Barry, that was awesome, all the valgrind error dissappeared after using the mpiexec from petsc folder, the more you know...
Anyway this is my output from valgrind running with those options: Last Update: 9/23/2016 12: 5:12 ucmsSeamount Entering MAIN loop. RHS loaded, size: 213120 / 213120 CSRMAt loaded, sizes: 213120 x 213120 8.32709217 s solveP pass: 1 RHS loaded, size: 213120 / 213120 CSRMAt loaded, sizes: 213120 x 0 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: Invalid argument [0]PETSC ERROR: Wrong type of object: Parameter # 1 [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.7.3, unknown [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 [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-fblaslapack=1 --download-mpich=1 --download-ml=1 [0]PETSC ERROR: #1 MatGetSize() line 6295 in /home/valera/v5PETSc/petsc/petsc/src/mat/interface/matrix.c [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: Invalid argument [0]PETSC ERROR: Wrong type of object: Parameter # 2 [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.7.3, unknown [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 [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-fblaslapack=1 --download-mpich=1 --download-ml=1 [0]PETSC ERROR: #2 KSPSetOperators() line 531 in /home/valera/v5PETSc/petsc/petsc/src/ksp/ksp/interface/itcreate.c [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: Nonconforming object sizes [0]PETSC ERROR: Preconditioner number of local rows -1 does not equal resulting vector number of rows 213120 [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.7.3, unknown [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 [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-fblaslapack=1 --download-mpich=1 --download-ml=1 [0]PETSC ERROR: #3 PCApply() line 474 in /home/valera/v5PETSc/petsc/petsc/src/ksp/pc/interface/precon.c [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: Object is in wrong state [0]PETSC ERROR: Mat object's type is not set: Argument # 1 [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.7.3, unknown [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 [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-fblaslapack=1 --download-mpich=1 --download-ml=1 [0]PETSC ERROR: #4 MatGetFactorAvailable() line 4286 in /home/valera/v5PETSc/petsc/petsc/src/mat/interface/matrix.c [0]PETSC ERROR: #5 PCGetDefaultType_Private() line 28 in /home/valera/v5PETSc/petsc/petsc/src/ksp/pc/interface/precon.c [0]PETSC ERROR: #6 PCSetFromOptions() line 159 in /home/valera/v5PETSc/petsc/petsc/src/ksp/pc/interface/pcset.c [0]PETSC ERROR: #7 KSPSetFromOptions() line 400 in /home/valera/v5PETSc/petsc/petsc/src/ksp/ksp/interface/itcl.c application called MPI_Abort(MPI_COMM_WORLD, 73) - process 0 [cli_0]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 73) - process 0 =================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = PID 6490 RUNNING AT valera-HP-xw4600-Workstation = EXIT CODE: 73 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES =================================================================================== ==6488== ==6488== HEAP SUMMARY: ==6488== in use at exit: 131,120 bytes in 2 blocks ==6488== total heap usage: 1,224 allocs, 1,222 frees, 249,285 bytes allocated ==6488== ==6488== LEAK SUMMARY: ==6488== definitely lost: 0 bytes in 0 blocks ==6488== indirectly lost: 0 bytes in 0 blocks ==6488== possibly lost: 0 bytes in 0 blocks ==6488== still reachable: 131,120 bytes in 2 blocks ==6488== suppressed: 0 bytes in 0 blocks ==6488== Rerun with --leak-check=full to see details of leaked memory ==6488== ==6488== For counts of detected and suppressed errors, rerun with: -v ==6488== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0) On Fri, Sep 23, 2016 at 11:15 AM, Barry Smith <bsm...@mcs.anl.gov> wrote: > > > On Sep 23, 2016, at 1:09 PM, Manuel Valera <mval...@mail.sdsu.edu> > wrote: > > > > Thanks Barry, for the quick reply, > > > > 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. > > 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. > > 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 > > So run with valgrind and email use the output and we may have > suggestions on the cause. > > Barry > > > > > > > Is there maybe an alternative approach ? or it would be better to just > get the model in better shape already ? > > > > Thanks > > > > On Fri, Sep 23, 2016 at 10:53 AM, Barry Smith <bsm...@mcs.anl.gov> > wrote: > > > > Run with valgrind to find the exact location of the first memory > corruption. http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind > > > > > On Sep 23, 2016, at 12:47 PM, Manuel Valera <mval...@mail.sdsu.edu> > wrote: > > > > > > Hello all, > > > > > > 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. > > > > > > Can you help me understand whats happening? > > > > > > The modules are attached, the error i get is the following, i bolded > the lines where i detected corruption: > > > > > > ucmsSeamount Entering MAIN loop. > > > RHS loaded, size: 213120 / 213120 > > > CSRMAt loaded, sizes: 213120 x 213120 > > > 8.39198399 s > > > solveP pass: 1 !Iteration number > > > RHS loaded, size: 213120 / 213120 > > > [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > > > [0]PETSC ERROR: Invalid argument > > > [0]PETSC ERROR: Wrong type of object: Parameter # 1 > > > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/ > documentation/faq.html for trouble shooting. > > > [0]PETSC ERROR: Petsc Release Version 3.7.3, unknown > > > [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 > > > [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++ > --with-fc=gfortran --download-fblaslapack=1 --download-mpich=1 > --download-ml=1 > > > [0]PETSC ERROR: #1 MatGetSize() line 6295 in > /home/valera/v5PETSc/petsc/petsc/src/mat/interface/matrix.c > > > CSRMAt loaded, sizes: 213120 x 0 > > > [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > > > [0]PETSC ERROR: Invalid argument > > > [0]PETSC ERROR: Wrong type of object: Parameter # 2 > > > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/ > documentation/faq.html for trouble shooting. > > > [0]PETSC ERROR: Petsc Release Version 3.7.3, unknown > > > [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 > > > [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++ > --with-fc=gfortran --download-fblaslapack=1 --download-mpich=1 > --download-ml=1 > > > [0]PETSC ERROR: #2 KSPSetOperators() line 531 in > /home/valera/v5PETSc/petsc/petsc/src/ksp/ksp/interface/itcreate.c > > > [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > > > [0]PETSC ERROR: Nonconforming object sizes > > > [0]PETSC ERROR: Preconditioner number of local rows -1 does not equal > resulting vector number of rows 213120 > > > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/ > documentation/faq.html for trouble shooting. > > > [0]PETSC ERROR: Petsc Release Version 3.7.3, unknown > > > [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 > > > [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++ > --with-fc=gfortran --download-fblaslapack=1 --download-mpich=1 > --download-ml=1 > > > [0]PETSC ERROR: #3 PCApply() line 474 in /home/valera/v5PETSc/petsc/ > petsc/src/ksp/pc/interface/precon.c > > > [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > > > [0]PETSC ERROR: Object is in wrong state > > > [0]PETSC ERROR: Mat object's type is not set: Argument # 1 > > > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/ > documentation/faq.html for trouble shooting. > > > [0]PETSC ERROR: Petsc Release Version 3.7.3, unknown > > > [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 > > > [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++ > --with-fc=gfortran --download-fblaslapack=1 --download-mpich=1 > --download-ml=1 > > > [0]PETSC ERROR: #4 MatGetFactorAvailable() line 4286 in > /home/valera/v5PETSc/petsc/petsc/src/mat/interface/matrix.c > > > [0]PETSC ERROR: #5 PCGetDefaultType_Private() line 28 in > /home/valera/v5PETSc/petsc/petsc/src/ksp/pc/interface/precon.c > > > [0]PETSC ERROR: #6 PCSetFromOptions() line 159 in > /home/valera/v5PETSc/petsc/petsc/src/ksp/pc/interface/pcset.c > > > [0]PETSC ERROR: #7 KSPSetFromOptions() line 400 in > /home/valera/v5PETSc/petsc/petsc/src/ksp/ksp/interface/itcl.c > > > application called MPI_Abort(MPI_COMM_WORLD, 73) - process 0 > > > [unset]: aborting job: > > > application called MPI_Abort(MPI_COMM_WORLD, 73) - process 0 > > > > > > <LoadPetscMatrix.f90><SolvePetscLinear.f90> > > > > > >
