine?
> 
> Thanks.
> Sincerely,
> Huq
> 
> 
> 
> On Thu, Nov 29, 2018 at 8:26 PM Fazlul Huq <huq2090 at gmail.com> wrote:
> Thanks.
> 
> I have configured with 64-bit and then when I run, I got the following error message:
> ***********************************************************************************************************************
> [0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
> [0]PETSC ERROR: Out of memory. This could be due to allocating
> [0]PETSC ERROR: too large an object or bleeding by not properly
> [0]PETSC ERROR: destroying unneeded objects.
> [0]PETSC ERROR: Memory allocated 41632 Memory used by process 13361152
> [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info.
> [0]PETSC ERROR: Memory requested 1614907707076
> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
> [0]PETSC ERROR: Petsc Release Version 3.10.2, Oct, 09, 2018 
> [0]PETSC ERROR: ./poisson_m on a arch-linux2-c-debug named huq2090-XPS-15-9570 by huq2090 Thu Nov 29 20:24:13 2018
> [0]PETSC ERROR: Configure options --download-hypre --download-mpich --with-64-bit-indices
> [0]PETSC ERROR: #1 VecCreate_Seq() line 35 in /home/huq2090/petsc-3.10.2/src/vec/vec/impls/seq/bvec3.c
> [0]PETSC ERROR: #2 PetscTrMallocDefault() line 183 in /home/huq2090/petsc-3.10.2/src/sys/memory/mtr.c
> [0]PETSC ERROR: #3 PetscMallocA() line 397 in /home/huq2090/petsc-3.10.2/src/sys/memory/mal.c
> [0]PETSC ERROR: #4 VecCreate_Seq() line 35 in /home/huq2090/petsc-3.10.2/src/vec/vec/impls/seq/bvec3.c
> [0]PETSC ERROR: #5 VecSetType() line 51 in /home/huq2090/petsc-3.10.2/src/vec/vec/interface/vecreg.c
> [0]PETSC ERROR: #6 VecSetTypeFromOptions_Private() line 1250 in /home/huq2090/petsc-3.10.2/src/vec/vec/interface/vector.c
> [0]PETSC ERROR: #7 VecSetFromOptions() line 1284 in /home/huq2090/petsc-3.10.2/src/vec/vec/interface/vector.c
> [0]PETSC ERROR: #8 main() line 57 in /home/huq2090/petsc-3.10.2/problems/ksp/poisson_m.c
> [0]PETSC ERROR: No PETSc Option Table entries
> [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov----------
> application called MPI_Abort(MPI_COMM_WORLD, 55) - process 0
> [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=55
> :
> system msg for write_line failure : Bad file descriptor
> ************************************************************************************************************************************
> 
> Thanks.
> Sincerely,
> Huq
> 
> On Thu, Nov 29, 2018 at 1:51 PM Smith, Barry F. <bsmith at mcs.anl.gov> wrote:
> 
> 
> > On Nov 29, 2018, at 1:46 PM, Fazlul Huq via petsc-users <petsc-users at mcs.anl.gov> wrote:
> > 
> > Hello PETSc Developers,
> > 
> > I am trying to run the code (attached herewith) with the following command and it works until the size of the matrix is 99999X99999. But when I try to run with 999999X999999 then I got weird result.
> 
>    What is that "weird result"? 
> 
>    My guess is for problems that large you need to ./configure PETSc with the additional option --with-64-bit-indices since for such large problems 32 bit integers are not large enough to contain values needed for storing and accessing the sparse matrix.
> 
>    Barry
> 
> > 
> > The command is: 
> > ./poisson_m -n 999999 -pc_type hypre -pc_hypre_type boomeramg -ksp_view_solution
> > Any suggestions is appreciated.
> > 
> > Thanks.
> > Sincerely,
> > Huq
> > 
> > 
> > -- 
> > 
> > Fazlul Huq
> > Graduate Research Assistant
> > Department of Nuclear, Plasma & Radiological Engineering (NPRE)
> > University of Illinois at Urbana-Champaign (UIUC)
> > E-mail: huq2090 at gmail.com
> > <poisson_m.c>
> 
> 
> 
> -- 
> 
> Fazlul Huq
> Graduate Research Assistant
> Department of Nuclear, Plasma & Radiological Engineering (NPRE)
> University of Illinois at Urbana-Champaign (UIUC)
> E-mail: huq2090 at gmail.com
> 
> 
> -- 
> 
> Fazlul Huq
> Graduate Research Assistant
> Department of Nuclear, Plasma & Radiological Engineering (NPRE)
> University of Illinois at Urbana-Champaign (UIUC)
> E-mail: huq2090 at gmail.com
> 
> 
> -- 
> 
> Fazlul Huq
> Graduate Research Assistant
> Department of Nuclear, Plasma & Radiological Engineering (NPRE)
> University of Illinois at Urbana-Champaign (UIUC)
> E-mail: huq2090 at gmail.com