<div dir="ltr"><span style="color:rgb(80,0,80);font-size:12.8000001907349px">Mahir,</span><div><font color="#500050"><span style="font-size:12.8000001907349px"><br></span></font></div><div><font color="#500050"><span style="font-size:12.8000001907349px">Sherry fixed several bugs in superlu_dist-v4.1.</span></font></div><div><font color="#500050"><span style="font-size:12.8000001907349px">The current petsc-release interfaces with superlu_dist-v4.0.</span></font></div><div><font color="#500050"><span style="font-size:12.8000001907349px">We do not know whether the reported issue (attached below) has been resolved or not. If not, c</span></font><font color="#500050"><span style="font-size:12.8000001907349px">an you test it with the latest </span></font><span style="color:rgb(80,0,80);font-size:12.8000001907349px">superlu_dist-v4.1?</span></div><div><span style="color:rgb(80,0,80);font-size:12.8000001907349px"><br></span></div><div><span style="color:rgb(80,0,80);font-size:12.8000001907349px">Here is how to do it:</span></div><div><span style="color:rgb(80,0,80);font-size:12.8000001907349px">1. download superlu_dist v4.1</span></div><div><span style="color:rgb(80,0,80);font-size:12.8000001907349px">2. remove existing PETSC_ARCH directory, then configure petsc with</span></div><div><font color="#500050"><span style="font-size:12.8000001907349px">'--download-superlu_dist=superlu_dist_4.1.tar.gz'</span></font><br></div><div><font color="#500050"><span style="font-size:12.8000001907349px">3. build petsc</span></font></div><div><font color="#500050"><span style="font-size:12.8000001907349px"><br></span></font></div><div><font color="#500050"><span style="font-size:12.8000001907349px">Let us know if the issue remains.</span></font></div><div><font color="#500050"><span style="font-size:12.8000001907349px"><br></span></font></div><div><font color="#500050"><span style="font-size:12.8000001907349px">Hong</span></font></div><div><span style="color:rgb(80,0,80);font-size:12.8000001907349px"><br></span></div><div><br></div><div><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">Xiaoye S. Li</b> <span dir="ltr"><<a href="mailto:xsli@lbl.gov">xsli@lbl.gov</a>></span><br>Date: Wed, Jul 29, 2015 at 2:24 PM<br>Subject: Fwd: [petsc-users] SuperLU MPI-problem<br>To: Hong Zhang <<a href="mailto:hzhang@mcs.anl.gov">hzhang@mcs.anl.gov</a>><br><br><br><div dir="ltr"><div style="font-family:arial,helvetica,sans-serif">Hong,<br></div><div style="font-family:arial,helvetica,sans-serif">I am cleaning the mailbox, and saw this unresolved issue. I am not sure whether the new fix to parallel symbolic factorization solves the problem. What bothers be is that he is getting the following error:<span class=""><br><br><span><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">Invalid ISPEC at line 484 in file get_perm_c.c<br><br></span></span></span></div>This has nothing to do with my bug fix.<div style="font-family:arial,helvetica,sans-serif;display:inline"> Shall we ask him to try the new version, or try to get him matrix?<br><br></div><div style="font-family:arial,helvetica,sans-serif;display:inline">Sherry<br></div><div style="font-family:arial,helvetica,sans-serif"><br></div><div class="gmail_quote"><span class="">---------- Forwarded message ----------<br>From: <b class="gmail_sendername"><a href="mailto:Mahir.Ulker-Kaustell@tyrens.se" target="_blank">Mahir.Ulker-Kaustell@tyrens.se</a></b> <span dir="ltr"><<a href="mailto:Mahir.Ulker-Kaustell@tyrens.se" target="_blank">Mahir.Ulker-Kaustell@tyrens.se</a>></span><br>Date: Wed, Jul 22, 2015 at 1:32 PM<br>Subject: RE: [petsc-users] SuperLU MPI-problem<br>To: Hong <<a href="mailto:hzhang@mcs.anl.gov" target="_blank">hzhang@mcs.anl.gov</a>>, "Xiaoye S. Li" <<a href="mailto:xsli@lbl.gov" target="_blank">xsli@lbl.gov</a>><br>Cc: petsc-users <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>><br><br><br>
</span><div link="blue" vlink="purple" lang="SV">
<div><span class="">
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d" lang="EN-US">The 1000 was just a conservative guess. The number of non-zeros per row is in the tens in general but certain constraints lead to non-diagonal
streaks in the sparsity-pattern.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d" lang="EN-US">Is it the reordering of the matrix that is killing me here? How can I set
</span><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">options.ColPerm</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d" lang="EN-US">?<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d" lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d" lang="EN-US">If i use -mat_superlu_dist_parsymbfact the program crashes with<u></u><u></u></span></p><span>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d" lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">Invalid ISPEC at line 484 in file get_perm_c.c<u></u><u></u></span></p>
</span><p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">-------------------------------------------------------<u></u><u></u></span></p></span><span><span class="">
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">Primary job terminated normally, but 1 process returned<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">a non-zero exit code.. Per user-direction, the job has been aborted.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">-------------------------------------------------------<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">[0]PETSC ERROR: ------------------------------------------------------------------------<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">[0]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the batch system) has told this process to end<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger<u></u><u></u></span></p>
</span><p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">[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><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">[0]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<u></u><u></u></span></p>
</span><span class=""><p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">[0]PETSC ERROR: to get more information on the crash.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">[0]PETSC ERROR: Signal received<u></u><u></u></span></p>
</span><p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">[0]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.<u></u><u></u></span></p><span class="">
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">[0]PETSC ERROR: Petsc Release Version 3.6.0, Jun, 09, 2015<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">[0]PETSC ERROR: ./solve on a cygwin-complex-nodebug named CZC5202SM2 by muk Wed Jul 22 21:59:23 2015<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">[0]PETSC ERROR: Configure options PETSC_DIR=/packages/petsc-3.6.0 PETSC_ARCH=cygwin-complex-nodebug --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --with-debugging=0
--with-fortran-kernels=1 --with-scalar-type=complex --download-fblaspack --download-mpich --download-scalapack --download-mumps --download-metis --download-parmetis --download-superlu --download-superlu_dist --download-fftw<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">[0]PETSC ERROR: #1 User provided function() line 0 in unknown file<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">[unset]: aborting job:<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">[0]PETSC ERROR: ------------------------------------------------------------------------<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d" lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d" lang="EN-US">If i use -mat_superlu_dist_parsymbfact=1 the program crashes (somewhat later) with<u></u><u></u></span></p><span>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d" lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">Malloc fails for Lnzval_bc_ptr[*][] at line 626 in file zdistribute.c<u></u><u></u></span></p>
</span><p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">col block 3006 -------------------------------------------------------<u></u><u></u></span></p><span>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">Primary job terminated normally, but 1 process returned<u></u><u></u></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">a non-zero exit code.. Per user-direction, the job has been aborted.<u></u><u></u></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">-------------------------------------------------------<u></u><u></u></span></p>
</span><p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">col block 1924 [0]PETSC ERROR: ------------------------------------------------------------------------<u></u><u></u></span></p></span><span><span class="">
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">[0]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the batch system) has told this process to
end<u></u><u></u></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger<u></u><u></u></span></p>
</span><p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">[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><u></u><u></u></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">[0]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<u></u><u></u></span></p>
</span><span class=""><p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run<u></u><u></u></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">[0]PETSC ERROR: to get more information on the crash.<u></u><u></u></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------<u></u><u></u></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">[0]PETSC ERROR: Signal received<u></u><u></u></span></p>
</span><p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">[0]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.<u></u><u></u></span></p><span class="">
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">[0]PETSC ERROR: Petsc Release Version 3.6.0, Jun, 09, 2015<u></u><u></u></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">[0]PETSC ERROR: ./solve on a cygwin-complex-nodebug named CZC5202SM2 by muk Wed Jul 22 21:59:58 2015<u></u><u></u></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">[0]PETSC ERROR: Configure options PETSC_DIR=/packages/petsc-3.6.0 PETSC_ARCH=cygwin-complex-nodebug --with-cc=gcc
--with-cxx=g++ --with-fc=gfortran --with-debugging=0 --with-fortran-kernels=1 --with-scalar-type=complex --download-fblaspack --download-mpich --download-scalapack --download-mumps --download-metis --download-parmetis --download-superlu --download-superlu_dist
--download-fftw<u></u><u></u></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">[0]PETSC ERROR: #1 User provided function() line 0 in unknown file<u></u><u></u></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0<u></u><u></u></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">[unset]: aborting job:<u></u><u></u></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Lucida Console"" lang="EN-US">application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0<u></u><u></u></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Lucida Console"">[0]PETSC ERROR: ------------------------------------------------------------------------<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d" lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="color:#1f497d">/Mahir<u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p>
</span><p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"" lang="EN-US">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"" lang="EN-US"> Hong [mailto:<a href="mailto:hzhang@mcs.anl.gov" target="_blank">hzhang@mcs.anl.gov</a>]
<br></span></p><div><div class="h5">
<b>Sent:</b> den 22 juli 2015 21:34<br>
<b>To:</b> Xiaoye S. Li<br>
<b>Cc:</b> Ülker-Kaustell, Mahir; petsc-users</div></div><p></p><div><div class="h5"><div><div><br>
<b>Subject:</b> Re: [petsc-users] SuperLU MPI-problem<u></u><u></u></div></div><p></p><div><div>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<div>
<p class="MsoNormal">In Petsc/superlu_dist interface, we set default <u></u><u></u></p>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
<div>
<div>
<p class="MsoNormal">options.ParSymbFact = NO;<u></u><u></u></p>
</div>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">When user raises the flag "-mat_superlu_dist_parsymbfact",<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">we set<u></u><u></u></p>
</div>
<div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal"> options.ParSymbFact = YES;<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"> options.ColPerm = PARMETIS; /* in v2.2, PARMETIS is forced for ParSymbFact regardless of user ordering setting */<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
</div>
<div>
<p class="MsoNormal">We do not change anything else.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Hong<u></u><u></u></p>
</div>
</div>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
<div>
<p class="MsoNormal">On Wed, Jul 22, 2015 at 2:19 PM, Xiaoye S. Li <<a href="mailto:xsli@lbl.gov" target="_blank">xsli@lbl.gov</a>> wrote:<u></u><u></u></p>
<div>
<div>
<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Arial","sans-serif"">I am trying to understand your problem. You said you are solving
</span>Naviers equation (elastodynamics) in the frequency domain, using finite element discretization. I wonder why you have about 1000 nonzeros per row. Usually in many PDE discretized matrices, the number of nonzeros per row is in the tens (even for 3D
problems), not in the thousands. So, your matrix is quite a bit denser than many sparse matrices we deal with.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">The number of nonzeros in the L and U factors is much more than that in original matrix A -- typically we see 10-20x fill ratio for 2D, or can be as bad as 50-100x fill ratio for 3D. But since your matrix starts much denser (i.e., the
underlying graph has many connections), it may not lend to any good ordering strategy to preserve sparsity of L and U; that is, the L and U fill ratio may be large. <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">I don't understand why you get the following error when you use <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">‘-mat_superlu_dist_parsymbfact’.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Lucida Console"">Invalid ISPEC at line 484 in file get_perm_c.c</span><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Perhaps Hong Zhang knows; she built the SuperLU_DIST interface for PETSc. <u></u><u></u></p>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif""><u></u> <u></u></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif"">Hong -- in order to use parallel symbolic factorization, is it sufficient to specify only <u></u><u></u></span></p>
</div>
<p class="MsoNormal">‘-mat_superlu_dist_parsymbfact’<u></u><u></u></p>
<div>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif""> ? (the default is to use sequential symbolic factorization.)<u></u><u></u></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif""><u></u> <u></u></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif""><u></u> <u></u></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif"">Sherry<u></u><u></u></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif""><u></u> <u></u></span></p>
</div>
</div>
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<p class="MsoNormal">On Wed, Jul 22, 2015 at 9:11 AM, <a href="mailto:Mahir.Ulker-Kaustell@tyrens.se" target="_blank">
Mahir.Ulker-Kaustell@tyrens.se</a> <<a href="mailto:Mahir.Ulker-Kaustell@tyrens.se" target="_blank">Mahir.Ulker-Kaustell@tyrens.se</a>> wrote:<u></u><u></u></p>
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<p class="MsoNormal">Thank you for your reply.<br>
<br>
As you have probably figured out already, I am not a computational scientist. I am a researcher in civil engineering (railways for high-speed traffic), trying to produce some, from my perspective, fairly large parametric studies based on finite element discretizations.<br>
<br>
I am working in a Windows-environment and have installed PETSc through Cygwin.<br>
Apparently, there is no support for Valgrind in this OS.<br>
<br>
If I have understood you correct, the memory issues are related to superLU and given my background, there is not much I can do. Is this correct?<br>
<br>
<br>
Best regards,<br>
Mahir<br>
<br>
______________________________________________<br>
Mahir Ülker-Kaustell, Kompetenssamordnare, Brokonstruktör, Tekn. Dr, Tyréns AB<br>
010 452 30 82, <a href="mailto:Mahir.Ulker-Kaustell@tyrens.se" target="_blank">Mahir.Ulker-Kaustell@tyrens.se</a><br>
______________________________________________<u></u><u></u></p>
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-----Original Message-----<br>
From: Barry Smith [mailto:<a href="mailto:bsmith@mcs.anl.gov" target="_blank">bsmith@mcs.anl.gov</a>]<br>
Sent: den 22 juli 2015 02:57<br>
To: Ülker-Kaustell, Mahir<br>
Cc: Xiaoye S. Li; petsc-users<br>
Subject: Re: [petsc-users] SuperLU MPI-problem<br>
<br>
<br>
Run the program under valgrind <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> . When I use the option -mat_superlu_dist_parsymbfact I get many scary memory problems some involving for example ddist_psymbtonum (pdsymbfact_distdata.c:1332)<br>
<br>
Note that I consider it unacceptable for running programs to EVER use uninitialized values; until these are all cleaned up I won't trust any runs like this.<br>
<br>
Barry<br>
<br>
<br>
<br>
<br>
==42050== Conditional jump or move depends on uninitialised value(s)<br>
==42050== at 0x10274C436: MPI_Allgatherv (allgatherv.c:1053)<br>
==42050== by 0x101557F60: get_perm_c_parmetis (get_perm_c_parmetis.c:285)<br>
==42050== by 0x101501192: pdgssvx (pdgssvx.c:934)<br>
==42050== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST (superlu_dist.c:414)<br>
==42050== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)<br>
==42050== by 0x100F09F2C: PCSetUp_LU (lu.c:152)<br>
==42050== by 0x100FF9036: PCSetUp (precon.c:982)<br>
==42050== by 0x1010F54EB: KSPSetUp (itfunc.c:332)<br>
==42050== by 0x1010F7985: KSPSolve (itfunc.c:546)<br>
==42050== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)<br>
==42050== by 0x1011C49B7: SNESSolve (snes.c:3906)<br>
==42050== by 0x100001B3C: main (in ./ex19)<br>
==42050== Uninitialised value was created by a stack allocation<br>
==42050== at 0x10155751B: get_perm_c_parmetis (get_perm_c_parmetis.c:96)<br>
==42050==<br>
==42050== Conditional jump or move depends on uninitialised value(s)<br>
==42050== at 0x102851C61: MPIR_Allgatherv_intra (allgatherv.c:651)<br>
==42050== by 0x102853EC7: MPIR_Allgatherv (allgatherv.c:903)<br>
==42050== by 0x102853F84: MPIR_Allgatherv_impl (allgatherv.c:944)<br>
==42050== by 0x10274CA41: MPI_Allgatherv (allgatherv.c:1107)<br>
==42050== by 0x101557F60: get_perm_c_parmetis (get_perm_c_parmetis.c:285)<br>
==42050== by 0x101501192: pdgssvx (pdgssvx.c:934)<br>
==42050== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST (superlu_dist.c:414)<br>
==42050== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)<br>
==42050== by 0x100F09F2C: PCSetUp_LU (lu.c:152)<br>
==42050== by 0x100FF9036: PCSetUp (precon.c:982)<br>
==42050== by 0x1010F54EB: KSPSetUp (itfunc.c:332)<br>
==42050== by 0x1010F7985: KSPSolve (itfunc.c:546)<br>
==42050== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)<br>
==42050== by 0x1011C49B7: SNESSolve (snes.c:3906)<br>
==42050== by 0x100001B3C: main (in ./ex19)<br>
==42050== Uninitialised value was created by a stack allocation<br>
==42050== at 0x10155751B: get_perm_c_parmetis (get_perm_c_parmetis.c:96)<br>
==42050==<br>
==42049== Syscall param writev(vector[...]) points to uninitialised byte(s)<br>
==42049== at 0x102DA1C3A: writev (in /usr/lib/system/libsystem_kernel.dylib)<br>
==42049== by 0x10296A0DC: MPL_large_writev (mplsock.c:32)<br>
==42049== by 0x10295F6AD: MPIDU_Sock_writev (sock_immed.i:610)<br>
==42049== by 0x102943FCA: MPIDI_CH3_iSendv (ch3_isendv.c:84)<br>
==42049== by 0x102934361: MPIDI_CH3_EagerContigIsend (ch3u_eager.c:556)<br>
==42049== by 0x102939531: MPID_Isend (mpid_isend.c:138)<br>
==42049== by 0x10277656E: MPI_Isend (isend.c:125)<br>
==42049== by 0x102088B66: libparmetis__gkMPI_Isend (gkmpi.c:63)<br>
==42049== by 0x10208140F: libparmetis__CommInterfaceData (comm.c:298)<br>
==42049== by 0x1020A8758: libparmetis__CompactGraph (ometis.c:553)<br>
==42049== by 0x1020A77BB: libparmetis__MultilevelOrder (ometis.c:225)<br>
==42049== by 0x1020A7493: ParMETIS_V32_NodeND (ometis.c:151)<br>
==42049== by 0x1020A6AFB: ParMETIS_V3_NodeND (ometis.c:34)<br>
==42049== by 0x101557CFC: get_perm_c_parmetis (get_perm_c_parmetis.c:241)<br>
==42049== by 0x101501192: pdgssvx (pdgssvx.c:934)<br>
==42049== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST (superlu_dist.c:414)<br>
==42049== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)<br>
==42049== by 0x100F09F2C: PCSetUp_LU (lu.c:152)<br>
==42049== by 0x100FF9036: PCSetUp (precon.c:982)<br>
==42048== Syscall param writev(vector[...]) points to uninitialised byte(s)<br>
==42049== by 0x1010F54EB: KSPSetUp (itfunc.c:332)<br>
==42049== Address 0x105edff70 is 1,424 bytes inside a block of size 752,720 alloc'd<br>
==42049== at 0x1000183B1: malloc (vg_replace_malloc.c:303)<br>
==42049== by 0x1020EB90C: gk_malloc (memory.c:147)<br>
==42049== by 0x1020EAA28: gk_mcoreCreate (mcore.c:28)<br>
==42048== at 0x102DA1C3A: writev (in /usr/lib/system/libsystem_kernel.dylib)<br>
==42048== by 0x10296A0DC: MPL_large_writev (mplsock.c:32)<br>
==42049== by 0x1020BA5CF: libparmetis__AllocateWSpace (wspace.c:23)<br>
==42049== by 0x1020A6E84: ParMETIS_V32_NodeND (ometis.c:98)<br>
==42048== by 0x10295F6AD: MPIDU_Sock_writev (sock_immed.i:610)<br>
==42048== by 0x102943FCA: MPIDI_CH3_iSendv (ch3_isendv.c:84)<br>
==42048== by 0x102934361: MPIDI_CH3_EagerContigIsend (ch3u_eager.c:556)<br>
==42049== by 0x1020A6AFB: ParMETIS_V3_NodeND (ometis.c:34)<br>
==42049== by 0x101557CFC: get_perm_c_parmetis (get_perm_c_parmetis.c:241)<br>
==42049== by 0x101501192: pdgssvx (pdgssvx.c:934)<br>
==42048== by 0x102939531: MPID_Isend (mpid_isend.c:138)<br>
==42048== by 0x10277656E: MPI_Isend (isend.c:125)<br>
==42049== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST (superlu_dist.c:414)<br>
==42049== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)<br>
==42049== by 0x100F09F2C: PCSetUp_LU (lu.c:152)<br>
==42049== by 0x100FF9036: PCSetUp (precon.c:982)<br>
==42049== by 0x1010F54EB: KSPSetUp (itfunc.c:332)<br>
==42048== by 0x102088B66: libparmetis__gkMPI_Isend (gkmpi.c:63)<br>
==42048== by 0x10208140F: libparmetis__CommInterfaceData (comm.c:298)<br>
==42049== by 0x1010F7985: KSPSolve (itfunc.c:546)<br>
==42049== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)<br>
==42048== by 0x1020A8758: libparmetis__CompactGraph (ometis.c:553)<br>
==42048== by 0x1020A77BB: libparmetis__MultilevelOrder (ometis.c:225)<br>
==42048== by 0x1020A7493: ParMETIS_V32_NodeND (ometis.c:151)<br>
==42049== by 0x1011C49B7: SNESSolve (snes.c:3906)<br>
==42049== by 0x100001B3C: main (in ./ex19)<br>
==42049== Uninitialised value was created by a heap allocation<br>
==42049== at 0x1000183B1: malloc (vg_replace_malloc.c:303)<br>
==42049== by 0x1020EB90C: gk_malloc (memory.c:147)<br>
==42048== by 0x1020A6AFB: ParMETIS_V3_NodeND (ometis.c:34)<br>
==42048== by 0x101557CFC: get_perm_c_parmetis (get_perm_c_parmetis.c:241)<br>
==42048== by 0x101501192: pdgssvx (pdgssvx.c:934)<br>
==42048== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST (superlu_dist.c:414)<br>
==42049== by 0x10211C50B: libmetis__imalloc (gklib.c:24)<br>
==42049== by 0x1020A8566: libparmetis__CompactGraph (ometis.c:519)<br>
==42049== by 0x1020A77BB: libparmetis__MultilevelOrder (ometis.c:225)<br>
==42048== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)<br>
==42049== by 0x1020A7493: ParMETIS_V32_NodeND (ometis.c:151)<br>
==42049== by 0x1020A6AFB: ParMETIS_V3_NodeND (ometis.c:34)<br>
==42049== by 0x101557CFC: get_perm_c_parmetis (get_perm_c_parmetis.c:241)<br>
==42049== by 0x101501192: pdgssvx (pdgssvx.c:934)<br>
==42049== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST (superlu_dist.c:414)<br>
==42049== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)<br>
==42048== by 0x100F09F2C: PCSetUp_LU (lu.c:152)<br>
==42049== by 0x100F09F2C: PCSetUp_LU (lu.c:152)<br>
==42049== by 0x100FF9036: PCSetUp (precon.c:982)<br>
==42049== by 0x1010F54EB: KSPSetUp (itfunc.c:332)<br>
==42049== by 0x1010F7985: KSPSolve (itfunc.c:546)<br>
==42049== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)<br>
==42048== by 0x100FF9036: PCSetUp (precon.c:982)<br>
==42048== by 0x1010F54EB: KSPSetUp (itfunc.c:332)<br>
==42048== Address 0x10597a860 is 1,408 bytes inside a block of size 752,720 alloc'd<br>
==42049== by 0x1011C49B7: SNESSolve (snes.c:3906)<br>
==42049== by 0x100001B3C: main (in ./ex19)<br>
==42049==<br>
==42048== at 0x1000183B1: malloc (vg_replace_malloc.c:303)<br>
==42048== by 0x1020EB90C: gk_malloc (memory.c:147)<br>
==42048== by 0x1020EAA28: gk_mcoreCreate (mcore.c:28)<br>
==42048== by 0x1020BA5CF: libparmetis__AllocateWSpace (wspace.c:23)<br>
==42048== by 0x1020A6E84: ParMETIS_V32_NodeND (ometis.c:98)<br>
==42048== by 0x1020A6AFB: ParMETIS_V3_NodeND (ometis.c:34)<br>
==42048== by 0x101557CFC: get_perm_c_parmetis (get_perm_c_parmetis.c:241)<br>
==42048== by 0x101501192: pdgssvx (pdgssvx.c:934)<br>
==42048== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST (superlu_dist.c:414)<br>
==42048== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)<br>
==42048== by 0x100F09F2C: PCSetUp_LU (lu.c:152)<br>
==42048== by 0x100FF9036: PCSetUp (precon.c:982)<br>
==42048== by 0x1010F54EB: KSPSetUp (itfunc.c:332)<br>
==42048== by 0x1010F7985: KSPSolve (itfunc.c:546)<br>
==42048== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)<br>
==42048== by 0x1011C49B7: SNESSolve (snes.c:3906)<br>
==42048== by 0x100001B3C: main (in ./ex19)<br>
==42048== Uninitialised value was created by a heap allocation<br>
==42048== at 0x1000183B1: malloc (vg_replace_malloc.c:303)<br>
==42048== by 0x1020EB90C: gk_malloc (memory.c:147)<br>
==42048== by 0x10211C50B: libmetis__imalloc (gklib.c:24)<br>
==42048== by 0x1020A8566: libparmetis__CompactGraph (ometis.c:519)<br>
==42048== by 0x1020A77BB: libparmetis__MultilevelOrder (ometis.c:225)<br>
==42048== by 0x1020A7493: ParMETIS_V32_NodeND (ometis.c:151)<br>
==42048== by 0x1020A6AFB: ParMETIS_V3_NodeND (ometis.c:34)<br>
==42048== by 0x101557CFC: get_perm_c_parmetis (get_perm_c_parmetis.c:241)<br>
==42048== by 0x101501192: pdgssvx (pdgssvx.c:934)<br>
==42048== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST (superlu_dist.c:414)<br>
==42048== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)<br>
==42048== by 0x100F09F2C: PCSetUp_LU (lu.c:152)<br>
==42048== by 0x100FF9036: PCSetUp (precon.c:982)<br>
==42048== by 0x1010F54EB: KSPSetUp (itfunc.c:332)<br>
==42048== by 0x1010F7985: KSPSolve (itfunc.c:546)<br>
==42048== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)<br>
==42048== by 0x1011C49B7: SNESSolve (snes.c:3906)<br>
==42048== by 0x100001B3C: main (in ./ex19)<br>
==42048==<br>
==42048== Syscall param write(buf) points to uninitialised byte(s)<br>
==42048== at 0x102DA1C22: write (in /usr/lib/system/libsystem_kernel.dylib)<br>
==42048== by 0x10295F5BD: MPIDU_Sock_write (sock_immed.i:525)<br>
==42048== by 0x102944839: MPIDI_CH3_iStartMsg (ch3_istartmsg.c:86)<br>
==42048== by 0x102933B80: MPIDI_CH3_EagerContigShortSend (ch3u_eager.c:257)<br>
==42048== by 0x10293ADBA: MPID_Send (mpid_send.c:130)<br>
==42048== by 0x10277A1FA: MPI_Send (send.c:127)<br>
==42048== by 0x10155802F: get_perm_c_parmetis (get_perm_c_parmetis.c:299)<br>
==42048== by 0x101501192: pdgssvx (pdgssvx.c:934)<br>
==42048== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST (superlu_dist.c:414)<br>
==42048== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)<br>
==42048== by 0x100F09F2C: PCSetUp_LU (lu.c:152)<br>
==42048== by 0x100FF9036: PCSetUp (precon.c:982)<br>
==42048== by 0x1010F54EB: KSPSetUp (itfunc.c:332)<br>
==42048== by 0x1010F7985: KSPSolve (itfunc.c:546)<br>
==42048== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)<br>
==42048== by 0x1011C49B7: SNESSolve (snes.c:3906)<br>
==42048== by 0x100001B3C: main (in ./ex19)<br>
==42048== Address 0x104810704 is on thread 1's stack<br>
==42048== in frame #3, created by MPIDI_CH3_EagerContigShortSend (ch3u_eager.c:218)<br>
==42048== Uninitialised value was created by a heap allocation<br>
==42048== at 0x1000183B1: malloc (vg_replace_malloc.c:303)<br>
==42048== by 0x10153B704: superlu_malloc_dist (memory.c:108)<br>
==42048== by 0x101557AB9: get_perm_c_parmetis (get_perm_c_parmetis.c:185)<br>
==42048== by 0x101501192: pdgssvx (pdgssvx.c:934)<br>
==42048== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST (superlu_dist.c:414)<br>
==42048== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)<br>
==42048== by 0x100F09F2C: PCSetUp_LU (lu.c:152)<br>
==42048== by 0x100FF9036: PCSetUp (precon.c:982)<br>
==42048== by 0x1010F54EB: KSPSetUp (itfunc.c:332)<br>
==42048== by 0x1010F7985: KSPSolve (itfunc.c:546)<br>
==42048== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)<br>
==42048== by 0x1011C49B7: SNESSolve (snes.c:3906)<br>
==42048== by 0x100001B3C: main (in ./ex19)<br>
==42048==<br>
==42050== Conditional jump or move depends on uninitialised value(s)<br>
==42050== at 0x102744CB8: MPI_Alltoallv (alltoallv.c:480)<br>
==42050== by 0x101510B3E: dist_symbLU (pdsymbfact_distdata.c:539)<br>
==42050== by 0x10150A5C6: ddist_psymbtonum (pdsymbfact_distdata.c:1275)<br>
==42050== by 0x1015018C2: pdgssvx (pdgssvx.c:1057)<br>
==42050== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST (superlu_dist.c:414)<br>
==42050== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)<br>
==42050== by 0x100F09F2C: PCSetUp_LU (lu.c:152)<br>
==42050== by 0x100FF9036: PCSetUp (precon.c:982)<br>
==42050== by 0x1010F54EB: KSPSetUp (itfunc.c:332)<br>
==42050== by 0x1010F7985: KSPSolve (itfunc.c:546)<br>
==42050== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)<br>
==42050== by 0x1011C49B7: SNESSolve (snes.c:3906)<br>
==42050== by 0x100001B3C: main (in ./ex19)<br>
==42050== Uninitialised value was created by a stack allocation<br>
==42050== at 0x10150E4C4: dist_symbLU (pdsymbfact_distdata.c:96)<br>
==42050==<br>
==42050== Conditional jump or move depends on uninitialised value(s)<br>
==42050== at 0x102744E43: MPI_Alltoallv (alltoallv.c:490)<br>
==42050== by 0x101510B3E: dist_symbLU (pdsymbfact_distdata.c:539)<br>
==42050== by 0x10150A5C6: ddist_psymbtonum (pdsymbfact_distdata.c:1275)<br>
==42050== by 0x1015018C2: pdgssvx (pdgssvx.c:1057)<br>
==42050== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST (superlu_dist.c:414)<br>
==42050== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)<br>
==42050== by 0x100F09F2C: PCSetUp_LU (lu.c:152)<br>
==42050== by 0x100FF9036: PCSetUp (precon.c:982)<br>
==42050== by 0x1010F54EB: KSPSetUp (itfunc.c:332)<br>
==42050== by 0x1010F7985: KSPSolve (itfunc.c:546)<br>
==42050== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)<br>
==42050== by 0x1011C49B7: SNESSolve (snes.c:3906)<br>
==42050== by 0x100001B3C: main (in ./ex19)<br>
==42050== Uninitialised value was created by a stack allocation<br>
==42050== at 0x10150E4C4: dist_symbLU (pdsymbfact_distdata.c:96)<br>
==42050==<br>
==42050== Conditional jump or move depends on uninitialised value(s)<br>
==42050== at 0x102744EBF: MPI_Alltoallv (alltoallv.c:497)<br>
==42050== by 0x101510B3E: dist_symbLU (pdsymbfact_distdata.c:539)<br>
==42050== by 0x10150A5C6: ddist_psymbtonum (pdsymbfact_distdata.c:1275)<br>
==42050== by 0x1015018C2: pdgssvx (pdgssvx.c:1057)<br>
==42050== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST (superlu_dist.c:414)<br>
==42050== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)<br>
==42050== by 0x100F09F2C: PCSetUp_LU (lu.c:152)<br>
==42050== by 0x100FF9036: PCSetUp (precon.c:982)<br>
==42050== by 0x1010F54EB: KSPSetUp (itfunc.c:332)<br>
==42050== by 0x1010F7985: KSPSolve (itfunc.c:546)<br>
==42050== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)<br>
==42050== by 0x1011C49B7: SNESSolve (snes.c:3906)<br>
==42050== by 0x100001B3C: main (in ./ex19)<br>
==42050== Uninitialised value was created by a stack allocation<br>
==42050== at 0x10150E4C4: dist_symbLU (pdsymbfact_distdata.c:96)<br>
==42050==<br>
==42050== Conditional jump or move depends on uninitialised value(s)<br>
==42050== at 0x1027450B1: MPI_Alltoallv (alltoallv.c:512)<br>
==42050== by 0x101510B3E: dist_symbLU (pdsymbfact_distdata.c:539)<br>
==42050== by 0x10150A5C6: ddist_psymbtonum (pdsymbfact_distdata.c:1275)<br>
==42050== by 0x1015018C2: pdgssvx (pdgssvx.c:1057)<br>
==42050== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST (superlu_dist.c:414)<br>
==42050== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)<br>
==42050== by 0x100F09F2C: PCSetUp_LU (lu.c:152)<br>
==42050== by 0x100FF9036: PCSetUp (precon.c:982)<br>
==42050== by 0x1010F54EB: KSPSetUp (itfunc.c:332)<br>
==42050== by 0x1010F7985: KSPSolve (itfunc.c:546)<br>
==42050== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)<br>
==42050== by 0x1011C49B7: SNESSolve (snes.c:3906)<br>
==42050== by 0x100001B3C: main (in ./ex19)<br>
==42050== Uninitialised value was created by a stack allocation<br>
==42050== at 0x10150E4C4: dist_symbLU (pdsymbfact_distdata.c:96)<br>
==42050==<br>
==42050== Conditional jump or move depends on uninitialised value(s)<br>
==42050== at 0x10283FB06: MPIR_Alltoallv_intra (alltoallv.c:92)<br>
==42050== by 0x1028407B6: MPIR_Alltoallv (alltoallv.c:343)<br>
==42050== by 0x102840884: MPIR_Alltoallv_impl (alltoallv.c:380)<br>
==42050== by 0x10274541B: MPI_Alltoallv (alltoallv.c:531)<br>
==42050== by 0x101510B3E: dist_symbLU (pdsymbfact_distdata.c:539)<br>
==42050== by 0x10150A5C6: ddist_psymbtonum (pdsymbfact_distdata.c:1275)<br>
==42050== by 0x1015018C2: pdgssvx (pdgssvx.c:1057)<br>
==42050== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST (superlu_dist.c:414)<br>
==42050== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)<br>
==42050== by 0x100F09F2C: PCSetUp_LU (lu.c:152)<br>
==42050== by 0x100FF9036: PCSetUp (precon.c:982)<br>
==42050== by 0x1010F54EB: KSPSetUp (itfunc.c:332)<br>
==42050== by 0x1010F7985: KSPSolve (itfunc.c:546)<br>
==42050== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)<br>
==42050== by 0x1011C49B7: SNESSolve (snes.c:3906)<br>
==42050== by 0x100001B3C: main (in ./ex19)<br>
==42050== Uninitialised value was created by a stack allocation<br>
==42050== at 0x10150E4C4: dist_symbLU (pdsymbfact_distdata.c:96)<br>
==42050==<br>
==42050== Syscall param writev(vector[...]) points to uninitialised byte(s)<br>
==42050== at 0x102DA1C3A: writev (in /usr/lib/system/libsystem_kernel.dylib)<br>
==42050== by 0x10296A0DC: MPL_large_writev (mplsock.c:32)<br>
==42050== by 0x10295F6AD: MPIDU_Sock_writev (sock_immed.i:610)<br>
==42050== by 0x102943FCA: MPIDI_CH3_iSendv (ch3_isendv.c:84)<br>
==42050== by 0x102934361: MPIDI_CH3_EagerContigIsend (ch3u_eager.c:556)<br>
==42050== by 0x102939531: MPID_Isend (mpid_isend.c:138)<br>
==42050== by 0x10277656E: MPI_Isend (isend.c:125)<br>
==42050== by 0x101524C41: pdgstrf2_trsm (pdgstrf2.c:201)<br>
==42050== by 0x10151ECBF: pdgstrf (pdgstrf.c:1082)<br>
==42050== by 0x1015019A5: pdgssvx (pdgssvx.c:1069)<br>
==42050== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST (superlu_dist.c:414)<br>
==42050== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)<br>
==42050== by 0x100F09F2C: PCSetUp_LU (lu.c:152)<br>
==42050== by 0x100FF9036: PCSetUp (precon.c:982)<br>
==42050== by 0x1010F54EB: KSPSetUp (itfunc.c:332)<br>
==42050== by 0x1010F7985: KSPSolve (itfunc.c:546)<br>
==42050== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)<br>
==42050== by 0x1011C49B7: SNESSolve (snes.c:3906)<br>
==42050== by 0x100001B3C: main (in ./ex19)<br>
==42050== Address 0x1060144d0 is 1,168 bytes inside a block of size 131,072 alloc'd<br>
==42050== at 0x1000183B1: malloc (vg_replace_malloc.c:303)<br>
==42050== by 0x10153B704: superlu_malloc_dist (memory.c:108)<br>
==42050== by 0x1014FD7AD: doubleMalloc_dist (dmemory.c:145)<br>
==42050== by 0x10151DA7D: pdgstrf (pdgstrf.c:735)<br>
==42050== by 0x1015019A5: pdgssvx (pdgssvx.c:1069)<br>
==42050== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST (superlu_dist.c:414)<br>
==42050== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)<br>
==42050== by 0x100F09F2C: PCSetUp_LU (lu.c:152)<br>
==42050== by 0x100FF9036: PCSetUp (precon.c:982)<br>
==42050== by 0x1010F54EB: KSPSetUp (itfunc.c:332)<br>
==42050== by 0x1010F7985: KSPSolve (itfunc.c:546)<br>
==42050== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)<br>
==42050== by 0x1011C49B7: SNESSolve (snes.c:3906)<br>
==42050== by 0x100001B3C: main (in ./ex19)<br>
==42050== Uninitialised value was created by a heap allocation<br>
==42050== at 0x1000183B1: malloc (vg_replace_malloc.c:303)<br>
==42050== by 0x10153B704: superlu_malloc_dist (memory.c:108)<br>
==42050== by 0x1014FD7AD: doubleMalloc_dist (dmemory.c:145)<br>
==42050== by 0x10151DA7D: pdgstrf (pdgstrf.c:735)<br>
==42050== by 0x1015019A5: pdgssvx (pdgssvx.c:1069)<br>
==42050== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST (superlu_dist.c:414)<br>
==42050== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)<br>
==42050== by 0x100F09F2C: PCSetUp_LU (lu.c:152)<br>
==42050== by 0x100FF9036: PCSetUp (precon.c:982)<br>
==42050== by 0x1010F54EB: KSPSetUp (itfunc.c:332)<br>
==42050== by 0x1010F7985: KSPSolve (itfunc.c:546)<br>
==42050== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)<br>
==42050== by 0x1011C49B7: SNESSolve (snes.c:3906)<br>
==42050== by 0x100001B3C: main (in ./ex19)<br>
==42050==<br>
==42048== Conditional jump or move depends on uninitialised value(s)<br>
==42048== at 0x10151F141: pdgstrf (pdgstrf.c:1139)<br>
==42048== by 0x1015019A5: pdgssvx (pdgssvx.c:1069)<br>
==42048== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST (superlu_dist.c:414)<br>
==42048== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)<br>
==42048== by 0x100F09F2C: PCSetUp_LU (lu.c:152)<br>
==42048== by 0x100FF9036: PCSetUp (precon.c:982)<br>
==42048== by 0x1010F54EB: KSPSetUp (itfunc.c:332)<br>
==42048== by 0x1010F7985: KSPSolve (itfunc.c:546)<br>
==42048== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)<br>
==42048== by 0x1011C49B7: SNESSolve (snes.c:3906)<br>
==42048== by 0x100001B3C: main (in ./ex19)<br>
==42048== Uninitialised value was created by a heap allocation<br>
==42048== at 0x1000183B1: malloc (vg_replace_malloc.c:303)<br>
==42048== by 0x10153B704: superlu_malloc_dist (memory.c:108)<br>
==42048== by 0x10150ABE2: ddist_psymbtonum (pdsymbfact_distdata.c:1332)<br>
==42048== by 0x1015018C2: pdgssvx (pdgssvx.c:1057)<br>
==42048== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST (superlu_dist.c:414)<br>
==42048== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)<br>
==42048== by 0x100F09F2C: PCSetUp_LU (lu.c:152)<br>
==42048== by 0x100FF9036: PCSetUp (precon.c:982)<br>
==42048== by 0x1010F54EB: KSPSetUp (itfunc.c:332)<br>
==42048== by 0x1010F7985: KSPSolve (itfunc.c:546)<br>
==42048== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)<br>
==42048== by 0x1011C49B7: SNESSolve (snes.c:3906)<br>
==42048== by 0x100001B3C: main (in ./ex19)<br>
==42048==<br>
==42049== Conditional jump or move depends on uninitialised value(s)<br>
==42049== at 0x10151F141: pdgstrf (pdgstrf.c:1139)<br>
==42049== by 0x1015019A5: pdgssvx (pdgssvx.c:1069)<br>
==42049== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST (superlu_dist.c:414)<br>
==42049== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)<br>
==42049== by 0x100F09F2C: PCSetUp_LU (lu.c:152)<br>
==42049== by 0x100FF9036: PCSetUp (precon.c:982)<br>
==42049== by 0x1010F54EB: KSPSetUp (itfunc.c:332)<br>
==42049== by 0x1010F7985: KSPSolve (itfunc.c:546)<br>
==42049== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)<br>
==42049== by 0x1011C49B7: SNESSolve (snes.c:3906)<br>
==42049== by 0x100001B3C: main (in ./ex19)<br>
==42049== Uninitialised value was created by a heap allocation<br>
==42049== at 0x1000183B1: malloc (vg_replace_malloc.c:303)<br>
==42049== by 0x10153B704: superlu_malloc_dist (memory.c:108)<br>
==42049== by 0x10150ABE2: ddist_psymbtonum (pdsymbfact_distdata.c:1332)<br>
==42049== by 0x1015018C2: pdgssvx (pdgssvx.c:1057)<br>
==42049== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST (superlu_dist.c:414)<br>
==42049== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)<br>
==42049== by 0x100F09F2C: PCSetUp_LU (lu.c:152)<br>
==42049== by 0x100FF9036: PCSetUp (precon.c:982)<br>
==42049== by 0x1010F54EB: KSPSetUp (itfunc.c:332)<br>
==42049== by 0x1010F7985: KSPSolve (itfunc.c:546)<br>
==42049== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)<br>
==42049== by 0x1011C49B7: SNESSolve (snes.c:3906)<br>
==42049== by 0x100001B3C: main (in ./ex19)<br>
==42049==<br>
==42048== Conditional jump or move depends on uninitialised value(s)<br>
==42048== at 0x101520054: pdgstrf (pdgstrf.c:1429)<br>
==42048== by 0x1015019A5: pdgssvx (pdgssvx.c:1069)<br>
==42048== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST (superlu_dist.c:414)<br>
==42048== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)<br>
==42048== by 0x100F09F2C: PCSetUp_LU (lu.c:152)<br>
==42048== by 0x100FF9036: PCSetUp (precon.c:982)<br>
==42048== by 0x1010F54EB: KSPSetUp (itfunc.c:332)<br>
==42048== by 0x1010F7985: KSPSolve (itfunc.c:546)<br>
==42049== Conditional jump or move depends on uninitialised value(s)<br>
==42048== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)<br>
==42048== by 0x1011C49B7: SNESSolve (snes.c:3906)<br>
==42048== by 0x100001B3C: main (in ./ex19)<br>
==42048== Uninitialised value was created by a heap allocation<br>
==42049== at 0x101520054: pdgstrf (pdgstrf.c:1429)<br>
==42048== at 0x1000183B1: malloc (vg_replace_malloc.c:303)<br>
==42048== by 0x10153B704: superlu_malloc_dist (memory.c:108)<br>
==42049== by 0x1015019A5: pdgssvx (pdgssvx.c:1069)<br>
==42049== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST (superlu_dist.c:414)<br>
==42048== by 0x10150ABE2: ddist_psymbtonum (pdsymbfact_distdata.c:1332)<br>
==42048== by 0x1015018C2: pdgssvx (pdgssvx.c:1057)<br>
==42048== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST (superlu_dist.c:414)<br>
==42049== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)<br>
==42049== by 0x100F09F2C: PCSetUp_LU (lu.c:152)<br>
==42048== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)<br>
==42048== by 0x100F09F2C: PCSetUp_LU (lu.c:152)<br>
==42049== by 0x100FF9036: PCSetUp (precon.c:982)<br>
==42049== by 0x1010F54EB: KSPSetUp (itfunc.c:332)<br>
==42049== by 0x1010F7985: KSPSolve (itfunc.c:546)<br>
==42048== by 0x100FF9036: PCSetUp (precon.c:982)<br>
==42048== by 0x1010F54EB: KSPSetUp (itfunc.c:332)<br>
==42048== by 0x1010F7985: KSPSolve (itfunc.c:546)<br>
==42049== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)<br>
==42049== by 0x1011C49B7: SNESSolve (snes.c:3906)<br>
==42048== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)<br>
==42048== by 0x1011C49B7: SNESSolve (snes.c:3906)<br>
==42049== by 0x100001B3C: main (in ./ex19)<br>
==42049== Uninitialised value was created by a heap allocation<br>
==42049== at 0x1000183B1: malloc (vg_replace_malloc.c:303)<br>
==42048== by 0x100001B3C: main (in ./ex19)<br>
==42048==<br>
==42049== by 0x10153B704: superlu_malloc_dist (memory.c:108)<br>
==42049== by 0x10150ABE2: ddist_psymbtonum (pdsymbfact_distdata.c:1332)<br>
==42049== by 0x1015018C2: pdgssvx (pdgssvx.c:1057)<br>
==42049== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST (superlu_dist.c:414)<br>
==42049== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)<br>
==42049== by 0x100F09F2C: PCSetUp_LU (lu.c:152)<br>
==42049== by 0x100FF9036: PCSetUp (precon.c:982)<br>
==42049== by 0x1010F54EB: KSPSetUp (itfunc.c:332)<br>
==42049== by 0x1010F7985: KSPSolve (itfunc.c:546)<br>
==42049== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)<br>
==42049== by 0x1011C49B7: SNESSolve (snes.c:3906)<br>
==42049== by 0x100001B3C: main (in ./ex19)<br>
==42049==<br>
==42050== Conditional jump or move depends on uninitialised value(s)<br>
==42050== at 0x10151FDE6: pdgstrf (pdgstrf.c:1382)<br>
==42050== by 0x1015019A5: pdgssvx (pdgssvx.c:1069)<br>
==42050== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST (superlu_dist.c:414)<br>
==42050== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)<br>
==42050== by 0x100F09F2C: PCSetUp_LU (lu.c:152)<br>
==42050== by 0x100FF9036: PCSetUp (precon.c:982)<br>
==42050== by 0x1010F54EB: KSPSetUp (itfunc.c:332)<br>
==42050== by 0x1010F7985: KSPSolve (itfunc.c:546)<br>
==42050== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)<br>
==42050== by 0x1011C49B7: SNESSolve (snes.c:3906)<br>
==42050== by 0x100001B3C: main (in ./ex19)<br>
==42050== Uninitialised value was created by a heap allocation<br>
==42050== at 0x1000183B1: malloc (vg_replace_malloc.c:303)<br>
==42050== by 0x10153B704: superlu_malloc_dist (memory.c:108)<br>
==42050== by 0x10150B241: ddist_psymbtonum (pdsymbfact_distdata.c:1389)<br>
==42050== by 0x1015018C2: pdgssvx (pdgssvx.c:1057)<br>
==42050== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST (superlu_dist.c:414)<br>
==42050== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)<br>
==42050== by 0x100F09F2C: PCSetUp_LU (lu.c:152)<br>
==42050== by 0x100FF9036: PCSetUp (precon.c:982)<br>
==42050== by 0x1010F54EB: KSPSetUp (itfunc.c:332)<br>
==42050== by 0x1010F7985: KSPSolve (itfunc.c:546)<br>
==42050== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)<br>
==42050== by 0x1011C49B7: SNESSolve (snes.c:3906)<br>
==42050== by 0x100001B3C: main (in ./ex19)<br>
==42050==<br>
<br>
<br>
> On Jul 20, 2015, at 12:03 PM, <a href="mailto:Mahir.Ulker-Kaustell@tyrens.se" target="_blank">
Mahir.Ulker-Kaustell@tyrens.se</a> wrote:<br>
><br>
> Ok. So I have been creating the full factorization on each process. That gives me some hope!<br>
><br>
> I followed your suggestion and tried to use the runtime option ‘-mat_superlu_dist_parsymbfact’.<br>
> However, now the program crashes with:<br>
><br>
> Invalid ISPEC at line 484 in file get_perm_c.c<br>
><br>
> And so on…<br>
><br>
> From the SuperLU manual; I should give the option either YES or NO, however -mat_superlu_dist_parsymbfact YES makes the program crash in the same way as above.<br>
> Also I can’t find any reference to -mat_superlu_dist_parsymbfact in the PETSc documentation<br>
><br>
> Mahir<br>
><br>
> Mahir Ülker-Kaustell, Kompetenssamordnare, Brokonstruktör, Tekn. Dr, Tyréns AB<br>
> 010 452 30 82, <a href="mailto:Mahir.Ulker-Kaustell@tyrens.se" target="_blank">
Mahir.Ulker-Kaustell@tyrens.se</a><br>
><br>
> From: Xiaoye S. Li [mailto:<a href="mailto:xsli@lbl.gov" target="_blank">xsli@lbl.gov</a>]<br>
> Sent: den 20 juli 2015 18:12<br>
> To: Ülker-Kaustell, Mahir<br>
> Cc: Hong; petsc-users<br>
> Subject: Re: [petsc-users] SuperLU MPI-problem<br>
><br>
> The default SuperLU_DIST setting is to serial symbolic factorization. Therefore, what matters is how much memory do you have per MPI task?<br>
><br>
> The code failed to malloc memory during redistribution of matrix A to {L\U} data struction (using result of serial symbolic factorization.)<br>
><br>
> You can use parallel symbolic factorization, by runtime option: '-mat_superlu_dist_parsymbfact'<br>
><br>
> Sherry Li<br>
><br>
><br>
> On Mon, Jul 20, 2015 at 8:59 AM, <a href="mailto:Mahir.Ulker-Kaustell@tyrens.se" target="_blank">
Mahir.Ulker-Kaustell@tyrens.se</a> <<a href="mailto:Mahir.Ulker-Kaustell@tyrens.se" target="_blank">Mahir.Ulker-Kaustell@tyrens.se</a>> wrote:<br>
> Hong:<br>
><br>
> Previous experiences with this equation have shown that it is very difficult to solve it iteratively. Hence the use of a direct solver.<br>
><br>
> The large test problem I am trying to solve has slightly less than 10^6 degrees of freedom. The matrices are derived from finite elements so they are sparse.<br>
> The machine I am working on has 128GB ram. I have estimated the memory needed to less than 20GB, so if the solver needs twice or even three times as much, it should still work well. Or have I completely misunderstood something here?<br>
><br>
> Mahir<br>
><br>
><br>
><br>
> From: Hong [mailto:<a href="mailto:hzhang@mcs.anl.gov" target="_blank">hzhang@mcs.anl.gov</a>]<br>
> Sent: den 20 juli 2015 17:39<br>
> To: Ülker-Kaustell, Mahir<br>
> Cc: petsc-users<br>
> Subject: Re: [petsc-users] SuperLU MPI-problem<br>
><br>
> Mahir:<br>
> Direct solvers consume large amount of memory. Suggest to try followings:<br>
><br>
> 1. A sparse iterative solver if [-omega^2M + K] is not too ill-conditioned. You may test it using the small matrix.<br>
><br>
> 2. Incrementally increase your matrix sizes. Try different matrix orderings.<br>
> Do you get memory crash in the 1st symbolic factorization?<br>
> In your case, matrix data structure stays same when omega changes, so you only need to do one matrix symbolic factorization and reuse it.<br>
><br>
> 3. Use a machine that gives larger memory.<br>
><br>
> Hong<br>
><br>
> Dear Petsc-Users,<br>
><br>
> I am trying to use PETSc to solve a set of linear equations arising from Naviers equation (elastodynamics) in the frequency domain.<br>
> The frequency dependency of the problem requires that the system<br>
><br>
> [-omega^2M + K]u = F<br>
><br>
> where M and K are constant, square, positive definite matrices (mass and stiffness respectively) is solved for each frequency omega of interest.<br>
> K is a complex matrix, including material damping.<br>
><br>
> I have written a PETSc program which solves this problem for a small (1000 degrees of freedom) test problem on one or several processors, but it keeps crashing when I try it on my full scale (in the order of 10^6 degrees of freedom) problem.<br>
><br>
> The program crashes at KSPSetUp() and from what I can see in the error messages, it appears as if it consumes too much memory.<br>
><br>
> I would guess that similar problems have occurred in this mail-list, so I am hoping that someone can push me in the right direction…<br>
><br>
> Mahir<br>
<br>
<u></u><u></u></p>
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</div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
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</div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
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