<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote">On Tue, Feb 20, 2018 at 7:54 PM, TAY wee-beng <span dir="ltr"><<a href="mailto:zonexo@gmail.com" target="_blank">zonexo@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
<br>
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.<br>
<br>
So I tried to compile PETSc again and then compile my CFD code with the newly compiled PETSc. However, now I got segmentation error:<br>
<br>
rm: cannot remove `log': No such file or directory<br>
[409]PETSC ERROR: ------------------------------<wbr>------------------------------<wbr>------------<br>
[409]PETSC ERROR: [535]PETSC ERROR: [410]PETSC ERROR: ------------------------------<wbr>------------------------------<wbr>------------<br>
[410]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range<br>
[410]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger<br>
[410]PETSC ERROR: [536]PETSC ERROR: ------------------------------<wbr>------------------------------<wbr>------------<br>
[536]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range<br>
[536]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger<br>
[536]PETSC ERROR: or see <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind" rel="noreferrer" target="_blank">http://www.mcs.anl.gov/petsc/d<wbr>ocumentation/faq.html#valgrind</a><br>
[536]PETSC ERROR: or try <a href="http://valgrind.org" rel="noreferrer" target="_blank">http://valgrind.org</a> on GNU/linux and Apple Mac OS X to find memory corruption errors<br>
[536]PETSC ERROR: likely location of problem given in stack below<br>
[536]PETSC ERROR: --------------------- Stack Frames ------------------------------<wbr>------<br>
[536]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,<br>
[536]PETSC ERROR: INSTEAD the line number of the start of the function<br>
[536]PETSC ERROR: is given.<br>
[536]PETSC ERROR: [536] DMDACheckOwnershipRanges_Priva<wbr>te line 581 /home/users/nus/tsltaywb/sourc<wbr>e/petsc-3.7.6/src/dm/impls/da/<wbr>da.c<br>
[536]PETSC ERROR: or see <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind" rel="noreferrer" target="_blank">http://www.mcs.anl.gov/petsc/d<wbr>ocumentation/faq.html#valgrind</a><br>
[410]PETSC ERROR: or try <a href="http://valgrind.org" rel="noreferrer" target="_blank">http://valgrind.org</a> on GNU/linux and Apple Mac OS X to find memory corruption errors<br>
[410]PETSC ERROR: likely location of problem given in stack below<br>
[410]PETSC ERROR: --------------------- Stack Frames ------------------------------<wbr>------<br>
[410]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,<br>
[897]PETSC ERROR: [536] DMDASetOwnershipRanges line 613 /home/users/nus/tsltaywb/sourc<wbr>e/petsc-3.7.6/src/dm/impls/da/<wbr>da.c<br>
[536]PETSC ERROR: [536] DMDACreate3d line 1434 /home/users/nus/tsltaywb/sourc<wbr>e/petsc-3.7.6/src/dm/impls/da/<wbr>da3.c<br>
[536]PETSC ERROR: --------------------- Error Message ------------------------------<wbr>------------------------------<wbr>--<br>
<br>
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?<br>
<br>
Besides, I want to know when and why do I have to use PETSc with 64-bit indices?<br></blockquote><div><br></div><div>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,</div><div> before you even start to count nonzero entries in the matrix. 64-bit integers allow you to handle these big sizes.</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Also, can I use the 64-bit indices version with smaller sized problems?<br></blockquote><div><br></div><div>2) Yes</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
And is there a speed difference between using the 32-bit and 64-bit indices ver?</blockquote><div><br></div><div>3) I have seen no evidence of this</div><div><br></div><div>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.</div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class="HOEnZb"><font color="#888888"><br>
-- <br>
Thank you very much.<br>
<br>
Yours sincerely,<br>
<br>
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TAY Wee-Beng (Zheng Weiming) 郑伟明<br>
Personal research webpage: <a href="http://tayweebeng.wixsite.com/website" rel="noreferrer" target="_blank">http://tayweebeng.wixsite.com/<wbr>website</a><br>
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</font></span></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener</div><div><br></div><div><a href="http://www.caam.rice.edu/~mk51/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div>
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