<div dir="ltr">It appears that you have an uninitialized variable (or more than one). When compiled with debugging, variables<div>are normally initialized to zero.</div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Dec 25, 2015 at 5:41 AM, 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>
Sorry, there seems to be some problems with my valgrind. I have repeated it again, with the optimized and debug version<div class="HOEnZb"><div class="h5"><br>
<br>
<br>
<br>
<br>
Thank you.<br>
<br>
Yours sincerely,<br>
<br>
TAY wee-beng<br>
<br>
On 25/12/2015 12:42 PM, Barry Smith wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
On Dec 24, 2015, at 10:37 PM, TAY wee-beng <<a href="mailto:zonexo@gmail.com" target="_blank">zonexo@gmail.com</a>> wrote:<br>
<br>
Hi,<br>
<br>
I tried valgrind in MPI but it aborts very early, with the error msg regarding PETSc initialize.<br>
</blockquote>
It shouldn't "abort" it should print some error message and continue. Please send all the output when running with valgrind.<br>
<br>
It is possible you are solving large enough problem that require configure --with-64-bit-indices . Does that resolve the problem?<br>
<br>
Barry<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I retry again, using a lower resolution.<br>
<br>
GAMG works, but BoomerAMG and hypre doesn't. Increasing cpu too high (80) also cause it to hang. 60 works fine.<br>
<br>
My grid size is 98x169x169<br>
<br>
But when I increase the resolution, GAMG can't work again.<br>
<br>
I tried to increase the cpu no but it still doesn't work.<br>
<br>
Previously, using single z direction partition, it work using GAMG and hypre. So what could be the problem?<br>
Thank you.<br>
<br>
Yours sincerely,<br>
<br>
TAY wee-beng<br>
<br>
On 25/12/2015 12:33 AM, Matthew Knepley wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
It sounds like you have memory corruption in a different part of the code. Run in valgrind.<br>
<br>
Matt<br>
<br>
On Thu, Dec 24, 2015 at 10:14 AM, TAY wee-beng <<a href="mailto:zonexo@gmail.com" target="_blank">zonexo@gmail.com</a>> wrote:<br>
Hi,<br>
<br>
I have this strange error. I converted my CFD code from a z directon only partition to the yz direction partition. The code works fine but when I increase the cpu no, strange things happen when solving the Poisson eqn.<br>
<br>
I increase cpu no from 24 to 40.<br>
<br>
Sometimes it works, sometimes it doesn't. When it doesn't, it just hangs there with no output, or it gives the error below:<br>
<br>
Using MPI_Barrier during debug shows that it hangs at<br>
<br>
call KSPSolve(ksp,b_rhs,xx,ierr).<br>
<br>
I use hypre BoomerAMG and GAMG (-poisson_pc_gamg_agg_nsmooths 1 -poisson_pc_type gamg)<br>
<br>
<br>
Why is this so random? Also how do I debug this type of problem.<br>
<br>
<br>
[32]PETSC ERROR: ------------------------------------------------------------------------<br>
[32]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range<br>
[32]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger<br>
[32]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/documentation/faq.html#valgrind</a><br>
[32]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>
[32]PETSC ERROR: likely location of problem given in stack below<br>
[32]PETSC ERROR: --------------------- Stack Frames ------------------------------------<br>
[32]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,<br>
[32]PETSC ERROR: INSTEAD the line number of the start of the function<br>
[32]PETSC ERROR: is given.<br>
[32]PETSC ERROR: [32] HYPRE_SetupXXX line 174 /home/wtay/Codes/petsc-3.6.2/src/ksp/pc/impls/hypre/hypre.c<br>
[32]PETSC ERROR: [32] PCSetUp_HYPRE line 122 /home/wtay/Codes/petsc-3.6.2/src/ksp/pc/impls/hypre/hypre.c<br>
[32]PETSC ERROR: [32] PCSetUp line 945 /home/wtay/Codes/petsc-3.6.2/src/ksp/pc/interface/precon.c<br>
[32]PETSC ERROR: [32] KSPSetUp line 247 /home/wtay/Codes/petsc-3.6.2/src/ksp/ksp/interface/itfunc.c<br>
[32]PETSC ERROR: [32] KSPSolve line 510 /home/wtay/Codes/petsc-3.6.2/src/ksp/ksp/interface/itfunc.c<br>
[32]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------<br>
[32]PETSC ERROR: Signal received<br>
[32]PETSC ERROR: See <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html" rel="noreferrer" target="_blank">http://www.mcs.anl.gov/petsc/documentation/faq.html</a> for trouble shooting.<br>
[32]PETSC ERROR: Petsc Release Version 3.6.2, Oct, 02, 2015<br>
[32]PETSC ERROR: ./a.out on a petsc-3.6.2_shared_gnu_debug named n12-40 by wtay Thu Dec 24 17:01:51 2015<br>
[32]PETSC ERROR: Configure options --with-mpi-dir=/opt/ud/openmpi-1.8.8/ --download-fblaslapack=1 --with-debugging=1 --download-hypre=1 --prefix=/home/wtay/Lib/petsc-3.6.2_shared_gnu_debug --known-mpi-shared=1 --with-shared-libraries --with-fortran-interfaces=1<br>
[32]PETSC ERROR: #1 User provided function() line 0 in unknown file<br>
--------------------------------------------------------------------------<br>
MPI_ABORT was invoked on rank 32 in communicator MPI_COMM_WORLD<br>
with errorcode 59.<br>
<br>
-- <br>
Thank you.<br>
<br>
Yours sincerely,<br>
<br>
TAY wee-beng<br>
<br>
<br>
<br>
<br>
-- <br>
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<br>
</blockquote></blockquote></blockquote>
<br>
</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature">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>