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

Re: [petsc-dev] error building with petsc-dev
by Mark F. Adams 30 Apr '12

30 Apr '12

Thanks Dmitry, I think there is something wrong with my kdiff3 (or something like that). I updated this AM and got 100+ conflicts and so I just kept all of my code, and lost the updates to gamg.c and agg.c. Mark On Apr 30, 2012, at 2:07 PM, Dmitry Karpeev wrote: > Mark, > PetscTypeCompare got renamed to PetscObjectTypeCompare in line with the PETSc naming guidelines: > http://petsc.cs.iit.edu/petsc/petsc-dev/rev/3fc8f665421d > The gamg source was part of this update. > Any chance you introduced a new instance of PetscTypeCompare() after that changeset? > If so, simply replace it with PetscObjectTypeCompare(). > > Dmitry. > > On Mon, Apr 30, 2012 at 1:03 PM, Mark F. Adams <mark.adams(a)columbia.edu> wrote: > I've built petsc-dev but when I try to make an example I get this: > > make ex54 > /Users/markadams/Codes/petsc-dev/arch-macosx-gnu-O/bin/mpicc -o ex54.o -c -malign-double -g3 -fno-inline -O0 -I/Users/markadams/Codes/petsc-dev/include -I/Users/markadams/Codes/petsc-dev/arch-macosx-gnu-O/include -D__INSDIR__=src/ksp/ksp/examples/tutorials/ ex54.c > /Users/markadams/Codes/petsc-dev/arch-macosx-gnu-O/bin/mpicc -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first -malign-double -g3 -fno-inline -O0 -o ex54 ex54.o -L/Users/markadams/Codes/petsc-dev/arch-macosx-gnu-O/lib -lpetsc -ltriangle -lparmetis -lmetis -lHYPRE -lmpichcxx -lstdc++ -lpthread -lflapack -lfblas -lhdf5_fortran -lhdf5 -lhdf5hl_fortran -lhdf5_hl -lz -L/sw/lib/gcc4.6/lib/gcc/i386-apple-darwin10.8.0/4.6.2 -L/sw/lib/gcc4.6/lib -lpmpich -lmpich -lopa -lmpl -lSystem -lgcc_ext.10.5 -ldl -lmpichf90 -lpthread -lgfortran -lgfortran -lquadmath -lm -lm -lmpichcxx -lstdc++ -lpmpich -lmpich -lopa -lmpl -lSystem -lgcc_ext.10.5 -ldl > Undefined symbols: > "_PetscTypeCompare", referenced from: > _PCSetUp_GAMG in libpetsc.a(gamg.c.o) > _PCSetUp_GAMG in libpetsc.a(gamg.c.o) > ld: symbol(s) not found > collect2: ld returned 1 exit status > > Any ideas? > > Mark >

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Re: [petsc-dev] error building with petsc-dev
by Dmitry Karpeev 30 Apr '12

30 Apr '12

Mark, PetscTypeCompare got renamed to PetscObjectTypeCompare in line with the PETSc naming guidelines: http://petsc.cs.iit.edu/petsc/petsc-dev/rev/3fc8f665421d The gamg source was part of this update. Any chance you introduced a new instance of PetscTypeCompare() after that changeset? If so, simply replace it with PetscObjectTypeCompare(). Dmitry. On Mon, Apr 30, 2012 at 1:03 PM, Mark F. Adams <mark.adams(a)columbia.edu>wrote: > I've built petsc-dev but when I try to make an example I get this: > > make ex54 > /Users/markadams/Codes/petsc-dev/arch-macosx-gnu-O/bin/mpicc -o ex54.o -c > -malign-double -g3 -fno-inline -O0 > -I/Users/markadams/Codes/petsc-dev/include > -I/Users/markadams/Codes/petsc-dev/arch-macosx-gnu-O/include > -D__INSDIR__=src/ksp/ksp/examples/tutorials/ ex54.c > /Users/markadams/Codes/petsc-dev/arch-macosx-gnu-O/bin/mpicc > -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress > -Wl,-commons,use_dylibs -Wl,-search_paths_first > -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress > -Wl,-commons,use_dylibs -Wl,-search_paths_first -malign-double -g3 > -fno-inline -O0 -o ex54 ex54.o > -L/Users/markadams/Codes/petsc-dev/arch-macosx-gnu-O/lib -lpetsc > -ltriangle -lparmetis -lmetis -lHYPRE -lmpichcxx -lstdc++ -lpthread > -lflapack -lfblas -lhdf5_fortran -lhdf5 -lhdf5hl_fortran -lhdf5_hl -lz > -L/sw/lib/gcc4.6/lib/gcc/i386-apple-darwin10.8.0/4.6.2 -L/sw/lib/gcc4.6/lib > -lpmpich -lmpich -lopa -lmpl -lSystem -lgcc_ext.10.5 -ldl -lmpichf90 > -lpthread -lgfortran -lgfortran -lquadmath -lm -lm -lmpichcxx -lstdc++ > -lpmpich -lmpich -lopa -lmpl -lSystem -lgcc_ext.10.5 -ldl > Undefined symbols: > "_PetscTypeCompare", referenced from: > _PCSetUp_GAMG in libpetsc.a(gamg.c.o) > _PCSetUp_GAMG in libpetsc.a(gamg.c.o) > ld: symbol(s) not found > collect2: ld returned 1 exit status > > Any ideas? > > Mark

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error building with petsc-dev
by Mark F. Adams 30 Apr '12

30 Apr '12

I've built petsc-dev but when I try to make an example I get this: make ex54 /Users/markadams/Codes/petsc-dev/arch-macosx-gnu-O/bin/mpicc -o ex54.o -c -malign-double -g3 -fno-inline -O0 -I/Users/markadams/Codes/petsc-dev/include -I/Users/markadams/Codes/petsc-dev/arch-macosx-gnu-O/include -D__INSDIR__=src/ksp/ksp/examples/tutorials/ ex54.c /Users/markadams/Codes/petsc-dev/arch-macosx-gnu-O/bin/mpicc -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first -malign-double -g3 -fno-inline -O0 -o ex54 ex54.o -L/Users/markadams/Codes/petsc-dev/arch-macosx-gnu-O/lib -lpetsc -ltriangle -lparmetis -lmetis -lHYPRE -lmpichcxx -lstdc++ -lpthread -lflapack -lfblas -lhdf5_fortran -lhdf5 -lhdf5hl_fortran -lhdf5_hl -lz -L/sw/lib/gcc4.6/lib/gcc/i386-apple-darwin10.8.0/4.6.2 -L/sw/lib/gcc4.6/lib -lpmpich -lmpich -lopa -lmpl -lSystem -lgcc_ext.10.5 -ldl -lmpichf90 -lpthread -lgfortran -lgfortran -lquadmath -lm -lm -lmpichcxx -lstdc++ -lpmpich -lmpich -lopa -lmpl -lSystem -lgcc_ext.10.5 -ldl Undefined symbols: "_PetscTypeCompare", referenced from: _PCSetUp_GAMG in libpetsc.a(gamg.c.o) _PCSetUp_GAMG in libpetsc.a(gamg.c.o) ld: symbol(s) not found collect2: ld returned 1 exit status Any ideas? Mark

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Re: [petsc-dev] What needs to be done before a release?
by Blaise Bourdin 30 Apr '12

30 Apr '12

Hi, I know I suggested it before and the idea did not get much traction, but it would be _really_ nice to add Real and Integer arrays to PetscBag. The idea is _not_ to add full fields in a bag. Instead, I would like to be able to pass material properties as command line arguments in a concise way. (Think of a Hooke's law in 3d and its 21 coefficients, passing it as -a 1,1,1,1,1,... is much nicer than having to pass -a_1111 1 -a 1122 1 etc). Also, fortran wrappers over PetscOptionsEnum and PetscBagRegisterEnum would be nice. I understand that it is a bit tricky since it involves passing fortran arrays of strings. Blaise On Apr 29, 2012, at 9:55 PM, Shri wrote: > > > ----- Original Message ----- >> What is left to be done before a release? >> >> - Replace 2 DMMG examples >> - Rework thread code > This should hopefully be done by friday. > > Shri > >> >> >> Barry -- 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] MetSetBlockSize issue
by Mark F. Adams 30 Apr '12

30 Apr '12

I have added MatGet(Set)BlockSizes. Given that the block size is in a map and MatSetBlockSize sets both maps with the same value, this was very natural to do. Hong, can you please make the matrix methods (PtAP and AAt, AtA, etc.) inherit block sizes? And MatGetSubmatrix also needs to have the matrix inherit the block sizes ... anyone want to do that or should I do it? Mark On Apr 25, 2012, at 8:41 PM, Barry Smith wrote: > > Ok, so add MatSetBlockSizes(). > > Reason we don't have implemented fully function different row and column block sizes or different block sizes in different parts of the matrix: with our current programming model (C+MPI) the code complexity would get higher increasing the time to write and maintain code hence it has not been done. Plus we have plenty of other high priority things to work on. Nothing is stopping anyone from writing a more general block implementation and putting it in PETSc. > > Barry > > On Apr 25, 2012, at 5:58 PM, Mark F. Adams wrote: > >> >> On Apr 25, 2012, at 6:10 PM, Barry Smith wrote: >> >>> >>> On Apr 25, 2012, at 4:58 PM, Jed Brown wrote: >>> >>>> On Wed, Apr 25, 2012 at 16:41, Barry Smith <bsmith(a)mcs.anl.gov> wrote: >>>> I admit MatSetVirtualColumnBlockSize() is clunky and would be happy to hear alternatives. >>>> >>>> What about having a separate row and column block size? The BAIJ and MAIJ formats can continue to store data using bs=gcd(rowbs,colbs), but those row and column block sizes indicate that redundancy exists in the data structure, so it can be utilized by appropriate operations. >>> >>> Mark told me in a earlier email that the "column block size" isn't really the column block size (except in some cases), since it is not really a column block size I don't want the matrix to list it as the column block size (hence my virtual column block size thing). >> >> The blocks are not always dense, so by what appears to be your definition of block size it is not (always) a 'column block size'. But I think that it is semantically a blocked matrix and hence it has a column block size. >> >>> >>> If it is truly a column block size then great, P is given the column block size with MatSetColumnBlockSize() or MatSetBlockSizes(mat,col,row) and PtAP automatically uses that column block size for the resulting matrix block size. >>> >> >> I think this solution is the best (eg, no 'virtual'). Column block size is a fundamental property of a blocked matrix. PETSc's current implementations do not exploit or accommodate this but since it is a fundamental property I do not mind cluttering up Mat with yet another parameter. You deal with rectangular matrices, and blocked matrices, why not rectangular blocks? You also have row block size on AIJ matrices that do not have dense blocks so why not column block size? >> >> Mark >> >>> So Mark I ask you again, in GAMG is it truly a column block size? >>> >>> Barry >>> >>> >>> >> > >

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Re: [petsc-dev] pull problem
by Mark F. Adams 30 Apr '12

30 Apr '12

Duh, sorry, just realized this mistake, Mark On Apr 30, 2012, at 9:30 AM, Satish Balay wrote: > On Mon, 30 Apr 2012, Mark F. Adams wrote: > >> I have been able to pull and update this AM but this (from the petsc web page) fails: >> >> ~/Codes>hg clone http://petsc.cs.iit.edu/petsc/petsc-dev-temp >> abort: HTTP Error 404: Not Found > > Why access petsc-dev-tmp? Perhaps it was a temporary repo thats now removed? > > Satish >

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Re: [petsc-dev] pull problem
by Satish Balay 30 Apr '12

30 Apr '12

On Mon, 30 Apr 2012, Mark F. Adams wrote: > I have been able to pull and update this AM but this (from the petsc web page) fails: > > ~/Codes>hg clone http://petsc.cs.iit.edu/petsc/petsc-dev-temp > abort: HTTP Error 404: Not Found Why access petsc-dev-tmp? Perhaps it was a temporary repo thats now removed? Satish

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pull problem
by Mark F. Adams 30 Apr '12

30 Apr '12

I have been able to pull and update this AM but this (from the petsc web page) fails: ~/Codes>hg clone http://petsc.cs.iit.edu/petsc/petsc-dev-temp abort: HTTP Error 404: Not Found Mark

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Re: [petsc-dev] What needs to be done before a release?
by Shri 29 Apr '12

29 Apr '12

----- Original Message ----- > What is left to be done before a release? > > - Replace 2 DMMG examples > - Rework thread code This should hopefully be done by friday. Shri > > > Barry

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What needs to be done before a release?
by Barry Smith 29 Apr '12

29 Apr '12

What is left to be done before a release? - Replace 2 DMMG examples - Rework thread code Barry

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