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

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

12 Jun '12

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 Matthew Knepley 12 Jun '12

12 Jun '12

On Wed, Jun 13, 2012 at 3:25 AM, Mark F. Adams <mark.adams(a)columbia.edu>wrote: > > On Jun 12, 2012, at 2:57 PM, Matthew Knepley wrote: > > On Wed, Jun 13, 2012 at 2:57 AM, Jed Brown <jedbrown(a)mcs.anl.gov> wrote: > >> On Tue, Jun 12, 2012 at 1:59 PM, Mark F. Adams <mark.adams(a)columbia.edu>wrote: >> >>> How does one do that? Blaise generated this mat/vec. >> >> >> Set a prefix in the info file (done automatically when you write it) and >> set a prefix on the Vec before you read it. >> > > I think its even simpler in this case. The option is coming too late. Give > it explicitly on the command line. > > > Still not sure what you mean. I added -vecload_block_size 3 to the > command line and I got the same error. > 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(). Matt > Also, shouldn't this just work? Blaise wrote a binary fine and I'm using > ex10 to read it. We are both using petsc-dev presumably. > > Mark > > > Matt > > -- > 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

On Jun 12, 2012, at 2:57 PM, Matthew Knepley wrote: > On Wed, Jun 13, 2012 at 2:57 AM, Jed Brown <jedbrown(a)mcs.anl.gov> wrote: > On Tue, Jun 12, 2012 at 1:59 PM, Mark F. Adams <mark.adams(a)columbia.edu> wrote: > How does one do that? Blaise generated this mat/vec. > > Set a prefix in the info file (done automatically when you write it) and set a prefix on the Vec before you read it. > > I think its even simpler in this case. The option is coming too late. Give it explicitly on the command line. Still not sure what you mean. I added -vecload_block_size 3 to the command line and I got the same error. Also, shouldn't this just work? Blaise wrote a binary fine and I'm using ex10 to read it. We are both using petsc-dev presumably. Mark > > Matt > > -- > 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

On Jun 12, 2012, at 1:53 PM, Matthew Knepley wrote: > On Wed, Jun 13, 2012 at 1:49 AM, Mark F. Adams <mark.adams(a)columbia.edu> wrote: > I have: ~/Desktop/GAMG>cat binaryoutput-sym.info > -vecload_block_size 3 > > I need the matrix block size to be set... > > Then you need to disambiguate among vectors with prefixes. How does one do that? Blaise generated this mat/vec. Mark > > Matt > > Mark > > On Jun 12, 2012, at 12:42 PM, Jed Brown wrote: > >> Look at the *.info file. >> >> On Tue, Jun 12, 2012 at 11:45 AM, Mark F. Adams <mark.adams(a)columbia.edu> wrote: >> I'm getting this error when I try to read a matrix/vector with block size 3: >> >> ~/Desktop/GAMG>./ex10 -f0 binaryoutput-sym >> [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: 4c35227011f74c2367a3a96a62bc4d6df701bcfb HG Date: Sun Jun 10 00:30:22 2012 -0500 >> [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: ./ex10 on a arch-maco named madams-macbk-3.local by markadams Tue Jun 12 12:39:02 2012 >> [0]PETSC ERROR: Libraries linked from /Users/markadams/Codes/petsc-dev/arch-macosx-gnu-O/lib >> [0]PETSC ERROR: Configure run at Mon Jun 11 15:15:38 2012 >> [0]PETSC ERROR: Configure options CXX=/sw/lib/gcc4.6/bin/g++-4 CC=/sw/lib/gcc4.6/bin/gcc-4 CFLAGS=-malign-double CXXFLAGS=-malign-double FC=/sw/lib/gcc4.6/bin/gfortran --download-parmetis=1 --download-metis=1 --download-hdf5=1 --download-hypre=1 --download-ml=1 --download-prometheus=1 --download-triangle=1 --with-x=0 --with-debugging=0 --download-mpich=1 PETSC_ARCH=arch-macosx-gnu-O >> [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 >> application called MPI_Abort(MPI_COMM_WORLD, 75) - process 0 >> [unset]: aborting job: >> application called MPI_Abort(MPI_COMM_WORLD, 75) - process 0 >> ~/Desktop/GAMG> >> >> I just want to check if anyone has any thoughts before I start digging into this. >> >> Mark >> > > > > > -- > 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 Matthew Knepley 12 Jun '12

12 Jun '12

On Wed, Jun 13, 2012 at 2:57 AM, Jed Brown <jedbrown(a)mcs.anl.gov> wrote: > On Tue, Jun 12, 2012 at 1:59 PM, Mark F. Adams <mark.adams(a)columbia.edu>wrote: > >> How does one do that? Blaise generated this mat/vec. > > > Set a prefix in the info file (done automatically when you write it) and > set a prefix on the Vec before you read it. > I think its even simpler in this case. The option is coming too late. Give it explicitly on the command line. Matt -- 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 Jed Brown 12 Jun '12

12 Jun '12

On Tue, Jun 12, 2012 at 1:59 PM, Mark F. Adams <mark.adams(a)columbia.edu>wrote: > How does one do that? Blaise generated this mat/vec. Set a prefix in the info file (done automatically when you write it) and set a prefix on the Vec before you read it.

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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 1:49 AM, Mark F. Adams <mark.adams(a)columbia.edu>wrote: > I have: ~/Desktop/GAMG>cat binaryoutput-sym.info > -vecload_block_size 3 > > I need the matrix block size to be set... > Then you need to disambiguate among vectors with prefixes. Matt > Mark > > On Jun 12, 2012, at 12:42 PM, Jed Brown wrote: > > Look at the *.info file. > > On Tue, Jun 12, 2012 at 11:45 AM, Mark F. Adams <mark.adams(a)columbia.edu>wrote: > >> I'm getting this error when I try to read a matrix/vector with block size >> 3: >> >> ~/Desktop/GAMG>./ex10 -f0 binaryoutput-sym >> [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: >> 4c35227011f74c2367a3a96a62bc4d6df701bcfb HG Date: Sun Jun 10 00:30:22 2012 >> -0500 >> [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: ./ex10 on a arch-maco named madams-macbk-3.local by >> markadams Tue Jun 12 12:39:02 2012 >> [0]PETSC ERROR: Libraries linked from >> /Users/markadams/Codes/petsc-dev/arch-macosx-gnu-O/lib >> [0]PETSC ERROR: Configure run at Mon Jun 11 15:15:38 2012 >> [0]PETSC ERROR: Configure options CXX=/sw/lib/gcc4.6/bin/g++-4 >> CC=/sw/lib/gcc4.6/bin/gcc-4 CFLAGS=-malign-double CXXFLAGS=-malign-double >> FC=/sw/lib/gcc4.6/bin/gfortran --download-parmetis=1 --download-metis=1 >> --download-hdf5=1 --download-hypre=1 --download-ml=1 >> --download-prometheus=1 --download-triangle=1 --with-x=0 --with-debugging=0 >> --download-mpich=1 PETSC_ARCH=arch-macosx-gnu-O >> [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 >> application called MPI_Abort(MPI_COMM_WORLD, 75) - process 0 >> [unset]: aborting job: >> application called MPI_Abort(MPI_COMM_WORLD, 75) - process 0 >> ~/Desktop/GAMG> >> >> I just want to check if anyone has any thoughts before I start digging >> into this. >> >> Mark > > > > -- 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 have: ~/Desktop/GAMG>cat binaryoutput-sym.info -vecload_block_size 3 I need the matrix block size to be set... Mark On Jun 12, 2012, at 12:42 PM, Jed Brown wrote: > Look at the *.info file. > > On Tue, Jun 12, 2012 at 11:45 AM, Mark F. Adams <mark.adams(a)columbia.edu> wrote: > I'm getting this error when I try to read a matrix/vector with block size 3: > > ~/Desktop/GAMG>./ex10 -f0 binaryoutput-sym > [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: 4c35227011f74c2367a3a96a62bc4d6df701bcfb HG Date: Sun Jun 10 00:30:22 2012 -0500 > [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: ./ex10 on a arch-maco named madams-macbk-3.local by markadams Tue Jun 12 12:39:02 2012 > [0]PETSC ERROR: Libraries linked from /Users/markadams/Codes/petsc-dev/arch-macosx-gnu-O/lib > [0]PETSC ERROR: Configure run at Mon Jun 11 15:15:38 2012 > [0]PETSC ERROR: Configure options CXX=/sw/lib/gcc4.6/bin/g++-4 CC=/sw/lib/gcc4.6/bin/gcc-4 CFLAGS=-malign-double CXXFLAGS=-malign-double FC=/sw/lib/gcc4.6/bin/gfortran --download-parmetis=1 --download-metis=1 --download-hdf5=1 --download-hypre=1 --download-ml=1 --download-prometheus=1 --download-triangle=1 --with-x=0 --with-debugging=0 --download-mpich=1 PETSC_ARCH=arch-macosx-gnu-O > [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 > application called MPI_Abort(MPI_COMM_WORLD, 75) - process 0 > [unset]: aborting job: > application called MPI_Abort(MPI_COMM_WORLD, 75) - process 0 > ~/Desktop/GAMG> > > I just want to check if anyone has any thoughts before I start digging into this. > > Mark >

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error reading binary file
by Mark F. Adams 12 Jun '12

12 Jun '12

I'm getting this error when I try to read a matrix/vector with block size 3: ~/Desktop/GAMG>./ex10 -f0 binaryoutput-sym [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: 4c35227011f74c2367a3a96a62bc4d6df701bcfb HG Date: Sun Jun 10 00:30:22 2012 -0500 [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: ./ex10 on a arch-maco named madams-macbk-3.local by markadams Tue Jun 12 12:39:02 2012 [0]PETSC ERROR: Libraries linked from /Users/markadams/Codes/petsc-dev/arch-macosx-gnu-O/lib [0]PETSC ERROR: Configure run at Mon Jun 11 15:15:38 2012 [0]PETSC ERROR: Configure options CXX=/sw/lib/gcc4.6/bin/g++-4 CC=/sw/lib/gcc4.6/bin/gcc-4 CFLAGS=-malign-double CXXFLAGS=-malign-double FC=/sw/lib/gcc4.6/bin/gfortran --download-parmetis=1 --download-metis=1 --download-hdf5=1 --download-hypre=1 --download-ml=1 --download-prometheus=1 --download-triangle=1 --with-x=0 --with-debugging=0 --download-mpich=1 PETSC_ARCH=arch-macosx-gnu-O [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 application called MPI_Abort(MPI_COMM_WORLD, 75) - process 0 [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 75) - process 0 ~/Desktop/GAMG> I just want to check if anyone has any thoughts before I start digging into this. Mark

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

12 Jun '12

Look at the *.info file. On Tue, Jun 12, 2012 at 11:45 AM, Mark F. Adams <mark.adams(a)columbia.edu>wrote: > I'm getting this error when I try to read a matrix/vector with block size > 3: > > ~/Desktop/GAMG>./ex10 -f0 binaryoutput-sym > [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: > 4c35227011f74c2367a3a96a62bc4d6df701bcfb HG Date: Sun Jun 10 00:30:22 2012 > -0500 > [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: ./ex10 on a arch-maco named madams-macbk-3.local by > markadams Tue Jun 12 12:39:02 2012 > [0]PETSC ERROR: Libraries linked from > /Users/markadams/Codes/petsc-dev/arch-macosx-gnu-O/lib > [0]PETSC ERROR: Configure run at Mon Jun 11 15:15:38 2012 > [0]PETSC ERROR: Configure options CXX=/sw/lib/gcc4.6/bin/g++-4 > CC=/sw/lib/gcc4.6/bin/gcc-4 CFLAGS=-malign-double CXXFLAGS=-malign-double > FC=/sw/lib/gcc4.6/bin/gfortran --download-parmetis=1 --download-metis=1 > --download-hdf5=1 --download-hypre=1 --download-ml=1 > --download-prometheus=1 --download-triangle=1 --with-x=0 --with-debugging=0 > --download-mpich=1 PETSC_ARCH=arch-macosx-gnu-O > [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 > application called MPI_Abort(MPI_COMM_WORLD, 75) - process 0 > [unset]: aborting job: > application called MPI_Abort(MPI_COMM_WORLD, 75) - process 0 > ~/Desktop/GAMG> > > I just want to check if anyone has any thoughts before I start digging > into this. > > Mark

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