On Dec 14, 2011, at 9:45 AM, M.Younas wrote:
> Dear Barry,
>
> Does BoomeAMG precondition (one v-cycle) the system after every iteration of
> GMRES(m)
It is not "after" every iteration of GMRES it is "as part of each iteration"
of preconditioned GMRES.
> OR
> it precondition the linear system once only and then GMRES(m) iterations
> until convergence is reached?
>
No.
You may want to read up on Krylov methods in a numerical analysis book.
Barry
> Kind regards, Younas
>
>
> On 14-12-11, petsc-users-request at mcs.anl.gov wrote:
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>> Today's Topics:
>>
>> 1. run successfully on 20 processors but failed on 24
>> processors (Xiangdong Liang)
>> 2. Re: run successfully on 20 processors but failed on 24
>> processors (Matthew Knepley)
>> 3. Two Questions about Matrix Preallocation (behzad baghapour)
>> 4. Multigrid as preconditioner (M.Younas)
>> 5. save vector to bin-file at each time step (robert)
>> 6. AMG as preconditioner (M.Younas)
>> 7. Re: Two Questions about Matrix Preallocation (Barry Smith)
>> 8. Re: Multigrid as preconditioner (Barry Smith)
>> 9. Re: save vector to bin-file at each time step (Barry Smith)
>> 10. Re: save vector to bin-file at each time step (robert)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Tue, 13 Dec 2011 22:49:40 -0500
>> From: Xiangdong Liang <xdliang at gmail.com>
>> Subject: [petsc-users] run successfully on 20 processors but failed on
>> 24 processors
>> To: PETSc users list <petsc-users at mcs.anl.gov>
>> Message-ID:
>> <CAGzjfYZMW3dY7-PDH8AReAnQRuUVC0W6Jtbfu-ETMTc5JaopcQ at mail.gmail.com>
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> Hello everyone,
>>
>> I am solving complex Ax=b with PaStix on 20 processors successfully
>> but failed on 24 processors. The relatively error indicated by
>> mat_pastix_verbose becomes "nan" for 24 processors. Where could be
>> wrong? Can someone give me some hints on how I can debug? Thanks.
>>
>> Xiangdong
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Tue, 13 Dec 2011 22:59:09 -0600
>> From: Matthew Knepley <knepley at gmail.com>
>> Subject: Re: [petsc-users] run successfully on 20 processors but
>> failed on 24 processors
>> To: PETSc users list <petsc-users at mcs.anl.gov>
>> Message-ID:
>> <CAMYG4Gm_fnVMEpks_wt07_fg8PF3q-oCNAzw4U1G48JTJVwvPA at mail.gmail.com>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> On Tue, Dec 13, 2011 at 9:49 PM, Xiangdong Liang <xdliang at gmail.com>
>> wrote:
>>
>> > Hello everyone,
>> >
>> > I am solving complex Ax=b with PaStix on 20 processors successfully
>> > but failed on 24 processors. The relatively error indicated by
>> > mat_pastix_verbose becomes "nan" for 24 processors. Where could be
>> > wrong? Can someone give me some hints on how I can debug? Thanks.
>>
>>
>> First, make sure you did not put any NaNs in your matrix or rhs.
>>
>> Matt
>>
>>
>> >
>> > Xiangdong
>>
>> --
>> 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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>>
>> ------------------------------
>>
>> Message: 3
>> Date: Wed, 14 Dec 2011 11:32:48 +0330
>> From: behzad baghapour <behzad.baghapour at gmail.com>
>> Subject: [petsc-users] Two Questions about Matrix Preallocation
>> To: PETSc users list <petsc-users at mcs.anl.gov>
>> Message-ID:
>> <CA+jOtDLYQy-2Xt8UsvNdnZySbqNBQTwyFi5vrp39=6j9hagD0Q at mail.gmail.com>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Dear Developers,
>>
>> I am facing with two questions about Block-Sparse Preallocation:
>>
>> 1- I set array "nnz[]" and did:
>>
>> MatSetType ( JAC, MATSEQBAIJ );
>> MatSetSizes( JAC, PETSC_DECIDE, PETSC_DECIDE, nt, nt );
>> MatSeqAIJSetPreallocation( JAC, 0, nnz );
>>
>> but when I saw log file with -info -mat_view_info, I found this message:
>>
>> [0] MatSetUpPreallocation(): Warning not preallocating matrix storage
>>
>> What this means? Did I correctly preallocate the matrix?
>>
>> 2- I need to test MatSeqBAIJSetPreallocation() too but I little confused
>> with descriptions of the command in man-page:
>>
>> what are "nz" and "nnz[]" in this case?
>>
>> what about number of blocks per row?
>>
>> Thanks bothering too much :-)
>> BehZad
>> -------------- next part --------------
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>>
>> ------------------------------
>>
>> Message: 4
>> Date: Wed, 14 Dec 2011 14:07:10 +0100
>> From: "M.Younas" <m.younas at rug.nl>
>> Subject: [petsc-users] Multigrid as preconditioner
>> To: petsc-users at mcs.anl.gov
>> Message-ID: <73f0f8e5cc491.4ee8ad8e at rug.nl>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> ?Hi, PETSc, Team,
>>
>> I have solved a non-symmetric Poisson problem using GMRES(m) as solver and
>> BoomerAMG (from Hypre) as preconditioner. But I don't understand how the
>> BoomerAMG works as preconditioner with GMRES(m). Can anyone explain the
>> procedure? Does it work like BoomerAMG precondition the liner system first
>> (once only) and then GMRES(m) is being used for stopping criterion?
>>
>> Kind regards,
>>
>> Younas
>>
>> RUG, Groningen, The Netherlands.
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
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>>
>> ------------------------------
>>
>> Message: 5
>> Date: Wed, 14 Dec 2011 15:00:03 +0100
>> From: robert <robert.bodner at unil.ch>
>> Subject: [petsc-users] save vector to bin-file at each time step
>> To: petsc-users at mcs.anl.gov
>> Message-ID: <4EE8ABE3.5050108 at unil.ch>
>> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>>
>> Hello,
>>
>> I am quite new to petsc and therefore my question might be quite trivial.
>>
>> I have a 1D finite difference code and want to store several vectors in
>> a binary:
>>
>> ierr = PetscViewerCreate(PETSC_COMM_WORLD,&viewer);CHKERRQ(ierr);
>> ierr =
>> PetscViewerBinaryOpen(PETSC_COMM_WORLD,"out.bin",FILE_MODE_APPEND,&viewer);
>> CHKERRQ(ierr);
>> ierr = PetscObjectSetName((PetscObject)u,"u");CHKERRQ(ierr);
>> ierr = PetscObjectSetName((PetscObject)rhs,"rhs");CHKERRQ(ierr);
>> ierr = VecView(u,viewer); CHKERRQ(ierr);
>> ierr = VecView(rhs,viewer);CHKERRQ(ierr);
>>
>> However, when I read the file with matlab (PetscBinaryRead.m) I only get
>> the first vector.
>>
>> In further application I would like to use something similar but putting
>> out the solution vector every timestep.
>>
>> Could someone just provide me some sample code?
>>
>> Thanks,
>> Robert
>>
>>
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
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>>
>> ------------------------------
>>
>> Message: 6
>> Date: Wed, 14 Dec 2011 15:04:47 +0100
>> From: "M.Younas" <m.younas at rug.nl>
>> Subject: [petsc-users] AMG as preconditioner
>> To: petsc-users at mcs.anl.gov
>> Message-ID: <7420f1bdca4d2.4ee8bb0f at rug.nl>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> ?Hi, PETSc, Team,
>>
>> I have
>> solved a non-symmetric Poisson problem using GMRES(m) as solver and
>> BoomerAMG (from Hypre) as preconditioner. But I don't understand how the
>> BoomerAMG works as preconditioner with GMRES(m). Can anyone explain the
>> procedure? Does it work like BoomerAMG precondition the liner system
>> first (once only) and then GMRES(m) is being used for stopping
>> criterion?
>>
>> Kind regards,
>>
>> Younas
>>
>> RUG, Groningen, The Netherlands.
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL:
>> <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20111214/70b57dea/attachment-0001.htm>
>>
>> ------------------------------
>>
>> Message: 7
>> Date: Wed, 14 Dec 2011 08:22:33 -0600
>> From: Barry Smith <bsmith at mcs.anl.gov>
>> Subject: Re: [petsc-users] Two Questions about Matrix Preallocation
>> To: PETSc users list <petsc-users at mcs.anl.gov>, behzad baghapour
>> <behzad.baghapour at gmail.com>
>> Message-ID: <CF31FC30-6E95-4F0E-AA13-6D7260172041 at mcs.anl.gov>
>> Content-Type: text/plain; charset=us-ascii
>>
>>
>> On Dec 14, 2011, at 2:02 AM, behzad baghapour wrote:
>>
>> > Dear Developers,
>> >
>> > I am facing with two questions about Block-Sparse Preallocation:
>> >
>> > 1- I set array "nnz[]" and did:
>> >
>> > MatSetType ( JAC, MATSEQBAIJ );
>> > MatSetSizes( JAC, PETSC_DECIDE, PETSC_DECIDE, nt, nt );
>> > MatSeqAIJSetPreallocation( JAC, 0, nnz );
>> >
>> > but when I saw log file with -info -mat_view_info, I found this message:
>> >
>> > [0] MatSetUpPreallocation(): Warning not preallocating matrix storage
>>
>> Since you are using BAIJ matrix type you need to also call
>> MatSeqBAIJSetPreallocation()
>>
>> >
>> > What this means? Did I correctly preallocate the matrix?
>> >
>> > 2- I need to test MatSeqBAIJSetPreallocation() too but I little confused
>> > with descriptions of the command in man-page:
>> >
>> > what are "nz" and "nnz[]" in this case?
>> >
>> > what about number of blocks per row?
>>
>> nz is the maximum number of blocks per row, just like with other matrix
>> formats or you can set nnz[] which for each row is the number of blocks from
>> the diagonal block to the end of the row. For example with a block size of
>> one the matrix
>>
>> 1 0 2
>> 0 3 4
>> 2 4 5
>>
>> would have a nnz[] = 2,2,1
>>
>> Barry
>>
>> >
>> > Thanks bothering too much :-)
>> > BehZad
>> >
>>
>>
>>
>> ------------------------------
>>
>> Message: 8
>> Date: Wed, 14 Dec 2011 08:26:27 -0600
>> From: Barry Smith <bsmith at mcs.anl.gov>
>> Subject: Re: [petsc-users] Multigrid as preconditioner
>> To: PETSc users list <petsc-users at mcs.anl.gov>
>> Message-ID: <2770E217-0CC1-4E85-AB40-35B00F705D53 at mcs.anl.gov>
>> Content-Type: text/plain; charset=us-ascii
>>
>>
>> On Dec 14, 2011, at 7:07 AM, M.Younas wrote:
>>
>> > Hi, PETSc, Team,
>> >
>> > I have solved a non-symmetric Poisson problem using GMRES(m) as solver and
>> > BoomerAMG (from Hypre) as preconditioner. But I don't understand how the
>> > BoomerAMG works as preconditioner with GMRES(m). Can anyone explain the
>> > procedure? Does it work like BoomerAMG precondition the liner system first
>> > (once only) and then GMRES(m) is being used for stopping criterion?
>>
>> By default PETSc uses ONE v-cycle of the BoomerAMG as a preconditioner
>> for GMRES.
>>
>> With the option -ksp_type richardson then PETSc is using a bunch of
>> BoomerAMG v-cycles until the convergence criteria is satisfied without using
>> a GMRES
>>
>> Barry
>>
>> Note that a preconditioner can be any stationary linear iterative scheme.
>> That is any linear operation that approximately solves A x = b, no matter
>> how complicated the stationary linear iterative scheme is it can be used as
>> a preconditioner.
>>
>>
>> >
>> > Kind regards,
>> >
>> > Younas
>> >
>> > RUG, Groningen, The Netherlands.
>>
>>
>>
>> ------------------------------
>>
>> Message: 9
>> Date: Wed, 14 Dec 2011 08:32:58 -0600
>> From: Barry Smith <bsmith at mcs.anl.gov>
>> Subject: Re: [petsc-users] save vector to bin-file at each time step
>> To: PETSc users list <petsc-users at mcs.anl.gov>
>> Message-ID: <76717B20-13EF-4FD2-BF50-CC12E9E87842 at mcs.anl.gov>
>> Content-Type: text/plain; charset=us-ascii
>>
>>
>> On Dec 14, 2011, at 8:00 AM, robert wrote:
>>
>> > Hello,
>> >
>> > I am quite new to petsc and therefore my question might be quite trivial.
>> >
>> > I have a 1D finite difference code and want to store several vectors in a
>> > binary:
>> >
>> > ierr = PetscViewerCreate(PETSC_COMM_WORLD,&viewer);CHKERRQ(ierr);
>> > ierr =
>> > PetscViewerBinaryOpen(PETSC_COMM_WORLD,"out.bin",FILE_MODE_APPEND,&viewer);
>> > CHKERRQ(ierr);
>> > ierr = PetscObjectSetName((PetscObject)u,"u");CHKERRQ(ierr);
>> > ierr = PetscObjectSetName((PetscObject)rhs,"rhs");CHKERRQ(ierr);
>> > ierr = VecView(u,viewer); CHKERRQ(ierr);
>> > ierr = VecView(rhs,viewer);CHKERRQ(ierr);
>> >
>> > However, when I read the file with matlab (PetscBinaryRead.m) I only get
>> > the first vector.
>>
>> 1) Did you call PetscViewerDestroy() before the end of the program? If
>> not called all the data may not be flushed into the file.
>>
>> 2) How are you reading the vectors into Matlab? For example [u,rhs] =
>> PetscBinaryRead('filename') will read in two vectors. If you want to call
>> PetscBinaryRead() repeatedly to read more information than read the help for
>> PetscBinaryRead() carefully, you cannot simply call u =
>> PetscBinaryRead('filename'); rhs = PetscBinaryRead('filename') and hope to
>> get the second vector
>>
>> For example: fd = PetscOpenFile('filename');
>> u = PetscBinaryRead(fd); % get first vector
>> rhs = PetscBinaryRead(fd); % get second vector
>>
>> Barry
>>
>>
>> >
>> > In further application I would like to use something similar but putting
>> > out the solution vector every timestep.
>> >
>> > Could someone just provide me some sample code?
>> >
>> > Thanks,
>> > Robert
>> >
>> >
>>
>>
>>
>> ------------------------------
>>
>> Message: 10
>> Date: Wed, 14 Dec 2011 15:44:39 +0100
>> From: robert <robert.bodner at unil.ch>
>> Subject: Re: [petsc-users] save vector to bin-file at each time step
>> To: PETSc users list <petsc-users at mcs.anl.gov>
>> Message-ID: <4EE8B657.4090506 at unil.ch>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> On 12/14/2011 03:32 PM, Barry Smith wrote:
>> > On Dec 14, 2011, at 8:00 AM, robert wrote:
>> >
>> >> Hello,
>> >>
>> >> I am quite new to petsc and therefore my question might be quite trivial.
>> >>
>> >> I have a 1D finite difference code and want to store several vectors in a
>> >> binary:
>> >>
>> >> ierr = PetscViewerCreate(PETSC_COMM_WORLD,&viewer);CHKERRQ(ierr);
>> >> ierr =
>> >> PetscViewerBinaryOpen(PETSC_COMM_WORLD,"out.bin",FILE_MODE_APPEND,&viewer);
>> >> CHKERRQ(ierr);
>> >> ierr = PetscObjectSetName((PetscObject)u,"u");CHKERRQ(ierr);
>> >> ierr = PetscObjectSetName((PetscObject)rhs,"rhs");CHKERRQ(ierr);
>> >> ierr = VecView(u,viewer); CHKERRQ(ierr);
>> >> ierr = VecView(rhs,viewer);CHKERRQ(ierr);
>> >>
>> >> However, when I read the file with matlab (PetscBinaryRead.m) I only get
>> >> the first vector.
>> >>
>> >>
>> >> 2) How are you reading the vectors into Matlab? For example [u,rhs]
>> >> = PetscBinaryRead('filename') will read in two vectors. If you want to
>> >> call PetscBinaryRead() repeatedly to read more information than ...
>>
>> Hi,
>>
>> thank you for your fast reply. It's as easy as that and I spent hours
>> ... :-)
>> >>
>>
>>
>> >> In further application I would like to use something similar but putting
>> >> out the solution vector every timestep.
>> >>
>> >> Could someone just provide me some sample code?
>> >>
>> >> Thanks,
>> >> Robert
>> >>
>> >>
>> >
>>
>>
>>
>> ------------------------------
>>
>> _______________________________________________
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>> petsc-users at mcs.anl.gov
>> https://lists.mcs.anl.gov/mailman/listinfo/petsc-users
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>>
>> End of petsc-users Digest, Vol 36, Issue 50
>> *******************************************
