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

PETSc communicators with MPI in Fortran
by Neelam Patel 31 Oct '17

31 Oct '17

Hello PETSc users, Working in Fortran, I created 2 disjoint communicators with MPI_Group operations using PETSC_COMM_WORLD as the "base" comm. I created parallel vectors on each communicator, and set values in them equal to their ranks on PETSC_COMM_WORLD. Everything seems to be working fine. My question is: Is this a valid thing to do? Or will it cause some undefined behaviour that I'm not seeing right now? I somehow thought that communicators created this way were not 'visible' to PETSc. Or is it that using PETSC_COMM_WORLD above eliminates that problem? Thank you in advance,Neelam

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Re: [petsc-dev] PetscSF in Fortran
by Smith, Barry F. 31 Oct '17

31 Oct '17

Please send the full traceback. Cut and paste > On Oct 31, 2017, at 3:37 PM, Adrian Croucher <a.croucher(a)auckland.ac.nz> wrote: > > > On 01/11/17 03:02, Smith, Barry F. wrote: >> Adrian, >> >> I fixed some bugs but apparently broke something at the same time. At a meeting now, maybe you could use -start_in_debugger and get the traceback where it crashes for you? > OK I did that, and it appears to be dying in src/vec/is/sf/impls/basic/sfbasic.c:497, which is: > > DEF_PackCmp(int) > > Dunno what that means though... > > - Adrian > > -- > Dr Adrian Croucher > Senior Research Fellow > Department of Engineering Science > University of Auckland, New Zealand > email: a.croucher(a)auckland.ac.nz > tel: +64 (0)9 923 4611 >

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Re: [petsc-dev] PetscSF in Fortran
by Adrian Croucher 31 Oct '17

31 Oct '17

On 01/11/17 03:02, Smith, Barry F. wrote: > Adrian, > > I fixed some bugs but apparently broke something at the same time. At a meeting now, maybe you could use -start_in_debugger and get the traceback where it crashes for you? OK I did that, and it appears to be dying in src/vec/is/sf/impls/basic/sfbasic.c:497, which is: DEF_PackCmp(int) Dunno what that means though... - Adrian -- Dr Adrian Croucher Senior Research Fellow Department of Engineering Science University of Auckland, New Zealand email: a.croucher(a)auckland.ac.nz tel: +64 (0)9 923 4611

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Re: [petsc-dev] Segfault in DMPlexVecGetClosure
by Blaise A Bourdin 31 Oct '17

31 Oct '17

On Oct 31, 2017, at 12:39 PM, Matthew Knepley <knepley(a)gmail.com<mailto:[email protected]>> wrote: On Tue, Oct 31, 2017 at 11:36 AM, Blaise A Bourdin <bourdin(a)lsu.edu<mailto:[email protected]>> wrote: Hi, I am losing my mind over segfaults in DMPlexVecGetClosure. In the example below, I get a segfault whenever cval is not set to NULL before calling DMPlexVecGetClosure. Is this expected? Yes. If cval is NULL, it allocates the necessary space and passes back the array. If it is not NULL, it uses the pointer that you passed in (so you can allocate your own temp storage if you are smarter). The documentations says nothing about this That is a problem. Also, after calling DMPlexVecRestoreClosure, the values of cval are discarded and neither global nor coord are changed. Ah, GetClosure() is not like GetArray(), in that it is a temp copy. You need SetClosure() in order to change values. So DMPlexVecGetClosure / DMPlexVecRestoreClosure behaves more like ISCreateGeneral / ISDestroy than as a standard PETSc XXXGet / XXXRestore. I’ll do my best to submit a pull request with an updated man page and an example. Blaise Matt I am obviously doing something wrong but cannot figure it out... Blaise -- Department of Mathematics and Center for Computation & Technology Louisiana State University, Baton Rouge, LA 70803, USA Tel. +1 (225) 578 1612<tel:(225)%20578-1612>, Fax +1 (225) 578 4276<tel:(225)%20578-4276> http://www.math.lsu.edu/~bourdin -- 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 https://www.cse.buffalo.edu/~knepley/<http://www.caam.rice.edu/~mk51/> -- 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] Segfault in DMPlexVecGetClosure
by Matthew Knepley 31 Oct '17

31 Oct '17

On Tue, Oct 31, 2017 at 11:36 AM, Blaise A Bourdin <bourdin(a)lsu.edu> wrote: > Hi, > > I am losing my mind over segfaults in DMPlexVecGetClosure. > > In the example below, I get a segfault whenever cval is not set to NULL > before calling DMPlexVecGetClosure. Is this expected? > Yes. If cval is NULL, it allocates the necessary space and passes back the array. If it is not NULL, it uses the pointer that you passed in (so you can allocate your own temp storage if you are smarter). > The documentations says nothing about this > That is a problem. > Also, after calling DMPlexVecRestoreClosure, the values of cval are > discarded and neither global nor coord are changed. > Ah, GetClosure() is not like GetArray(), in that it is a temp copy. You need SetClosure() in order to change values. Matt > I am obviously doing something wrong but cannot figure it out... > > Blaise > > > -- > Department of Mathematics and Center for Computation & Technology > Louisiana State University, Baton Rouge, LA 70803, USA > Tel. +1 (225) 578 1612 <(225)%20578-1612>, Fax +1 (225) 578 4276 > <(225)%20578-4276> http://www.math.lsu.edu/~bourdin > > > > > > > > -- 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 https://www.cse.buffalo.edu/~knepley/ <http://www.caam.rice.edu/~mk51/>

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Re: [petsc-dev] Segfault in DMPlexVecGetClosure
by Lawrence Mitchell 31 Oct '17

31 Oct '17

> On 31 Oct 2017, at 15:36, Blaise A Bourdin <bourdin(a)lsu.edu> wrote: > > Hi, > > I am losing my mind over segfaults in DMPlexVecGetClosure. > > In the example below, I get a segfault whenever cval is not set to NULL before calling DMPlexVecGetClosure. Is this expected? The documentations says nothing about this > Also, after calling DMPlexVecRestoreClosure, the values of cval are discarded and neither global nor coord are changed. > > I am obviously doing something wrong but cannot figure it out... The interface is similar to DMPlexGetClosure. DMPlexVecGetClosure fills the array you provide it with values. It can allocate a work array for you if you don't provide one, but you must indicate so explicitly by setting it to NULL: so PetscScalar *values = NULL; DMPlexVecGetClosure(...., &values); Do things with values Now you need to release the work array, you do that with the matching restore closure call. DMPlexVecRestoreClosure(...., &values); Now, these arrays you get are *not* pointers into the global Vec array, instead they are local buffers. If you want to update the Vec with the values you've put in values, you need to call DMPlexVecSetClosure: e.g. DMPlexVecSetClosure(..., values, INSERT_VALUES); So the calling sequence should be something like: PetscScalar *values = NULL; for ( int p = 0; p < ...; p++ ) { DMPlexVecGetClosure(..., p, ..., &values); // do stuff with values. DMPlexVecSetClosure(..., p, ..., values, INSERT_VALUES); } // Finally, restore work array DMPlexVecRestoreClosure(..., 0, ..., &values); Cheers, Lawrence

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Segfault in DMPlexVecGetClosure
by Blaise A Bourdin 31 Oct '17

31 Oct '17

Hi, I am losing my mind over segfaults in DMPlexVecGetClosure. In the example below, I get a segfault whenever cval is not set to NULL before calling DMPlexVecGetClosure. Is this expected? The documentations says nothing about this Also, after calling DMPlexVecRestoreClosure, the values of cval are discarded and neither global nor coord are changed. I am obviously doing something wrong but cannot figure it out... Blaise -- 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] QR factorization of dense matrix
by Franck Houssen 31 Oct '17

31 Oct '17

OK, got it. Thanks. Franck ----- Mail original ----- > De: "Jose E. Roman" <jroman(a)dsic.upv.es> > À: "Franck Houssen" <franck.houssen(a)inria.fr> > Cc: "For users of the development version of PETSc" <petsc-dev(a)mcs.anl.gov> > Envoyé: Lundi 30 Octobre 2017 17:37:52 > Objet: Re: [petsc-dev] QR factorization of dense matrix > > Any BV type will do. The default BVSVEC is generally best. > Jose > > > > El 30 oct 2017, a las 17:18, Franck Houssen <franck.houssen(a)inria.fr> > > escribió: > > > > It was not clear to me when I read the doc. That's OK now: got it to work, > > thanks Jose ! > > Just to make sure, to make it work, I had to set a BV type: I chose BVMAT > > as I use BVCreateFromMat. Is that the good type ? (BVVECS works too) > > > > Franck > > > > ----- Mail original ----- > >> De: "Jose E. Roman" <jroman(a)dsic.upv.es> > >> À: "Franck Houssen" <franck.houssen(a)inria.fr> > >> Cc: "For users of the development version of PETSc" > >> <petsc-dev(a)mcs.anl.gov> > >> Envoyé: Samedi 28 Octobre 2017 16:56:22 > >> Objet: Re: [petsc-dev] QR factorization of dense matrix > >> > >> Matrix R must be mxm. > >> BVOrthogonalize computes Z=Q*R, where Q overwrites Z. > >> Jose > >> > >>> El 28 oct 2017, a las 13:11, Franck Houssen <franck.houssen(a)inria.fr> > >>> escribió: > >>> > >>> I've seen that !... But can't get BVOrthogonalize to work. > >>> > >>> I tried: > >>> Mat Z; MatCreateSeqDense(PETSC_COMM_SELF, n, m, NULL, &Z); > >>> ...; // MatSetValues(Z, ...) > >>> BVCreate(PETSC_COMM_SELF, &bv); > >>> BVCreateFromMat(Z, &bv); // Z is tall-skinny > >>> Mat R; MatCreateSeqDense(PETSC_COMM_SELF, n, m, NULL, &R); // Same n, m > >>> than Z. > >>> BVOrthogonalize(bv, R); > >>> > >>> But BVOrthogonalize fails with : > >>>> [0]PETSC ERROR: Nonconforming object sizes > >>>> [0]PETSC ERROR: Mat argument is not square, it has 1 rows and 3 columns > >>> > >>> So, as I didn't get what's wrong, I was looking for another way to do > >>> this. > >>> > >>> Franck > >>> > >>> ----- Mail original ----- > >>>> De: "Jose E. Roman" <jroman(a)dsic.upv.es> > >>>> À: "Franck Houssen" <franck.houssen(a)inria.fr> > >>>> Cc: "For users of the development version of PETSc" > >>>> <petsc-dev(a)mcs.anl.gov> > >>>> Envoyé: Vendredi 27 Octobre 2017 19:03:37 > >>>> Objet: Re: [petsc-dev] QR factorization of dense matrix > >>>> > >>>> Franck, > >>>> > >>>> SLEPc has some support for this, but it is intended only for tall-skinny > >>>> matrices, that is, when the number of columns is much smaller than rows. > >>>> For > >>>> an almost square matrix you should not use it. > >>>> > >>>> Have a look at this > >>>> http://slepc.upv.es/documentation/current/docs/manualpages/BV/BVOrthogonali… > >>>> http://slepc.upv.es/documentation/current/docs/manualpages/BV/BVOrthogBlock… > >>>> > >>>> You can see there are three methods. All of them have drawbacks: > >>>> GS: This is a Gram-Schmidt QR, computed column by column, so it is > >>>> slower > >>>> than the other two. However, it is robust. > >>>> CHOL: Cholesky QR, it is not numerically stable. In the future we will > >>>> add > >>>> Cholesky QR2. > >>>> TSQR: Unfortunately this is not implemented in parallel. I wanted to add > >>>> the > >>>> parallel version for 3.8, but didn't have time. It will be added soon. > >>>> > >>>> You can use BVCreateFromMat() to create a BV object from a Mat. > >>>> > >>>> Jose > >>>> > >>>> > >>>>> El 27 oct 2017, a las 18:39, Franck Houssen <franck.houssen(a)inria.fr> > >>>>> escribió: > >>>>> > >>>>> I am looking for QR factorization of (sequential) dense matrix: is this > >>>>> available in PETSc ? I "just" need the diagonal of R (I do not need > >>>>> neither the full content of R, nor Q) > >>>>> > >>>>> I found that (old !) thread > >>>>> https://lists.mcs.anl.gov/pipermail/petsc-users/2013-November/019577.html > >>>>> that says it could be implemented: has it been done ? > >>>>> As for a direct solve, the way to go is "KSPSetType(ksp, KSPPREONLY); > >>>>> PCSetType(pc, PCLU);", I was expecting something like "KSPSetType(ksp, > >>>>> KSPPREONLY); PCSetType(pc, PCQR);"... But it seems there is no PCQR > >>>>> available. Or is it possible to do that using "an iterative way" with a > >>>>> specific kind of KSP that triggers a Gram Schmidt orthogonalization in > >>>>> back-end ? (I have seen a KSPLSQR but could I get Q and R back ? As I > >>>>> understand this, I would say no: I would say the user can only get the > >>>>> solution) > >>>>> > >>>>> Is it possible to QR a (sequential) dense matrix in PETSc ? If yes, > >>>>> what > >>>>> are the steps to follow ? > >>>>> > >>>>> Franck > >>>>> > >>>>> My understanding is that DGEQRF from lapack can do "more" than what I > >>>>> need, > >>>>> but, no sure to get if I can use it from PETSc through a KSP: > >>>>>>> git grep DGEQRF > >>>>> include/petscblaslapack_stdcall.h:# define LAPACKgeqrf_ DGEQRF > >>>>>>> git grep LAPACKgeqrf_ > >>>>> include/petscblaslapack.h:PETSC_EXTERN void > >>>>> LAPACKgeqrf_(PetscBLASInt*,PetscBLASInt*,PetscScalar*,PetscBLASInt*,PetscScalar*,PetscScalar*,PetscBLASInt*,PetscBLASInt*); > >>>>> include/petscblaslapack_mangle.h:#define LAPACKgeqrf_ > >>>>> PETSCBLAS(geqrf,GEQRF) > >>>>> include/petscblaslapack_stdcall.h:# define LAPACKgeqrf_ SGEQRF > >>>>> include/petscblaslapack_stdcall.h:# define LAPACKgeqrf_ DGEQRF > >>>>> include/petscblaslapack_stdcall.h:# define LAPACKgeqrf_ CGEQRF > >>>>> include/petscblaslapack_stdcall.h:# define LAPACKgeqrf_ ZGEQRF > >>>>> include/petscblaslapack_stdcall.h:PETSC_EXTERN void PETSC_STDCALL > >>>>> LAPACKgeqrf_(PetscBLASInt*,PetscBLASInt*,PetscScalar*,PetscBLASInt*,PetscScalar*,PetscScalar*,PetscBLASInt*,PetscBLASInt*); > >>>>> src/dm/dt/interface/dt.c: > >>>>> PetscStackCallBLAS("LAPACKgeqrf",LAPACKgeqrf_(&M,&N,A,&lda,tau,work,&ldwork,&info)); > >>>>> src/dm/dt/interface/dtfv.c: > >>>>> LAPACKgeqrf_(&M,&N,A,&lda,tau,work,&ldwork,&info); > >>>>> src/ksp/ksp/impls/gmres/agmres/agmres.c: > >>>>> PetscStackCallBLAS("LAPACKgeqrf",LAPACKgeqrf_(&lC, &KspSize, > >>>>> agmres->hh_origin, &ldH, agmres->tau, agmres->work, &lwork, &info)); > >>>>> src/ksp/pc/impls/bddc/bddcprivate.c: > >>>>> PetscStackCallBLAS("LAPACKgeqrf",LAPACKgeqrf_(&Blas_M,&Blas_N,qr_basis,&Blas_LDA,qr_tau,&lqr_work_t,&lqr_work,&lierr)); > >>>>> src/ksp/pc/impls/bddc/bddcprivate.c: > >>>>> PetscStackCallBLAS("LAPACKgeqrf",LAPACKgeqrf_(&Blas_M,&Blas_N,qr_basis,&Blas_LDA,qr_tau,qr_work,&lqr_work,&lierr)); > >>>>> src/ksp/pc/impls/gamg/agg.c: > >>>>> PetscStackCallBLAS("LAPACKgeqrf",LAPACKgeqrf_(&Mdata, &N, qqc, &LDA, > >>>>> TAU, WORK, &LWORK, &INFO)); > >>>>> src/tao/leastsquares/impls/pounders/pounders.c: > >>>>> PetscStackCallBLAS("LAPACKgeqrf",LAPACKgeqrf_(&blasnp,&blasnplus1,mfqP->Q_tmp,&blasnpmax,mfqP->tau_tmp,mfqP->mwork,&blasmaxmn,&info)); > >>>>> src/tao/leastsquares/impls/pounders/pounders.c: > >>>>> PetscStackCallBLAS("LAPACKgeqrf",LAPACKgeqrf_(&blasn,&blask,mfqP->Q,&blasnpmax,mfqP->tau,mfqP->mwork,&blasmaxmn,&info)); > >>>> > >>>> > >> > >> > >

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Re: [petsc-dev] SLEPc failure
by Franck Houssen 31 Oct '17

31 Oct '17

Thanks, this is helpful ! At least, I have some clues to dig deeper into. The data set I have seems to be very sensitive: I knew B would likely be close to singular (even arpack, which seems to be the most stable, is not always robust enough depending on use cases and/or number of domains). To get things stable with arpack, I had to add "-mat_mumps_cntl_1 0.01 -mat_mumps_cntl_3 -0.0001 -mat_mumps_cntl_4 0.0001": so I let all that also when testing with krylovschur. I've just tried to suppress these extra options: I get the MUMPS error in numerical factorization. At least, it make sense... Now, I added -eps_gen_non_hermitian and failed with EPS_DIVERGED_ITS. Increasing -eps_max_it does not help. So, I guess this is the end of the road. Would you consider to expose (in future release) the tolerance of this check ? Or is this something you really want to keep private ? (whatever B is or not singular - I guess in my case, this would have not helped anyway) Franck ----- Mail original ----- > De: "Jose E. Roman" <jroman(a)dsic.upv.es> > À: "Franck Houssen" <franck.houssen(a)inria.fr> > Cc: "For users of the development version of PETSc" <petsc-dev(a)mcs.anl.gov> > Envoyé: Lundi 30 Octobre 2017 18:11:48 > Objet: Re: [petsc-dev] SLEPc failure > > I am getting a MUMPS error in numerical factorization... > Anyway, your B matrix is singular, with a high-dimensional nullspace. Maybe > this is producing small negative values when computing v'*B*v. > There is no way to relax the check. You should solve the problem as > non-symmetric. Or use Arpack if it works for you. > > Jose > > > > > El 30 oct 2017, a las 17:16, Franck Houssen <franck.houssen(a)inria.fr> > > escribió: > > > > I deal with domain decomposition. It was faster/easier to generate files > > with 1 proc: I guess the "dirichlet" and "neumann" matrices are the same > > in this case, so one get the same files in the end... I didn't realized > > that when I sent the files. My mistake. > > > > At my side, when I use krylovschur, SLEPc fails using 1, 2, 4, 8, ... procs > > (each proc performs a SLEPc solve that may fail or not - difficult to > > catch one). For instance, I attached data of one failed domain out of 8 (8 > > MPI procs): matrices are very close but different. Moreover, I added EPS > > logs of the same run and domain but replacing krylovschur with arpack when > > SLEPc does not fail (regarding your remark that B could be indefinite, I > > added -mat_mumps_icntl_33 1 to get the determinant). > > > > Anyway, I don't expect you spend too much time on this. My understanding is > > that there is no way to relax this check ? Correct ? > > > > Franck > > > > ----- Mail original ----- > >> De: "Jose E. Roman" <jroman(a)dsic.upv.es> > >> À: "Franck Houssen" <franck.houssen(a)inria.fr> > >> Cc: "For users of the development version of PETSc" > >> <petsc-dev(a)mcs.anl.gov> > >> Envoyé: Samedi 28 Octobre 2017 17:40:41 > >> Objet: Re: [petsc-dev] SLEPc failure > >> > >> The two matrices are the same ... > >> > >>> El 28 oct 2017, a las 13:11, Franck Houssen <franck.houssen(a)inria.fr> > >>> escribió: > >>> > >>> I just added that before EPSSetOperators: > >>> PetscViewer viewerA; > >>> PetscViewerBinaryOpen(PETSC_COMM_WORLD,"Atau.out",FILE_MODE_WRITE,&viewerA); > >>> MatView(A,viewerA); > >>> PetscViewer viewerB; > >>> PetscViewerBinaryOpen(PETSC_COMM_WORLD,"Btau.out",FILE_MODE_WRITE,&viewerB); > >>> MatView(B,viewerB); > >>> > >>> At first, I avoided binary as I didn't know if the format handles > >>> big/little endianness... So I prefered ASCII. > >>> > >>> Binary data are attached. > >>> > >>> Franck > >>> > >>> PS : running debian with little endian. > >>>>> python -c "import sys;print(0 if sys.byteorder=='big' else 1)" > >>> 1 > >>> > >>> > >>> ----- Mail original ----- > >>>> De: "Jose E. Roman" <jroman(a)dsic.upv.es> > >>>> À: "Franck Houssen" <franck.houssen(a)inria.fr> > >>>> Cc: "For users of the development version of PETSc" > >>>> <petsc-dev(a)mcs.anl.gov> > >>>> Envoyé: Vendredi 27 Octobre 2017 18:52:56 > >>>> Objet: Re: [petsc-dev] SLEPc failure > >>>> > >>>> I cannot load the files you sent. Please send the matrices in binary > >>>> format. > >>>> The easiest way is to run your program with -eps_view_mat0 > >>>> binary:Atau.bin > >>>> -eps_view_mat1 binary:Btau.bin > >>>> > >>>> However, the files are written at the end of EPSSolve() so if the solve > >>>> fails > >>>> then it will not create the files. You can try running with -eps_max_it > >>>> 1 > >>>> or add code in your main program to write the matrices. > >>>> > >>>> Jose > >>>> > >>>> > >>>>> El 27 oct 2017, a las 12:28, Franck Houssen <franck.houssen(a)inria.fr> > >>>>> escribió: > >>>>> > >>>>> Maybe could be convenient for the users to have an option (or an > >>>>> EPSSetXXX) > >>>>> to relax that check ? > >>>>> Data are attached. > >>>>> > >>>>> Franck > >>>>> > >>>>> ----- Mail original ----- > >>>>>> De: "Jose E. Roman" <jroman(a)dsic.upv.es> > >>>>>> À: "Franck Houssen" <franck.houssen(a)inria.fr> > >>>>>> Cc: "For users of the development version of PETSc" > >>>>>> <petsc-dev(a)mcs.anl.gov> > >>>>>> Envoyé: Vendredi 27 Octobre 2017 10:15:44 > >>>>>> Objet: Re: [petsc-dev] SLEPc failure > >>>>>> > >>>>>> There is no new option. What I mean is that from 3.7 to 3.8 we changed > >>>>>> the > >>>>>> line that produces this error. But it seems that it is still failing > >>>>>> in > >>>>>> your > >>>>>> problem. Maybe your B matrix is indefinite or not exactly symmetric. > >>>>>> Can > >>>>>> you > >>>>>> send me the matrices? > >>>>>> Jose > >>>>>> > >>>>>>> El 27 oct 2017, a las 9:57, Franck Houssen <franck.houssen(a)inria.fr> > >>>>>>> escribió: > >>>>>>> > >>>>>>> I use the development version (bitbucket clone). How to relax the > >>>>>>> check > >>>>>>> ? > >>>>>>> At command line option ? > >>>>>>> > >>>>>>> Franck > >>>>>>> > >>>>>>> ----- Mail original ----- > >>>>>>>> De: "Jose E. Roman" <jroman(a)dsic.upv.es> > >>>>>>>> À: "Franck Houssen" <franck.houssen(a)inria.fr> > >>>>>>>> Cc: "For users of the development version of PETSc" > >>>>>>>> <petsc-dev(a)mcs.anl.gov> > >>>>>>>> Envoyé: Jeudi 26 Octobre 2017 18:49:22 > >>>>>>>> Objet: Re: [petsc-dev] SLEPc failure > >>>>>>>> > >>>>>>>> > >>>>>>>>> El 26 oct 2017, a las 18:36, Franck Houssen > >>>>>>>>> <franck.houssen(a)inria.fr> > >>>>>>>>> escribió: > >>>>>>>>> > >>>>>>>>> Here is a stack I end up with when trying to solve an eigen problem > >>>>>>>>> (real, > >>>>>>>>> sym, generalized) with SLEPc. My understanding is that, during the > >>>>>>>>> Gram > >>>>>>>>> Schmidt orthogonalisation, the projection of one basis vector turns > >>>>>>>>> out > >>>>>>>>> to > >>>>>>>>> be null. > >>>>>>>>> First, is this correct ? Second, in such cases, are there some > >>>>>>>>> recommended > >>>>>>>>> "recipe" to test/try (options) to get a clue on the problem ? (I > >>>>>>>>> would > >>>>>>>>> unfortunately perfectly understand the answer could be no !... As > >>>>>>>>> this > >>>>>>>>> totally depends on A/B). > >>>>>>>>> > >>>>>>>>> With arpack, the eigen problem is solved (so the matrix A and B I > >>>>>>>>> use > >>>>>>>>> seems > >>>>>>>>> to be relevant). But, when I change from arpack to > >>>>>>>>> krylovschur/ciss/arnoldi, I get the stack below. > >>>>>>>>> > >>>>>>>>> Franck > >>>>>>>>> > >>>>>>>>> [0]PETSC ERROR: #1 BV_SafeSqrt() > >>>>>>>>> [0]PETSC ERROR: #2 BVNorm_Private() > >>>>>>>>> [0]PETSC ERROR: #3 BVNormColumn() > >>>>>>>>> [0]PETSC ERROR: #4 BV_NormVecOrColumn() > >>>>>>>>> [0]PETSC ERROR: #5 BVOrthogonalizeCGS1() > >>>>>>>>> [0]PETSC ERROR: #6 BVOrthogonalizeGS() > >>>>>>>>> [0]PETSC ERROR: #7 BVOrthonormalizeColumn() > >>>>>>>>> [0]PETSC ERROR: #8 EPSFullLanczos() > >>>>>>>>> [0]PETSC ERROR: #9 EPSSolve_KrylovSchur_Symm() > >>>>>>>>> [0]PETSC ERROR: #10 EPSSolve() > >>>>>>>> > >>>>>>>> Is this with SLEPc 3.8? In SLEPc 3.8 we relaxed this check so I > >>>>>>>> would > >>>>>>>> suggest > >>>>>>>> trying with it. > >>>>>>>> Jose > >>>>>>>> > >>>>>>>> > >>>>>> > >>>>>> > >>>>> <ABtau.tar.gz> > >>>> > >>>> > >>> <ABtau.tar.gz> > >> > >> > > <slepc.tar.gz> > >

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Re: [petsc-dev] PetscSF in Fortran
by Smith, Barry F. 31 Oct '17

31 Oct '17

Adrian, I fixed some bugs but apparently broke something at the same time. At a meeting now, maybe you could use -start_in_debugger and get the traceback where it crashes for you? Barry > On Oct 30, 2017, at 5:21 PM, Adrian Croucher <a.croucher(a)auckland.ac.nz> wrote: > > hi, > > I just pulled the latest next branch and found that the PetscSF stuff doesn't appear to work in Fortran anymore for me. > > When I run the ex1f example it gives: > > [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 erro > rs > [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] PetscSFBcastBegin_Basic line 922 /home/acro018/software/PETSc/code/src/vec/is/sf/impl > s/basic/sfbasic.c > [0]PETSC ERROR: [0] PetscSFBcastBegin line 972 /home/acro018/software/PETSc/code/src/vec/is/sf/interface/ > sf.c > [0]PETSC ERROR: --------------------- Error Message ----------------------------------------------------- > > And the same thing happens with my own code. > > Should this example still work? Or is there something else I need to do? > > I did make allfortranstubs and make. > > - Adrian > > -- > Dr Adrian Croucher > Senior Research Fellow > Department of Engineering Science > University of Auckland, New Zealand > email: a.croucher(a)auckland.ac.nz > tel: +64 (0)9 923 4611 >

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