August 2012 - petsc-dev - mailman3.cels.anl.gov

Re: [petsc-dev] DMSetDefaultSection destroys old sections
by Jed Brown 30 Aug '12

30 Aug '12

You must have something else going on. The following works fine, for example. diff --git a/src/snes/examples/tutorials/ex5f.F b/src/snes/examples/tutorials/ex5f.F --- a/src/snes/examples/tutorials/ex5f.F +++ b/src/snes/examples/tutorials/ex5f.F @@ -58,6 +58,7 @@ PetscErrorCode ierr PetscReal lambda_max,lambda_min PetscBool flg + DM da2 ! Note: Any user-defined Fortran routines (such as FormJacobianLocal) @@ -144,6 +145,9 @@ call DMDASetLocalFunction(da,FormFunctionLocal,ierr) call DMDASetLocalJacobian(da,FormJacobianLocal,ierr) call SNESSetDM(snes,da,ierr) + da2 = da + call PetscObjectReference(da2,ierr) + call DMDestroy(da2,ierr) ! - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ! Customize nonlinear solver; set runtime options On Thu, Aug 30, 2012 at 5:36 PM, Chris Eldred <chris.eldred(a)gmail.com>wrote: > I get an error when I try to use that: > > [0]PETSC ERROR: --------------------- Error Message > ------------------------------------ > [0]PETSC ERROR: Corrupt argument: > see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind! > [0]PETSC ERROR: Invalid type of object: Parameter # 1! > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Petsc Development HG revision: > 56f27b189e4fd57f5a4b7ffd6aa6bb08bd8a4d5b HG Date: Wed Aug 29 12:03:50 > 2012 -0500 > [0]PETSC ERROR: See docs/changes/index.html for recent updates. > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > [0]PETSC ERROR: See docs/index.html for manual pages. > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: ./swe on a arch-linu named Puget-101334 by user Thu > Aug 30 16:35:51 2012 > [0]PETSC ERROR: Libraries linked from > /home/user/Desktop/LIBRARIES/petsc-dev/arch-linux2-cxx-debug/lib > [0]PETSC ERROR: Configure run at Wed Aug 29 12:49:26 2012 > [0]PETSC ERROR: Configure options --download-boost --download-chaco > --download-ctetgen --download-f-blas-lapack --download-fiat > --download-generator --download-metis --download-ml --download-mpich > --download-parmetis --download-scientificpython --download-triangle > --with-clanguage=cxx --with-dynamic-loading --with-shared-libraries > --with-sieve PETSC_ARCH=arch-linux2-cxx-debug > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: PetscObjectReference() line 378 in > /home/user/Desktop/LIBRARIES/petsc-dev/src/sys/objects/inherit.c > application called MPI_Abort(MPI_COMM_WORLD, 64) - process 0 > [unset]: aborting job: > application called MPI_Abort(MPI_COMM_WORLD, 64) - process 0 > > > On Thu, Aug 30, 2012 at 4:32 PM, Jed Brown <jedbrown(a)mcs.anl.gov> wrote: > > On Thu, Aug 30, 2012 at 5:30 PM, Chris Eldred <chris.eldred(a)gmail.com> > > wrote: > >> > >> How would I use PetscObjectReference((PetscObject)section) in Fortran? > > > > > > call PetscObjectReference(section,ierr) > > > >> > >> > >> On Thu, Aug 30, 2012 at 4:16 PM, Jed Brown <jedbrown(a)mcs.anl.gov> > wrote: > >> > On Thu, Aug 30, 2012 at 5:12 PM, Matthew Knepley <knepley(a)gmail.com> > >> > wrote: > >> >> > >> >> Its not wrong. This is the way I wanted it. You set the PetscSection > >> >> and > >> >> give up control. If you > >> >> do not want to give up control, then call PetscObjectReference() > before > >> >> passing it in. > >> > > >> > > >> > Since this is (a) different from everything else in PETSc and (b) not > >> > explicitly documented, it is doubly wrong. > >> > >> > >> > >> -- > >> Chris Eldred > >> DOE Computational Science Graduate Fellow > >> Graduate Student, Atmospheric Science, Colorado State University > >> B.S. Applied Computational Physics, Carnegie Mellon University, 2009 > >> chris.eldred(a)gmail.com > > > > > > > > -- > Chris Eldred > DOE Computational Science Graduate Fellow > Graduate Student, Atmospheric Science, Colorado State University > B.S. Applied Computational Physics, Carnegie Mellon University, 2009 > chris.eldred(a)gmail.com >

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Re: [petsc-dev] DMSetDefaultSection destroys old sections
by Chris Eldred 30 Aug '12

30 Aug '12

I get an error when I try to use that: [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Corrupt argument: see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind! [0]PETSC ERROR: Invalid type of object: Parameter # 1! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Development HG revision: 56f27b189e4fd57f5a4b7ffd6aa6bb08bd8a4d5b HG Date: Wed Aug 29 12:03:50 2012 -0500 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: ./swe on a arch-linu named Puget-101334 by user Thu Aug 30 16:35:51 2012 [0]PETSC ERROR: Libraries linked from /home/user/Desktop/LIBRARIES/petsc-dev/arch-linux2-cxx-debug/lib [0]PETSC ERROR: Configure run at Wed Aug 29 12:49:26 2012 [0]PETSC ERROR: Configure options --download-boost --download-chaco --download-ctetgen --download-f-blas-lapack --download-fiat --download-generator --download-metis --download-ml --download-mpich --download-parmetis --download-scientificpython --download-triangle --with-clanguage=cxx --with-dynamic-loading --with-shared-libraries --with-sieve PETSC_ARCH=arch-linux2-cxx-debug [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: PetscObjectReference() line 378 in /home/user/Desktop/LIBRARIES/petsc-dev/src/sys/objects/inherit.c application called MPI_Abort(MPI_COMM_WORLD, 64) - process 0 [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 64) - process 0 On Thu, Aug 30, 2012 at 4:32 PM, Jed Brown <jedbrown(a)mcs.anl.gov> wrote: > On Thu, Aug 30, 2012 at 5:30 PM, Chris Eldred <chris.eldred(a)gmail.com> > wrote: >> >> How would I use PetscObjectReference((PetscObject)section) in Fortran? > > > call PetscObjectReference(section,ierr) > >> >> >> On Thu, Aug 30, 2012 at 4:16 PM, Jed Brown <jedbrown(a)mcs.anl.gov> wrote: >> > On Thu, Aug 30, 2012 at 5:12 PM, Matthew Knepley <knepley(a)gmail.com> >> > wrote: >> >> >> >> Its not wrong. This is the way I wanted it. You set the PetscSection >> >> and >> >> give up control. If you >> >> do not want to give up control, then call PetscObjectReference() before >> >> passing it in. >> > >> > >> > Since this is (a) different from everything else in PETSc and (b) not >> > explicitly documented, it is doubly wrong. >> >> >> >> -- >> Chris Eldred >> DOE Computational Science Graduate Fellow >> Graduate Student, Atmospheric Science, Colorado State University >> B.S. Applied Computational Physics, Carnegie Mellon University, 2009 >> chris.eldred(a)gmail.com > > -- Chris Eldred DOE Computational Science Graduate Fellow Graduate Student, Atmospheric Science, Colorado State University B.S. Applied Computational Physics, Carnegie Mellon University, 2009 chris.eldred(a)gmail.com

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Re: [petsc-dev] DMSetDefaultSection destroys old sections
by Jed Brown 30 Aug '12

30 Aug '12

On Thu, Aug 30, 2012 at 5:30 PM, Chris Eldred <chris.eldred(a)gmail.com>wrote: > How would I use PetscObjectReference((PetscObject)section) in Fortran? > call PetscObjectReference(section,ierr) > > On Thu, Aug 30, 2012 at 4:16 PM, Jed Brown <jedbrown(a)mcs.anl.gov> wrote: > > On Thu, Aug 30, 2012 at 5:12 PM, Matthew Knepley <knepley(a)gmail.com> > wrote: > >> > >> Its not wrong. This is the way I wanted it. You set the PetscSection and > >> give up control. If you > >> do not want to give up control, then call PetscObjectReference() before > >> passing it in. > > > > > > Since this is (a) different from everything else in PETSc and (b) not > > explicitly documented, it is doubly wrong. > > > > -- > Chris Eldred > DOE Computational Science Graduate Fellow > Graduate Student, Atmospheric Science, Colorado State University > B.S. Applied Computational Physics, Carnegie Mellon University, 2009 > chris.eldred(a)gmail.com >

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Re: [petsc-dev] DMSetDefaultSection destroys old sections
by Matthew Knepley 30 Aug '12

30 Aug '12

On Thu, Aug 30, 2012 at 5:30 PM, Chris Eldred <chris.eldred(a)gmail.com>wrote: > How would I use PetscObjectReference((PetscObject)section) in Fortran? > call PetscObjectReference(section) Matt > On Thu, Aug 30, 2012 at 4:16 PM, Jed Brown <jedbrown(a)mcs.anl.gov> wrote: > > On Thu, Aug 30, 2012 at 5:12 PM, Matthew Knepley <knepley(a)gmail.com> > wrote: > >> > >> Its not wrong. This is the way I wanted it. You set the PetscSection and > >> give up control. If you > >> do not want to give up control, then call PetscObjectReference() before > >> passing it in. > > > > > > Since this is (a) different from everything else in PETSc and (b) not > > explicitly documented, it is doubly wrong. > > > > -- > Chris Eldred > DOE Computational Science Graduate Fellow > Graduate Student, Atmospheric Science, Colorado State University > B.S. Applied Computational Physics, Carnegie Mellon University, 2009 > chris.eldred(a)gmail.com > -- 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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Re: [petsc-dev] DMSetDefaultSection destroys old sections
by Chris Eldred 30 Aug '12

30 Aug '12

How would I use PetscObjectReference((PetscObject)section) in Fortran? On Thu, Aug 30, 2012 at 4:16 PM, Jed Brown <jedbrown(a)mcs.anl.gov> wrote: > On Thu, Aug 30, 2012 at 5:12 PM, Matthew Knepley <knepley(a)gmail.com> wrote: >> >> Its not wrong. This is the way I wanted it. You set the PetscSection and >> give up control. If you >> do not want to give up control, then call PetscObjectReference() before >> passing it in. > > > Since this is (a) different from everything else in PETSc and (b) not > explicitly documented, it is doubly wrong. -- Chris Eldred DOE Computational Science Graduate Fellow Graduate Student, Atmospheric Science, Colorado State University B.S. Applied Computational Physics, Carnegie Mellon University, 2009 chris.eldred(a)gmail.com

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Re: [petsc-dev] DMSetDefaultSection destroys old sections
by Jed Brown 30 Aug '12

30 Aug '12

On Thu, Aug 30, 2012 at 5:12 PM, Matthew Knepley <knepley(a)gmail.com> wrote: > Its not wrong. This is the way I wanted it. You set the PetscSection and > give up control. If you > do not want to give up control, then call PetscObjectReference() before > passing it in. > Since this is (a) different from everything else in PETSc and (b) not explicitly documented, it is doubly wrong.

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Re: [petsc-dev] DMSetDefaultSection destroys old sections
by Matthew Knepley 30 Aug '12

30 Aug '12

On Thu, Aug 30, 2012 at 5:10 PM, Jed Brown <jedbrown(a)mcs.anl.gov> wrote: > On Thu, Aug 30, 2012 at 5:06 PM, Chris Eldred <chris.eldred(a)gmail.com>wrote: > >> The code for DMSetDefaultSection is: >> >> 3016: PetscSectionDestroy(&dm->defaultSection); >> 3017: PetscSectionDestroy(&dm->defaultGlobalSection); >> 3018: dm->defaultSection = section; >> 3019: return(0); >> > > This code is wrong. It should likely have used > PetscObjectReference((PetscObject)section) before these lines. > Its not wrong. This is the way I wanted it. You set the PetscSection and give up control. If you do not want to give up control, then call PetscObjectReference() before passing it in. Matt > > >> >> which destroys the "current" default section before setting the new >> one. Since my sections are passed by reference in Fortran, the only >> recourse I can see is to create a copy of the section before it is >> passed to DMSetDefaultSection. Any other ideas? >> >> On Thu, Aug 30, 2012 at 4:03 PM, Jed Brown <jedbrown(a)mcs.anl.gov> wrote: >> > I think the bug is not that the old section is destroyed, but that the >> new >> > one is not referenced. >> > >> > >> > On Thu, Aug 30, 2012 at 5:00 PM, Chris Eldred <chris.eldred(a)gmail.com> >> > wrote: >> >> >> >> I am using DMSetDefaultSection and DMCreateLocalVector to create >> >> vectors in my code, but errors are occurring because >> >> DMSetDefaultSection destroys old sections. My usage pattern is >> >> >> >> for each variable >> >> call DMSetDefaultSection >> >> call DMCreateLocalVector >> >> >> >> which fails if there is more than one 1 variable that uses the same >> >> section since the sections are being destroyed when a new one is set. >> >> Is there a reason for this behavior in DMSetDefaultSection (ie can a >> >> version of DMSetDefaultSection that does not destroy the old sections >> >> be provided)? >> >> >> >> -- >> >> Chris Eldred >> >> DOE Computational Science Graduate Fellow >> >> Graduate Student, Atmospheric Science, Colorado State University >> >> B.S. Applied Computational Physics, Carnegie Mellon University, 2009 >> >> chris.eldred(a)gmail.com >> > >> > >> >> >> >> -- >> Chris Eldred >> DOE Computational Science Graduate Fellow >> Graduate Student, Atmospheric Science, Colorado State University >> B.S. Applied Computational Physics, Carnegie Mellon University, 2009 >> chris.eldred(a)gmail.com >> > > -- 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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Re: [petsc-dev] DMSetDefaultSection destroys old sections
by Jed Brown 30 Aug '12

30 Aug '12

On Thu, Aug 30, 2012 at 5:06 PM, Chris Eldred <chris.eldred(a)gmail.com>wrote: > The code for DMSetDefaultSection is: > > 3016: PetscSectionDestroy(&dm->defaultSection); > 3017: PetscSectionDestroy(&dm->defaultGlobalSection); > 3018: dm->defaultSection = section; > 3019: return(0); > This code is wrong. It should likely have used PetscObjectReference((PetscObject)section) before these lines. > > which destroys the "current" default section before setting the new > one. Since my sections are passed by reference in Fortran, the only > recourse I can see is to create a copy of the section before it is > passed to DMSetDefaultSection. Any other ideas? > > On Thu, Aug 30, 2012 at 4:03 PM, Jed Brown <jedbrown(a)mcs.anl.gov> wrote: > > I think the bug is not that the old section is destroyed, but that the > new > > one is not referenced. > > > > > > On Thu, Aug 30, 2012 at 5:00 PM, Chris Eldred <chris.eldred(a)gmail.com> > > wrote: > >> > >> I am using DMSetDefaultSection and DMCreateLocalVector to create > >> vectors in my code, but errors are occurring because > >> DMSetDefaultSection destroys old sections. My usage pattern is > >> > >> for each variable > >> call DMSetDefaultSection > >> call DMCreateLocalVector > >> > >> which fails if there is more than one 1 variable that uses the same > >> section since the sections are being destroyed when a new one is set. > >> Is there a reason for this behavior in DMSetDefaultSection (ie can a > >> version of DMSetDefaultSection that does not destroy the old sections > >> be provided)? > >> > >> -- > >> Chris Eldred > >> DOE Computational Science Graduate Fellow > >> Graduate Student, Atmospheric Science, Colorado State University > >> B.S. Applied Computational Physics, Carnegie Mellon University, 2009 > >> chris.eldred(a)gmail.com > > > > > > > > -- > Chris Eldred > DOE Computational Science Graduate Fellow > Graduate Student, Atmospheric Science, Colorado State University > B.S. Applied Computational Physics, Carnegie Mellon University, 2009 > chris.eldred(a)gmail.com >

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Re: [petsc-dev] DMSetDefaultSection destroys old sections
by Chris Eldred 30 Aug '12

30 Aug '12

The code for DMSetDefaultSection is: 3016: PetscSectionDestroy(&dm->defaultSection); 3017: PetscSectionDestroy(&dm->defaultGlobalSection); 3018: dm->defaultSection = section; 3019: return(0); which destroys the "current" default section before setting the new one. Since my sections are passed by reference in Fortran, the only recourse I can see is to create a copy of the section before it is passed to DMSetDefaultSection. Any other ideas? On Thu, Aug 30, 2012 at 4:03 PM, Jed Brown <jedbrown(a)mcs.anl.gov> wrote: > I think the bug is not that the old section is destroyed, but that the new > one is not referenced. > > > On Thu, Aug 30, 2012 at 5:00 PM, Chris Eldred <chris.eldred(a)gmail.com> > wrote: >> >> I am using DMSetDefaultSection and DMCreateLocalVector to create >> vectors in my code, but errors are occurring because >> DMSetDefaultSection destroys old sections. My usage pattern is >> >> for each variable >> call DMSetDefaultSection >> call DMCreateLocalVector >> >> which fails if there is more than one 1 variable that uses the same >> section since the sections are being destroyed when a new one is set. >> Is there a reason for this behavior in DMSetDefaultSection (ie can a >> version of DMSetDefaultSection that does not destroy the old sections >> be provided)? >> >> -- >> Chris Eldred >> DOE Computational Science Graduate Fellow >> Graduate Student, Atmospheric Science, Colorado State University >> B.S. Applied Computational Physics, Carnegie Mellon University, 2009 >> chris.eldred(a)gmail.com > > -- Chris Eldred DOE Computational Science Graduate Fellow Graduate Student, Atmospheric Science, Colorado State University B.S. Applied Computational Physics, Carnegie Mellon University, 2009 chris.eldred(a)gmail.com

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Re: [petsc-dev] DMSetDefaultSection destroys old sections
by Jed Brown 30 Aug '12

30 Aug '12

I think the bug is not that the old section is destroyed, but that the new one is not referenced. On Thu, Aug 30, 2012 at 5:00 PM, Chris Eldred <chris.eldred(a)gmail.com>wrote: > I am using DMSetDefaultSection and DMCreateLocalVector to create > vectors in my code, but errors are occurring because > DMSetDefaultSection destroys old sections. My usage pattern is > > for each variable > call DMSetDefaultSection > call DMCreateLocalVector > > which fails if there is more than one 1 variable that uses the same > section since the sections are being destroyed when a new one is set. > Is there a reason for this behavior in DMSetDefaultSection (ie can a > version of DMSetDefaultSection that does not destroy the old sections > be provided)? > > -- > Chris Eldred > DOE Computational Science Graduate Fellow > Graduate Student, Atmospheric Science, Colorado State University > B.S. Applied Computational Physics, Carnegie Mellon University, 2009 > chris.eldred(a)gmail.com >

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