<div dir="ltr"><div dir="ltr"><div class="gmail_quote"><div dir="ltr">On Wed, Jan 16, 2019 at 3:52 AM Sal Am via petsc-users <<a href="mailto:petsc-users@mcs.anl.gov">petsc-users@mcs.anl.gov</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
The memory requested is an insane number. You may need to use 64 bit integers.
</blockquote><div>Thanks Mark, I reconfigured it to use 64bit, however in the process it says I can no longer use MUMPS and SuperLU as they are not supported (I see on MUMPS webpage it supports 64int). However it does not exactly solve the problem.</div></div></div></div></div></blockquote><div><br></div><div>SuperLU_dist supports 64-bit ints. Are you not running in parallel?</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div>
This time, it crashes at
<span class="gmail-m_-3814543233888417572gmail-im"><div>[6]PETSC ERROR: #1 MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ() line 1989 in /lustre/home/vef002/petsc/src/mat/impls/aij/mpi/mpimatmatmult.c<br>
</div>
</span><div>ierr = PetscMalloc1(bi[pn]+1,&bj);<br>
</div>
<div>which allocates local portion of B^T*A. </div>
<div>You may also try to increase number of cores to reduce local matrix size.</div></div></blockquote><div><br></div><div>So I increased the number of cores to 16 on one node and ran it by :</div><div>mpiexec valgrind --tool=memcheck -q --num-callers=20 --log-file=valgrind.log-osa.%p ./solveCSys -malloc off -ksp_type bcgs -pc_type gamg -mattransposematmult_via scalable -ksp_monitor -log_view <br></div><div>It crashed after reading in the matrix and before starting to solve. The error: <br></div><div><br></div><div>[15]PETSC ERROR: [0]PETSC ERROR: ------------------------------------------------------------------------<br>[0]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the batch system) has told this process to end<br>[0]PETSC ERROR: [1]PETSC ERROR: ------------------------------------------------------------------------<br>[2]PETSC ERROR: ------------------------------------------------------------------------<br>[2]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the batch system) has told this process to end<br>[3]PETSC ERROR: ------------------------------------------------------------------------<br>[4]PETSC ERROR: ------------------------------------------------------------------------<br>[4]PETSC ERROR: [5]PETSC ERROR: [6]PETSC ERROR: ------------------------------------------------------------------------<br>[8]PETSC ERROR: ------------------------------------------------------------------------<br>[12]PETSC ERROR: ------------------------------------------------------------------------<br>[12]PETSC ERROR: [14]PETSC ERROR: ------------------------------------------------------------------------<br>[14]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the batch system) has told this process to end<br>--------------------------------------------------------------------------<br>mpiexec noticed that process rank 10 with PID 0 on node r03n01 exited on signal 9 (Killed).</div><div><br></div><div>Now I was running this with valgrind as someone had previously suggested and the 16 files created all contain the same type of error:</div></div></div></div></div></blockquote><div><br></div><div>Okay, its possible that there are bugs in the MPI implementation. So</div><div><br></div><div>1) Try using -build_twosided allreduce on this run</div><div><br></div><div>2) Is it possible to get something that fails here but we can run. None of our tests show this problem.</div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div>==25940== Invalid read of size 8<br>==25940== at 0x5103326: PetscCheckPointer (checkptr.c:81)<br>==25940== by 0x4F42058: PetscCommGetNewTag (tagm.c:77)<br>==25940== by 0x4FC952D: PetscCommBuildTwoSidedFReq_Ibarrier (mpits.c:373)<br>==25940== by 0x4FCB29B: PetscCommBuildTwoSidedFReq (mpits.c:572)<br>==25940== by 0x52BBFF4: VecAssemblyBegin_MPI_BTS (pbvec.c:251)<br>==25940== by 0x52D6B42: VecAssemblyBegin (vector.c:140)<br>==25940== by 0x5328C97: VecLoad_Binary (vecio.c:141)<br>==25940== by 0x5329051: VecLoad_Default (vecio.c:516)<br>==25940== by 0x52E0BAB: VecLoad (vector.c:933)<br>==25940== by 0x4013D5: main (solveCmplxLinearSys.cpp:31)<br>==25940== Address 0x19f807fc is 12 bytes inside a block of size 16 alloc'd<br>==25940== at 0x4C2A603: memalign (vg_replace_malloc.c:899)<br>==25940== by 0x4FD0B0E: PetscMallocAlign (mal.c:41)<br>==25940== by 0x4FD23E7: PetscMallocA (mal.c:397)<br>==25940== by 0x4FC948E: PetscCommBuildTwoSidedFReq_Ibarrier (mpits.c:371)<br>==25940== by 0x4FCB29B: PetscCommBuildTwoSidedFReq (mpits.c:572)<br>==25940== by 0x52BBFF4: VecAssemblyBegin_MPI_BTS (pbvec.c:251)<br>==25940== by 0x52D6B42: VecAssemblyBegin (vector.c:140)<br>==25940== by 0x5328C97: VecLoad_Binary (vecio.c:141)<br>==25940== by 0x5329051: VecLoad_Default (vecio.c:516)<br>==25940== by 0x52E0BAB: VecLoad (vector.c:933)<br>==25940== by 0x4013D5: main (solveCmplxLinearSys.cpp:31)<br>==25940==<br><br></div></div></div></div></div><br><div class="gmail_quote"><div dir="ltr">On Mon, Jan 14, 2019 at 7:29 PM Zhang, Hong <<a href="mailto:hzhang@mcs.anl.gov" target="_blank">hzhang@mcs.anl.gov</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<div dir="ltr">
<div dir="ltr">Fande:<br>
</div>
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div dir="ltr">
<div>According to this PR <a href="https://bitbucket.org/petsc/petsc/pull-requests/1061/a_selinger-feature-faster-scalable/diff" target="_blank">https://bitbucket.org/petsc/petsc/pull-requests/1061/a_selinger-feature-faster-scalable/diff</a><br>
</div>
<div><br>
</div>
<div>Should we set the scalable algorithm as default?</div>
</div>
</div>
</blockquote>
<div>Sure, we can. But I feel we need do more tests to compare scalable and non-scalable algorithms. </div>
<div>On theory, for small to medium matrices, non-scalable matmatmult() algorithm enables more efficient </div>
<div>data accessing. Andreas optimized scalable implementation. Our non-scalable implementation might have room to be further optimized. </div>
<div>Hong</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<br>
<div class="gmail_quote">
<div dir="ltr">On Fri, Jan 11, 2019 at 10:34 AM Zhang, Hong via petsc-users <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">
<div>Add option '-mattransposematmult_via scalable'</div>
<div>Hong</div>
<br>
<div class="gmail_quote">
<div dir="ltr">On Fri, Jan 11, 2019 at 9:52 AM Zhang, Junchao via petsc-users <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">I saw the following error message in your first email.</div>
</div>
<blockquote style="margin:0px 0px 0px 40px;border:medium none;padding:0px">
<div>
<div>
<div>
<div>[0]PETSC ERROR: Out of memory. This could be due to allocating</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>[0]PETSC ERROR: too large an object or bleeding by not properly</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>[0]PETSC ERROR: destroying unneeded objects.</div>
</div>
</div>
</div>
</blockquote>
<div dir="ltr">
<div dir="ltr">
<div>Probably the matrix is too large. You can try with more compute nodes, for example, use 8 nodes instead of 2, and see what happens.</div>
<div><br clear="all">
<div>
<div dir="ltr" class="gmail-m_-3814543233888417572gmail-m_3659884561732865489gmail-m_3948349922729883348gmail-m_-4238683586953860770gmail-m_-3160957232454552718gmail_signature">
<div dir="ltr">--Junchao Zhang</div>
</div>
</div>
<br>
</div>
</div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr">On Fri, Jan 11, 2019 at 7:45 AM Sal Am via petsc-users <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">
<div>Using a larger problem set with 2B non-zero elements and a matrix of 25M x 25M I get the following error:</div>
<div>[4]PETSC ERROR: ------------------------------------------------------------------------<br>
[4]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range<br>
[4]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger<br>
[4]PETSC ERROR: or see <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind" target="_blank">
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind</a><br>
[4]PETSC ERROR: or try <a href="http://valgrind.org" target="_blank">http://valgrind.org</a> on GNU/linux and Apple Mac OS X to find memory corruption errors<br>
[4]PETSC ERROR: likely location of problem given in stack below<br>
[4]PETSC ERROR: --------------------- Stack Frames ------------------------------------<br>
[4]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,<br>
[4]PETSC ERROR: INSTEAD the line number of the start of the function<br>
[4]PETSC ERROR: is given.<br>
[4]PETSC ERROR: [4] MatCreateSeqAIJWithArrays line 4422 /lustre/home/vef002/petsc/src/mat/impls/aij/seq/aij.c<br>
[4]PETSC ERROR: [4] MatMatMultSymbolic_SeqAIJ_SeqAIJ line 747 /lustre/home/vef002/petsc/src/mat/impls/aij/seq/matmatmult.c<br>
[4]PETSC ERROR: [4] MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable line 1256 /lustre/home/vef002/petsc/src/mat/impls/aij/mpi/mpimatmatmult.c<br>
[4]PETSC ERROR: [4] MatTransposeMatMult_MPIAIJ_MPIAIJ line 1156 /lustre/home/vef002/petsc/src/mat/impls/aij/mpi/mpimatmatmult.c<br>
[4]PETSC ERROR: [4] MatTransposeMatMult line 9950 /lustre/home/vef002/petsc/src/mat/interface/matrix.c<br>
[4]PETSC ERROR: [4] PCGAMGCoarsen_AGG line 871 /lustre/home/vef002/petsc/src/ksp/pc/impls/gamg/agg.c<br>
[4]PETSC ERROR: [4] PCSetUp_GAMG line 428 /lustre/home/vef002/petsc/src/ksp/pc/impls/gamg/gamg.c<br>
[4]PETSC ERROR: [4] PCSetUp line 894 /lustre/home/vef002/petsc/src/ksp/pc/interface/precon.c<br>
[4]PETSC ERROR: [4] KSPSetUp line 304 /lustre/home/vef002/petsc/src/ksp/ksp/interface/itfunc.c<br>
[4]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------<br>
[4]PETSC ERROR: Signal received<br>
[4]PETSC ERROR: See <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html" target="_blank">
http://www.mcs.anl.gov/petsc/documentation/faq.html</a> for trouble shooting.<br>
[4]PETSC ERROR: Petsc Release Version 3.10.2, unknown <br>
[4]PETSC ERROR: ./solveCSys on a linux-cumulus-debug named r02g03 by vef002 Fri Jan 11 09:13:23 2019<br>
[4]PETSC ERROR: Configure options PETSC_ARCH=linux-cumulus-debug --with-cc=/usr/local/depot/openmpi-3.1.1-gcc-7.3.0/bin/mpicc --with-fc=/usr/local/depot/openmpi-3.1.1-gcc-7.3.0/bin/mpifort --with-cxx=/usr/local/depot/openmpi-3.1.1-gcc-7.3.0/bin/mpicxx --download-parmetis
--download-metis --download-ptscotch --download-superlu_dist --download-mumps --with-scalar-type=complex --with-debugging=yes --download-scalapack --download-superlu --download-fblaslapack=1 --download-cmake<br>
[4]PETSC ERROR: #1 User provided function() line 0 in unknown file<br>
--------------------------------------------------------------------------<br>
MPI_ABORT was invoked on rank 4 in communicator MPI_COMM_WORLD<br>
with errorcode 59.<br>
<br>
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.<br>
You may or may not see output from other processes, depending on<br>
exactly when Open MPI kills them.<br>
--------------------------------------------------------------------------<br>
[0]PETSC ERROR: ------------------------------------------------------------------------<br>
[0]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the batch system) has told this process to end<br>
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger<br>
[0]PETSC ERROR: or see <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind" target="_blank">
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind</a><br>
</div>
<div><br>
</div>
<div>Using Valgrind on only one of the valgrind files the following error was written:</div>
<div><br>
</div>
<div>==9053== Invalid read of size 4<br>
==9053== at 0x5B8067E: MatCreateSeqAIJWithArrays (aij.c:4445)<br>
==9053== by 0x5BC2608: MatMatMultSymbolic_SeqAIJ_SeqAIJ (matmatmult.c:790)<br>
==9053== by 0x5D106F8: MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable (mpimatmatmult.c:1337)<br>
==9053== by 0x5D0E84E: MatTransposeMatMult_MPIAIJ_MPIAIJ (mpimatmatmult.c:1186)<br>
==9053== by 0x5457C57: MatTransposeMatMult (matrix.c:9984)<br>
==9053== by 0x64DD99D: PCGAMGCoarsen_AGG (agg.c:882)<br>
==9053== by 0x64C7527: PCSetUp_GAMG (gamg.c:522)<br>
==9053== by 0x6592AA0: PCSetUp (precon.c:932)<br>
==9053== by 0x66B1267: KSPSetUp (itfunc.c:391)<br>
==9053== by 0x4019A2: main (solveCmplxLinearSys.cpp:68)<br>
==9053== Address 0x8386997f4 is not stack'd, malloc'd or (recently) free'd<br>
==9053==<br>
<br>
</div>
</div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr">On Fri, Jan 11, 2019 at 8:41 AM Sal Am <<a href="mailto:tempohoper@gmail.com" target="_blank">tempohoper@gmail.com</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div dir="ltr">
<div>Thank you Dave,</div>
<div><br>
</div>
<div>I reconfigured PETSc with valgrind and debugging mode, I ran the code again with the following options:</div>
<div>mpiexec -n 8 valgrind --tool=memcheck -q --num-callers=20 --log-file=valgrind.log.%p ./solveCSys -malloc off -ksp_type bcgs -pc_type gamg -log_view</div>
<div>(as on the petsc website you linked)</div>
<div><br>
</div>
<div>It finished solving using the iterative solver, but the resulting valgrind.log.%p files (all 8 corresponding to each processor) are all empty. And it took a whooping ~15hours, for what used to take ~10-20min. Maybe this is because of valgrind? I am not
sure. Attached is the log_view.<br>
</div>
<div><br>
</div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr">On Thu, Jan 10, 2019 at 8:59 AM Dave May <<a href="mailto:dave.mayhem23@gmail.com" target="_blank">dave.mayhem23@gmail.com</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div dir="ltr">
<div dir="ltr"><br>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr">On Thu, 10 Jan 2019 at 08:55, Sal Am via petsc-users <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">
<div>I am not sure what is exactly is wrong as the error changes slightly every time I run it (without changing the parameters).</div>
</div>
</div>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>This likely implies that you have a memory error in your code (a memory leak would not cause this behaviour).</div>
<div>I strongly suggest you make sure your code is free of memory errors.</div>
<div>You can do this using valgrind. See here </div>
<div><br>
</div>
<div><a href="https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind" target="_blank">https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind</a><br>
</div>
<div><br>
</div>
<div>for an explanation of how to use valgrind.</div>
<div> <br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">
<div>I have attached the first two run's errors and my code. <br>
</div>
<div><br>
</div>
<div>Is there a memory leak somewhere? I have tried running it with -malloc_dump, but not getting anything printed out, however, when run with -log_view I see that Viewer is created 4 times, but destroyed 3 times. The way I see it, I have destroyed it where
I see I no longer have use for it so not sure if I am wrong. Could this be the reason why it keeps crashing? It crashes as soon as it reads the matrix, before entering the solving mode (I have a print statement before solving starts that never prints).<br>
</div>
<div><br>
</div>
<div>how I run it in the job script on 2 node with 32 processors using the clusters OpenMPI.
<br>
</div>
<div><br>
</div>
<div>mpiexec ./solveCSys -ksp_type bcgs -pc_type gamg -ksp_converged_reason -ksp_monitor_true_residual -log_view -ksp_error_if_not_converged -ksp_monitor -malloc_log -ksp_view</div>
<div><br>
</div>
<div>the matrix:</div>
<div>2 122 821 366 (non-zero elements)<br>
</div>
<div>25 947 279 x 25 947 279<br>
</div>
<div><br>
</div>
<div>Thanks and all the best<br>
</div>
</div>
</div>
</div>
</div>
</blockquote>
</div>
</div>
</div>
</blockquote>
</div>
</blockquote>
</div>
</blockquote>
</div>
</div>
</blockquote>
</div>
</div>
</div>
</div>
</div>
</blockquote>
</div>
</blockquote>
</div>
</div>
</div>
</blockquote></div>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><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.cse.buffalo.edu/~knepley/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div></div></div></div></div>