July 2012 - petsc-dev - mailman3.cels.anl.gov

Re: [petsc-dev] downtime for petsc.cs.iit.edu
by Jed Brown 19 Jul '12

19 Jul '12

Still down. Does anyone know how long the power outage was expected to take? On Thu, Jul 19, 2012 at 12:06 AM, Satish Balay <balay(a)mcs.anl.gov> wrote: > There is a scheduled power outage at IIT for early morning [5am] of > 19th. I believe some of the labs are switching off hardware in > anticipation of this outage. > > petsc.cs.iit.edu is unreachable now. I expect it to come back up in > the morning. [when power is restored after the outage] > > Satish > > >

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downtime for petsc.cs.iit.edu
by Satish Balay 19 Jul '12

19 Jul '12

There is a scheduled power outage at IIT for early morning [5am] of 19th. I believe some of the labs are switching off hardware in anticipation of this outage. petsc.cs.iit.edu is unreachable now. I expect it to come back up in the morning. [when power is restored after the outage] Satish

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Re: [petsc-dev] where is type(Mat) defined?
by Satish Balay 18 Jul '12

18 Jul '12

sorry forgot to push petsc-3.3. Its pushed now. Satish On Wed, 18 Jul 2012, Blaise Bourdin wrote: > Satish, > > Sorry for the typo. Actually I think that you committed to petsc-dev and not 3.3 > > Blaise > > On Jul 18, 2012, at 5:00 PM, Satish Balay wrote: > > > I've changed the filename to 'zmatnullf.c' - per convention - and > > commited to petsc-3.3 [and merged to petsc-dev] > > > > Satish > > > > On Wed, 18 Jul 2012, Barry Smith wrote: > > > >> > >> Satish, > >> > >> Please apply this patch if it makes sense. > >> > >> Thanks > >> > >> Barry > >> > >> On Jul 17, 2012, at 11:25 PM, Blaise Bourdin wrote: > >> > >>> > >>> On Jul 17, 2012, at 10:51 PM, Barry Smith wrote: > >>> > >>>> > >>>> If you are using Fortran modules (and being a FORTRAN lover you are :-). Then you have to rebuild the modules whenever you change these files. Do make cmake after you edit the file > >>> > >>> You bet I am... > >>> make cmake is what I was missing. > >>> > >>> Is it possible to apply the attached patch to petsc-3.3 and petsc-dev? > >>> It adds the data type, and the fortran binding for MatNullSpaceView. > >>> > >>> Blaise > >>> > >>> <MatNullSpace.patch> > >>> > >>>> > >>>> Barry > >>>> > >>>> On Jul 17, 2012, at 10:41 PM, Blaise Bourdin wrote: > >>>> > >>>>> Hi, > >>>>> > >>>>> I am still trying to figure out how to add support for MatNullSpace with fortran data types. As I said in a previous email, adding the statement > >>>>> type MatNullSpace > >>>>> PetscFortranAddr:: v > >>>>> end type MatNullSpace > >>>>> in include/finclude/ftn-custom/petscmatdef.h90 > >>>>> > >>>>> is not enough. > >>>>> > >>>>> Furthermore, if I remove the corresponding statement > >>>>> type Mat > >>>>> PetscFortranAddr:: v > >>>>> end type Mat > >>>>> for Mat, I can still compile code with a statement like > >>>>> Type(Mat) :: M > >>>>> > >>>>> It looks like the fortran data type for Mat is defined somewhere else, but I can't figure out where. Can anybody shine some light for me? > >>>>> > >>>>> 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 > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>> > >>> > >>> -- > >>> 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] where is type(Mat) defined?
by Blaise Bourdin 18 Jul '12

18 Jul '12

Satish, Sorry for the typo. Actually I think that you committed to petsc-dev and not 3.3 Blaise On Jul 18, 2012, at 5:00 PM, Satish Balay wrote: > I've changed the filename to 'zmatnullf.c' - per convention - and > commited to petsc-3.3 [and merged to petsc-dev] > > Satish > > On Wed, 18 Jul 2012, Barry Smith wrote: > >> >> Satish, >> >> Please apply this patch if it makes sense. >> >> Thanks >> >> Barry >> >> On Jul 17, 2012, at 11:25 PM, Blaise Bourdin wrote: >> >>> >>> On Jul 17, 2012, at 10:51 PM, Barry Smith wrote: >>> >>>> >>>> If you are using Fortran modules (and being a FORTRAN lover you are :-). Then you have to rebuild the modules whenever you change these files. Do make cmake after you edit the file >>> >>> You bet I am... >>> make cmake is what I was missing. >>> >>> Is it possible to apply the attached patch to petsc-3.3 and petsc-dev? >>> It adds the data type, and the fortran binding for MatNullSpaceView. >>> >>> Blaise >>> >>> <MatNullSpace.patch> >>> >>>> >>>> Barry >>>> >>>> On Jul 17, 2012, at 10:41 PM, Blaise Bourdin wrote: >>>> >>>>> Hi, >>>>> >>>>> I am still trying to figure out how to add support for MatNullSpace with fortran data types. As I said in a previous email, adding the statement >>>>> type MatNullSpace >>>>> PetscFortranAddr:: v >>>>> end type MatNullSpace >>>>> in include/finclude/ftn-custom/petscmatdef.h90 >>>>> >>>>> is not enough. >>>>> >>>>> Furthermore, if I remove the corresponding statement >>>>> type Mat >>>>> PetscFortranAddr:: v >>>>> end type Mat >>>>> for Mat, I can still compile code with a statement like >>>>> Type(Mat) :: M >>>>> >>>>> It looks like the fortran data type for Mat is defined somewhere else, but I can't figure out where. Can anybody shine some light for me? >>>>> >>>>> 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 >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>> >>> -- >>> 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 >>> >>> >>> >>> >>> >>> >>> >> >> > -- 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] where is type(Mat) defined?
by Satish Balay 18 Jul '12

18 Jul '12

I've changed the filename to 'zmatnullf.c' - per convention - and commited to petsc-3.3 [and merged to petsc-dev] Satish On Wed, 18 Jul 2012, Barry Smith wrote: > > Satish, > > Please apply this patch if it makes sense. > > Thanks > > Barry > > On Jul 17, 2012, at 11:25 PM, Blaise Bourdin wrote: > > > > > On Jul 17, 2012, at 10:51 PM, Barry Smith wrote: > > > >> > >> If you are using Fortran modules (and being a FORTRAN lover you are :-). Then you have to rebuild the modules whenever you change these files. Do make cmake after you edit the file > > > > You bet I am... > > make cmake is what I was missing. > > > > Is it possible to apply the attached patch to petsc-3.3 and petsc-dev? > > It adds the data type, and the fortran binding for MatNullSpaceView. > > > > Blaise > > > > <MatNullSpace.patch> > > > >> > >> Barry > >> > >> On Jul 17, 2012, at 10:41 PM, Blaise Bourdin wrote: > >> > >>> Hi, > >>> > >>> I am still trying to figure out how to add support for MatNullSpace with fortran data types. As I said in a previous email, adding the statement > >>> type MatNullSpace > >>> PetscFortranAddr:: v > >>> end type MatNullSpace > >>> in include/finclude/ftn-custom/petscmatdef.h90 > >>> > >>> is not enough. > >>> > >>> Furthermore, if I remove the corresponding statement > >>> type Mat > >>> PetscFortranAddr:: v > >>> end type Mat > >>> for Mat, I can still compile code with a statement like > >>> Type(Mat) :: M > >>> > >>> It looks like the fortran data type for Mat is defined somewhere else, but I can't figure out where. Can anybody shine some light for me? > >>> > >>> 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 > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >> > > > > -- > > 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] where is type(Mat) defined?
by Barry Smith 18 Jul '12

18 Jul '12

Satish, Please apply this patch if it makes sense. Thanks Barry On Jul 17, 2012, at 11:25 PM, Blaise Bourdin wrote: > > On Jul 17, 2012, at 10:51 PM, Barry Smith wrote: > >> >> If you are using Fortran modules (and being a FORTRAN lover you are :-). Then you have to rebuild the modules whenever you change these files. Do make cmake after you edit the file > > You bet I am... > make cmake is what I was missing. > > Is it possible to apply the attached patch to petsc-3.3 and petsc-dev? > It adds the data type, and the fortran binding for MatNullSpaceView. > > Blaise > > <MatNullSpace.patch> > >> >> Barry >> >> On Jul 17, 2012, at 10:41 PM, Blaise Bourdin wrote: >> >>> Hi, >>> >>> I am still trying to figure out how to add support for MatNullSpace with fortran data types. As I said in a previous email, adding the statement >>> type MatNullSpace >>> PetscFortranAddr:: v >>> end type MatNullSpace >>> in include/finclude/ftn-custom/petscmatdef.h90 >>> >>> is not enough. >>> >>> Furthermore, if I remove the corresponding statement >>> type Mat >>> PetscFortranAddr:: v >>> end type Mat >>> for Mat, I can still compile code with a statement like >>> Type(Mat) :: M >>> >>> It looks like the fortran data type for Mat is defined somewhere else, but I can't figure out where. Can anybody shine some light for me? >>> >>> 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 >>> >>> >>> >>> >>> >>> >>> >> > > -- > 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] MatMultHermitianTranspose
by Barry Smith 18 Jul '12

18 Jul '12

I am pushing to petsc-3.3 and petsc-dev for MatConjugate to be a no-op (like VecConjugate already is) in the case of complex numbers so you do not need the #ifdef below Will be there in minutes Barry On Jul 18, 2012, at 1:42 PM, Jose E. Roman wrote: > > El 18/07/2012, a las 20:07, Jed Brown escribió: > >> On Wed, Jul 18, 2012 at 11:09 AM, Jose E. Roman <jroman(a)dsic.upv.es> wrote: >> Er... well, now that I see better: it is not always safe, it will error out if mat->ops->conjugate is not available, for instance in BAIJ. >> >> There is MatMultHermitianTranspose_SeqBAIJ so that would only an issue for parallel BAIJ, but you were just going to use VecConjugate, right? In Matlab notation, A'*x = (x'*A)', so you only need VecConjugate. > > No, the problem with mat->ops->conjugate is in the "explicit" transpose case. For instance this code: > ierr = MatTranspose(svd->OP,MAT_INITIAL_MATRIX,&svd->A);CHKERRQ(ierr); > #if defined(PETSC_USE_COMPLEX) > ierr = MatConjugate(svd->A);CHKERRQ(ierr); > #endif > > You were suggesting to remove the #ifdef, right? What I was saying is that in real scalars the MatConjugate operation would fail in some matrix types (parallel BAIJ), but this operation is only necessary in complex scalars. So I will not remove the #ifdef > > Jose >

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Re: [petsc-dev] MatMultHermitianTranspose
by Jose E. Roman 18 Jul '12

18 Jul '12

El 18/07/2012, a las 20:07, Jed Brown escribió: > On Wed, Jul 18, 2012 at 11:09 AM, Jose E. Roman <jroman(a)dsic.upv.es> wrote: > Er... well, now that I see better: it is not always safe, it will error out if mat->ops->conjugate is not available, for instance in BAIJ. > > There is MatMultHermitianTranspose_SeqBAIJ so that would only an issue for parallel BAIJ, but you were just going to use VecConjugate, right? In Matlab notation, A'*x = (x'*A)', so you only need VecConjugate. No, the problem with mat->ops->conjugate is in the "explicit" transpose case. For instance this code: ierr = MatTranspose(svd->OP,MAT_INITIAL_MATRIX,&svd->A);CHKERRQ(ierr); #if defined(PETSC_USE_COMPLEX) ierr = MatConjugate(svd->A);CHKERRQ(ierr); #endif You were suggesting to remove the #ifdef, right? What I was saying is that in real scalars the MatConjugate operation would fail in some matrix types (parallel BAIJ), but this operation is only necessary in complex scalars. So I will not remove the #ifdef Jose

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Re: [petsc-dev] MatMultHermitianTranspose
by Jed Brown 18 Jul '12

18 Jul '12

On Wed, Jul 18, 2012 at 11:09 AM, Jose E. Roman <jroman(a)dsic.upv.es> wrote: > Er... well, now that I see better: it is not always safe, it will error > out if mat->ops->conjugate is not available, for instance in BAIJ. There is MatMultHermitianTranspose_SeqBAIJ so that would only an issue for parallel BAIJ, but you were just going to use VecConjugate, right? In Matlab notation, A'*x = (x'*A)', so you only need VecConjugate.

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Re: [petsc-dev] MatMultHermitianTranspose
by Jose E. Roman 18 Jul '12

18 Jul '12

El 18/07/2012, a las 18:05, Jose E. Roman escribió: >> >> Also, I notice this in your current code. It is always safe to call MatConjugate(), the function will just do nothing if not using complex. > > I see. Thanks. Er... well, now that I see better: it is not always safe, it will error out if mat->ops->conjugate is not available, for instance in BAIJ. Jose

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