<div dir="ltr"><div dir="ltr">On Sun, Apr 30, 2023 at 2:57 AM Danyang Su <<a href="mailto:danyang.su@gmail.com">danyang.su@gmail.com</a>> wrote:<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 class="msg7185785732288196194"><div lang="EN-CA" style="overflow-wrap: break-word;"><div class="m_7185785732288196194WordSection1"><p class="MsoNormal">Hi Matt,<u></u><u></u></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">Just let you know that the error problem in <span lang="EN-US">DMGetLocalBoundingBox seems fixed in the latest dev version. I didn’t catch the error information any more.</span></p></div></div></div></blockquote><div><br></div><div>Sorry, I forgot to mail back. Thanks for reporting that.</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 class="msg7185785732288196194"><div lang="EN-CA" style="overflow-wrap: break-word;"><div class="m_7185785732288196194WordSection1"><p class="MsoNormal"> </p><p class="MsoNormal">Regards,<u></u><u></u></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">Danyang<u></u><u></u></p><p class="MsoNormal"><u></u> <u></u></p><div style="border-right:none;border-bottom:none;border-left:none;border-top:1pt solid rgb(181,196,223);padding:3pt 0cm 0cm"><p class="MsoNormal"><b><span style="font-size:12pt;color:black">From: </span></b><span style="font-size:12pt;color:black"><<a href="mailto:danyang.su@gmail.com" target="_blank">danyang.su@gmail.com</a>><br><b>Date: </b>Friday, March 17, 2023 at 11:02 AM<br><b>To: </b>'Matthew Knepley' <<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>><br><b>Cc: </b><<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>><br><b>Subject: </b>RE: [petsc-users] PETSC ERROR in DMGetLocalBoundingBox?<u></u><u></u></span></p></div><div><p class="MsoNormal"><u></u> <u></u></p></div><p class="MsoNormal">Hi Matt,<u></u><u></u></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">I am following up to check if you can reproduce the problem on your side. <u></u><u></u></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">Thanks and have a great weekend,<u></u><u></u></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">Danyang<u></u><u></u></p><p class="MsoNormal"><u></u> <u></u></p><div><div style="border-right:none;border-bottom:none;border-left:none;border-top:1pt solid rgb(225,225,225);padding:3pt 0cm 0cm"><p class="MsoNormal"><b><span lang="EN-US">From:</span></b><span lang="EN-US"> Danyang Su <<a href="mailto:danyang.su@gmail.com" target="_blank">danyang.su@gmail.com</a>> <br><b>Sent:</b> March 4, 2023 4:38 PM<br><b>To:</b> Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>><br><b>Cc:</b> <a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a><br><b>Subject:</b> Re: [petsc-users] PETSC ERROR in DMGetLocalBoundingBox?<u></u><u></u></span></p></div></div><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">Hi Matt,<u></u><u></u></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">Attached is the source code and example. I have deleted most of the unused source code but it is still a bit length. Sorry about that. The errors come <span style="color:black">after </span><span style="font-size:10.5pt;font-family:Consolas;color:black">DMGetLocalBoundingBox and DMGetBoundingBox.<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black">-> To compile the code<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black">Please type 'make exe' and the executable file petsc_bounding will be created under the same folder.<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black">-> To test the code<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black">Please go to fold 'test' and type 'mpiexec -n 1 ../petsc_bounding'.<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black">-> The output from PETSc 3.18, error information<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black">input file: stedvs.dat<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black">------------------------------------------------------------------------<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black">global control parameters<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black">------------------------------------------------------------------------<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black">[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black">[0]PETSC ERROR: Corrupt argument: <a href="https://petsc.org/release/faq/#valgrind" target="_blank">https://petsc.org/release/faq/#valgrind</a><u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black">[0]PETSC ERROR: Object already free: Parameter # 1<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black">[0]PETSC ERROR: See <a href="https://petsc.org/release/faq/" target="_blank">https://petsc.org/release/faq/</a> for trouble shooting.<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black">[0]PETSC ERROR: Petsc Release Version 3.18.3, Dec 28, 2022 <u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black">[0]PETSC ERROR: ../petsc_bounding on a linux-gnu-dbg named starblazer by dsu Sat Mar 4 16:20:51 2023<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black">[0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-mpich --download-scalapack --download-parmetis --download-metis --download-mumps --download-ptscotch --download-chaco --download-fblaslapack --download-hypre --download-superlu_dist --download-hdf5=yes --download-ctetgen --download-zlib --download-pnetcdf --download-cmake --with-hdf5-fortran-bindings --with-debugging=1<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black">[0]PETSC ERROR: #1 VecGetArrayRead() at /home/dsu/Soft/petsc/petsc-3.18.3/src/vec/vec/interface/rvector.c:1928<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black">[0]PETSC ERROR: #2 DMGetLocalBoundingBox() at /home/dsu/Soft/petsc/petsc-3.18.3/src/dm/interface/dmcoordinates.c:897<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black">[0]PETSC ERROR: #3 /home/dsu/Work/bug-check/petsc_bounding/src/solver_ddmethod.F90:1920<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black">Total volume of simulation domain 0.20000000E+01<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black">Total volume of simulation domain 0.20000000E+01<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black">-> The output from PETSc 3.17 and earlier, no error<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black">input file: stedvs.dat<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black">------------------------------------------------------------------------<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black">global control parameters<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black">------------------------------------------------------------------------<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black">Total volume of simulation domain 0.20000000E+01<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black">Total volume of simulation domain 0.20000000E+01<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:black"><u></u> <u></u></span></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">Thanks,<u></u><u></u></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">Danyang<u></u><u></u></p><div style="border-right:none;border-bottom:none;border-left:none;border-top:1pt solid rgb(181,196,223);padding:3pt 0cm 0cm"><p class="MsoNormal"><b><span style="font-size:12pt;color:black">From: </span></b><span style="font-size:12pt;color:black">Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>><br><b>Date: </b>Friday, March 3, 2023 at 8:58 PM<br><b>To: </b><<a href="mailto:danyang.su@gmail.com" target="_blank">danyang.su@gmail.com</a>><br><b>Cc: </b><<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>><br><b>Subject: </b>Re: [petsc-users] PETSC ERROR in DMGetLocalBoundingBox?<u></u><u></u></span></p></div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><div><p class="MsoNormal">On Sat, Mar 4, 2023 at 1:35 AM <<a href="mailto:danyang.su@gmail.com" target="_blank">danyang.su@gmail.com</a>> wrote:<u></u><u></u></p></div><div><blockquote style="border-top:none;border-right:none;border-bottom:none;border-left:1pt solid rgb(204,204,204);padding:0cm 0cm 0cm 6pt;margin:5pt 0cm 5pt 4.8pt"><div><div><div><p class="MsoNormal">Hi All,<u></u><u></u></p><p class="MsoNormal"> <u></u><u></u></p><p class="MsoNormal">I get a very strange error after upgrading PETSc version to 3.18.3, indicating some object is already free. The error is begin and does not crash the code. There is no error before PETSc 3.17.5 versions.<u></u><u></u></p></div></div></div></blockquote><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">We have changed the way coordinates are handled in order to support higher order coordinate fields. Is it possible<u></u><u></u></p></div><div><p class="MsoNormal">to send something that we can run that has this error? It could be on our end, but it could also be that you are<u></u><u></u></p></div><div><p class="MsoNormal">destroying a coordinate vector accidentally.<u></u><u></u></p></div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal"> Thanks,<u></u><u></u></p></div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal"> Matt<u></u><u></u></p></div><div><p class="MsoNormal"> <u></u><u></u></p></div><blockquote style="border-top:none;border-right:none;border-bottom:none;border-left:1pt solid rgb(204,204,204);padding:0cm 0cm 0cm 6pt;margin:5pt 0cm 5pt 4.8pt"><div><div><div><p class="MsoNormal"> <u></u><u></u></p><p class="MsoNormal" style="line-height:14.25pt;background:rgb(30,30,30)"><span style="font-size:10.5pt;font-family:Consolas;color:rgb(212,212,212)"> </span><span style="font-size:10.5pt;font-family:Consolas;color:rgb(106,153,85)">!Check coordinates</span><u></u><u></u></p><p class="MsoNormal" style="line-height:14.25pt;background:rgb(30,30,30)"><span style="font-size:10.5pt;font-family:Consolas;color:rgb(212,212,212)"> </span><span style="font-size:10.5pt;font-family:Consolas;color:rgb(197,134,192)">call</span><span style="font-size:10.5pt;font-family:Consolas;color:rgb(212,212,212)"> DMGetCoordinateDM(dmda_flow%da,cda,ierr)</span><u></u><u></u></p><p class="MsoNormal" style="line-height:14.25pt;background:rgb(30,30,30)"><span style="font-size:10.5pt;font-family:Consolas;color:rgb(212,212,212)"> CHKERRQ(ierr)</span><u></u><u></u></p><p class="MsoNormal" style="line-height:14.25pt;background:rgb(30,30,30)"><span style="font-size:10.5pt;font-family:Consolas;color:rgb(212,212,212)"> </span><span style="font-size:10.5pt;font-family:Consolas;color:rgb(197,134,192)">call</span><span style="font-size:10.5pt;font-family:Consolas;color:rgb(212,212,212)"> DMGetCoordinates(dmda_flow%da,gc,ierr)</span><u></u><u></u></p><p class="MsoNormal" style="line-height:14.25pt;background:rgb(30,30,30)"><span style="font-size:10.5pt;font-family:Consolas;color:rgb(212,212,212)"> CHKERRQ(ierr)</span><u></u><u></u></p><p class="MsoNormal" style="line-height:14.25pt;background:rgb(30,30,30)"><span style="font-size:10.5pt;font-family:Consolas;color:rgb(212,212,212)"> </span><span style="font-size:10.5pt;font-family:Consolas;color:rgb(197,134,192)">call</span><span style="font-size:10.5pt;font-family:Consolas;color:rgb(212,212,212)"> DMGetLocalBoundingBox(dmda_flow%da,lmin,lmax,ierr)</span><u></u><u></u></p><p class="MsoNormal" style="line-height:14.25pt;background:rgb(30,30,30)"><span style="font-size:10.5pt;font-family:Consolas;color:rgb(212,212,212)"> CHKERRQ(ierr)</span><u></u><u></u></p><p class="MsoNormal" style="line-height:14.25pt;background:rgb(30,30,30)"><span style="font-size:10.5pt;font-family:Consolas;color:rgb(212,212,212)"> </span><span style="font-size:10.5pt;font-family:Consolas;color:rgb(197,134,192)">call</span><span style="font-size:10.5pt;font-family:Consolas;color:rgb(212,212,212)"> DMGetBoundingBox(dmda_flow%da,gmin,gmax,ierr)</span><u></u><u></u></p><p class="MsoNormal" style="line-height:14.25pt;background:rgb(30,30,30)"><span style="font-size:10.5pt;font-family:Consolas;color:rgb(212,212,212)"> CHKERRQ(ierr)</span><u></u><u></u></p><p class="MsoNormal"> <u></u><u></u></p><p class="MsoNormal"> <u></u><u></u></p><p class="MsoNormal">[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------<u></u><u></u></p><p class="MsoNormal">[0]PETSC ERROR: Corrupt argument: <a href="https://petsc.org/release/faq/#valgrind" target="_blank">https://petsc.org/release/faq/#valgrind</a><u></u><u></u></p><p class="MsoNormal">[0]PETSC ERROR: Object already free: Parameter # 1<u></u><u></u></p><p class="MsoNormal">[0]PETSC ERROR: See <a href="https://petsc.org/release/faq/" target="_blank">https://petsc.org/release/faq/</a> for trouble shooting.<u></u><u></u></p><p class="MsoNormal">[0]PETSC ERROR: Petsc Release Version 3.18.3, Dec 28, 2022<u></u><u></u></p><p class="MsoNormal">[0]PETSC ERROR: ../min3p-hpc-mpi-petsc-3.18.3 on a linux-gnu-dbg named starblazer by dsu Fri Mar 3 16:26:03 2023<u></u><u></u></p><p class="MsoNormal">[0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-mpich --download-scalapack --download-parmetis --download-metis --download-mumps --download-ptscotch --download-chaco --download-fblaslapack --download-hypre --download-superlu_dist --download-hdf5=yes --download-ctetgen --download-zlib --download-pnetcdf --download-cmake --with-hdf5-fortran-bindings --with-debugging=1<u></u><u></u></p><p class="MsoNormal">[0]PETSC ERROR: #1 VecGetArrayRead() at /home/dsu/Soft/petsc/petsc-3.18.3/src/vec/vec/interface/rvector.c:1928<u></u><u></u></p><p class="MsoNormal">[0]PETSC ERROR: #2 DMGetLocalBoundingBox() at /home/dsu/Soft/petsc/petsc-3.18.3/src/dm/interface/dmcoordinates.c:897<u></u><u></u></p><p class="MsoNormal">[0]PETSC ERROR: #3 /home/dsu/Work/min3p-dbs-backup/src/project/makefile_p/../../solver/solver_ddmethod.F90:2140<u></u><u></u></p><p class="MsoNormal"> <u></u><u></u></p><p class="MsoNormal">Any suggestion on this?<u></u><u></u></p><p class="MsoNormal"> <u></u><u></u></p><p class="MsoNormal">Thanks,<u></u><u></u></p><p class="MsoNormal"> <u></u><u></u></p><p class="MsoNormal">Danyang<u></u><u></u></p></div></div></div></blockquote></div><p class="MsoNormal"><br clear="all"><u></u><u></u></p><div><p class="MsoNormal"><u></u> <u></u></p></div><p class="MsoNormal">-- <u></u><u></u></p><div><div><div><div><div><div><div><p class="MsoNormal">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<u></u><u></u></p></div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal"><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><u></u><u></u></p></div></div></div></div></div></div></div></div></div></div>
</div></blockquote></div><br clear="all"><div><br></div><span class="gmail_signature_prefix">-- </span><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>