Dear Barry, Does BoomeAMG precondition (one v-cycle) the system after every iteration of GMRES(m) OR it precondition the linear system once only and then GMRES(m) iterations until convergence is reached?
Kind regards, Younas ? On 14-12-11, petsc-users-request at mcs.anl.gov wrote: > Send petsc-users mailing list submissions to > petsc-users at mcs.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.mcs.anl.gov/mailman/listinfo/petsc-users > or, via email, send a message with subject or body 'help' to > petsc-users-request at mcs.anl.gov > > You can reach the person managing the list at > petsc-users-owner at mcs.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of petsc-users digest..." > > > 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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20111213/339c4743/attachment-0001.htm> > > ------------------------------ > > 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 -------------- > An HTML attachment was scrubbed... > URL: > <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20111214/abec449b/attachment-0001.htm> > > ------------------------------ > > 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... > URL: > <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20111214/684a66f7/attachment-0001.htm> > > ------------------------------ > > 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... > URL: > <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20111214/5a31167d/attachment-0001.htm> > > ------------------------------ > > 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 > >> > >> > > > > > > ------------------------------ > > _______________________________________________ > petsc-users mailing list > petsc-users at mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/petsc-users > > > End of petsc-users Digest, Vol 36, Issue 50 > ******************************************* > > -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20111214/8446d198/attachment-0001.htm>
