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" <jro...@dsic.upv.es> > À: "Franck Houssen" <franck.hous...@inria.fr> > Cc: "For users of the development version of PETSc" <petsc-dev@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/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 <franck.hous...@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)); > >