December 2014 - petsc-dev - mailman3.cels.anl.gov

PETSc conference and tutorials June 15 - 18, 2015 at ANL
by Barry Smith 21 Dec '14

21 Dec '14

We are excited to invite you to the PETSc 20th anniversary conference and tutorial from June 15 to June 18 2014 at Argonne National Laboratory. The conference announcement can be found at http://www.mcs.anl.gov/petsc-20 and in the attached PDE document. Thanks to the generosity of the Computing, Environment, and Life Sciences (CELS) directorate of Argonne, there are no registration fees, and we can provide some travel support for students, post-docs and those with limited travel budgets. Please register soon so we can include you in the program. Hope to see you there, Barry

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Re: [petsc-dev] More Fortran Interfaces
by John O'Sullivan 21 Dec '14

21 Dec '14

Hi Matt, Merry Christmas! I was wondering if you had a chance to put in the Fortran interfaces? No worries if you haven’t. We’re breaking up from work on Tuesday and won’t be back until the 7th of Jan so I won’t be working on it for a couple of weeks. It would be great to be able to get back to working on out Petsc code once we’re back though. Is there anyway I can tell that I need to pull a new dev version or should I just wait for you to email me? Anyway I hope you have a good break and its not too freezing where you are. We’ll be heading to the beach down here. Cheers John -- Dr John O'Sullivan Lecturer Department of Engineering Science University of Auckland, New Zealand email: jp.osullivan at auckland.ac.nz<https://lists.mcs.anl.gov/mailman/listinfo/petsc-dev> tel: +64 (0)9 923 85353 From: Matthew Knepley [mailto:[email protected]] Sent: Sunday, 14 December 2014 4:52 p.m. To: John O'Sullivan Cc: petsc-dev(a)mcs.anl.gov Subject: Re: [petsc-dev] More Fortran Interfaces On Mon, Dec 8, 2014 at 4:00 AM, John O'Sullivan <jp.osullivan(a)auckland.ac.nz<mailto:[email protected]>> wrote: Hi, I'm working with Adrian on our PetSc project at the University of Auckland. I think I've found a couple more fortran interfaces that are missing: DMPlexGetFaceFields DMPlexGefFaceGeometry I get the error: Undefined symbols for architecture x86_64: "_dmplexgetfacefields_", referenced from: _rhs_darcy_local.2542 in darcy.o "_dmplexgetfacegeometry_", referenced from: _rhs_darcy_local.2542 in darcy.o I haven't got to the restore stage yet but I think probably these ones are missing too: DMPlexRestoreFaceFields DMPlexRestoreFaceGeometry Also I'm having trouble declaring a pointer to a PetscFVFaceGeom type to use with the DMPlexGetFaceGeometry. Is there a trick to this or maybe its definition in fortran is missing too? Sorry, this is a really bad time of year for me with family and work travel. I can put in the Fortran bindings this week I think. I do not know how to handle structs in Fortran (will ask Fortran gurus). Right now, I am just going to make a PetscScalar array with one more dimension since the struct is a bunch of Scalars, and you will have to index into it treating the struct as another dim. Thanks, Matt Thanks very much! Cheers John -- Dr John O'Sullivan Lecturer Department of Engineering Science University of Auckland, New Zealand email: jp.osullivan at auckland.ac.nz<https://lists.mcs.anl.gov/mailman/listinfo/petsc-dev> tel: +64 (0)9 923 85353 -- 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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memory leaks and other problems with cusp tests in master
by Barry Smith 21 Dec '14

21 Dec '14

http://ftp.mcs.anl.gov/pub/petsc/nightlylogs/archive/2014/12/20/examples_ma…

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Re: [petsc-dev] Patch to fix vector allocation in ksp-fcg
by Sascha Schnepp 20 Dec '14

20 Dec '14

Hello, yes, I am sorry, there was a bug in the patch. The problem occurred when the number of preallocated vectors was bigger than the max number of old directions to store - as in the options in runex60. It hadn’t checked this case. Again, sorry for that. I prepared a new patch which also replaces a PetscMin for a PetscMax but also swaps argument positions. I ran ex2, ex43 and ex60 with appropriate options in valgrind and got no errors. BTW: valgrind is available for Mac through MacPorts again. Sascha On 20 Dec 2014, at 18:17, Barry Smith <bsmith(a)mcs.anl.gov> wrote: > > When I added this change src/ksp/ksp/examples/tutorials/ex60 make runex60 failed with valgrind errors. > > bsmith@es:/sandbox/bsmith/petsc/src/ksp/ksp/examples/tutorials$ /sandbox/bsmith/petsc/bin/petscmpiexec -valgrind -n 1 ./ex60 -ksp_monitor_short -ksp_rtol 1e-6 -diagfunc 1 -ksp_type fcg -ksp_fcg_mmax 1 -eta 0.1 > ==14854== Invalid write of size 8 > ==14854== at 0x5C32987: KSPAllocateVectors_FCG (fcg.c:37) > ==14854== by 0x5C32FE2: KSPSetUp_FCG (fcg.c:77) > ==14854== by 0x5BEBD69: KSPSetUp (itfunc.c:267) > ==14854== by 0x5BED3E3: KSPSolve (itfunc.c:419) > ==14854== by 0x403599: main (ex60.c:219) > ==14854== Address 0xa49f720 is 0 bytes after a block of size 16 alloc'd > ==14854== at 0x4C29BE8: memalign (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so) > ==14854== by 0x4F33A45: PetscMallocAlign (mal.c:27) > ==14854== by 0x5C32D96: KSPSetUp_FCG (fcg.c:63) > ==14854== by 0x5BEBD69: KSPSetUp (itfunc.c:267) > ==14854== by 0x5BED3E3: KSPSolve (itfunc.c:419) > ==14854== by 0x403599: main (ex60.c:219) > ==14854== > > Thus I have removed this change. > > Barry > >> On Dec 19, 2014, at 8:18 AM, Sascha Schnepp <mail(a)saschaschnepp.net> wrote: >> >> Hello developers, >> >> I prepared a patch to fix the allocation of direction vectors in >> KSPAllocateVectors_FCG within ksp-fcg. >> >> The fix consists only of replacing a PetscMin with a PetscMax. This >> prevents vectors being allocated one-by-one instead of chunksize >> of them once the preallocated ones (nprealloc) are exhausted. >> >> Let me know if you prefer a PR. >> >> Best, >> Sascha >> >> >> >> -------------------------------------- >> ETH Zurich >> Sascha Schnepp >> Institute of Geophysics - Geophysical Fluid Dynamics >> NO H23, Sonneggstrasse 5, 8092 Zurich, Switzerland >> >> schnepps(a)ethz.ch >> www.gfd.ethz.ch; www.saschaschnepp.net >> >> +41 44 632 0244 phone >> >> Consider encrypting your mail >> Public Key ID: 0x67AC24EF >> -------------------------------------- >> >> <Fix-to-KSPAllocateVectors_FCG.patch> >

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Re: [petsc-dev] MatPermute definition
by Matthew Knepley 20 Dec '14

20 Dec '14

On Sat, Dec 20, 2014 at 7:51 AM, Victor Magri @Sinmec < victorapm(a)sinmec.ufsc.br> wrote: > > Hello! > > I'm using MatPermute function to create a permuted matrix from two given > index sets. According to line 4711 of > ${PETSC_DIR}/src/mat/interface/matrix.c they map from row/col of permuted > matrix to row/col of the original one. So, the index sets are inverted > before the act of permutation. Shouldn't it be better to call this function > MatInvertPermute or something like this in oppose to MatPermute? Besides > that, I think it would be good to define a new function which does not > invert the index sets before permutation. > The old ordering routines of Alan George, which we wrap up in MatOrdering give back p[new number] = old number Thus this is what we use for input. We get the inverse, because for parallelism, it makes sense to have p[old number] = new number Thanks, Matt > Thank you! > -- 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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why jed/fix-mat-convert-basic-bs not in master?
by Barry Smith 20 Dec '14

20 Dec '14

Jed, Could you please merge jed/fix-mat-convert-basic-bs into master? Master is still broken on MatConvert Thanks Barry

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Re: [petsc-dev] Patch to fix vector allocation in ksp-fcg
by Barry Smith 20 Dec '14

20 Dec '14

When I added this change src/ksp/ksp/examples/tutorials/ex60 make runex60 failed with valgrind errors. bsmith@es:/sandbox/bsmith/petsc/src/ksp/ksp/examples/tutorials$ /sandbox/bsmith/petsc/bin/petscmpiexec -valgrind -n 1 ./ex60 -ksp_monitor_short -ksp_rtol 1e-6 -diagfunc 1 -ksp_type fcg -ksp_fcg_mmax 1 -eta 0.1 ==14854== Invalid write of size 8 ==14854== at 0x5C32987: KSPAllocateVectors_FCG (fcg.c:37) ==14854== by 0x5C32FE2: KSPSetUp_FCG (fcg.c:77) ==14854== by 0x5BEBD69: KSPSetUp (itfunc.c:267) ==14854== by 0x5BED3E3: KSPSolve (itfunc.c:419) ==14854== by 0x403599: main (ex60.c:219) ==14854== Address 0xa49f720 is 0 bytes after a block of size 16 alloc'd ==14854== at 0x4C29BE8: memalign (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so) ==14854== by 0x4F33A45: PetscMallocAlign (mal.c:27) ==14854== by 0x5C32D96: KSPSetUp_FCG (fcg.c:63) ==14854== by 0x5BEBD69: KSPSetUp (itfunc.c:267) ==14854== by 0x5BED3E3: KSPSolve (itfunc.c:419) ==14854== by 0x403599: main (ex60.c:219) ==14854== Thus I have removed this change. Barry > On Dec 19, 2014, at 8:18 AM, Sascha Schnepp <mail(a)saschaschnepp.net> wrote: > > Hello developers, > > I prepared a patch to fix the allocation of direction vectors in > KSPAllocateVectors_FCG within ksp-fcg. > > The fix consists only of replacing a PetscMin with a PetscMax. This > prevents vectors being allocated one-by-one instead of chunksize > of them once the preallocated ones (nprealloc) are exhausted. > > Let me know if you prefer a PR. > > Best, > Sascha > > > > -------------------------------------- > ETH Zurich > Sascha Schnepp > Institute of Geophysics - Geophysical Fluid Dynamics > NO H23, Sonneggstrasse 5, 8092 Zurich, Switzerland > > schnepps(a)ethz.ch > www.gfd.ethz.ch; www.saschaschnepp.net > > +41 44 632 0244 phone > > Consider encrypting your mail > Public Key ID: 0x67AC24EF > -------------------------------------- > > <Fix-to-KSPAllocateVectors_FCG.patch>

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MatPermute definition
by Victor Magri ＠Sinmec 20 Dec '14

20 Dec '14

Hello! I'm using MatPermute function to create a permuted matrix from two given index sets. According to line 4711 of ${PETSC_DIR}/src/mat/interface/matrix.c they map from row/col of permuted matrix to row/col of the original one. So, the index sets are inverted before the act of permutation. Shouldn't it be better to call this function MatInvertPermute or something like this in oppose to MatPermute? Besides that, I think it would be good to define a new function which does not invert the index sets before permutation. Thank you!

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Re: [petsc-dev] Fwd: [Bitbucket] Issue #84: pastix compilation error when custom compiler flags are set (petsc/petsc)
by Satish Balay 19 Dec '14

19 Dec '14

Added to branch 'balay/update-pastix_5.2.2.20' off 'maint' - and merged to next for now. https://bitbucket.org/petsc/petsc/commits/c7c61743d300979d95f7cd246d0504c36… Satish On Thu, 18 Dec 2014, Barry Smith wrote: > > Satish, > > Can you update maint and master to use this new version (after testing in next of course :-) > > Barry > > > > Begin forwarded message: > > > > Subject: Re: [Bitbucket] Issue #84: pastix compilation error when custom compiler flags are set (petsc/petsc) > > From: XL <issues-reply(a)bitbucket.org> > > To: <bsmith(a)mcs.anl.gov> > > Date: December 18, 2014 at 8:57:38 AM CST > > > > > > XL commented on issue #84: > > pastix compilation error when custom compiler flags are set <https://bitbucket.org/petsc/petsc/issue/84/pastix-compilation-error-when-cu…> > > I just released a new version that should fix the issue: https://gforge.inria.fr/frs/download.php/file/34392/pastix_5.2.2.20.tar.bz2 <https://gforge.inria.fr/frs/download.php/file/34392/pastix_5.2.2.20.tar.bz2>. > > View this issue <https://bitbucket.org/petsc/petsc/issue/84/pastix-compilation-error-when-cu…> or add a comment by replying to this email. > > Unsubscribe from issue emails <https://bitbucket.org/api/1.0/petsc/petsc/issue/84/unsubscribe/BarryFSmith/…> for this repository. <https://bitbucket.org/> > >

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Re: [petsc-dev] Patch to fix vector allocation in ksp-fcg
by Barry Smith 19 Dec '14

19 Dec '14

Fixed in master and next Thanks Barry > On Dec 19, 2014, at 8:18 AM, Sascha Schnepp <mail(a)saschaschnepp.net> wrote: > > Hello developers, > > I prepared a patch to fix the allocation of direction vectors in > KSPAllocateVectors_FCG within ksp-fcg. > > The fix consists only of replacing a PetscMin with a PetscMax. This > prevents vectors being allocated one-by-one instead of chunksize > of them once the preallocated ones (nprealloc) are exhausted. > > Let me know if you prefer a PR. > > Best, > Sascha > > > > -------------------------------------- > ETH Zurich > Sascha Schnepp > Institute of Geophysics - Geophysical Fluid Dynamics > NO H23, Sonneggstrasse 5, 8092 Zurich, Switzerland > > schnepps(a)ethz.ch > www.gfd.ethz.ch; www.saschaschnepp.net > > +41 44 632 0244 phone > > Consider encrypting your mail > Public Key ID: 0x67AC24EF > -------------------------------------- > > <Fix-to-KSPAllocateVectors_FCG.patch>

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