[petsc-users] Best way to share variables in fortran ?
Manuel Valera
mvalera at mail.sdsu.edu
Sat Nov 5 20:38:57 CDT 2016
Great ! it worked, im carrying out tests,
Btw, any of you developers and users are attending SC16 next week ? i will
be there as a volunteer and a big group from CSRC-SDSU also, we would like
to share some thoughts,
Regards and many thanks,
Manuel
On Fri, Nov 4, 2016 at 8:19 PM, Matthew Knepley <knepley at gmail.com> wrote:
> On Fri, Nov 4, 2016 at 7:37 PM, Manuel Valera <mvalera at mail.sdsu.edu>
> wrote:
>
>> Hello all,
>>
>> I'm reviving this old post because we are trying to share the petsc
>> objects from outside our iteration routine, this means several levels
>> outside the linear solver script where they are created now,
>>
>> we have tried with fortran modules but right now we have conflicts while
>> taking the includes, if we make the #include in the module it conflicts
>> with the rest of the routines, so we wanted to ask you guys what other
>> option to make the petsc objects available for the entire program we have,
>> carrying them as arguments seems maybe too cumbersome,
>>
>
> Use the Fortran modules
>
> http://www.mcs.anl.gov/petsc/petsc-current/docs/
> manualpages/Sys/UsingFortran.html
>
> although I would delicately recommend a language with a non-broken scoping
> model.
>
> Matt
>
>
>> Thanks for your help,
>>
>> Manuel
>>
>>
>>
>> On Fri, Sep 23, 2016 at 12:39 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>>
>>>
>>> I don't know much about modules so can't help, but PETSc variables
>>> are just like any other variables and so should behave in the same way.
>>>
>>> Barry
>>>
>>> > On Sep 23, 2016, at 2:31 PM, Manuel Valera <mvalera at mail.sdsu.edu>
>>> wrote:
>>> >
>>> > Ok, i got this:
>>> >
>>> > RHS loaded, size: 213120 / 213120
>>> > CSRMAt loaded, sizes: 213120 x 213120
>>> > 8.43036175 s
>>> > solveP pass: 1
>>> > RHS loaded, size: 213120 / 213120
>>> > [0]PETSC ERROR: MatGetSize() line 6295 in
>>> /home/valera/v5PETSc/petsc/petsc/src/mat/interface/matrix.c Wrong type
>>> of object: Parameter # 1
>>> >
>>> > Program received signal SIGABRT: Process abort signal.
>>> >
>>> > Backtrace for this error:
>>> > #0 0x7F2A35AEA777
>>> > #1 0x7F2A35AEAD7E
>>> > #2 0x7F2A34FC6CAF
>>> > #3 0x7F2A34FC6C37
>>> > #4 0x7F2A34FCA027
>>> > #5 0x7F2A35F6F6AA
>>> > #6 0x7F2A35F6A2EA
>>> > #7 0x7F2A362E2FEF
>>> > #8 0x7F2A36326681
>>> > #9 0x799AFF in solvepetsclinear_ at SolvePetscLinear.f90:137
>>> (discriminator 2)
>>> > #10 0x798F6A in solvep_rhs_ at SolveP_Rhs.f90:284
>>> > #11 0x80D028 in ucmsmain at ucmsMain.f90:472
>>> >
>>> > .-.-.-.-.-.-.-.-
>>> >
>>> > What is weird for me is why it loads everything as it should for the
>>> first timestep of the problem and then it breaks on the second one,
>>> shouldnt the matrix be loaded at modules and shared with all subroutines?
>>> also, shouldnt the matrix be locked after assembly_final was used ? that
>>> matrix call is Ap which is inside LoadPetscMatrix module, and it looks like
>>> its changed after the first timestep.
>>> >
>>> >
>>> > On Fri, Sep 23, 2016 at 12:18 PM, Barry Smith <bsmith at mcs.anl.gov>
>>> wrote:
>>> >
>>> > Ok, so the problem is not memory corruption.
>>> >
>>> > > 0]PETSC ERROR: --------------------- Error Message
>>> --------------------------------------------------------------
>>> > > [0]PETSC ERROR: Invalid argument
>>> > > [0]PETSC ERROR: Wrong type of object: Parameter # 1
>>> > > [0]PETSC ERROR: #1 MatGetSize() line 6295 in
>>> /home/valera/v5PETSc/petsc/petsc/src/mat/interface/matrix.c
>>> >
>>> > So it looks like the matrix has not been created yet in this call.
>>> You can run with -start_in_debugger noxterm and then type cont in the
>>> debugger and it should stop at this error so you can look at the mat object
>>> to see what its value is.
>>> >
>>> > Barry
>>> >
>>> >
>>> >
>>> > > On Sep 23, 2016, at 2:07 PM, Manuel Valera <mvalera at mail.sdsu.edu>
>>> wrote:
>>> > >
>>> > > 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/d
>>> ocumentation/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/d
>>> ocumentation/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/d
>>> ocumentation/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/d
>>> ocumentation/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 <bsmith at mcs.anl.gov>
>>> wrote:
>>> > >
>>> > > > On Sep 23, 2016, at 1:09 PM, Manuel Valera <mvalera at 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 <bsmith at 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 <
>>> mvalera at 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/d
>>> ocumentation/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/d
>>> ocumentation/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/d
>>> ocumentation/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/d
>>> ocumentation/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>
>>> > > >
>>> > > >
>>> > >
>>> > >
>>> >
>>> >
>>>
>>>
>>
>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>
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