[petsc-users] Compiling with PETSc 64-bit indices
TAY wee-beng
zonexo at gmail.com
Thu Feb 22 00:24:11 CST 2018
On 21/2/2018 9:12 AM, Matthew Knepley wrote:
> On Tue, Feb 20, 2018 at 8:08 PM, TAY wee-beng <zonexo at gmail.com
> <mailto:zonexo at gmail.com>> wrote:
>
>
> On 21/2/2018 9:00 AM, Matthew Knepley wrote:
>> On Tue, Feb 20, 2018 at 7:54 PM, TAY wee-beng <zonexo at gmail.com
>> <mailto:zonexo at gmail.com>> wrote:
>>
>> Hi,
>>
>> When I run my CFD code with a grid size of 1119x1119x499 (
>> total grid size = 624828339 ), I got the error saying I
>> need to compile PETSc with 64-bit indices.
>>
>> So I tried to compile PETSc again and then compile my CFD
>> code with the newly compiled PETSc. However, now I got
>> segmentation error:
>>
>> rm: cannot remove `log': No such file or directory
>> [409]PETSC ERROR:
>> ------------------------------------------------------------------------
>> [409]PETSC ERROR: [535]PETSC ERROR: [410]PETSC ERROR:
>> ------------------------------------------------------------------------
>> [410]PETSC ERROR: Caught signal number 11 SEGV: Segmentation
>> Violation, probably memory access out of range
>> [410]PETSC ERROR: Try option -start_in_debugger or
>> -on_error_attach_debugger
>> [410]PETSC ERROR: [536]PETSC ERROR:
>> ------------------------------------------------------------------------
>> [536]PETSC ERROR: Caught signal number 11 SEGV: Segmentation
>> Violation, probably memory access out of range
>> [536]PETSC ERROR: Try option -start_in_debugger or
>> -on_error_attach_debugger
>> [536]PETSC ERROR: or see
>> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
>> <http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind>
>> [536]PETSC ERROR: or try http://valgrind.org on GNU/linux and
>> Apple Mac OS X to find memory corruption errors
>> [536]PETSC ERROR: likely location of problem given in stack below
>> [536]PETSC ERROR: --------------------- Stack Frames
>> ------------------------------------
>> [536]PETSC ERROR: Note: The EXACT line numbers in the stack
>> are not available,
>> [536]PETSC ERROR: INSTEAD the line number of the start
>> of the function
>> [536]PETSC ERROR: is given.
>> [536]PETSC ERROR: [536] DMDACheckOwnershipRanges_Private line
>> 581
>> /home/users/nus/tsltaywb/source/petsc-3.7.6/src/dm/impls/da/da.c
>> [536]PETSC ERROR: or see
>> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
>> <http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind>
>> [410]PETSC ERROR: or try http://valgrind.org on GNU/linux and
>> Apple Mac OS X to find memory corruption errors
>> [410]PETSC ERROR: likely location of problem given in stack below
>> [410]PETSC ERROR: --------------------- Stack Frames
>> ------------------------------------
>> [410]PETSC ERROR: Note: The EXACT line numbers in the stack
>> are not available,
>> [897]PETSC ERROR: [536] DMDASetOwnershipRanges line 613
>> /home/users/nus/tsltaywb/source/petsc-3.7.6/src/dm/impls/da/da.c
>> [536]PETSC ERROR: [536] DMDACreate3d line 1434
>> /home/users/nus/tsltaywb/source/petsc-3.7.6/src/dm/impls/da/da3.c
>> [536]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>>
>> The CFD code worked previously but increasing the problem
>> size results in segmentation error. It seems to be related to
>> DMDACreate3d and DMDASetOwnershipRanges. Any idea where the
>> problem lies?
>>
>> Besides, I want to know when and why do I have to use PETSc
>> with 64-bit indices?
>>
>>
>> 1) A 32-bit integer can hold numbers up to 2^32 = 4.2e9, so if
>> you have a 3D velocity, pressure, and energy, you already have
>> 3e9 unknowns,
>> before you even start to count nonzero entries in the matrix.
>> 64-bit integers allow you to handle these big sizes.
>>
>> Also, can I use the 64-bit indices version with smaller sized
>> problems?
>>
>>
>> 2) Yes
>>
>> And is there a speed difference between using the 32-bit and
>> 64-bit indices ver?
>>
>>
>> 3) I have seen no evidence of this
>>
>> 4) My guess is that you have defines regular integers in your
>> code and passed them to PETSc, rather than using PetscInt as the
>> type.
> Oh that seems probable. So I am still using integer(4) when it
> should be integer(8) for some values, is that so? If I use
> PetscInt, is it the same as integer(8)? Or does it depend on the
> actual number?
>
>
> PetscInt will be integer(4) if you configure with 32-bit ints, and
> integer(8) if you configure with 64-bit ints. If you use it
> consistently, you can avoid problems
> with matching the PETSc API.
>
> I wonder if I replace all my integer to PetscInt, will there be a
> large increase in memory usage, because all integer(4) now becomes
> integer(8)?
>
>
> Only if you have large integer storage. Most codes do not.
Hi,
What do you mean by "large integer storage"?
Btw, I got the following error when I ran a simple small test case with
my CFD code:
[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 0 Memory used by process 52858880
[0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info.
[0]PETSC ERROR: Memory requested 6917565139726106624
[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: ./a.out on a petsc-3.8.3_intel_64_rel named nus02 by
tsltaywb Thu Feb 22 10:34:29 2018
[0]PETSC ERROR: Configure options
--with-mpi-dir=/app/intel/xe2018/compilers_and_libraries_2018.0.128/linux/mpi/intel64
--with-blaslapack-dir=/app/intel/xe2018/compilers_and_libraries_2018.0.128/linux/mkl/lib/intel64
--download-hypre=/home/users/nus/tsltaywb/source/git.hypre.tar.gz
--with-debugging=0
--prefix=/home/users/nus/tsltaywb/lib/petsc-3.8.3_intel_64_rel
--with-shared-libraries=0 --known-mpi-shared-libraries=0
--with-fortran-interfaces=1 --CFLAGS="-xHost -g -O3" --CXXFLAGS="-xHost
-g -O3" --FFLAGS="-xHost -g -O3" --with-64-bit-indices
[0]PETSC ERROR: #105 DMSetUp_DA() line 18 in
/home/users/nus/tsltaywb/source/petsc-3.8.3/src/dm/impls/da/dareg.c
[0]PETSC ERROR: #106 DMSetUp_DA() line 18 in
/home/users/nus/tsltaywb/source/petsc-3.8.3/src/dm/impls/da/dareg.c
[0]PETSC ERROR: #107 DMSetUp() line 720 in
/home/users/nus/tsltaywb/source/petsc-3.8.3/src/dm/interface/dm.c
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: Arguments are incompatible
[0]PETSC ERROR: Ownership ranges sum to 4294967337 but global dimension
is 41
[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: ./a.out on a petsc-3.8.3_intel_64_rel named nus02 by
tsltaywb Thu Feb 22 10:34:29 2018
[0]PETSC ERROR: Configure options
--with-mpi-dir=/app/intel/xe2018/compilers_and_libraries_2018.0.128/linux/mpi/intel64
--with-blaslapack-dir=/app/intel/xe2018/compilers_and_libraries_2018.0.128/linux/mkl/lib/intel64
--download-hypre=/home/users/nus/tsltaywb/source/git.hypre.tar.gz
--with-debugging=0
--prefix=/home/users/nus/tsltaywb/lib/petsc-3.8.3_intel_64_rel
--with-shared-libraries=0 --known-mpi-shared-libraries=0
--with-fortran-interfaces=1 --CFLAGS="-xHost -g -O3" --CXXFLAGS="-xHost
-g -O3" --FFLAGS="-xHost -g -O3" --with-64-bit-indices
[0]PETSC ERROR: #108 DMDACheckOwnershipRanges_Private() line 548 in
/home/users/nus/tsltaywb/source/petsc-3.8.3/src/dm/impls/da/da.c
[0]PETSC ERROR: #109 DMDASetOwnershipRanges() line 580 in
/home/users/nus/tsltaywb/source/petsc-3.8.3/src/dm/impls/da/da.c
[0]PETSC ERROR: #110 DMDACreate3d() line 1444 in
/home/users/nus/tsltaywb/source/petsc-3.8.3/src/dm/impls/da/da3.c
What's the problem?
Thanks.
>
> Thanks,
>
> Matt
>
> Thanks.
>>
>> Thanks,
>>
>> Matt
>>
>>
>> --
>> Thank you very much.
>>
>> Yours sincerely,
>>
>> ================================================
>> TAY Wee-Beng (Zheng Weiming) 郑伟明
>> Personal research webpage:
>> http://tayweebeng.wixsite.com/website
>> <http://tayweebeng.wixsite.com/website>
>> Youtube research showcase:
>> https://www.youtube.com/channel/UC72ZHtvQNMpNs2uRTSToiLA
>> <https://www.youtube.com/channel/UC72ZHtvQNMpNs2uRTSToiLA>
>> linkedin: www.linkedin.com/in/tay-weebeng
>> <http://www.linkedin.com/in/tay-weebeng>
>> ================================================
>>
>>
>>
>>
>> --
>> What most experimenters take for granted before they begin their
>> experiments is infinitely more interesting than any results to
>> which their experiments lead.
>> -- Norbert Wiener
>>
>> https://www.cse.buffalo.edu/~knepley/
>> <http://www.caam.rice.edu/%7Emk51/>
>
>
>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which
> their experiments lead.
> -- Norbert Wiener
>
> https://www.cse.buffalo.edu/~knepley/ <http://www.caam.rice.edu/%7Emk51/>
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