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

Re: [petsc-dev] error reading binary file
by Jed Brown 12 Jun '12

12 Jun '12

On Tue, Jun 12, 2012 at 4:06 PM, Mark F. Adams <mark.adams(a)columbia.edu>wrote: > There is a vector load, at least ex10 loads a vec and its seems to work > (so I assume Blaise put one in there). Fixed here, someone can merge it to petsc-dev (I have a dirty tree and don't want to mess with it). http://petsc.cs.iit.edu/petsc/releases/petsc-3.3/rev/9e1563b28611

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Re: [petsc-dev] error reading binary file
by Mark F. Adams 12 Jun '12

12 Jun '12

On Jun 12, 2012, at 4:56 PM, Jed Brown wrote: > On Tue, Jun 12, 2012 at 3:54 PM, Mark F. Adams <mark.adams(a)columbia.edu> wrote: > How is what? The ex10 code or "I set the block size for matrices before SetFromOptions". > > This how I create matrices with blocks sizes: > > ierr = MatCreate( wcomm, &Prol ); CHKERRQ(ierr); > ierr = MatSetSizes(Prol,nloc*bs,nLocalSelected*col_bs,PETSC_DETERMINE,PETSC_DETERMINE); > CHKERRQ(ierr); > ierr = MatSetBlockSizes( Prol, bs, col_bs ); CHKERRQ(ierr); > > Sorry, I thought you were talking about vectors because the error is coming from a vector load. > There is a vector load, at least ex10 loads a vec and its seems to work (so I assume Blaise put one in there). > Where is this input file? I'll grab it sort out the issue. You can get an archive containing the KSP and the data files at https://filestogeaux.lsu.edu/public/download.php?FILE=bourdin/52338Q0at2Y These are just standard "binaryoutput" files I think, Mark

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Re: [petsc-dev] error reading binary file
by Jed Brown 12 Jun '12

12 Jun '12

On Tue, Jun 12, 2012 at 3:54 PM, Mark F. Adams <mark.adams(a)columbia.edu>wrote: > How is what? The ex10 code or "I set the block size for matrices before > SetFromOptions". > > This how I create matrices with blocks sizes: > > ierr = MatCreate( wcomm, &Prol ); CHKERRQ(ierr); > ierr = > MatSetSizes(Prol,nloc*bs,nLocalSelected*col_bs,PETSC_DETERMINE,PETSC_DETERMINE); > CHKERRQ(ierr); > ierr = MatSetBlockSizes( Prol, bs, col_bs ); CHKERRQ(ierr); > Sorry, I thought you were talking about vectors because the error is coming from a vector load. Where is this input file? I'll grab it sort out the issue.

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Re: [petsc-dev] error reading binary file
by Mark F. Adams 12 Jun '12

12 Jun '12

On Jun 12, 2012, at 4:25 PM, Jed Brown wrote: > On Tue, Jun 12, 2012 at 3:18 PM, Mark F. Adams <mark.adams(a)columbia.edu> wrote: > This is the calling sequence in ex10: > > ierr = VecCreate(PETSC_COMM_WORLD,&b);CHKERRQ(ierr); > ierr = VecSetFromOptions(b);CHKERRQ(ierr); > ierr = VecLoad(b,fd);CHKERRQ(ierr); > > I set the block size for matrices before SetFromOptions. > > How is that? You don't even know the Vec type. How is what? The ex10 code or "I set the block size for matrices before SetFromOptions". This how I create matrices with blocks sizes: ierr = MatCreate( wcomm, &Prol ); CHKERRQ(ierr); ierr = MatSetSizes(Prol,nloc*bs,nLocalSelected*col_bs,PETSC_DETERMINE,PETSC_DETERMINE); CHKERRQ(ierr); ierr = MatSetBlockSizes( Prol, bs, col_bs ); CHKERRQ(ierr);

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Re: [petsc-dev] error reading binary file
by Jed Brown 12 Jun '12

12 Jun '12

On Tue, Jun 12, 2012 at 3:18 PM, Mark F. Adams <mark.adams(a)columbia.edu>wrote: > This is the calling sequence in ex10: > > ierr = VecCreate(PETSC_COMM_WORLD,&b);CHKERRQ(ierr); > ierr = VecSetFromOptions(b);CHKERRQ(ierr); > ierr = VecLoad(b,fd);CHKERRQ(ierr); > > I set the block size for matrices before SetFromOptions. > How is that? You don't even know the Vec type.

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Re: [petsc-dev] error reading binary file
by Mark F. Adams 12 Jun '12

12 Jun '12

On Jun 12, 2012, at 4:05 PM, Matthew Knepley wrote: > On Wed, Jun 13, 2012 at 3:57 AM, Mark F. Adams <mark.adams(a)columbia.edu> wrote: > This seems to be the first call to VecSetBlockSize: > > If that were true, how could we ever change the block size for any vector? > This is the calling sequence in ex10: ierr = VecCreate(PETSC_COMM_WORLD,&b);CHKERRQ(ierr); ierr = VecSetFromOptions(b);CHKERRQ(ierr); ierr = VecLoad(b,fd);CHKERRQ(ierr); I set the block size for matrices before SetFromOptions. I never set vectors as blocked so I'm not sure _if_ anyone changes vector block size... Anyway I just deleted the vector block thing in .info and it seems to work. Thanks, Mark > Matt > > Breakpoint 1 at 0x1dbcee: file /Users/markadams/Codes/petsc-dev/src/vec/vec/interface/vector.c, line 1523. > (gdb) r > Starting program: /Users/markadams/Desktop/GAMG/ex10 -f0 binaryoutput-sym -vecload_block_size 3 > Reading symbols for shared libraries .++++++ done > > Breakpoint 1, VecSetBlockSize (v=0x18c1850, bs=3) at /Users/markadams/Codes/petsc-dev/src/vec/vec/interface/vector.c:1523 > 1523 PetscFunctionBegin; > (gdb) where > #0 VecSetBlockSize (v=0x18c1850, bs=3) at /Users/markadams/Codes/petsc-dev/src/vec/vec/interface/vector.c:1523 > #1 0x00246e6f in VecLoad_Binary (vec=0x18c1850, viewer=0x180d850) at /Users/markadams/Codes/petsc-dev/src/vec/vec/utils/vecio.c:104 > #2 0x00247c85 in VecLoad_Default (newvec=0x18c1850, viewer=0x180d850) at /Users/markadams/Codes/petsc-dev/src/vec/vec/utils/vecio.c:348 > #3 0x001d7ed8 in VecLoad (newvec=0x18c1850, viewer=0x180d850) at /Users/markadams/Codes/petsc-dev/src/vec/vec/interface/vector.c:1111 > #4 0x00003a91 in main () > (gdb) n > 1524 PetscValidHeaderSpecific(v,VEC_CLASSID,1); > (gdb) > 1525 if (bs == v->map->bs) PetscFunctionReturn(0); > (gdb) > 1526 ierr = PetscLayoutSetBlockSize(v->map,bs);CHKERRQ(ierr); > (gdb) > [0]PETSC ERROR: --------------------- Error Message ------------------------------------ > [0]PETSC ERROR: Arguments are incompatible! > [0]PETSC ERROR: Cannot change block size 1 to 3! > [0]PETSC ERROR: ------------------------------------------------------------------------ > [0]PETSC ERROR: Petsc Development HG revision: 73637941c41b51aa3e638c914e6cb05248ece8b0 HG Date: Mon Jun 11 14:55:24 2012 -0400 > [0]PETSC ERROR: See docs/changes/index.html for recent updates. > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > [0]PETSC ERROR: See docs/index.html for manual pages. > [0]PETSC ERROR: ------------------------------------------------------------------------ > [0]PETSC ERROR: /Users/markadams/Desktop/GAMG/ex10 on a arch-maco named madams-macbk-3.local by markadams Tue Jun 12 15:52:56 2012 > [0]PETSC ERROR: Libraries linked from /Users/markadams/Codes/petsc-dev/arch-macosx-gnu-g/lib > [0]PETSC ERROR: Configure run at Mon Jun 11 17:03:36 2012 > [0]PETSC ERROR: Configure options CXX=/sw/lib/gcc4.4/bin/g++-4 CC=/sw/lib/gcc4.4/bin/gcc-4 CFLAGS=-malign-double CXXFLAGS=-malign-double FC=/sw/lib/gcc4.4/bin/gfortran --download-hypre=1 --download-parmetis=1 --download-metis=1 --download-triangle=1 --with-x=0 --with-debugging=1 --download-mpich=1 PETSC_ARCH=arch-macosx-gnu-g > [0]PETSC ERROR: ------------------------------------------------------------------------ > [0]PETSC ERROR: PetscLayoutSetBlockSize() line 460 in /Users/markadams/Codes/petsc-dev/src/vec/vec/impls/mpi/pmap.c > [0]PETSC ERROR: VecSetBlockSize() line 1526 in /Users/markadams/Codes/petsc-dev/src/vec/vec/interface/vector.c > > > On Jun 12, 2012, at 3:42 PM, Matthew Knepley wrote: > >> On Wed, Jun 13, 2012 at 3:45 AM, Mark F. Adams <mark.adams(a)columbia.edu> wrote: >> > >> > I thought there would be a -vec_block_size option, but alas its missing. Can you check in the debugger >> > when the block size is getting set? I cannot find it in VecSetFromOptions(). >> >> Its in the stack trace right? >> >> That is the second time, I want the first. >> >> Matt >> >> Thanks, >> mark >> >> [0]PETSC ERROR: ------------------------------------------------------------------------ >> [0]PETSC ERROR: PetscLayoutSetBlockSize() line 460 in /Users/markadams/Codes/petsc-dev/src/vec/vec/impls/mpi/pmap.c >> [0]PETSC ERROR: VecSetBlockSize() line 1526 in /Users/markadams/Codes/petsc-dev/src/vec/vec/interface/vector.c >> [0]PETSC ERROR: VecLoad_Binary() line 104 in /Users/markadams/Codes/petsc-dev/src/vec/vec/utils/vecio.c >> [0]PETSC ERROR: VecLoad_Default() line 348 in /Users/markadams/Codes/petsc-dev/src/vec/vec/utils/vecio.c >> [0]PETSC ERROR: VecLoad() line 1111 in /Users/markadams/Codes/petsc-dev/src/vec/vec/interface/vector.c >> [0]PETSC ERROR: main() line 132 in src/ksp/ksp/examples/tutorials/ex10.c >> >> >> >> >> >> -- >> 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 > > > > > -- > 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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Re: [petsc-dev] error reading binary file
by Mark F. Adams 12 Jun '12

12 Jun '12

It looks like I have a bigger problem. Mat is not passing the blocksize through .info. So I added -mat_block_size 3 and that seemed to work. Mark

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Re: [petsc-dev] error reading binary file
by Matthew Knepley 12 Jun '12

12 Jun '12

On Wed, Jun 13, 2012 at 3:57 AM, Mark F. Adams <mark.adams(a)columbia.edu>wrote: > This seems to be the first call to VecSetBlockSize: > If that were true, how could we ever change the block size for any vector? Matt > Breakpoint 1 at 0x1dbcee: file > /Users/markadams/Codes/petsc-dev/src/vec/vec/interface/vector.c, line 1523. > (gdb) r > Starting program: /Users/markadams/Desktop/GAMG/ex10 -f0 binaryoutput-sym > -vecload_block_size 3 > Reading symbols for shared libraries .++++++ done > > Breakpoint 1, VecSetBlockSize (v=0x18c1850, bs=3) at > /Users/markadams/Codes/petsc-dev/src/vec/vec/interface/vector.c:1523 > 1523 PetscFunctionBegin; > (gdb) where > #0 VecSetBlockSize (v=0x18c1850, bs=3) at > /Users/markadams/Codes/petsc-dev/src/vec/vec/interface/vector.c:1523 > #1 0x00246e6f in VecLoad_Binary (vec=0x18c1850, viewer=0x180d850) at > /Users/markadams/Codes/petsc-dev/src/vec/vec/utils/vecio.c:104 > #2 0x00247c85 in VecLoad_Default (newvec=0x18c1850, viewer=0x180d850) at > /Users/markadams/Codes/petsc-dev/src/vec/vec/utils/vecio.c:348 > #3 0x001d7ed8 in VecLoad (newvec=0x18c1850, viewer=0x180d850) at > /Users/markadams/Codes/petsc-dev/src/vec/vec/interface/vector.c:1111 > #4 0x00003a91 in main () > (gdb) n > 1524 PetscValidHeaderSpecific(v,VEC_CLASSID,1); > (gdb) > 1525 if (bs == v->map->bs) PetscFunctionReturn(0); > (gdb) > 1526 ierr = PetscLayoutSetBlockSize(v->map,bs);CHKERRQ(ierr); > (gdb) > [0]PETSC ERROR: --------------------- Error Message > ------------------------------------ > [0]PETSC ERROR: Arguments are incompatible! > [0]PETSC ERROR: Cannot change block size 1 to 3! > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Petsc Development HG revision: > 73637941c41b51aa3e638c914e6cb05248ece8b0 HG Date: Mon Jun 11 14:55:24 2012 > -0400 > [0]PETSC ERROR: See docs/changes/index.html for recent updates. > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > [0]PETSC ERROR: See docs/index.html for manual pages. > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: /Users/markadams/Desktop/GAMG/ex10 on a arch-maco named > madams-macbk-3.local by markadams Tue Jun 12 15:52:56 2012 > [0]PETSC ERROR: Libraries linked from > /Users/markadams/Codes/petsc-dev/arch-macosx-gnu-g/lib > [0]PETSC ERROR: Configure run at Mon Jun 11 17:03:36 2012 > [0]PETSC ERROR: Configure options CXX=/sw/lib/gcc4.4/bin/g++-4 > CC=/sw/lib/gcc4.4/bin/gcc-4 CFLAGS=-malign-double CXXFLAGS=-malign-double > FC=/sw/lib/gcc4.4/bin/gfortran --download-hypre=1 --download-parmetis=1 > --download-metis=1 --download-triangle=1 --with-x=0 --with-debugging=1 > --download-mpich=1 PETSC_ARCH=arch-macosx-gnu-g > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: PetscLayoutSetBlockSize() line 460 in > /Users/markadams/Codes/petsc-dev/src/vec/vec/impls/mpi/pmap.c > [0]PETSC ERROR: VecSetBlockSize() line 1526 in > /Users/markadams/Codes/petsc-dev/src/vec/vec/interface/vector.c > > > On Jun 12, 2012, at 3:42 PM, Matthew Knepley wrote: > > On Wed, Jun 13, 2012 at 3:45 AM, Mark F. Adams <mark.adams(a)columbia.edu>wrote: > >> > >> > I thought there would be a -vec_block_size option, but alas its >> missing. Can you check in the debugger >> > when the block size is getting set? I cannot find it in >> VecSetFromOptions(). >> >> Its in the stack trace right? >> > > That is the second time, I want the first. > > Matt > > >> Thanks, >> mark >> >> [0]PETSC ERROR: >> ------------------------------------------------------------------------ >> [0]PETSC ERROR: PetscLayoutSetBlockSize() line 460 in >> /Users/markadams/Codes/petsc-dev/src/vec/vec/impls/mpi/pmap.c >> [0]PETSC ERROR: VecSetBlockSize() line 1526 in >> /Users/markadams/Codes/petsc-dev/src/vec/vec/interface/vector.c >> [0]PETSC ERROR: VecLoad_Binary() line 104 in >> /Users/markadams/Codes/petsc-dev/src/vec/vec/utils/vecio.c >> [0]PETSC ERROR: VecLoad_Default() line 348 in >> /Users/markadams/Codes/petsc-dev/src/vec/vec/utils/vecio.c >> [0]PETSC ERROR: VecLoad() line 1111 in >> /Users/markadams/Codes/petsc-dev/src/vec/vec/interface/vector.c >> [0]PETSC ERROR: main() line 132 in src/ksp/ksp/examples/tutorials/ex10.c >> >> >> > > > -- > 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 > > > -- 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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Re: [petsc-dev] error reading binary file
by Mark F. Adams 12 Jun '12

12 Jun '12

This seems to be the first call to VecSetBlockSize: Breakpoint 1 at 0x1dbcee: file /Users/markadams/Codes/petsc-dev/src/vec/vec/interface/vector.c, line 1523. (gdb) r Starting program: /Users/markadams/Desktop/GAMG/ex10 -f0 binaryoutput-sym -vecload_block_size 3 Reading symbols for shared libraries .++++++ done Breakpoint 1, VecSetBlockSize (v=0x18c1850, bs=3) at /Users/markadams/Codes/petsc-dev/src/vec/vec/interface/vector.c:1523 1523 PetscFunctionBegin; (gdb) where #0 VecSetBlockSize (v=0x18c1850, bs=3) at /Users/markadams/Codes/petsc-dev/src/vec/vec/interface/vector.c:1523 #1 0x00246e6f in VecLoad_Binary (vec=0x18c1850, viewer=0x180d850) at /Users/markadams/Codes/petsc-dev/src/vec/vec/utils/vecio.c:104 #2 0x00247c85 in VecLoad_Default (newvec=0x18c1850, viewer=0x180d850) at /Users/markadams/Codes/petsc-dev/src/vec/vec/utils/vecio.c:348 #3 0x001d7ed8 in VecLoad (newvec=0x18c1850, viewer=0x180d850) at /Users/markadams/Codes/petsc-dev/src/vec/vec/interface/vector.c:1111 #4 0x00003a91 in main () (gdb) n 1524 PetscValidHeaderSpecific(v,VEC_CLASSID,1); (gdb) 1525 if (bs == v->map->bs) PetscFunctionReturn(0); (gdb) 1526 ierr = PetscLayoutSetBlockSize(v->map,bs);CHKERRQ(ierr); (gdb) [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Arguments are incompatible! [0]PETSC ERROR: Cannot change block size 1 to 3! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Development HG revision: 73637941c41b51aa3e638c914e6cb05248ece8b0 HG Date: Mon Jun 11 14:55:24 2012 -0400 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: /Users/markadams/Desktop/GAMG/ex10 on a arch-maco named madams-macbk-3.local by markadams Tue Jun 12 15:52:56 2012 [0]PETSC ERROR: Libraries linked from /Users/markadams/Codes/petsc-dev/arch-macosx-gnu-g/lib [0]PETSC ERROR: Configure run at Mon Jun 11 17:03:36 2012 [0]PETSC ERROR: Configure options CXX=/sw/lib/gcc4.4/bin/g++-4 CC=/sw/lib/gcc4.4/bin/gcc-4 CFLAGS=-malign-double CXXFLAGS=-malign-double FC=/sw/lib/gcc4.4/bin/gfortran --download-hypre=1 --download-parmetis=1 --download-metis=1 --download-triangle=1 --with-x=0 --with-debugging=1 --download-mpich=1 PETSC_ARCH=arch-macosx-gnu-g [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: PetscLayoutSetBlockSize() line 460 in /Users/markadams/Codes/petsc-dev/src/vec/vec/impls/mpi/pmap.c [0]PETSC ERROR: VecSetBlockSize() line 1526 in /Users/markadams/Codes/petsc-dev/src/vec/vec/interface/vector.c On Jun 12, 2012, at 3:42 PM, Matthew Knepley wrote: > On Wed, Jun 13, 2012 at 3:45 AM, Mark F. Adams <mark.adams(a)columbia.edu> wrote: > > > > I thought there would be a -vec_block_size option, but alas its missing. Can you check in the debugger > > when the block size is getting set? I cannot find it in VecSetFromOptions(). > > Its in the stack trace right? > > That is the second time, I want the first. > > Matt > > Thanks, > mark > > [0]PETSC ERROR: ------------------------------------------------------------------------ > [0]PETSC ERROR: PetscLayoutSetBlockSize() line 460 in /Users/markadams/Codes/petsc-dev/src/vec/vec/impls/mpi/pmap.c > [0]PETSC ERROR: VecSetBlockSize() line 1526 in /Users/markadams/Codes/petsc-dev/src/vec/vec/interface/vector.c > [0]PETSC ERROR: VecLoad_Binary() line 104 in /Users/markadams/Codes/petsc-dev/src/vec/vec/utils/vecio.c > [0]PETSC ERROR: VecLoad_Default() line 348 in /Users/markadams/Codes/petsc-dev/src/vec/vec/utils/vecio.c > [0]PETSC ERROR: VecLoad() line 1111 in /Users/markadams/Codes/petsc-dev/src/vec/vec/interface/vector.c > [0]PETSC ERROR: main() line 132 in src/ksp/ksp/examples/tutorials/ex10.c > > > > > > -- > 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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Re: [petsc-dev] error reading binary file
by Mark F. Adams 12 Jun '12

12 Jun '12

> > I thought there would be a -vec_block_size option, but alas its missing. Can you check in the debugger > when the block size is getting set? I cannot find it in VecSetFromOptions(). Its in the stack trace right? Thanks, mark [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: PetscLayoutSetBlockSize() line 460 in /Users/markadams/Codes/petsc-dev/src/vec/vec/impls/mpi/pmap.c [0]PETSC ERROR: VecSetBlockSize() line 1526 in /Users/markadams/Codes/petsc-dev/src/vec/vec/interface/vector.c [0]PETSC ERROR: VecLoad_Binary() line 104 in /Users/markadams/Codes/petsc-dev/src/vec/vec/utils/vecio.c [0]PETSC ERROR: VecLoad_Default() line 348 in /Users/markadams/Codes/petsc-dev/src/vec/vec/utils/vecio.c [0]PETSC ERROR: VecLoad() line 1111 in /Users/markadams/Codes/petsc-dev/src/vec/vec/interface/vector.c [0]PETSC ERROR: main() line 132 in src/ksp/ksp/examples/tutorials/ex10.c

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