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 <[email protected]> > 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" <[email protected]> >> À: "Franck Houssen" <[email protected]> >> Cc: "For users of the development version of PETSc" <[email protected]> >> 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/BVOrthogonalize.html >> http://slepc.upv.es/documentation/current/docs/manualpages/BV/BVOrthogBlockType.html >> >> 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 <[email protected]> >>> 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)); >> >>
