February 2017 - petsc-dev - mailman3.cels.anl.gov

Re: [petsc-dev] every test example runs in a new directory with new test harness
by Jed Brown 09 Feb '17

09 Feb '17

Matthew Knepley <knepley(a)gmail.com> writes: > So I need to check in this checkpoint file in order to test reading it in, > and also the diffing? I am not sure I like that better. > Shouldn't we design our test system to do this simple thing, rather than > clutter our repository for all time? Shouldn't we do the stronger test that guarantees the file format does not silently change?

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Re: [petsc-dev] every test example runs in a new directory with new test harness
by Matthew Knepley 09 Feb '17

09 Feb '17

On Thu, Feb 9, 2017 at 5:54 PM, Barry Smith <bsmith(a)mcs.anl.gov> wrote: > > I had no idea what a subtest was (horrible name BTW) so I said all > subtests should have the same output. > > I now understand what Scott meant by a subtest but I am still not sure > that it is a good idea. The benefits/features of subtests are > > 1) you don't need to type the base command line arguments multiple times > > 2) subtests need to be run sequentially in the same work directory > > 3) others? > > Now 1) seems like a nice but not crucial feature. 2) seems like a horrible > idea. 2) seems to exist only so we can have test cases like this particular > one of yours where the first run generates a file and the second run reads > in the file. This type of test is useful because it provides some assurance > that the "writing" actually wrote a suitable file (instead of possible > garbage that does not get tested). Jed proposed an alternative approach for > making sure output files are correct that does not require one test case be > run after another. Instead the test harness does a diff (for example > hdf5diff) on the output file with a "known" file. > > I don't see a downside to Jed's proposal. So I need to check in this checkpoint file in order to test reading it in, and also the diffing? I am not sure I like that better. Shouldn't we design our test system to do this simple thing, rather than clutter our repository for all time? Matt > > Barry > > > > > On Feb 9, 2017, at 4:32 PM, Matthew Knepley <knepley(a)gmail.com> wrote: > > > > On Mon, Feb 6, 2017 at 9:15 AM, Scott Kruger <kruger(a)txcorp.com> wrote: > > > > The basic idea of running multiple commands within a single shell > > script was what I called a subtest (for lack of a better word). > > So: > > > > This almost works. However, the two tests create separate output, but > the text below checks both > > runs against the same output. I tried using a "subsuffix", but it did > not change the output filename. > > > > Thanks, > > > > Matt > > > > > > test: > > suffix: restart > > requires: hdf5 > > args: -run_type test -refinement_limit 0.0 -bc_type dirichlet > -interpolate 1 -petscspace_order 1 > > test: > > args: -dm_view hdf5:sol.h5 -vec_view hdf5:sol.h5::append > > test: > > args: -f sol.h5 -restart > > > > The args in the subtest inherit from the parent test. This seems > > to be generally useful as a testing idiom in petsc tests as this > > example nicely shows. > > > > Each mpiexec would be tested separately and reported separately. > > This would give you want you want, and should work as is. > > > > > > Tobin pointed out that I broke the for loops and some of the subtest > > functionality in some of the other feature implementations. We > > have come to consensus (right, Tobin?) on the > > desired functionality and implementation. A pull request > > is planned this week. It doesn't affect this directly, but > > should have some minor improvements (like in the reporting). > > > > Scott > > > > > > On 2/6/17 7:10 AM, Matthew Knepley wrote: > > On Mon, Feb 6, 2017 at 1:05 AM, Jed Brown <jed(a)jedbrown.org > > <mailto:[email protected]>> wrote: > > > > > > Barry Smith <bsmith(a)mcs.anl.gov <mailto:[email protected]>> writes: > > > > > test: > > > suffix: restart_0 > > > requires: hdf5 > > > args: -run_type test -refinement_limit 0.0 -bc_type > dirichlet -interpolate 1 -petscspace_order 1 -dm_view hdf5:sol.h5 -vec_view > hdf5:sol.h5::append > > > > > > test: > > > suffix: restart_1 > > > requires: hdf5 > > > args: -run_type test -refinement_limit 0.0 -bc_type > dirichlet -interpolate 1 -petscspace_order 1 -f sol.h5 -restart > > > > > > See a problem? > > > > > > Should the same run of the example view the files and then load > them back in? versus trying to read in a data file from another run that > may not even have been created before and even if it was, the file was > definitely created in a different directory? > > > > So if write only is broken, do you want both to fail? I think it's > > better to read and write separately, with comparison using h5diff, > since > > that independently tests read vs write and establishes backward > > compatibility, which you'd really like the test system to make you > deal > > with explicitly. > > > > > > I know the test is broken, but I did already mail the list about this > > and was waiting for an answer > > to be worked out. > > > > I agree with Satish that running two commands would be great. I could > > rewrite the example to > > both write and load it, but it would complicate it. Also, I am trying to > > get the pattern I expect the > > user to follow for checkpointing. > > > > 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 > > > > -- > > Tech-X Corporation kruger(a)txcorp.com > > 5621 Arapahoe Ave, Suite A Phone: (720) 974-1841 > > Boulder, CO 80303 Fax: (303) 448-7756 > > > > > > > > -- > > 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 > > -- 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] every test example runs in a new directory with new test harness
by Barry Smith 09 Feb '17

09 Feb '17

I had no idea what a subtest was (horrible name BTW) so I said all subtests should have the same output. I now understand what Scott meant by a subtest but I am still not sure that it is a good idea. The benefits/features of subtests are 1) you don't need to type the base command line arguments multiple times 2) subtests need to be run sequentially in the same work directory 3) others? Now 1) seems like a nice but not crucial feature. 2) seems like a horrible idea. 2) seems to exist only so we can have test cases like this particular one of yours where the first run generates a file and the second run reads in the file. This type of test is useful because it provides some assurance that the "writing" actually wrote a suitable file (instead of possible garbage that does not get tested). Jed proposed an alternative approach for making sure output files are correct that does not require one test case be run after another. Instead the test harness does a diff (for example hdf5diff) on the output file with a "known" file. I don't see a downside to Jed's proposal. Barry > On Feb 9, 2017, at 4:32 PM, Matthew Knepley <knepley(a)gmail.com> wrote: > > On Mon, Feb 6, 2017 at 9:15 AM, Scott Kruger <kruger(a)txcorp.com> wrote: > > The basic idea of running multiple commands within a single shell > script was what I called a subtest (for lack of a better word). > So: > > This almost works. However, the two tests create separate output, but the text below checks both > runs against the same output. I tried using a "subsuffix", but it did not change the output filename. > > Thanks, > > Matt > > > test: > suffix: restart > requires: hdf5 > args: -run_type test -refinement_limit 0.0 -bc_type dirichlet -interpolate 1 -petscspace_order 1 > test: > args: -dm_view hdf5:sol.h5 -vec_view hdf5:sol.h5::append > test: > args: -f sol.h5 -restart > > The args in the subtest inherit from the parent test. This seems > to be generally useful as a testing idiom in petsc tests as this > example nicely shows. > > Each mpiexec would be tested separately and reported separately. > This would give you want you want, and should work as is. > > > Tobin pointed out that I broke the for loops and some of the subtest > functionality in some of the other feature implementations. We > have come to consensus (right, Tobin?) on the > desired functionality and implementation. A pull request > is planned this week. It doesn't affect this directly, but > should have some minor improvements (like in the reporting). > > Scott > > > On 2/6/17 7:10 AM, Matthew Knepley wrote: > On Mon, Feb 6, 2017 at 1:05 AM, Jed Brown <jed(a)jedbrown.org > <mailto:[email protected]>> wrote: > > > Barry Smith <bsmith(a)mcs.anl.gov <mailto:[email protected]>> writes: > > > test: > > suffix: restart_0 > > requires: hdf5 > > args: -run_type test -refinement_limit 0.0 -bc_type dirichlet -interpolate 1 -petscspace_order 1 -dm_view hdf5:sol.h5 -vec_view hdf5:sol.h5::append > > > > test: > > suffix: restart_1 > > requires: hdf5 > > args: -run_type test -refinement_limit 0.0 -bc_type dirichlet -interpolate 1 -petscspace_order 1 -f sol.h5 -restart > > > > See a problem? > > > > Should the same run of the example view the files and then load them back in? versus trying to read in a data file from another run that may not even have been created before and even if it was, the file was definitely created in a different directory? > > So if write only is broken, do you want both to fail? I think it's > better to read and write separately, with comparison using h5diff, since > that independently tests read vs write and establishes backward > compatibility, which you'd really like the test system to make you deal > with explicitly. > > > I know the test is broken, but I did already mail the list about this > and was waiting for an answer > to be worked out. > > I agree with Satish that running two commands would be great. I could > rewrite the example to > both write and load it, but it would complicate it. Also, I am trying to > get the pattern I expect the > user to follow for checkpointing. > > 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 > > -- > Tech-X Corporation kruger(a)txcorp.com > 5621 Arapahoe Ave, Suite A Phone: (720) 974-1841 > Boulder, CO 80303 Fax: (303) 448-7756 > > > > -- > 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] Segmentation fault GAMG + MatView
by Hong 09 Feb '17

09 Feb '17

Change below fixed the problem. I'll turn off additional ops later. Hong diff --git a/src/mat/impls/aij/seq/aij.c b/src/mat/impls/aij/seq/aij.c index 1e0b0b8..5cee782 100644 --- a/src/mat/impls/aij/seq/aij.c +++ b/src/mat/impls/aij/seq/aij.c @@ -4169,6 +4169,11 @@ PetscErrorCode MatCreateSeqAIJWithArrays(MPI_Comm comm,PetscInt m,PetscInt n,Pe } #endif + if (!a) { + (*mat)->ops->view = 0; + } + ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); Hong On Thu, Feb 9, 2017 at 4:53 PM, Hong <hzhang(a)mcs.anl.gov> wrote: > I'll check it tomorrow and fix it. > Hong > > On Thu, Feb 9, 2017 at 4:27 PM, Barry Smith <bsmith(a)mcs.anl.gov> wrote: > >> >> When called with a NULL set of numerical values >> MatCreateSeqAIJWithArrays() should turn off the function pointers for >> things that don't make sense for matrices without numerical values, for >> example MatMult() and MatView(), in fact most function pointers don't make >> sense and should be turned off. >> This could be done with a >> if (!a) { >> ... >> } >> after the call to MatSetType(). >> >> Barry >> >> > On Feb 9, 2017, at 4:08 PM, Matthew Knepley <knepley(a)gmail.com> wrote: >> > >> > On Thu, Feb 9, 2017 at 4:00 PM, Pierre Jolivet < >> pierre.jolivet(a)enseeiht.fr> wrote: >> > Oh my, this example also segfaults (at least on my Mac) when running: >> > mpirun -np 1 ./ex1 -pc_type gamg -mat_view >> > >> > Hong, in >> > >> > MatTransposeMatMultSymbolic_SeqAIJ_SeqAIJ() on line 1015 >> > >> > you create a matrix without values, not surprising since this is the >> symbolic phase. However, >> > it calls MatAssemblyEnd(), which calls ViewFromOptions(), which gets an >> SEGV because >> > it does not think to check if a->a is NULL. >> > >> > a) Should we make View robust to missing matrix values? >> > >> > b) I don't think this internal matrix should really be viewed like >> this, so maybe change its prefix? >> > >> > Thanks, >> > >> > Matt >> > >> > [0]PETSC ERROR: [0] MatView_SeqAIJ_ASCII line 560 >> /Volumes/Data/Repositories/petsc/src/mat/impls/aij/seq/aij.c >> > [0]PETSC ERROR: [0] MatView_SeqAIJ line 915 >> /Volumes/Data/Repositories/petsc/src/mat/impls/aij/seq/aij.c >> > [0]PETSC ERROR: [0] MatView line 920 /Volumes/Data/Repositories/pet >> sc/src/mat/interface/matrix.c >> > [0]PETSC ERROR: [0] PetscObjectView line 92 >> /Volumes/Data/Repositories/petsc/src/sys/objects/destroy.c >> > [0]PETSC ERROR: [0] PetscObjectViewFromOptions line 2702 >> /Volumes/Data/Repositories/petsc/src/sys/objects/options.c >> > [0]PETSC ERROR: [0] MatAssemblyEnd line 5151 >> /Volumes/Data/Repositories/petsc/src/mat/interface/matrix.c >> > [0]PETSC ERROR: [0] MatCreateSeqAIJWithArrays line 4137 >> /Volumes/Data/Repositories/petsc/src/mat/impls/aij/seq/aij.c >> > [0]PETSC ERROR: [0] MatTransposeMatMultSymbolic_SeqAIJ_SeqAIJ line >> 1012 /Volumes/Data/Repositories/petsc/src/mat/impls/aij/seq/matmatmult.c >> > [0]PETSC ERROR: [0] MatTransposeMatMult_SeqAIJ_SeqAIJ line 994 >> /Volumes/Data/Repositories/petsc/src/mat/impls/aij/seq/matmatmult.c >> > [0]PETSC ERROR: [0] MatTransposeMatMult line 9607 >> /Volumes/Data/Repositories/petsc/src/mat/interface/matrix.c >> > [0]PETSC ERROR: [0] PCGAMGCoarsen_AGG line 914 >> /Volumes/Data/Repositories/petsc/src/ksp/pc/impls/gamg/agg.c >> > [0]PETSC ERROR: [0] PCSetUp_GAMG line 425 /Volumes/Data/Repositories/pet >> sc/src/ksp/pc/impls/gamg/gamg.c >> > [0]PETSC ERROR: [0] PCSetUp line 886 /Volumes/Data/Repositories/pet >> sc/src/ksp/pc/interface/precon.c >> > [0]PETSC ERROR: [0] KSPSetUp line 291 /Volumes/Data/Repositories/pet >> sc/src/ksp/ksp/interface/itfunc.c >> > >> > [0]PETSC ERROR: Petsc Development GIT revision: v3.7.5-3046-gde967d2 >> GIT Date: 2017-02-09 18:59:37 +0000 >> > [0]PETSC ERROR: Configure options --LDFLAGS=-L/opt/intel/lib >> --download-hypre --download-metis --download-mumps --download-parmetis >> --download-pastix --download-ptscotch --with-blacs-include=/opt/intel/mkl/include >> --with-blacs-lib=/opt/intel/mkl/lib/libmkl_blacs_mpich_lp64.so >> --with-blaslapack-dir=/opt/intel/mkl --with-chtml=0 >> --with-mkl_pardiso-include=/opt/intel/mkl/include --with-mkl_pardiso=1 >> --with-scalapack-include=/opt/intel/mkl/include >> --with-scalapack-lib="[/opt/intel/mkl/lib/libmkl_scalapack_ >> lp64.so,/opt/intel/mkl/lib/libmkl_blacs_mpich_lp64.so]" >> --with-shared-libraries=1 --with-x=1 PETSC_ARCH=arch-darwin-c-debug >> > >> >> On Feb 9, 2017, at 10:52 PM, Pierre Jolivet < >> pierre.jolivet(a)enseeiht.fr> wrote: >> >> >> >> There, attached. >> >> >> >> Thanks. >> >> >> >> PS: here is the patch also, just in case >> >> diff --git a/src/ksp/ksp/examples/tutorials/ex1.c >> b/src/ksp/ksp/examples/tutorials/ex1.c >> >> index 6382c09..d9dc69a 100644 >> >> --- a/src/ksp/ksp/examples/tutorials/ex1.c >> >> +++ b/src/ksp/ksp/examples/tutorials/ex1.c >> >> @@ -123,6 +123,11 @@ int main(int argc,char **args) >> >> routines. >> >> */ >> >> ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr); >> >> + ierr = KSPSetUp(ksp);CHKERRQ(ierr); >> >> + char right_options[] = "-ksp_norm_type unpreconditioned >> -ksp_pc_side right"; >> >> + PetscOptionsInsertString(NULL,right_options); >> >> + ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr); >> >> + ierr = KSPSetUp(ksp);CHKERRQ(ierr); >> >> >> >> if (nonzeroguess) { >> >> PetscScalar p = .5; >> >> >> >> <ex1.c> >> >> >> >>> On Feb 9, 2017, at 2:56 PM, Matthew Knepley <knepley(a)gmail.com> >> wrote: >> >>> >> >>> On Thu, Feb 9, 2017 at 7:48 AM, Pierre Jolivet < >> pierre.jolivet(a)enseeiht.fr> wrote: >> >>>> On Feb 9, 2017, at 2:31 PM, Matthew Knepley <knepley(a)gmail.com> >> wrote: >> >>>> >> >>>> On Thu, Feb 9, 2017 at 7:29 AM, Pierre Jolivet < >> pierre.jolivet(a)enseeiht.fr> wrote: >> >>>> >> >>>>> On Feb 9, 2017, at 2:17 PM, Matthew Knepley <knepley(a)gmail.com> >> wrote: >> >>>>> >> >>>>> On Thu, Feb 9, 2017 at 7:06 AM, Pierre Jolivet < >> pierre.jolivet(a)enseeiht.fr> wrote: >> >>>>> >> >>>>>> On Feb 9, 2017, at 1:37 PM, Matthew Knepley <knepley(a)gmail.com> >> wrote: >> >>>>>> >> >>>>>> On Thu, Feb 9, 2017 at 4:56 AM, Pierre Jolivet < >> pierre.jolivet(a)enseeiht.fr> wrote: >> >>>>>> Hello, >> >>>>>> I _might_ be doing something wrong when calling >> KSPSetFromOptions/KSPSetUp, but still, am I supposed to get this kind of >> error? >> >>>>>> [0]PETSC ERROR: No support for this operation for this object type >> >>>>>> [0]PETSC ERROR: KSP gmres does not support PRECONDITIONED with >> RIGHT >> >>>>>> >> >>>>>> If not, I’ll try to send a MWE (it basically depends on where I >> set the option -ksp_pc_side right). >> >>>>>> >> >>>>>> I believe its telling you that it cannot display the >> preconditioned residual with right preconditioning, which is true. >> >>>>>> Are you requesting both? >> >>>>> >> >>>>> No, I’m just using -ksp_view and -ksp_pc_side right. In the >> “standard” case, it obviously work. >> >>>>> However, the error is triggered if I set -ksp_pc_side right after a >> first call to KSPSetOperators()/KSPSetUp() without destroying the KSP. >> >>>>> Should I destroy my KSP before changing from left- (default) to >> right-preconditioning if KSPSetOperators()/KSPSetUp has already been called? >> >>>>> >> >>>>> Its likely you have to use >> >>>>> >> >>>>> http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages >> /KSP/KSPSetNormType.html >> >>>>> >> >>>>> or >> >>>>> >> >>>>> -ksp_norm_type unpreconditioned >> >>>> >> >>>> If I use this after my first call to KSPSetUp, I now end up with: >> >>>> [0]PETSC ERROR: KSP gmres does not support UNPRECONDITIONED with LEFT >> >>>> >> >>>> Yes, you would need to use it at the same time that you change the >> preconditioning side. >> >>> >> >>> Yes, I’m using PetscOptionsInsert, and whether I let PETSc parse >> "-ksp_pc_side right -ksp_norm_type unpreconditioned” or "-ksp_norm_type >> unpreconditioned -ksp_pc_side right” I end up with the same error >> afterwards. >> >>> >> >>> Can you make an example do it (SNES ex5)? Or can you send a small >> example that does it? >> >>> >> >>> Thanks, >> >>> >> >>> Matt >> >>> >> >>> Thanks. >> >>> >> >>>> Thanks, >> >>>> >> >>>> Matt >> >>>>> since we would not have a chance to change it since its been set >> already. >> >>>>> >> >>>>> Thanks, >> >>>>> >> >>>>> Matt >> >>>>> >> >>>>> Thanks. >> >>>>> >> >>>>>> Thanks, >> >>>>>> >> >>>>>> Matt >> >>>>>> >> >>>>>> Thanks, >> >>>>>> Pierre >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> -- >> >>>>>> 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 >> >>>>> >> >>>>> >> >>>>> >> >>>>> >> >>>>> -- >> >>>>> 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 >> >>>> >> >>>> >> >>>> >> >>>> >> >>>> -- >> >>>> 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 >> >>> >> >>> >> >>> >> >>> >> >>> -- >> >>> 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 >> >> >> > >> > >> > >> > >> > -- >> > 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] Segmentation fault GAMG + MatView
by Hong 09 Feb '17

09 Feb '17

I'll check it tomorrow and fix it. Hong On Thu, Feb 9, 2017 at 4:27 PM, Barry Smith <bsmith(a)mcs.anl.gov> wrote: > > When called with a NULL set of numerical values > MatCreateSeqAIJWithArrays() should turn off the function pointers for > things that don't make sense for matrices without numerical values, for > example MatMult() and MatView(), in fact most function pointers don't make > sense and should be turned off. > This could be done with a > if (!a) { > ... > } > after the call to MatSetType(). > > Barry > > > On Feb 9, 2017, at 4:08 PM, Matthew Knepley <knepley(a)gmail.com> wrote: > > > > On Thu, Feb 9, 2017 at 4:00 PM, Pierre Jolivet < > pierre.jolivet(a)enseeiht.fr> wrote: > > Oh my, this example also segfaults (at least on my Mac) when running: > > mpirun -np 1 ./ex1 -pc_type gamg -mat_view > > > > Hong, in > > > > MatTransposeMatMultSymbolic_SeqAIJ_SeqAIJ() on line 1015 > > > > you create a matrix without values, not surprising since this is the > symbolic phase. However, > > it calls MatAssemblyEnd(), which calls ViewFromOptions(), which gets an > SEGV because > > it does not think to check if a->a is NULL. > > > > a) Should we make View robust to missing matrix values? > > > > b) I don't think this internal matrix should really be viewed like this, > so maybe change its prefix? > > > > Thanks, > > > > Matt > > > > [0]PETSC ERROR: [0] MatView_SeqAIJ_ASCII line 560 > /Volumes/Data/Repositories/petsc/src/mat/impls/aij/seq/aij.c > > [0]PETSC ERROR: [0] MatView_SeqAIJ line 915 /Volumes/Data/Repositories/ > petsc/src/mat/impls/aij/seq/aij.c > > [0]PETSC ERROR: [0] MatView line 920 /Volumes/Data/Repositories/ > petsc/src/mat/interface/matrix.c > > [0]PETSC ERROR: [0] PetscObjectView line 92 /Volumes/Data/Repositories/ > petsc/src/sys/objects/destroy.c > > [0]PETSC ERROR: [0] PetscObjectViewFromOptions line 2702 > /Volumes/Data/Repositories/petsc/src/sys/objects/options.c > > [0]PETSC ERROR: [0] MatAssemblyEnd line 5151 /Volumes/Data/Repositories/ > petsc/src/mat/interface/matrix.c > > [0]PETSC ERROR: [0] MatCreateSeqAIJWithArrays line 4137 > /Volumes/Data/Repositories/petsc/src/mat/impls/aij/seq/aij.c > > [0]PETSC ERROR: [0] MatTransposeMatMultSymbolic_SeqAIJ_SeqAIJ line 1012 > /Volumes/Data/Repositories/petsc/src/mat/impls/aij/seq/matmatmult.c > > [0]PETSC ERROR: [0] MatTransposeMatMult_SeqAIJ_SeqAIJ line 994 > /Volumes/Data/Repositories/petsc/src/mat/impls/aij/seq/matmatmult.c > > [0]PETSC ERROR: [0] MatTransposeMatMult line 9607 > /Volumes/Data/Repositories/petsc/src/mat/interface/matrix.c > > [0]PETSC ERROR: [0] PCGAMGCoarsen_AGG line 914 > /Volumes/Data/Repositories/petsc/src/ksp/pc/impls/gamg/agg.c > > [0]PETSC ERROR: [0] PCSetUp_GAMG line 425 /Volumes/Data/Repositories/ > petsc/src/ksp/pc/impls/gamg/gamg.c > > [0]PETSC ERROR: [0] PCSetUp line 886 /Volumes/Data/Repositories/ > petsc/src/ksp/pc/interface/precon.c > > [0]PETSC ERROR: [0] KSPSetUp line 291 /Volumes/Data/Repositories/ > petsc/src/ksp/ksp/interface/itfunc.c > > > > [0]PETSC ERROR: Petsc Development GIT revision: v3.7.5-3046-gde967d2 > GIT Date: 2017-02-09 18:59:37 +0000 > > [0]PETSC ERROR: Configure options --LDFLAGS=-L/opt/intel/lib > --download-hypre --download-metis --download-mumps --download-parmetis > --download-pastix --download-ptscotch --with-blacs-include=/opt/intel/mkl/include > --with-blacs-lib=/opt/intel/mkl/lib/libmkl_blacs_mpich_lp64.so > --with-blaslapack-dir=/opt/intel/mkl --with-chtml=0 > --with-mkl_pardiso-include=/opt/intel/mkl/include --with-mkl_pardiso=1 > --with-scalapack-include=/opt/intel/mkl/include > --with-scalapack-lib="[/opt/intel/mkl/lib/libmkl_ > scalapack_lp64.so,/opt/intel/mkl/lib/libmkl_blacs_mpich_lp64.so]" > --with-shared-libraries=1 --with-x=1 PETSC_ARCH=arch-darwin-c-debug > > > >> On Feb 9, 2017, at 10:52 PM, Pierre Jolivet <pierre.jolivet(a)enseeiht.fr> > wrote: > >> > >> There, attached. > >> > >> Thanks. > >> > >> PS: here is the patch also, just in case > >> diff --git a/src/ksp/ksp/examples/tutorials/ex1.c > b/src/ksp/ksp/examples/tutorials/ex1.c > >> index 6382c09..d9dc69a 100644 > >> --- a/src/ksp/ksp/examples/tutorials/ex1.c > >> +++ b/src/ksp/ksp/examples/tutorials/ex1.c > >> @@ -123,6 +123,11 @@ int main(int argc,char **args) > >> routines. > >> */ > >> ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr); > >> + ierr = KSPSetUp(ksp);CHKERRQ(ierr); > >> + char right_options[] = "-ksp_norm_type unpreconditioned -ksp_pc_side > right"; > >> + PetscOptionsInsertString(NULL,right_options); > >> + ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr); > >> + ierr = KSPSetUp(ksp);CHKERRQ(ierr); > >> > >> if (nonzeroguess) { > >> PetscScalar p = .5; > >> > >> <ex1.c> > >> > >>> On Feb 9, 2017, at 2:56 PM, Matthew Knepley <knepley(a)gmail.com> wrote: > >>> > >>> On Thu, Feb 9, 2017 at 7:48 AM, Pierre Jolivet < > pierre.jolivet(a)enseeiht.fr> wrote: > >>>> On Feb 9, 2017, at 2:31 PM, Matthew Knepley <knepley(a)gmail.com> > wrote: > >>>> > >>>> On Thu, Feb 9, 2017 at 7:29 AM, Pierre Jolivet < > pierre.jolivet(a)enseeiht.fr> wrote: > >>>> > >>>>> On Feb 9, 2017, at 2:17 PM, Matthew Knepley <knepley(a)gmail.com> > wrote: > >>>>> > >>>>> On Thu, Feb 9, 2017 at 7:06 AM, Pierre Jolivet < > pierre.jolivet(a)enseeiht.fr> wrote: > >>>>> > >>>>>> On Feb 9, 2017, at 1:37 PM, Matthew Knepley <knepley(a)gmail.com> > wrote: > >>>>>> > >>>>>> On Thu, Feb 9, 2017 at 4:56 AM, Pierre Jolivet < > pierre.jolivet(a)enseeiht.fr> wrote: > >>>>>> Hello, > >>>>>> I _might_ be doing something wrong when calling > KSPSetFromOptions/KSPSetUp, but still, am I supposed to get this kind of > error? > >>>>>> [0]PETSC ERROR: No support for this operation for this object type > >>>>>> [0]PETSC ERROR: KSP gmres does not support PRECONDITIONED with RIGHT > >>>>>> > >>>>>> If not, I’ll try to send a MWE (it basically depends on where I set > the option -ksp_pc_side right). > >>>>>> > >>>>>> I believe its telling you that it cannot display the preconditioned > residual with right preconditioning, which is true. > >>>>>> Are you requesting both? > >>>>> > >>>>> No, I’m just using -ksp_view and -ksp_pc_side right. In the > “standard” case, it obviously work. > >>>>> However, the error is triggered if I set -ksp_pc_side right after a > first call to KSPSetOperators()/KSPSetUp() without destroying the KSP. > >>>>> Should I destroy my KSP before changing from left- (default) to > right-preconditioning if KSPSetOperators()/KSPSetUp has already been called? > >>>>> > >>>>> Its likely you have to use > >>>>> > >>>>> http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/KSP/ > KSPSetNormType.html > >>>>> > >>>>> or > >>>>> > >>>>> -ksp_norm_type unpreconditioned > >>>> > >>>> If I use this after my first call to KSPSetUp, I now end up with: > >>>> [0]PETSC ERROR: KSP gmres does not support UNPRECONDITIONED with LEFT > >>>> > >>>> Yes, you would need to use it at the same time that you change the > preconditioning side. > >>> > >>> Yes, I’m using PetscOptionsInsert, and whether I let PETSc parse > "-ksp_pc_side right -ksp_norm_type unpreconditioned” or "-ksp_norm_type > unpreconditioned -ksp_pc_side right” I end up with the same error > afterwards. > >>> > >>> Can you make an example do it (SNES ex5)? Or can you send a small > example that does it? > >>> > >>> Thanks, > >>> > >>> Matt > >>> > >>> Thanks. > >>> > >>>> Thanks, > >>>> > >>>> Matt > >>>>> since we would not have a chance to change it since its been set > already. > >>>>> > >>>>> Thanks, > >>>>> > >>>>> Matt > >>>>> > >>>>> Thanks. > >>>>> > >>>>>> Thanks, > >>>>>> > >>>>>> Matt > >>>>>> > >>>>>> Thanks, > >>>>>> Pierre > >>>>>> > >>>>>> > >>>>>> > >>>>>> -- > >>>>>> 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 > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> -- > >>>>> 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 > >>>> > >>>> > >>>> > >>>> > >>>> -- > >>>> 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 > >>> > >>> > >>> > >>> > >>> -- > >>> 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 > >> > > > > > > > > > > -- > > 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] every test example runs in a new directory with new test harness
by Matthew Knepley 09 Feb '17

09 Feb '17

On Mon, Feb 6, 2017 at 9:15 AM, Scott Kruger <kruger(a)txcorp.com> wrote: > > The basic idea of running multiple commands within a single shell > script was what I called a subtest (for lack of a better word). > So: > This almost works. However, the two tests create separate output, but the text below checks both runs against the same output. I tried using a "subsuffix", but it did not change the output filename. Thanks, Matt > > test: > suffix: restart > requires: hdf5 > args: -run_type test -refinement_limit 0.0 -bc_type dirichlet > -interpolate 1 -petscspace_order 1 > test: > args: -dm_view hdf5:sol.h5 -vec_view hdf5:sol.h5::append > test: > args: -f sol.h5 -restart > > The args in the subtest inherit from the parent test. This seems > to be generally useful as a testing idiom in petsc tests as this > example nicely shows. > > Each mpiexec would be tested separately and reported separately. > This would give you want you want, and should work as is. > > > Tobin pointed out that I broke the for loops and some of the subtest > functionality in some of the other feature implementations. We > have come to consensus (right, Tobin?) on the > desired functionality and implementation. A pull request > is planned this week. It doesn't affect this directly, but > should have some minor improvements (like in the reporting). > > Scott > > > On 2/6/17 7:10 AM, Matthew Knepley wrote: > >> On Mon, Feb 6, 2017 at 1:05 AM, Jed Brown <jed(a)jedbrown.org >> <mailto:[email protected]>> wrote: >> >> >> Barry Smith <bsmith(a)mcs.anl.gov <mailto:[email protected]>> writes: >> >> > test: >> > suffix: restart_0 >> > requires: hdf5 >> > args: -run_type test -refinement_limit 0.0 -bc_type >> dirichlet -interpolate 1 -petscspace_order 1 -dm_view hdf5:sol.h5 -vec_view >> hdf5:sol.h5::append >> > >> > test: >> > suffix: restart_1 >> > requires: hdf5 >> > args: -run_type test -refinement_limit 0.0 -bc_type >> dirichlet -interpolate 1 -petscspace_order 1 -f sol.h5 -restart >> > >> > See a problem? >> > >> > Should the same run of the example view the files and then load >> them back in? versus trying to read in a data file from another run that >> may not even have been created before and even if it was, the file was >> definitely created in a different directory? >> >> So if write only is broken, do you want both to fail? I think it's >> better to read and write separately, with comparison using h5diff, >> since >> that independently tests read vs write and establishes backward >> compatibility, which you'd really like the test system to make you >> deal >> with explicitly. >> >> >> I know the test is broken, but I did already mail the list about this >> and was waiting for an answer >> to be worked out. >> >> I agree with Satish that running two commands would be great. I could >> rewrite the example to >> both write and load it, but it would complicate it. Also, I am trying to >> get the pattern I expect the >> user to follow for checkpointing. >> >> 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 >> > > -- > Tech-X Corporation kruger(a)txcorp.com > 5621 Arapahoe Ave, Suite A Phone: (720) 974-1841 > Boulder, CO 80303 Fax: (303) 448-7756 > -- 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] Segmentation fault GAMG + MatView
by Barry Smith 09 Feb '17

09 Feb '17

When called with a NULL set of numerical values MatCreateSeqAIJWithArrays() should turn off the function pointers for things that don't make sense for matrices without numerical values, for example MatMult() and MatView(), in fact most function pointers don't make sense and should be turned off. This could be done with a if (!a) { ... } after the call to MatSetType(). Barry > On Feb 9, 2017, at 4:08 PM, Matthew Knepley <knepley(a)gmail.com> wrote: > > On Thu, Feb 9, 2017 at 4:00 PM, Pierre Jolivet <pierre.jolivet(a)enseeiht.fr> wrote: > Oh my, this example also segfaults (at least on my Mac) when running: > mpirun -np 1 ./ex1 -pc_type gamg -mat_view > > Hong, in > > MatTransposeMatMultSymbolic_SeqAIJ_SeqAIJ() on line 1015 > > you create a matrix without values, not surprising since this is the symbolic phase. However, > it calls MatAssemblyEnd(), which calls ViewFromOptions(), which gets an SEGV because > it does not think to check if a->a is NULL. > > a) Should we make View robust to missing matrix values? > > b) I don't think this internal matrix should really be viewed like this, so maybe change its prefix? > > Thanks, > > Matt > > [0]PETSC ERROR: [0] MatView_SeqAIJ_ASCII line 560 /Volumes/Data/Repositories/petsc/src/mat/impls/aij/seq/aij.c > [0]PETSC ERROR: [0] MatView_SeqAIJ line 915 /Volumes/Data/Repositories/petsc/src/mat/impls/aij/seq/aij.c > [0]PETSC ERROR: [0] MatView line 920 /Volumes/Data/Repositories/petsc/src/mat/interface/matrix.c > [0]PETSC ERROR: [0] PetscObjectView line 92 /Volumes/Data/Repositories/petsc/src/sys/objects/destroy.c > [0]PETSC ERROR: [0] PetscObjectViewFromOptions line 2702 /Volumes/Data/Repositories/petsc/src/sys/objects/options.c > [0]PETSC ERROR: [0] MatAssemblyEnd line 5151 /Volumes/Data/Repositories/petsc/src/mat/interface/matrix.c > [0]PETSC ERROR: [0] MatCreateSeqAIJWithArrays line 4137 /Volumes/Data/Repositories/petsc/src/mat/impls/aij/seq/aij.c > [0]PETSC ERROR: [0] MatTransposeMatMultSymbolic_SeqAIJ_SeqAIJ line 1012 /Volumes/Data/Repositories/petsc/src/mat/impls/aij/seq/matmatmult.c > [0]PETSC ERROR: [0] MatTransposeMatMult_SeqAIJ_SeqAIJ line 994 /Volumes/Data/Repositories/petsc/src/mat/impls/aij/seq/matmatmult.c > [0]PETSC ERROR: [0] MatTransposeMatMult line 9607 /Volumes/Data/Repositories/petsc/src/mat/interface/matrix.c > [0]PETSC ERROR: [0] PCGAMGCoarsen_AGG line 914 /Volumes/Data/Repositories/petsc/src/ksp/pc/impls/gamg/agg.c > [0]PETSC ERROR: [0] PCSetUp_GAMG line 425 /Volumes/Data/Repositories/petsc/src/ksp/pc/impls/gamg/gamg.c > [0]PETSC ERROR: [0] PCSetUp line 886 /Volumes/Data/Repositories/petsc/src/ksp/pc/interface/precon.c > [0]PETSC ERROR: [0] KSPSetUp line 291 /Volumes/Data/Repositories/petsc/src/ksp/ksp/interface/itfunc.c > > [0]PETSC ERROR: Petsc Development GIT revision: v3.7.5-3046-gde967d2 GIT Date: 2017-02-09 18:59:37 +0000 > [0]PETSC ERROR: Configure options --LDFLAGS=-L/opt/intel/lib --download-hypre --download-metis --download-mumps --download-parmetis --download-pastix --download-ptscotch --with-blacs-include=/opt/intel/mkl/include --with-blacs-lib=/opt/intel/mkl/lib/libmkl_blacs_mpich_lp64.so --with-blaslapack-dir=/opt/intel/mkl --with-chtml=0 --with-mkl_pardiso-include=/opt/intel/mkl/include --with-mkl_pardiso=1 --with-scalapack-include=/opt/intel/mkl/include --with-scalapack-lib="[/opt/intel/mkl/lib/libmkl_scalapack_lp64.so,/opt/intel/mkl/lib/libmkl_blacs_mpich_lp64.so]" --with-shared-libraries=1 --with-x=1 PETSC_ARCH=arch-darwin-c-debug > >> On Feb 9, 2017, at 10:52 PM, Pierre Jolivet <pierre.jolivet(a)enseeiht.fr> wrote: >> >> There, attached. >> >> Thanks. >> >> PS: here is the patch also, just in case >> diff --git a/src/ksp/ksp/examples/tutorials/ex1.c b/src/ksp/ksp/examples/tutorials/ex1.c >> index 6382c09..d9dc69a 100644 >> --- a/src/ksp/ksp/examples/tutorials/ex1.c >> +++ b/src/ksp/ksp/examples/tutorials/ex1.c >> @@ -123,6 +123,11 @@ int main(int argc,char **args) >> routines. >> */ >> ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr); >> + ierr = KSPSetUp(ksp);CHKERRQ(ierr); >> + char right_options[] = "-ksp_norm_type unpreconditioned -ksp_pc_side right"; >> + PetscOptionsInsertString(NULL,right_options); >> + ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr); >> + ierr = KSPSetUp(ksp);CHKERRQ(ierr); >> >> if (nonzeroguess) { >> PetscScalar p = .5; >> >> <ex1.c> >> >>> On Feb 9, 2017, at 2:56 PM, Matthew Knepley <knepley(a)gmail.com> wrote: >>> >>> On Thu, Feb 9, 2017 at 7:48 AM, Pierre Jolivet <pierre.jolivet(a)enseeiht.fr> wrote: >>>> On Feb 9, 2017, at 2:31 PM, Matthew Knepley <knepley(a)gmail.com> wrote: >>>> >>>> On Thu, Feb 9, 2017 at 7:29 AM, Pierre Jolivet <pierre.jolivet(a)enseeiht.fr> wrote: >>>> >>>>> On Feb 9, 2017, at 2:17 PM, Matthew Knepley <knepley(a)gmail.com> wrote: >>>>> >>>>> On Thu, Feb 9, 2017 at 7:06 AM, Pierre Jolivet <pierre.jolivet(a)enseeiht.fr> wrote: >>>>> >>>>>> On Feb 9, 2017, at 1:37 PM, Matthew Knepley <knepley(a)gmail.com> wrote: >>>>>> >>>>>> On Thu, Feb 9, 2017 at 4:56 AM, Pierre Jolivet <pierre.jolivet(a)enseeiht.fr> wrote: >>>>>> Hello, >>>>>> I _might_ be doing something wrong when calling KSPSetFromOptions/KSPSetUp, but still, am I supposed to get this kind of error? >>>>>> [0]PETSC ERROR: No support for this operation for this object type >>>>>> [0]PETSC ERROR: KSP gmres does not support PRECONDITIONED with RIGHT >>>>>> >>>>>> If not, I’ll try to send a MWE (it basically depends on where I set the option -ksp_pc_side right). >>>>>> >>>>>> I believe its telling you that it cannot display the preconditioned residual with right preconditioning, which is true. >>>>>> Are you requesting both? >>>>> >>>>> No, I’m just using -ksp_view and -ksp_pc_side right. In the “standard” case, it obviously work. >>>>> However, the error is triggered if I set -ksp_pc_side right after a first call to KSPSetOperators()/KSPSetUp() without destroying the KSP. >>>>> Should I destroy my KSP before changing from left- (default) to right-preconditioning if KSPSetOperators()/KSPSetUp has already been called? >>>>> >>>>> Its likely you have to use >>>>> >>>>> http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/KSP/KSPSetNormT… >>>>> >>>>> or >>>>> >>>>> -ksp_norm_type unpreconditioned >>>> >>>> If I use this after my first call to KSPSetUp, I now end up with: >>>> [0]PETSC ERROR: KSP gmres does not support UNPRECONDITIONED with LEFT >>>> >>>> Yes, you would need to use it at the same time that you change the preconditioning side. >>> >>> Yes, I’m using PetscOptionsInsert, and whether I let PETSc parse "-ksp_pc_side right -ksp_norm_type unpreconditioned” or "-ksp_norm_type unpreconditioned -ksp_pc_side right” I end up with the same error afterwards. >>> >>> Can you make an example do it (SNES ex5)? Or can you send a small example that does it? >>> >>> Thanks, >>> >>> Matt >>> >>> Thanks. >>> >>>> Thanks, >>>> >>>> Matt >>>>> since we would not have a chance to change it since its been set already. >>>>> >>>>> Thanks, >>>>> >>>>> Matt >>>>> >>>>> Thanks. >>>>> >>>>>> Thanks, >>>>>> >>>>>> Matt >>>>>> >>>>>> Thanks, >>>>>> Pierre >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> 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 >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> 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 >>>> >>>> >>>> >>>> >>>> -- >>>> 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 >>> >>> >>> >>> >>> -- >>> 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 >> > > > > > -- > 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] Segmentation fault GAMG + MatView
by Matthew Knepley 09 Feb '17

09 Feb '17

On Thu, Feb 9, 2017 at 4:00 PM, Pierre Jolivet <pierre.jolivet(a)enseeiht.fr> wrote: > Oh my, this example also segfaults (at least on my Mac) when running: > mpirun -np 1 ./ex1 -pc_type gamg -mat_view > Hong, in MatTransposeMatMultSymbolic_SeqAIJ_SeqAIJ() on line 1015 you create a matrix without values, not surprising since this is the symbolic phase. However, it calls MatAssemblyEnd(), which calls ViewFromOptions(), which gets an SEGV because it does not think to check if a->a is NULL. a) Should we make View robust to missing matrix values? b) I don't think this internal matrix should really be viewed like this, so maybe change its prefix? Thanks, Matt > [0]PETSC ERROR: [0] MatView_SeqAIJ_ASCII line 560 > /Volumes/Data/Repositories/petsc/src/mat/impls/aij/seq/aij.c > [0]PETSC ERROR: [0] MatView_SeqAIJ line 915 /Volumes/Data/Repositories/ > petsc/src/mat/impls/aij/seq/aij.c > [0]PETSC ERROR: [0] MatView line 920 /Volumes/Data/Repositories/ > petsc/src/mat/interface/matrix.c > [0]PETSC ERROR: [0] PetscObjectView line 92 /Volumes/Data/Repositories/ > petsc/src/sys/objects/destroy.c > [0]PETSC ERROR: [0] PetscObjectViewFromOptions line 2702 > /Volumes/Data/Repositories/petsc/src/sys/objects/options.c > [0]PETSC ERROR: [0] MatAssemblyEnd line 5151 /Volumes/Data/Repositories/ > petsc/src/mat/interface/matrix.c > [0]PETSC ERROR: [0] MatCreateSeqAIJWithArrays line 4137 > /Volumes/Data/Repositories/petsc/src/mat/impls/aij/seq/aij.c > [0]PETSC ERROR: [0] MatTransposeMatMultSymbolic_SeqAIJ_SeqAIJ line 1012 > /Volumes/Data/Repositories/petsc/src/mat/impls/aij/seq/matmatmult.c > [0]PETSC ERROR: [0] MatTransposeMatMult_SeqAIJ_SeqAIJ line 994 > /Volumes/Data/Repositories/petsc/src/mat/impls/aij/seq/matmatmult.c > [0]PETSC ERROR: [0] MatTransposeMatMult line 9607 > /Volumes/Data/Repositories/petsc/src/mat/interface/matrix.c > [0]PETSC ERROR: [0] PCGAMGCoarsen_AGG line 914 /Volumes/Data/Repositories/ > petsc/src/ksp/pc/impls/gamg/agg.c > [0]PETSC ERROR: [0] PCSetUp_GAMG line 425 /Volumes/Data/Repositories/ > petsc/src/ksp/pc/impls/gamg/gamg.c > [0]PETSC ERROR: [0] PCSetUp line 886 /Volumes/Data/Repositories/ > petsc/src/ksp/pc/interface/precon.c > [0]PETSC ERROR: [0] KSPSetUp line 291 /Volumes/Data/Repositories/ > petsc/src/ksp/ksp/interface/itfunc.c > > [0]PETSC ERROR: Petsc Development GIT revision: v3.7.5-3046-gde967d2 GIT > Date: 2017-02-09 18:59:37 +0000 > [0]PETSC ERROR: Configure options --LDFLAGS=-L/opt/intel/lib > --download-hypre --download-metis --download-mumps --download-parmetis > --download-pastix --download-ptscotch --with-blacs-include=/opt/intel/mkl/include > --with-blacs-lib=/opt/intel/mkl/lib/libmkl_blacs_mpich_lp64.so > --with-blaslapack-dir=/opt/intel/mkl --with-chtml=0 > --with-mkl_pardiso-include=/opt/intel/mkl/include --with-mkl_pardiso=1 > --with-scalapack-include=/opt/intel/mkl/include > --with-scalapack-lib="[/opt/intel/mkl/lib/libmkl_ > scalapack_lp64.so,/opt/intel/mkl/lib/libmkl_blacs_mpich_lp64.so]" > --with-shared-libraries=1 --with-x=1 PETSC_ARCH=arch-darwin-c-debug > > On Feb 9, 2017, at 10:52 PM, Pierre Jolivet <pierre.jolivet(a)enseeiht.fr> > wrote: > > There, attached. > > Thanks. > > PS: here is the patch also, just in case > diff --git a/src/ksp/ksp/examples/tutorials/ex1.c b/src/ksp/ksp/examples/ > tutorials/ex1.c > index 6382c09..d9dc69a 100644 > --- a/src/ksp/ksp/examples/tutorials/ex1.c > +++ b/src/ksp/ksp/examples/tutorials/ex1.c > @@ -123,6 +123,11 @@ int main(int argc,char **args) > routines. > */ > ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr); > + ierr = KSPSetUp(ksp);CHKERRQ(ierr); > + char right_options[] = "-ksp_norm_type unpreconditioned -ksp_pc_side > right"; > + PetscOptionsInsertString(NULL,right_options); > + ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr); > + ierr = KSPSetUp(ksp);CHKERRQ(ierr); > > if (nonzeroguess) { > PetscScalar p = .5; > > <ex1.c> > > On Feb 9, 2017, at 2:56 PM, Matthew Knepley <knepley(a)gmail.com> wrote: > > On Thu, Feb 9, 2017 at 7:48 AM, Pierre Jolivet <pierre.jolivet(a)enseeiht.fr > > wrote: > >> On Feb 9, 2017, at 2:31 PM, Matthew Knepley <knepley(a)gmail.com> wrote: >> >> On Thu, Feb 9, 2017 at 7:29 AM, Pierre Jolivet <pierre.jolivet@enseei >> ht.fr> wrote: >> >>> >>> On Feb 9, 2017, at 2:17 PM, Matthew Knepley <knepley(a)gmail.com> wrote: >>> >>> On Thu, Feb 9, 2017 at 7:06 AM, Pierre Jolivet <pierre.jolivet@enseei >>> ht.fr> wrote: >>> >>>> >>>> On Feb 9, 2017, at 1:37 PM, Matthew Knepley <knepley(a)gmail.com> wrote: >>>> >>>> On Thu, Feb 9, 2017 at 4:56 AM, Pierre Jolivet <pierre.jolivet@enseei >>>> ht.fr> wrote: >>>> >>>>> Hello, >>>>> I _might_ be doing something wrong when calling >>>>> KSPSetFromOptions/KSPSetUp, but still, am I supposed to get this kind of >>>>> error? >>>>> [0]PETSC ERROR: No support for this operation for this object type >>>>> [0]PETSC ERROR: KSP gmres does not support PRECONDITIONED with RIGHT >>>>> >>>>> If not, I’ll try to send a MWE (it basically depends on where I set >>>>> the option -ksp_pc_side right). >>>>> >>>> >>>> I believe its telling you that it cannot display the preconditioned >>>> residual with right preconditioning, which is true. >>>> Are you requesting both? >>>> >>>> >>>> No, I’m just using -ksp_view and -ksp_pc_side right. In the “standard” >>>> case, it obviously work. >>>> However, the error is triggered if I set -ksp_pc_side right after a >>>> first call to KSPSetOperators()/KSPSetUp() without destroying the KSP. >>>> Should I destroy my KSP before changing from left- (default) to >>>> right-preconditioning if KSPSetOperators()/KSPSetUp has already been called? >>>> >>> >>> Its likely you have to use >>> >>> http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpage >>> s/KSP/KSPSetNormType.html >>> >>> or >>> >>> *-ksp_norm_type unpreconditioned* >>> >>> >>> If I use this after my first call to KSPSetUp, I now end up with: >>> [0]PETSC ERROR: KSP gmres does not support UNPRECONDITIONED with LEFT >>> >> >> Yes, you would need to use it at the same time that you change the >> preconditioning side. >> >> >> Yes, I’m using PetscOptionsInsert, and whether I let PETSc parse >> "-ksp_pc_side right -ksp_norm_type unpreconditioned” or "-ksp_norm_type >> unpreconditioned -ksp_pc_side right” I end up with the same error >> afterwards. >> > > Can you make an example do it (SNES ex5)? Or can you send a small example > that does it? > > Thanks, > > Matt > > >> Thanks. >> >> Thanks, >> >> Matt >> >>> since we would not have a chance to change it since its been set already. >>> >>> Thanks, >>> >>> Matt >>> >>> Thanks. >>>> >>>> Thanks, >>>> >>>> Matt >>>> >>>> >>>>> Thanks, >>>>> Pierre >>>> >>>> >>>> >>>> >>>> -- >>>> 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 >>>> >>>> >>>> >>> >>> >>> -- >>> 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 >>> >>> >>> >> >> >> -- >> 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 >> >> >> > > > -- > 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 > > > > -- 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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Segmentation fault GAMG + MatView
by Pierre Jolivet 09 Feb '17

09 Feb '17

Oh my, this example also segfaults (at least on my Mac) when running: mpirun -np 1 ./ex1 -pc_type gamg -mat_view [0]PETSC ERROR: [0] MatView_SeqAIJ_ASCII line 560 /Volumes/Data/Repositories/petsc/src/mat/impls/aij/seq/aij.c [0]PETSC ERROR: [0] MatView_SeqAIJ line 915 /Volumes/Data/Repositories/petsc/src/mat/impls/aij/seq/aij.c [0]PETSC ERROR: [0] MatView line 920 /Volumes/Data/Repositories/petsc/src/mat/interface/matrix.c [0]PETSC ERROR: [0] PetscObjectView line 92 /Volumes/Data/Repositories/petsc/src/sys/objects/destroy.c [0]PETSC ERROR: [0] PetscObjectViewFromOptions line 2702 /Volumes/Data/Repositories/petsc/src/sys/objects/options.c [0]PETSC ERROR: [0] MatAssemblyEnd line 5151 /Volumes/Data/Repositories/petsc/src/mat/interface/matrix.c [0]PETSC ERROR: [0] MatCreateSeqAIJWithArrays line 4137 /Volumes/Data/Repositories/petsc/src/mat/impls/aij/seq/aij.c [0]PETSC ERROR: [0] MatTransposeMatMultSymbolic_SeqAIJ_SeqAIJ line 1012 /Volumes/Data/Repositories/petsc/src/mat/impls/aij/seq/matmatmult.c [0]PETSC ERROR: [0] MatTransposeMatMult_SeqAIJ_SeqAIJ line 994 /Volumes/Data/Repositories/petsc/src/mat/impls/aij/seq/matmatmult.c [0]PETSC ERROR: [0] MatTransposeMatMult line 9607 /Volumes/Data/Repositories/petsc/src/mat/interface/matrix.c [0]PETSC ERROR: [0] PCGAMGCoarsen_AGG line 914 /Volumes/Data/Repositories/petsc/src/ksp/pc/impls/gamg/agg.c [0]PETSC ERROR: [0] PCSetUp_GAMG line 425 /Volumes/Data/Repositories/petsc/src/ksp/pc/impls/gamg/gamg.c [0]PETSC ERROR: [0] PCSetUp line 886 /Volumes/Data/Repositories/petsc/src/ksp/pc/interface/precon.c [0]PETSC ERROR: [0] KSPSetUp line 291 /Volumes/Data/Repositories/petsc/src/ksp/ksp/interface/itfunc.c [0]PETSC ERROR: Petsc Development GIT revision: v3.7.5-3046-gde967d2 GIT Date: 2017-02-09 18:59:37 +0000 [0]PETSC ERROR: Configure options --LDFLAGS=-L/opt/intel/lib --download-hypre --download-metis --download-mumps --download-parmetis --download-pastix --download-ptscotch --with-blacs-include=/opt/intel/mkl/include --with-blacs-lib=/opt/intel/mkl/lib/libmkl_blacs_mpich_lp64.so --with-blaslapack-dir=/opt/intel/mkl --with-chtml=0 --with-mkl_pardiso-include=/opt/intel/mkl/include --with-mkl_pardiso=1 --with-scalapack-include=/opt/intel/mkl/include --with-scalapack-lib="[/opt/intel/mkl/lib/libmkl_scalapack_lp64.so,/opt/intel/mkl/lib/libmkl_blacs_mpich_lp64.so]" --with-shared-libraries=1 --with-x=1 PETSC_ARCH=arch-darwin-c-debug > On Feb 9, 2017, at 10:52 PM, Pierre Jolivet <pierre.jolivet(a)enseeiht.fr> wrote: > > There, attached. > > Thanks. > > PS: here is the patch also, just in case > diff --git a/src/ksp/ksp/examples/tutorials/ex1.c b/src/ksp/ksp/examples/tutorials/ex1.c > index 6382c09..d9dc69a 100644 > --- a/src/ksp/ksp/examples/tutorials/ex1.c > +++ b/src/ksp/ksp/examples/tutorials/ex1.c > @@ -123,6 +123,11 @@ int main(int argc,char **args) > routines. > */ > ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr); > + ierr = KSPSetUp(ksp);CHKERRQ(ierr); > + char right_options[] = "-ksp_norm_type unpreconditioned -ksp_pc_side right"; > + PetscOptionsInsertString(NULL,right_options); > + ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr); > + ierr = KSPSetUp(ksp);CHKERRQ(ierr); > > if (nonzeroguess) { > PetscScalar p = .5; > > <ex1.c> > >> On Feb 9, 2017, at 2:56 PM, Matthew Knepley <knepley(a)gmail.com <mailto:[email protected]>> wrote: >> >> On Thu, Feb 9, 2017 at 7:48 AM, Pierre Jolivet <pierre.jolivet(a)enseeiht.fr <mailto:[email protected]>> wrote: >>> On Feb 9, 2017, at 2:31 PM, Matthew Knepley <knepley(a)gmail.com <mailto:[email protected]>> wrote: >>> >>> On Thu, Feb 9, 2017 at 7:29 AM, Pierre Jolivet <pierre.jolivet(a)enseeiht.fr <mailto:[email protected]>> wrote: >>> >>>> On Feb 9, 2017, at 2:17 PM, Matthew Knepley <knepley(a)gmail.com <mailto:[email protected]>> wrote: >>>> >>>> On Thu, Feb 9, 2017 at 7:06 AM, Pierre Jolivet <pierre.jolivet(a)enseeiht.fr <mailto:[email protected]>> wrote: >>>> >>>>> On Feb 9, 2017, at 1:37 PM, Matthew Knepley <knepley(a)gmail.com <mailto:[email protected]>> wrote: >>>>> >>>>> On Thu, Feb 9, 2017 at 4:56 AM, Pierre Jolivet <pierre.jolivet(a)enseeiht.fr <mailto:[email protected]>> wrote: >>>>> Hello, >>>>> I _might_ be doing something wrong when calling KSPSetFromOptions/KSPSetUp, but still, am I supposed to get this kind of error? >>>>> [0]PETSC ERROR: No support for this operation for this object type >>>>> [0]PETSC ERROR: KSP gmres does not support PRECONDITIONED with RIGHT >>>>> >>>>> If not, I’ll try to send a MWE (it basically depends on where I set the option -ksp_pc_side right). >>>>> >>>>> I believe its telling you that it cannot display the preconditioned residual with right preconditioning, which is true. >>>>> Are you requesting both? >>>> >>>> No, I’m just using -ksp_view and -ksp_pc_side right. In the “standard” case, it obviously work. >>>> However, the error is triggered if I set -ksp_pc_side right after a first call to KSPSetOperators()/KSPSetUp() without destroying the KSP. >>>> Should I destroy my KSP before changing from left- (default) to right-preconditioning if KSPSetOperators()/KSPSetUp has already been called? >>>> >>>> Its likely you have to use >>>> >>>> http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/KSP/KSPSetNormT… <http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/KSP/KSPSetNormT…> >>>> >>>> or >>>> >>>> -ksp_norm_type unpreconditioned >>> >>> If I use this after my first call to KSPSetUp, I now end up with: >>> [0]PETSC ERROR: KSP gmres does not support UNPRECONDITIONED with LEFT >>> >>> Yes, you would need to use it at the same time that you change the preconditioning side. >> >> Yes, I’m using PetscOptionsInsert, and whether I let PETSc parse "-ksp_pc_side right -ksp_norm_type unpreconditioned” or "-ksp_norm_type unpreconditioned -ksp_pc_side right” I end up with the same error afterwards. >> >> Can you make an example do it (SNES ex5)? Or can you send a small example that does it? >> >> Thanks, >> >> Matt >> >> Thanks. >> >>> Thanks, >>> >>> Matt >>>> since we would not have a chance to change it since its been set already. >>>> >>>> Thanks, >>>> >>>> Matt >>>> >>>> Thanks. >>>> >>>>> Thanks, >>>>> >>>>> Matt >>>>> >>>>> Thanks, >>>>> Pierre >>>>> >>>>> >>>>> >>>>> -- >>>>> 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 >>>> >>>> >>>> >>>> >>>> -- >>>> 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 >>> >>> >>> >>> >>> -- >>> 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 >> >> >> >> >> -- >> 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] Right-preconditioned GMRES
by Pierre Jolivet 09 Feb '17

09 Feb '17

There, attached. Thanks. PS: here is the patch also, just in case diff --git a/src/ksp/ksp/examples/tutorials/ex1.c b/src/ksp/ksp/examples/tutorials/ex1.c index 6382c09..d9dc69a 100644 --- a/src/ksp/ksp/examples/tutorials/ex1.c +++ b/src/ksp/ksp/examples/tutorials/ex1.c @@ -123,6 +123,11 @@ int main(int argc,char **args) routines. */ ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr); + ierr = KSPSetUp(ksp);CHKERRQ(ierr); + char right_options[] = "-ksp_norm_type unpreconditioned -ksp_pc_side right"; + PetscOptionsInsertString(NULL,right_options); + ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr); + ierr = KSPSetUp(ksp);CHKERRQ(ierr); if (nonzeroguess) { PetscScalar p = .5; > On Feb 9, 2017, at 2:56 PM, Matthew Knepley <knepley(a)gmail.com> wrote: > > On Thu, Feb 9, 2017 at 7:48 AM, Pierre Jolivet <pierre.jolivet(a)enseeiht.fr <mailto:[email protected]>> wrote: >> On Feb 9, 2017, at 2:31 PM, Matthew Knepley <knepley(a)gmail.com <mailto:[email protected]>> wrote: >> >> On Thu, Feb 9, 2017 at 7:29 AM, Pierre Jolivet <pierre.jolivet(a)enseeiht.fr <mailto:[email protected]>> wrote: >> >>> On Feb 9, 2017, at 2:17 PM, Matthew Knepley <knepley(a)gmail.com <mailto:[email protected]>> wrote: >>> >>> On Thu, Feb 9, 2017 at 7:06 AM, Pierre Jolivet <pierre.jolivet(a)enseeiht.fr <mailto:[email protected]>> wrote: >>> >>>> On Feb 9, 2017, at 1:37 PM, Matthew Knepley <knepley(a)gmail.com <mailto:[email protected]>> wrote: >>>> >>>> On Thu, Feb 9, 2017 at 4:56 AM, Pierre Jolivet <pierre.jolivet(a)enseeiht.fr <mailto:[email protected]>> wrote: >>>> Hello, >>>> I _might_ be doing something wrong when calling KSPSetFromOptions/KSPSetUp, but still, am I supposed to get this kind of error? >>>> [0]PETSC ERROR: No support for this operation for this object type >>>> [0]PETSC ERROR: KSP gmres does not support PRECONDITIONED with RIGHT >>>> >>>> If not, I’ll try to send a MWE (it basically depends on where I set the option -ksp_pc_side right). >>>> >>>> I believe its telling you that it cannot display the preconditioned residual with right preconditioning, which is true. >>>> Are you requesting both? >>> >>> No, I’m just using -ksp_view and -ksp_pc_side right. In the “standard” case, it obviously work. >>> However, the error is triggered if I set -ksp_pc_side right after a first call to KSPSetOperators()/KSPSetUp() without destroying the KSP. >>> Should I destroy my KSP before changing from left- (default) to right-preconditioning if KSPSetOperators()/KSPSetUp has already been called? >>> >>> Its likely you have to use >>> >>> http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/KSP/KSPSetNormT… <http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/KSP/KSPSetNormT…> >>> >>> or >>> >>> -ksp_norm_type unpreconditioned >> >> If I use this after my first call to KSPSetUp, I now end up with: >> [0]PETSC ERROR: KSP gmres does not support UNPRECONDITIONED with LEFT >> >> Yes, you would need to use it at the same time that you change the preconditioning side. > > Yes, I’m using PetscOptionsInsert, and whether I let PETSc parse "-ksp_pc_side right -ksp_norm_type unpreconditioned” or "-ksp_norm_type unpreconditioned -ksp_pc_side right” I end up with the same error afterwards. > > Can you make an example do it (SNES ex5)? Or can you send a small example that does it? > > Thanks, > > Matt > > Thanks. > >> Thanks, >> >> Matt >>> since we would not have a chance to change it since its been set already. >>> >>> Thanks, >>> >>> Matt >>> >>> Thanks. >>> >>>> Thanks, >>>> >>>> Matt >>>> >>>> Thanks, >>>> Pierre >>>> >>>> >>>> >>>> -- >>>> 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 >>> >>> >>> >>> >>> -- >>> 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 >> >> >> >> >> -- >> 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 > > > > > -- > 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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