[petsc-users] Problem with large grid size

Thu Nov 29 20:55:35 CST 2018

So, if I try to run the same code in a super computer then I can run with
even larger matrix?

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
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