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

Re: [petsc-dev] Partial build
by Satish Balay 02 May '12

02 May '12

Normally both should work. Looks like 'lib' is broken. Satish On Wed, 2 May 2012, John Fettig wrote: > To answer my own question, it looks like you have to use libfast, not lib. > > John > > On Wed, May 2, 2012 at 4:54 PM, John Fettig <john.fettig(a)gmail.com> wrote: > > > If I modify src/vec/vec/impls/seq/seqcusp/veccusp.cu and then (in that > > directory) type "make lib", shouldn't it rebuild the library? I have also > > tried "make ACTION=lib tree" from higher up, and it still doesn't rebuild. > > What's the secret? This works for .c files. > > > > Thanks, > > John > > > > >

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Re: [petsc-dev] Partial build
by John Fettig 02 May '12

02 May '12

To answer my own question, it looks like you have to use libfast, not lib. John On Wed, May 2, 2012 at 4:54 PM, John Fettig <john.fettig(a)gmail.com> wrote: > If I modify src/vec/vec/impls/seq/seqcusp/veccusp.cu and then (in that > directory) type "make lib", shouldn't it rebuild the library? I have also > tried "make ACTION=lib tree" from higher up, and it still doesn't rebuild. > What's the secret? This works for .c files. > > Thanks, > John > >

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Partial build
by John Fettig 02 May '12

02 May '12

If I modify src/vec/vec/impls/seq/seqcusp/veccusp.cu and then (in that directory) type "make lib", shouldn't it rebuild the library? I have also tried "make ACTION=lib tree" from higher up, and it still doesn't rebuild. What's the secret? This works for .c files. Thanks, John

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Re: [petsc-dev] What needs to be done before a release?
by Blaise Bourdin 02 May '12

02 May '12

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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Re: [petsc-dev] PETSc MG Solvers vs agmg
by Mark F. Adams 02 May '12

02 May '12

For structure grids you can use geometric MG which is very good. Mark On May 2, 2012, at 12:44 AM, Dave Nystrom wrote: > Barry Smith writes: >> On May 1, 2012, at 7:22 PM, Dave Nystrom wrote: >>> >>>>> 2. Is anyone on this list sufficiently familiar with agmg and the other >>>>> PETSc mg solvers to know how to configure the PETSc mg solvers to work more >>>>> like agmg? It seems that agmg gives better performance than the PETSc mg >>>>> solvers but I also have issues with agmg including fragility. >>>> >>>> Please send a link for information on agmg; I've never heard of that. >>> >>> http://homepages.ulb.ac.be/~ynotay/AGMG >> >> Ok, this general approach is what the Trilinos ML solver users (which is a >> fairly good) and what Mark Adams is adding to PETSc in PCGAMG. > > Thanks for this info. > >> You can start by ./configure PETSc with --download-ml and then run the >> program with -pc_type mg > > I assume you mean "-pc_type ml". I have actually configured and run > petsc-dev with gamg, ml and hypre-boomeramg. I have just used the default > parameters because I am not sure which of the parameters would be most useful > to try and tune. It has seemed that ML has given the best results so far but > those results in terms of run time performance are not as good as agmg. > > I'd like to somehow get educated on how to intelligently tune the adjustable > parameters on these various MG packages and ML seems a good place to start. > But I'm not quite sure how to get started since there are enough adjustable > parameters that exploring parameter space could be challenge. > > Perhaps there is some good documentation on this. I guess I should google > "Trilinos ML documentation" and see what I find. My solves are on a 2d > structured mesh and I have 8 of them of various flavors. > >> You can run with -ksp_view to see the number of levels etc it ended up >> with and >> http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/PC/PCML.html >> for some options. > > Thanks again. > > Dave > >> Barry >> >>> >>>> Barry >>>> >>>>> >>>>> Thanks, >>>>> >>>>> Dave >> >

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Re: [petsc-dev] PETSc MG Solvers vs agmg
by Dave Nystrom 01 May '12

01 May '12

Barry Smith writes: > On May 1, 2012, at 7:22 PM, Dave Nystrom wrote: > > > >>> 2. Is anyone on this list sufficiently familiar with agmg and the other > >>> PETSc mg solvers to know how to configure the PETSc mg solvers to work more > >>> like agmg? It seems that agmg gives better performance than the PETSc mg > >>> solvers but I also have issues with agmg including fragility. > >> > >> Please send a link for information on agmg; I've never heard of that. > > > > http://homepages.ulb.ac.be/~ynotay/AGMG > > Ok, this general approach is what the Trilinos ML solver users (which is a > fairly good) and what Mark Adams is adding to PETSc in PCGAMG. Thanks for this info. > You can start by ./configure PETSc with --download-ml and then run the > program with -pc_type mg I assume you mean "-pc_type ml". I have actually configured and run petsc-dev with gamg, ml and hypre-boomeramg. I have just used the default parameters because I am not sure which of the parameters would be most useful to try and tune. It has seemed that ML has given the best results so far but those results in terms of run time performance are not as good as agmg. I'd like to somehow get educated on how to intelligently tune the adjustable parameters on these various MG packages and ML seems a good place to start. But I'm not quite sure how to get started since there are enough adjustable parameters that exploring parameter space could be challenge. Perhaps there is some good documentation on this. I guess I should google "Trilinos ML documentation" and see what I find. My solves are on a 2d structured mesh and I have 8 of them of various flavors. > You can run with -ksp_view to see the number of levels etc it ended up > with and > http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/PC/PCML.html > for some options. Thanks again. Dave > Barry > > > > >> Barry > >> > >>> > >>> Thanks, > >>> > >>> Dave >

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Re: [petsc-dev] PETSc MG Solvers vs agmg
by Barry Smith 01 May '12

01 May '12

On May 1, 2012, at 7:22 PM, Dave Nystrom wrote: > > >>> 2. Is anyone on this list sufficiently familiar with agmg and the other >>> PETSc mg solvers to know how to configure the PETSc mg solvers to work more >>> like agmg? It seems that agmg gives better performance than the PETSc mg >>> solvers but I also have issues with agmg including fragility. >> >> Please send a link for information on agmg; I've never heard of that. > > http://homepages.ulb.ac.be/~ynotay/AGMG Ok, this general approach is what the Trilinos ML solver users (which is a fairly good) and what Mark Adams is adding to PETSc in PCGAMG. You can start by ./configure PETSc with --download-ml and then run the program with -pc_type mg You can run with -ksp_view to see the number of levels etc it ended up with and http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/PC/PCML.html for some options. Barry > >> Barry >> >>> >>> Thanks, >>> >>> Dave

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Re: [petsc-dev] PETSc MG Solvers vs agmg
by Dave Nystrom 01 May '12

01 May '12

Barry Smith writes: > > On May 1, 2012, at 8:34 AM, Dave Nystrom wrote: > > > I have a 2d resistive mhd code that has an interface to both agmg and various > > multigrid solvers available from PETSc including gamg, hypre and ml. I'm not > > that familiar with multigrid and so it is difficult for me to know how to > > experiment with the various mg packages and tune them to my particular > > problems. In my code, agmg is a stand alone solver. I have a couple of > > questions. > > > > 1. Is it possible to use the PETSc mg solvers effectively without an > > iterative method by choosing preonly as the iterative method - like I do for > > the PETSc direct solves? > > Use -ksp_type richardson Note that using -ksp_type preonly would result in > only 1 iteration of the multigrid method and hence not what you want. > > Note that algebraic multigrid methods are generally designed to be used > with a Krylov accelerator and convergence may suffer (i.e. it will take > longer or not even converge) without a Krylov accelerator. Though, of > course, experimenting to find the fastest is a good idea. Thanks for the info. > > 2. Is anyone on this list sufficiently familiar with agmg and the other > > PETSc mg solvers to know how to configure the PETSc mg solvers to work more > > like agmg? It seems that agmg gives better performance than the PETSc mg > > solvers but I also have issues with agmg including fragility. > > Please send a link for information on agmg; I've never heard of that. http://homepages.ulb.ac.be/~ynotay/AGMG > Barry > > > > > Thanks, > > > > Dave

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Re: [petsc-dev] make test error
by Matthew Knepley 01 May '12

01 May '12

On Tue, May 1, 2012 at 3:28 PM, John Mousel <john.mousel(a)gmail.com> wrote: > I just pulled petsc-dev and am getting the following error in the tests. > Pushed fix. Matt > John > > > Running test examples to verify correct installation > Using PETSC_DIR=/home/vchivukula/NumericalLibraries/petsc-dev and > PETSC_ARCH=linux-intel > Possible error running C/C++ src/snes/examples/tutorials/ex19 with 1 MPI > process > See http://www.mcs.anl.gov/petsc/documentation/faq.html > lid velocity = 0.0016, prandtl # = 1, grashof # = 1 > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > [0]PETSC ERROR: or see > http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[0]PETSCERROR: or try > http://valgrind.org on GNU/linux and Apple Mac OS X to find memory > corruption errors > [0]PETSC ERROR: likely location of problem given in stack below > [0]PETSC ERROR: --------------------- Stack Frames > ------------------------------------ > [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not > available, > [0]PETSC ERROR: INSTEAD the line number of the start of the function > [0]PETSC ERROR: is given. > [0]PETSC ERROR: [0] PetscSectionCreateGlobalSection line 440 > src/vec/vec/impls/seq/vsection.c > [0]PETSC ERROR: [0] DMGetDefaultGlobalSection line 2624 > src/dm/interface/dm.c > [0]PETSC ERROR: [0] DMGetDefaultSF line 2656 src/dm/interface/dm.c > [0]PETSC ERROR: [0] DMGlobalToLocalBegin line 1012 src/dm/interface/dm.c > [0]PETSC ERROR: [0] DMDAFunction line 177 src/dm/impls/da/da2.c > [0]PETSC ERROR: [0] DM user function line 0 unknownunknown > [0]PETSC ERROR: [0] DMComputeFunction line 1896 src/dm/interface/dm.c > [0]PETSC ERROR: [0] SNESDefaultComputeFunction_DMLegacy line 379 > src/snes/utils/dmsnes.c > [0]PETSC ERROR: [0] SNES user function line 0 unknownunknown > [0]PETSC ERROR: [0] SNESComputeFunction line 1821 src/snes/interface/snes.c > [0]PETSC ERROR: [0] SNESSolve_LS line 143 src/snes/impls/ls/ls.c > [0]PETSC ERROR: [0] SNESSolve line 3395 src/snes/interface/snes.c > > -- 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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make test error
by John Mousel 01 May '12

01 May '12

I just pulled petsc-dev and am getting the following error in the tests. John Running test examples to verify correct installation Using PETSC_DIR=/home/vchivukula/NumericalLibraries/petsc-dev and PETSC_ARCH=linux-intel Possible error running C/C++ src/snes/examples/tutorials/ex19 with 1 MPI process See http://www.mcs.anl.gov/petsc/documentation/faq.html lid velocity = 0.0016, prandtl # = 1, grashof # = 1 [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors [0]PETSC ERROR: likely location of problem given in stack below [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------ [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available, [0]PETSC ERROR: INSTEAD the line number of the start of the function [0]PETSC ERROR: is given. [0]PETSC ERROR: [0] PetscSectionCreateGlobalSection line 440 src/vec/vec/impls/seq/vsection.c [0]PETSC ERROR: [0] DMGetDefaultGlobalSection line 2624 src/dm/interface/dm.c [0]PETSC ERROR: [0] DMGetDefaultSF line 2656 src/dm/interface/dm.c [0]PETSC ERROR: [0] DMGlobalToLocalBegin line 1012 src/dm/interface/dm.c [0]PETSC ERROR: [0] DMDAFunction line 177 src/dm/impls/da/da2.c [0]PETSC ERROR: [0] DM user function line 0 unknownunknown [0]PETSC ERROR: [0] DMComputeFunction line 1896 src/dm/interface/dm.c [0]PETSC ERROR: [0] SNESDefaultComputeFunction_DMLegacy line 379 src/snes/utils/dmsnes.c [0]PETSC ERROR: [0] SNES user function line 0 unknownunknown [0]PETSC ERROR: [0] SNESComputeFunction line 1821 src/snes/interface/snes.c [0]PETSC ERROR: [0] SNESSolve_LS line 143 src/snes/impls/ls/ls.c [0]PETSC ERROR: [0] SNESSolve line 3395 src/snes/interface/snes.c

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