<div dir="ltr">Barry, that was awesome, all the valgrind error dissappeared after using the mpiexec from petsc folder, the more you know...<div><br></div><div>Anyway this is my output from valgrind running with those options:</div><div><br></div><div><div><font face="monospace, monospace"> Last Update: 9/23/2016 12: 5:12</font></div><div><font face="monospace, monospace"> ucmsSeamount Entering MAIN loop.</font></div><div><font face="monospace, monospace"> RHS loaded, size: 213120 / 213120</font></div><div><font face="monospace, monospace"> CSRMAt loaded, sizes: 213120 x 213120</font></div><div><font face="monospace, monospace"> 8.32709217 s</font></div><div><font face="monospace, monospace"> solveP pass: 1</font></div><div><font face="monospace, monospace"> RHS loaded, size: 213120 / 213120</font></div><div><font face="monospace, monospace"> CSRMAt loaded, sizes: 213120 x 0</font></div><div><font face="monospace, monospace">[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------</font></div><div><font face="monospace, monospace">[0]PETSC ERROR: Invalid argument</font></div><div><font face="monospace, monospace">[0]PETSC ERROR: Wrong type of object: Parameter # 1</font></div><div><font face="monospace, monospace">[0]PETSC ERROR: See <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html">http://www.mcs.anl.gov/petsc/documentation/faq.html</a> for trouble shooting.</font></div><div><font face="monospace, monospace">[0]PETSC ERROR: Petsc Release Version 3.7.3, unknown </font></div><div><font face="monospace, monospace">[0]PETSC ERROR: ./ucmsSeamount �J� on a arch-linux2-c-debug named valera-HP-xw4600-Workstation by valera Fri Sep 23 12:05:03 2016</font></div><div><font face="monospace, monospace">[0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-fblaslapack=1 --download-mpich=1 --download-ml=1</font></div><div><font face="monospace, monospace">[0]PETSC ERROR: #1 MatGetSize() line 6295 in /home/valera/v5PETSc/petsc/petsc/src/mat/interface/matrix.c</font></div><div><font face="monospace, monospace">[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------</font></div><div><font face="monospace, monospace">[0]PETSC ERROR: Invalid argument</font></div><div><font face="monospace, monospace">[0]PETSC ERROR: Wrong type of object: Parameter # 2</font></div><div><font face="monospace, monospace">[0]PETSC ERROR: See <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html">http://www.mcs.anl.gov/petsc/documentation/faq.html</a> for trouble shooting.</font></div><div><font face="monospace, monospace">[0]PETSC ERROR: Petsc Release Version 3.7.3, unknown </font></div><div><font face="monospace, monospace">[0]PETSC ERROR: ./ucmsSeamount �J� on a arch-linux2-c-debug named valera-HP-xw4600-Workstation by valera Fri Sep 23 12:05:03 2016</font></div><div><font face="monospace, monospace">[0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-fblaslapack=1 --download-mpich=1 --download-ml=1</font></div><div><font face="monospace, monospace">[0]PETSC ERROR: #2 KSPSetOperators() line 531 in /home/valera/v5PETSc/petsc/petsc/src/ksp/ksp/interface/itcreate.c</font></div><div><font face="monospace, monospace">[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------</font></div><div><font face="monospace, monospace">[0]PETSC ERROR: Nonconforming object sizes</font></div><div><font face="monospace, monospace">[0]PETSC ERROR: Preconditioner number of local rows -1 does not equal resulting vector number of rows 213120</font></div><div><font face="monospace, monospace">[0]PETSC ERROR: See <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html">http://www.mcs.anl.gov/petsc/documentation/faq.html</a> for trouble shooting.</font></div><div><font face="monospace, monospace">[0]PETSC ERROR: Petsc Release Version 3.7.3, unknown </font></div><div><font face="monospace, monospace">[0]PETSC ERROR: ./ucmsSeamount �J� on a arch-linux2-c-debug named valera-HP-xw4600-Workstation by valera Fri Sep 23 12:05:03 2016</font></div><div><font face="monospace, monospace">[0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-fblaslapack=1 --download-mpich=1 --download-ml=1</font></div><div><font face="monospace, monospace">[0]PETSC ERROR: #3 PCApply() line 474 in /home/valera/v5PETSc/petsc/petsc/src/ksp/pc/interface/precon.c</font></div><div><font face="monospace, monospace">[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------</font></div><div><font face="monospace, monospace">[0]PETSC ERROR: Object is in wrong state</font></div><div><font face="monospace, monospace">[0]PETSC ERROR: Mat object's type is not set: Argument # 1</font></div><div><font face="monospace, monospace">[0]PETSC ERROR: See <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html">http://www.mcs.anl.gov/petsc/documentation/faq.html</a> for trouble shooting.</font></div><div><font face="monospace, monospace">[0]PETSC ERROR: Petsc Release Version 3.7.3, unknown </font></div><div><font face="monospace, monospace">[0]PETSC ERROR: ./ucmsSeamount �J� on a arch-linux2-c-debug named valera-HP-xw4600-Workstation by valera Fri Sep 23 12:05:03 2016</font></div><div><font face="monospace, monospace">[0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-fblaslapack=1 --download-mpich=1 --download-ml=1</font></div><div><font face="monospace, monospace">[0]PETSC ERROR: #4 MatGetFactorAvailable() line 4286 in /home/valera/v5PETSc/petsc/petsc/src/mat/interface/matrix.c</font></div><div><font face="monospace, monospace">[0]PETSC ERROR: #5 PCGetDefaultType_Private() line 28 in /home/valera/v5PETSc/petsc/petsc/src/ksp/pc/interface/precon.c</font></div><div><font face="monospace, monospace">[0]PETSC ERROR: #6 PCSetFromOptions() line 159 in /home/valera/v5PETSc/petsc/petsc/src/ksp/pc/interface/pcset.c</font></div><div><font face="monospace, monospace">[0]PETSC ERROR: #7 KSPSetFromOptions() line 400 in /home/valera/v5PETSc/petsc/petsc/src/ksp/ksp/interface/itcl.c</font></div><div><font face="monospace, monospace">application called MPI_Abort(MPI_COMM_WORLD, 73) - process 0</font></div><div><font face="monospace, monospace">[cli_0]: aborting job:</font></div><div><font face="monospace, monospace">application called MPI_Abort(MPI_COMM_WORLD, 73) - process 0</font></div><div><font face="monospace, monospace"><br></font></div><div><font face="monospace, monospace">===================================================================================</font></div><div><font face="monospace, monospace">= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES</font></div><div><font face="monospace, monospace">= PID 6490 RUNNING AT valera-HP-xw4600-Workstation</font></div><div><font face="monospace, monospace">= EXIT CODE: 73</font></div><div><font face="monospace, monospace">= CLEANING UP REMAINING PROCESSES</font></div><div><font face="monospace, monospace">= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES</font></div><div><font face="monospace, monospace">===================================================================================</font></div><div><font face="monospace, monospace">==6488== </font></div><div><font face="monospace, monospace">==6488== HEAP SUMMARY:</font></div><div><font face="monospace, monospace">==6488== in use at exit: 131,120 bytes in 2 blocks</font></div><div><font face="monospace, monospace">==6488== total heap usage: 1,224 allocs, 1,222 frees, 249,285 bytes allocated</font></div><div><font face="monospace, monospace">==6488== </font></div><div><font face="monospace, monospace">==6488== LEAK SUMMARY:</font></div><div><font face="monospace, monospace">==6488== definitely lost: 0 bytes in 0 blocks</font></div><div><font face="monospace, monospace">==6488== indirectly lost: 0 bytes in 0 blocks</font></div><div><font face="monospace, monospace">==6488== possibly lost: 0 bytes in 0 blocks</font></div><div><font face="monospace, monospace">==6488== still reachable: 131,120 bytes in 2 blocks</font></div><div><font face="monospace, monospace">==6488== suppressed: 0 bytes in 0 blocks</font></div><div><font face="monospace, monospace">==6488== Rerun with --leak-check=full to see details of leaked memory</font></div><div><font face="monospace, monospace">==6488== </font></div><div><font face="monospace, monospace">==6488== For counts of detected and suppressed errors, rerun with: -v</font></div><div><font face="monospace, monospace">==6488== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)</font></div></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Sep 23, 2016 at 11:15 AM, Barry Smith <span dir="ltr"><<a href="mailto:bsmith@mcs.anl.gov" target="_blank">bsmith@mcs.anl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class=""><br>
> On Sep 23, 2016, at 1:09 PM, Manuel Valera <<a href="mailto:mvalera@mail.sdsu.edu">mvalera@mail.sdsu.edu</a>> wrote:<br>
><br>
> Thanks Barry, for the quick reply,<br>
><br>
> I tried doing that once recently, not for this problem though, but it looks like the model i'm working on isn't optimized at all for memory leaks, and valgrind stopped with thousands of errors before reaching this part of the execution.<br>
<br>
</span> Some MPI implementations by default produce many meaningless valgrind messages. So make sure you ./configure PETSc with --download-mpich this version will not produce any meaningless valgrind messages about MPI.<br>
<br>
You are not concerned with "memory leaks" in this exercise, only with using uninitialized memory or overwriting memory you should not overwrite. So you want valgrind arguments like -q --tool=memcheck --num-callers=20 --track-origins=yes you do not need --leak-check=yes<br>
<br>
So run with valgrind and email use the output and we may have suggestions on the cause.<br>
<span class="HOEnZb"><font color="#888888"><br>
Barry<br>
</font></span><div class="HOEnZb"><div class="h5"><br>
<br>
<br>
><br>
> Is there maybe an alternative approach ? or it would be better to just get the model in better shape already ?<br>
><br>
> Thanks<br>
><br>
> On Fri, Sep 23, 2016 at 10:53 AM, Barry Smith <<a href="mailto:bsmith@mcs.anl.gov">bsmith@mcs.anl.gov</a>> wrote:<br>
><br>
> Run with valgrind to find the exact location of the first memory corruption. <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind" rel="noreferrer" target="_blank">http://www.mcs.anl.gov/petsc/<wbr>documentation/faq.html#<wbr>valgrind</a><br>
><br>
> > On Sep 23, 2016, at 12:47 PM, Manuel Valera <<a href="mailto:mvalera@mail.sdsu.edu">mvalera@mail.sdsu.edu</a>> wrote:<br>
> ><br>
> > Hello all,<br>
> ><br>
> > I'm trying to load my laplacian matrix into a fortran module, and i have implemented it and it works for the first iteration of laplacian solver, but when starts the second step the laplacian matrix object becomes corrupts and looks like it loses one of it's dimensions.<br>
> ><br>
> > Can you help me understand whats happening?<br>
> ><br>
> > The modules are attached, the error i get is the following, i bolded the lines where i detected corruption:<br>
> ><br>
> > ucmsSeamount Entering MAIN loop.<br>
> > RHS loaded, size: 213120 / 213120<br>
> > CSRMAt loaded, sizes: 213120 x 213120<br>
> > 8.39198399 s<br>
> > solveP pass: 1 !Iteration number<br>
> > RHS loaded, size: 213120 / 213120<br>
> > [0]PETSC ERROR: --------------------- Error Message ------------------------------<wbr>------------------------------<wbr>--<br>
> > [0]PETSC ERROR: Invalid argument<br>
> > [0]PETSC ERROR: Wrong type of object: Parameter # 1<br>
> > [0]PETSC ERROR: See <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html" rel="noreferrer" target="_blank">http://www.mcs.anl.gov/petsc/<wbr>documentation/faq.html</a> for trouble shooting.<br>
> > [0]PETSC ERROR: Petsc Release Version 3.7.3, unknown<br>
> > [0]PETSC ERROR: ./ucmsSeamount �J� on a arch-linux2-c-debug named valera-HP-xw4600-Workstation by valera Fri Sep 23 10:27:21 2016<br>
> > [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-fblaslapack=1 --download-mpich=1 --download-ml=1<br>
> > [0]PETSC ERROR: #1 MatGetSize() line 6295 in /home/valera/v5PETSc/petsc/<wbr>petsc/src/mat/interface/<wbr>matrix.c<br>
> > CSRMAt loaded, sizes: 213120 x 0<br>
> > [0]PETSC ERROR: --------------------- Error Message ------------------------------<wbr>------------------------------<wbr>--<br>
> > [0]PETSC ERROR: Invalid argument<br>
> > [0]PETSC ERROR: Wrong type of object: Parameter # 2<br>
> > [0]PETSC ERROR: See <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html" rel="noreferrer" target="_blank">http://www.mcs.anl.gov/petsc/<wbr>documentation/faq.html</a> for trouble shooting.<br>
> > [0]PETSC ERROR: Petsc Release Version 3.7.3, unknown<br>
> > [0]PETSC ERROR: ./ucmsSeamount �J� on a arch-linux2-c-debug named valera-HP-xw4600-Workstation by valera Fri Sep 23 10:27:21 2016<br>
> > [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-fblaslapack=1 --download-mpich=1 --download-ml=1<br>
> > [0]PETSC ERROR: #2 KSPSetOperators() line 531 in /home/valera/v5PETSc/petsc/<wbr>petsc/src/ksp/ksp/interface/<wbr>itcreate.c<br>
> > [0]PETSC ERROR: --------------------- Error Message ------------------------------<wbr>------------------------------<wbr>--<br>
> > [0]PETSC ERROR: Nonconforming object sizes<br>
> > [0]PETSC ERROR: Preconditioner number of local rows -1 does not equal resulting vector number of rows 213120<br>
> > [0]PETSC ERROR: See <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html" rel="noreferrer" target="_blank">http://www.mcs.anl.gov/petsc/<wbr>documentation/faq.html</a> for trouble shooting.<br>
> > [0]PETSC ERROR: Petsc Release Version 3.7.3, unknown<br>
> > [0]PETSC ERROR: ./ucmsSeamount �J� on a arch-linux2-c-debug named valera-HP-xw4600-Workstation by valera Fri Sep 23 10:27:21 2016<br>
> > [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-fblaslapack=1 --download-mpich=1 --download-ml=1<br>
> > [0]PETSC ERROR: #3 PCApply() line 474 in /home/valera/v5PETSc/petsc/<wbr>petsc/src/ksp/pc/interface/<wbr>precon.c<br>
> > [0]PETSC ERROR: --------------------- Error Message ------------------------------<wbr>------------------------------<wbr>--<br>
> > [0]PETSC ERROR: Object is in wrong state<br>
> > [0]PETSC ERROR: Mat object's type is not set: Argument # 1<br>
> > [0]PETSC ERROR: See <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html" rel="noreferrer" target="_blank">http://www.mcs.anl.gov/petsc/<wbr>documentation/faq.html</a> for trouble shooting.<br>
> > [0]PETSC ERROR: Petsc Release Version 3.7.3, unknown<br>
> > [0]PETSC ERROR: ./ucmsSeamount �J� on a arch-linux2-c-debug named valera-HP-xw4600-Workstation by valera Fri Sep 23 10:27:21 2016<br>
> > [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-fblaslapack=1 --download-mpich=1 --download-ml=1<br>
> > [0]PETSC ERROR: #4 MatGetFactorAvailable() line 4286 in /home/valera/v5PETSc/petsc/<wbr>petsc/src/mat/interface/<wbr>matrix.c<br>
> > [0]PETSC ERROR: #5 PCGetDefaultType_Private() line 28 in /home/valera/v5PETSc/petsc/<wbr>petsc/src/ksp/pc/interface/<wbr>precon.c<br>
> > [0]PETSC ERROR: #6 PCSetFromOptions() line 159 in /home/valera/v5PETSc/petsc/<wbr>petsc/src/ksp/pc/interface/<wbr>pcset.c<br>
> > [0]PETSC ERROR: #7 KSPSetFromOptions() line 400 in /home/valera/v5PETSc/petsc/<wbr>petsc/src/ksp/ksp/interface/<wbr>itcl.c<br>
> > application called MPI_Abort(MPI_COMM_WORLD, 73) - process 0<br>
> > [unset]: aborting job:<br>
> > application called MPI_Abort(MPI_COMM_WORLD, 73) - process 0<br>
> ><br>
> > <LoadPetscMatrix.f90><<wbr>SolvePetscLinear.f90><br>
><br>
><br>
<br>
</div></div></blockquote></div><br></div>