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

Re: [petsc-dev] What needs to be done before a release?
by Barry Smith 05 May '12

05 May '12

So long as DMMG is gone, I'm fine by that. Certain things, at least GPUs and threads, will still have the "you must use PETSc-dev" warning attached to them. Barry On May 5, 2012, at 9:51 PM, Matthew Knepley wrote: > On Sat, May 5, 2012 at 10:32 PM, Jed Brown <jedbrown(a)mcs.anl.gov> wrote: > On Fri, May 4, 2012 at 12:57 PM, Peter Brune <prbrune(a)gmail.com> wrote: > Jed, what else needs to be done with respect to getting all the SNES context into DM? I notice that, for instance, SNESSet/GetFunction is still mostly using the ops in SNES rather than the ones in SNESDM. > > I had a temporary option -snes_kspcompute to make the dispatch go through SNESDM. The main holdup now is -snes_grid_sequence, but I'm banging away at ex48 again, so I should be able to get it all working shortly. (I have ex48 running without DMMG, but some functionality is missing now, like changing the physics in the middle of the MG hierarchy.) > > Can we commit to a hard deadline? I would like the freeze for testing May 11, and clone and release May 14. > > Matt > > -- > 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] What needs to be done before a release?
by Matthew Knepley 05 May '12

05 May '12

On Sat, May 5, 2012 at 10:32 PM, Jed Brown <jedbrown(a)mcs.anl.gov> wrote: > On Fri, May 4, 2012 at 12:57 PM, Peter Brune <prbrune(a)gmail.com> wrote: > >> Jed, what else needs to be done with respect to getting all the SNEScontext into DM? I notice that, for instance, SNESSet/GetFunction is still >> mostly using the ops in SNES rather than the ones in SNESDM. >> > > I had a temporary option -snes_kspcompute to make the dispatch go through > SNESDM. The main holdup now is -snes_grid_sequence, but I'm banging away at > ex48 again, so I should be able to get it all working shortly. (I have ex48 > running without DMMG, but some functionality is missing now, like changing > the physics in the middle of the MG hierarchy.) > Can we commit to a hard deadline? I would like the freeze for testing May 11, and clone and release May 14. Matt -- 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] What needs to be done before a release?
by Jed Brown 05 May '12

05 May '12

On Fri, May 4, 2012 at 12:57 PM, Peter Brune <prbrune(a)gmail.com> wrote: > Jed, what else needs to be done with respect to getting all the SNEScontext into DM? I notice that, for instance, SNESSet/GetFunction is still > mostly using the ops in SNES rather than the ones in SNESDM. > I had a temporary option -snes_kspcompute to make the dispatch go through SNESDM. The main holdup now is -snes_grid_sequence, but I'm banging away at ex48 again, so I should be able to get it all working shortly. (I have ex48 running without DMMG, but some functionality is missing now, like changing the physics in the middle of the MG hierarchy.)

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Re: [petsc-dev] Error in make test
by Stefano Zampini 05 May '12

05 May '12

I reverted to 23244. 2012/5/5 Shri <abhyshr(a)mcs.anl.gov> > I've disabled the threadcomm code temporarily, so hopefully your code > should run as before now. Please pull and retry. > > Thanks, > Shri > > ------------------------------ > > Same error on make test. > > Moreover, I got some mpi errors running my fortran codes and PETSc doesn't > show the traceback > I can only see that the problem occurs in PetscInitialize > Here is the cryptic output from MPI (openmpi.1.4.5) > > [neo155:25438] *** An error occurred in MPI_Attr_get > [neo155:25438] *** on communicator MPI COMMUNICATOR 3 DUP FROM 1 > [neo155:25438] *** MPI_ERR_OTHER: known error not in list > [neo155:25438] *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort) > > > 2012/5/5 Shri <abhyshr(a)mcs.anl.gov> > >> I pushed some changes to fix these errors. Can you please pull and retry. >> >> >> ------------------------------ >> >> I had pulled some hours ago from >> http://petsc.cs.iit.edu/petsc/petsc-dev/rev/61898f35c333 and obtained >> the following error on make test >> >> [0]PETSC ERROR: PetscCommDuplicate() line 200 in >> /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/objects/tagm.c >> [0]PETSC ERROR: PetscHeaderCreate_Private() line 51 in >> /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/objects/inherit.c >> [0]PETSC ERROR: SNESCreate() line 1293 in >> /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/snes/interface/snes.c >> [0]PETSC ERROR: main() line 102 in src/snes/examples/tutorials/ex19.c >> >> I've just pulled and got the following error after typing make test >> >> [0]PETSC ERROR: PetscCommDestroy() line 246 in >> /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/objects/tagm.c >> [0]PETSC ERROR: PetscThreadCommFinalizePackage() line 36 in >> /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/threadcomm/interface/dlregisthreadcomm.c >> [0]PETSC ERROR: PetscRegisterFinalizeAll() line 313 in >> /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/objects/destroy.c >> [0]PETSC ERROR: PetscFinalize() line 1080 in >> /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/objects/pinit. >> >> I did not configure for a threaded version of PETSc. >> >> -- >> Stefano >> >> >> > > > -- > Stefano > > > -- Stefano

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Re: [petsc-dev] Error in make test
by Shri 05 May '12

05 May '12

I've disabled the threadcomm code temporarily, so hopefully your code should run as before now. Please pull and retry. Thanks, Shri ----- Original Message ----- > Same error on make test. > Moreover, I got some mpi errors running my fortran codes and PETSc > doesn't show the traceback > I can only see that the problem occurs in PetscInitialize > Here is the cryptic output from MPI (openmpi.1.4.5) > [neo155:25438] *** An error occurred in MPI_Attr_get > [neo155:25438] *** on communicator MPI COMMUNICATOR 3 DUP FROM 1 > [neo155:25438] *** MPI_ERR_OTHER: known error not in list > [neo155:25438] *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort) > 2012/5/5 Shri < abhyshr(a)mcs.anl.gov > > > I pushed some changes to fix these errors. Can you please pull and > > retry. > > > I had pulled some hours ago from > > > http://petsc.cs.iit.edu/petsc/petsc-dev/rev/61898f35c333 and > > > obtained > > > the following error on make test > > > [0]PETSC ERROR: PetscCommDuplicate() line 200 in > > > /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/objects/tagm.c > > > [0]PETSC ERROR: PetscHeaderCreate_Private() line 51 in > > > /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/objects/inherit.c > > > [0]PETSC ERROR: SNESCreate() line 1293 in > > > /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/snes/interface/snes.c > > > [0]PETSC ERROR: main() line 102 in > > > src/snes/examples/tutorials/ex19.c > > > I've just pulled and got the following error after typing make > > > test > > > [0]PETSC ERROR: PetscCommDestroy() line 246 in > > > /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/objects/tagm.c > > > [0]PETSC ERROR: PetscThreadCommFinalizePackage() line 36 in > > > /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/threadcomm/interface/dlregisthreadcomm.c > > > [0]PETSC ERROR: PetscRegisterFinalizeAll() line 313 in > > > /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/objects/destroy.c > > > [0]PETSC ERROR: PetscFinalize() line 1080 in > > > /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/objects/pinit. > > > I did not configure for a threaded version of PETSc. > > > -- > > > Stefano > -- > Stefano

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Re: [petsc-dev] Error in make test
by Stefano Zampini 05 May '12

05 May '12

Same error on make test. Moreover, I got some mpi errors running my fortran codes and PETSc doesn't show the traceback I can only see that the problem occurs in PetscInitialize Here is the cryptic output from MPI (openmpi.1.4.5) [neo155:25438] *** An error occurred in MPI_Attr_get [neo155:25438] *** on communicator MPI COMMUNICATOR 3 DUP FROM 1 [neo155:25438] *** MPI_ERR_OTHER: known error not in list [neo155:25438] *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort) 2012/5/5 Shri <abhyshr(a)mcs.anl.gov> > I pushed some changes to fix these errors. Can you please pull and retry. > > > ------------------------------ > > I had pulled some hours ago from > http://petsc.cs.iit.edu/petsc/petsc-dev/rev/61898f35c333 and obtained the > following error on make test > > [0]PETSC ERROR: PetscCommDuplicate() line 200 in > /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/objects/tagm.c > [0]PETSC ERROR: PetscHeaderCreate_Private() line 51 in > /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/objects/inherit.c > [0]PETSC ERROR: SNESCreate() line 1293 in > /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/snes/interface/snes.c > [0]PETSC ERROR: main() line 102 in src/snes/examples/tutorials/ex19.c > > I've just pulled and got the following error after typing make test > > [0]PETSC ERROR: PetscCommDestroy() line 246 in > /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/objects/tagm.c > [0]PETSC ERROR: PetscThreadCommFinalizePackage() line 36 in > /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/threadcomm/interface/dlregisthreadcomm.c > [0]PETSC ERROR: PetscRegisterFinalizeAll() line 313 in > /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/objects/destroy.c > [0]PETSC ERROR: PetscFinalize() line 1080 in > /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/objects/pinit. > > I did not configure for a threaded version of PETSc. > > -- > Stefano > > > -- Stefano

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Re: [petsc-dev] Error in make test
by Shri 05 May '12

05 May '12

I pushed some changes to fix these errors. Can you please pull and retry. ----- Original Message ----- > I had pulled some hours ago from > http://petsc.cs.iit.edu/petsc/petsc-dev/rev/61898f35c333 and obtained > the following error on make test > [0]PETSC ERROR: PetscCommDuplicate() line 200 in > /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/objects/tagm.c > [0]PETSC ERROR: PetscHeaderCreate_Private() line 51 in > /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/objects/inherit.c > [0]PETSC ERROR: SNESCreate() line 1293 in > /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/snes/interface/snes.c > [0]PETSC ERROR: main() line 102 in src/snes/examples/tutorials/ex19.c > I've just pulled and got the following error after typing make test > [0]PETSC ERROR: PetscCommDestroy() line 246 in > /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/objects/tagm.c > [0]PETSC ERROR: PetscThreadCommFinalizePackage() line 36 in > /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/threadcomm/interface/dlregisthreadcomm.c > [0]PETSC ERROR: PetscRegisterFinalizeAll() line 313 in > /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/objects/destroy.c > [0]PETSC ERROR: PetscFinalize() line 1080 in > /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/objects/pinit. > I did not configure for a threaded version of PETSc. > -- > Stefano

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Error in make test
by Stefano Zampini 05 May '12

05 May '12

I had pulled some hours ago from http://petsc.cs.iit.edu/petsc/petsc-dev/rev/61898f35c333 and obtained the following error on make test [0]PETSC ERROR: PetscCommDuplicate() line 200 in /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/objects/tagm.c [0]PETSC ERROR: PetscHeaderCreate_Private() line 51 in /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/objects/inherit.c [0]PETSC ERROR: SNESCreate() line 1293 in /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/snes/interface/snes.c [0]PETSC ERROR: main() line 102 in src/snes/examples/tutorials/ex19.c I've just pulled and got the following error after typing make test [0]PETSC ERROR: PetscCommDestroy() line 246 in /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/objects/tagm.c [0]PETSC ERROR: PetscThreadCommFinalizePackage() line 36 in /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/threadcomm/interface/dlregisthreadcomm.c [0]PETSC ERROR: PetscRegisterFinalizeAll() line 313 in /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/objects/destroy.c [0]PETSC ERROR: PetscFinalize() line 1080 in /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/objects/pinit. I did not configure for a threaded version of PETSc. -- Stefano

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Re: [petsc-dev] Petsc VecCopy code.
by Yoo, Andy 04 May '12

04 May '12

Thanks, Mathew. From: petsc-dev-bounces(a)mcs.anl.gov [mailto:[email protected]] On Behalf Of Matthew Knepley Sent: Friday, May 04, 2012 11:41 AM To: For users of the development version of PETSc Subject: Re: [petsc-dev] Petsc VecCopy code. On Fri, May 4, 2012 at 2:27 PM, Yoo, Andy <yoo2(a)llnl.gov<mailto:[email protected]>> wrote: Hi, I have written a two-dimensional MatVec routine (http://dl.acm.org/citation.cfm?id=2063469) a while ago. Any chance of getting that into PETSc proper? Now, I am noticing there is a small memory leak that appears to come from VecCopy. It is small, as it only appears like after 300000 MatVecs. I looked at the Petsc sources, but was not able to locate the default copy function for VecMPI. Can you please point me to the right direction? Its here: http://petsc.cs.iit.edu/petsc/petsc-dev/annotate/95406d5a1c14/src/vec/vec/i… set here in the vtable: http://petsc.cs.iit.edu/petsc/petsc-dev/annotate/95406d5a1c14/src/vec/vec/i… Matt Thank you for your help in advance. Andy Yoo, Ph.D. Center for Applied Scientific Computing Lawrence Livermore National Laboratory -- 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] What needs to be done before a release?
by Peter Brune 04 May '12

04 May '12

Jed, what else needs to be done with respect to getting all the SNES context into DM? I notice that, for instance, SNESSet/GetFunction is still mostly using the ops in SNES rather than the ones in SNESDM. - Peter On Wed, May 2, 2012 at 12:02 PM, Blaise Bourdin <bourdin(a)lsu.edu> wrote: > Barry, > > >> Also, fortran wrappers over PetscOptionsEnum and PetscBagRegisterEnum > would be nice. I understand that it > >> is a bit tricky since it involves passing fortran arrays of strings. > > > > Yup. We'd be willing to support these from FORTRAN but someone else > has to do the dirty work of figuring out how to handle those array of > strings (maybe F2003?). > > I am attaching a simple proof of concept example that demonstrates how to > write a fortran interface and call petsc C functions from fortran using > F2003 C-interoperability instead of going through the fortran bindings. > > Don't be put off by all the warnings if you use gfortran. They would be > easy to avoid. Basically, right now, you detect the fortran integer and > real kinds that match that of the C ones. It would be quite simple to get > the fortran C-interoperable integer and real types associated with the C > type of PetscInt, PetscReal etc. > > Basically, we (I?) could write a fortran interface and a fortran function > for the tricky functions involving arrays of string, instead of creating a > custom binding in C. Are you willing to let some fortran pollution into the > petsc code? Where would these function have to be? > > Blaise > > PS: you need FCFLAGS='-ffixed-line-length-none -ffree-line-length-none > -ffree-form' or some subset of these to compile with gfortran. I'm not sure > why these are not the default with a file suffix .F90 > > > > -- > Department of Mathematics and Center for Computation & Technology > Louisiana State University, Baton Rouge, LA 70803, USA > Tel. +1 (225) 578 1612, Fax +1 (225) 578 4276 > http://www.math.lsu.edu/~bourdin > > > > > > > > >

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