[petsc-dev] sieve examples seem totally broken?

Wed May 25 18:37:06 CDT 2011

On Mon, May 9, 2011 at 9:35 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:

>
> There doesn't seem to be a systematic way to run all the sieve examples.
> For example in  src/dm/impls/mesh/examples/tutorials and tests there are no
> TESTEXAMPLES_XXXX variables listing all the examples. In the tutorial
> directory a few are listed in TESTEXAMPLES_SIEVE but they don't compile.
>
> How can we test sieve for a release without the right infrastructure in
> place?
>

We can't. That is being fixed now. There is at least one example that
halfway runs with vanilla PETSc. SNES ex12.
I am fixing it up to do everything right, for Dirichlet and Neumann. Once
that is done, I will fix it for higher order.

   Matt

>   Barry
>
>
> barry-smiths-macbook-pro:tutorials barrysmith$ make testexamples_SIEVE
> --------------Error detected during compile or link!-----------------------
> See http://www.mcs.anl.gov/petsc/petsc-2/documentation/faq.html
> /Users/barrysmith/Src/petsc-dev/arch-sieve/bin/mpicxx -o ex1.o -c -Wall
> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g
> -I/Users/barrysmith/Src/petsc-dev/include
> -I/Users/barrysmith/Src/petsc-dev/arch-sieve/include
> -I/Users/barrysmith/Src/petsc-dev/include/sieve -I/opt/local/include -I/src
> -I. -DDIMENSION=3 -DNUM_TERMS=10 -DNUM_COEFFICIENTS=10*10*3
> -D__INSDIR__=src/dm/mesh/examples/tutorials/ ex1.c
> ex1.c:35:24: error: petscmesh.hh: No such file or directory
> ex1.c:36:32: error: petscmesh_formats.hh: No such file or directory
> ex1.c:40: error: ‘ALE’ has not been declared
> ex1.c:46: error: ‘PetscInt’ does not name a type
> ex1.c:47: error: ‘PetscBool’ does not name a type
> ex1.c:51: error: ‘PetscBool’ does not name a type
> ex1.c:52: error: ‘PetscBool’ does not name a type
> ex1.c:53: error: ‘PetscBool’ does not name a type
> ex1.c:54: error: ‘PetscBool’ does not name a type
> ex1.c:56: error: ‘PetscBool’ does not name a type
> ex1.c:57: error: ‘PetscBool’ does not name a type
> ex1.c:58: error: ‘SectionInt’ does not name a type
> ex1.c:59: error: ‘PetscBool’ does not name a type
> ex1.c:60: error: ‘SectionInt’ does not name a type
> ex1.c:63: error: ‘PetscErrorCode’ does not name a type
> ex1.c:67: error: ‘PetscErrorCode’ does not name a type
> ex1.c:152: error: ‘PetscErrorCode’ does not name a type
> ex1.c:176: error: ‘PetscErrorCode’ does not name a type
> ex1.c:203: error: ‘PetscErrorCode’ does not name a type
> ex1.c:241: error: ‘PetscErrorCode’ does not name a type
> ex1.c:275: error: ‘PetscErrorCode’ does not name a type
> ex1.c: In function ‘int main(int, char**)’:
> ex1.c:333: error: ‘MPI_Comm’ was not declared in this scope
> ex1.c:333: error: expected `;' before ‘comm’
> ex1.c:335: error: ‘PetscErrorCode’ was not declared in this scope
> ex1.c:335: error: expected `;' before ‘ierr’
> ex1.c:337: error: ‘PetscFunctionBegin’ was not declared in this scope
> ex1.c:338: error: ‘ierr’ was not declared in this scope
> ex1.c:338: error: ‘PetscInitialize’ was not declared in this scope
> ex1.c:338: error: ‘CHKERRQ’ was not declared in this scope
> ex1.c:339: error: ‘comm’ was not declared in this scope
> ex1.c:339: error: ‘PETSC_COMM_WORLD’ was not declared in this scope
> ex1.c:342: error: ‘Mesh’ was not declared in this scope
> ex1.c:342: error: expected `;' before ‘mesh’
> ex1.c:344: error: ‘ProcessOptions’ was not declared in this scope
> ex1.c:345: error: ‘mesh’ was not declared in this scope
> ex1.c:345: error: ‘CreateMesh’ was not declared in this scope
> ex1.c:346: error: ‘DistributeMesh’ was not declared in this scope
> ex1.c:347: error: ‘OutputVTK’ was not declared in this scope
> ex1.c:349: error: ‘struct Options’ has no member named ‘doPartition’
> ex1.c:350: error: ‘struct Options’ has no member named ‘partition’
> ex1.c:350: error: ‘SectionIntDestroy’ was not declared in this scope
> ex1.c:352: error: ‘MeshDestroy’ was not declared in this scope
> ex1.c:353: error: expected type-specifier before ‘ALE’
> ex1.c:353: error: expected `)' before ‘::’ token
> ex1.c:353: error: expected `{' before ‘::’ token
> ex1.c:353: error: ‘::Exception’ has not been declared
> ex1.c:353: error: expected `;' before ‘e’
> ex1.c:357: error: ‘PetscFinalize’ was not declared in this scope
> ex1.c:358: error: ‘PetscFunctionReturn’ was not declared in this scope
> make[1]: [ex1.o] Error 1 (ignored)
> /Users/barrysmith/Src/petsc-dev/arch-sieve/bin/mpicxx
> -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   -Wall -Wwrite-strings
> -Wno-strict-aliasing -Wno-unknown-pragmas -g  -o ex1 ex1.o
>  -L/Users/barrysmith/Src/petsc-dev/arch-sieve/lib  -lpetsc -L/usr/X11R6/lib
> -lX11 -llapack -lblas -L/usr/lib/gcc/i686-apple-darwin10/4.2.1/x86_64
> -L/usr/lib/i686-apple-darwin10/4.2.1
> -L/usr/lib/gcc/i686-apple-darwin10/4.2.1 -ldl -lpmpich -lmpich -lopa -lmpl
> -lpthread -lSystem -lmpichf90 -lgfortran
> -L/usr/local/lib/gcc/x86_64-apple-darwin10.4.0/4.6.0 -L/usr/local/lib
> -lgfortran -lgcc_ext.10.5 -lmpichcxx -lstdc++ -lmpichcxx -lstdc++ -ldl
> -lpmpich -lmpich -lopa -lmpl -lpthread -lSystem -ldl
> i686-apple-darwin10-g++-4.2.1: ex1.o: No such file or directory
> make[1]: [ex1] Error 1 (ignored)
> /bin/rm -f -f ex1.o
> /usr/bin/diff: testMesh.lcon: No such file or directory
> Possible problem with ex1_1, diffs above
> /usr/bin/diff: testMesh.nodes: No such file or directory
> Possible problem with ex1_1, diffs above
> /usr/bin/diff: testMesh.lcon: No such file or directory
> Possible problem with ex1_2, diffs above
> /usr/bin/diff: testMesh.nodes: No such file or directory
> Possible problem with ex1_2, diffs above
> /usr/bin/diff: testMesh.lcon: No such file or directory
> Possible problem with ex1_3, diffs above
> /usr/bin/diff: testMesh.nodes: No such file or directory
> Possible problem with ex1_3, diffs above
> /usr/bin/diff: data/bm1b/bm1b.0.connect: No such file or directory
> /usr/bin/diff: testMesh.0.connect: No such file or directory
> Possible problem with ex1_4, diffs above
> /usr/bin/diff: data/bm1b/bm1b.0.coord: No such file or directory
> /usr/bin/diff: testMesh.0.coord: No such file or directory
> Possible problem with ex1_4, diffs above
> /usr/bin/diff: data/bm1b/bm1b.1.connect: No such file or directory
> /usr/bin/diff: testMesh.1.connect: No such file or directory
> Possible problem with ex1_4, diffs above
> /usr/bin/diff: data/bm1b/bm1b.1.coord: No such file or directory
> /usr/bin/diff: testMesh.1.coord: No such file or directory
> Possible problem with ex1_4, diffs above
> /usr/bin/diff: data/bm1b/bm1b.2.connect: No such file or directory
> /usr/bin/diff: testMesh.2.connect: No such file or directory
> Possible problem with ex1_4, diffs above
> /usr/bin/diff: data/bm1b/bm1b.2.coord: No such file or directory
> /usr/bin/diff: testMesh.2.coord: No such file or directory
> Possible problem with ex1_4, diffs above
> /usr/bin/diff: data/bm1b/bm1b.3.connect: No such file or directory
> /usr/bin/diff: testMesh.3.connect: No such file or directory
> Possible problem with ex1_4, diffs above
> /usr/bin/diff: data/bm1b/bm1b.3.coord: No such file or directory
> /usr/bin/diff: testMesh.3.coord: No such file or directory
> Possible problem with ex1_4, diffs above
> /usr/bin/diff: data/bm1b/bm1b.4.connect: No such file or directory
> /usr/bin/diff: testMesh.4.connect: No such file or directory
> Possible problem with ex1_4, diffs above
> /usr/bin/diff: data/bm1b/bm1b.4.coord: No such file or directory
> /usr/bin/diff: testMesh.4.coord: No such file or directory
> Possible problem with ex1_4, diffs above
> --------------Error detected during compile or link!-----------------------
> See http://www.mcs.anl.gov/petsc/petsc-2/documentation/faq.html
> /Users/barrysmith/Src/petsc-dev/arch-sieve/bin/mpicxx -o ex2.o -c -Wall
> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g
> -I/Users/barrysmith/Src/petsc-dev/include
> -I/Users/barrysmith/Src/petsc-dev/arch-sieve/include
> -I/Users/barrysmith/Src/petsc-dev/include/sieve -I/opt/local/include -I/src
> -I. -DDIMENSION=3 -DNUM_TERMS=10 -DNUM_COEFFICIENTS=10*10*3
> -D__INSDIR__=src/dm/mesh/examples/tutorials/ ex2.c
> ex2.c:20:23: error: petscmesh.h: No such file or directory
> ex2.c:22:38: error: ../src/dm/mesh/meshpcice.h: No such file or directory
> ex2.c:42: error: type/value mismatch at argument 1 in template parameter
> list for ‘template<class X, class A> class ALE::Obj’
> ex2.c:42: error:   expected a type, got ‘Mesh’
> ex2.c:42: error: template argument 2 is invalid
> ex2.c:43: error: type/value mismatch at argument 1 in template parameter
> list for ‘template<class X, class A> class ALE::Obj’
> ex2.c:43: error:   expected a type, got ‘Mesh’
> ex2.c:43: error: template argument 2 is invalid
> ex2.c:45: error: ‘Mesh’ has not been declared
> ex2.c:46: error: ‘Mesh’ was not declared in this scope
> ex2.c:46: error: ‘Mesh’ was not declared in this scope
> ex2.c:46: error: expected primary-expression before ‘,’ token
> ex2.c:46: error: expected primary-expression before ‘*’ token
> ex2.c:46: error: expected primary-expression before ‘)’ token
> ex2.c:46: error: initializer expression list treated as compound expression
> ex2.c:47: error: ‘Mesh’ was not declared in this scope
> ex2.c:48: error: ‘Mesh’ was not declared in this scope
> ex2.c:48: error: expected primary-expression before ‘,’ token
> ex2.c:48: error: expected primary-expression before ‘*’ token
> ex2.c:48: error: expected primary-expression before ‘)’ token
> ex2.c:48: error: initializer expression list treated as compound expression
> ex2.c:49: error: ‘Mesh’ was not declared in this scope
> ex2.c:49: error: expected primary-expression before ‘,’ token
> ex2.c:49: error: expected primary-expression before ‘*’ token
> ex2.c:49: error: expected primary-expression before ‘)’ token
> ex2.c:49: error: initializer expression list treated as compound expression
> ex2.c:50: error: ‘Mesh’ was not declared in this scope
> ex2.c:50: error: expected primary-expression before ‘*’ token
> ex2.c:50: error: expected primary-expression before ‘)’ token
> ex2.c:50: error: initializer expression list treated as compound expression
> ex2.c: In function ‘int main(int, char**)’:
> ex2.c:65: error: ‘Mesh’ was not declared in this scope
> ex2.c:65: error: expected `;' before ‘meshBoundary’
> ex2.c:66: error: expected `;' before ‘mesh’
> ex2.c:69: error: ‘meshBoundary’ was not declared in this scope
> ex2.c:70: error: ‘mesh’ was not declared in this scope
> ex2.c:70: error: ‘CreateMesh’ cannot be used as a function
> ex2.c:71: error: ‘DistributeMesh’ cannot be used as a function
> ex2.c:72: error: ‘RefineMesh’ cannot be used as a function
> ex2.c:73: error: ‘OutputVTK’ cannot be used as a function
> ex2.c:74: error: ‘MeshDestroy’ was not declared in this scope
> ex2.c: At global scope:
> ex2.c:137: error: type/value mismatch at argument 1 in template parameter
> list for ‘template<class X, class A> class ALE::Obj’
> ex2.c:137: error:   expected a type, got ‘Mesh’
> ex2.c:137: error: template argument 2 is invalid
> ex2.c: In function ‘PetscErrorCode CreateSquareBoundary(const int&)’:
> ex2.c:148: error: ‘template<class IndexType, class ScalarType> class
> ALE::Mesh’ used without template parameters
> ex2.c:148: error: expected initializer before ‘patch’
> ex2.c:151: error: ‘template<class IndexType, class ScalarType> class
> ALE::Mesh’ used without template parameters
> ex2.c:151: error: expected `;' before ‘vertices’
> ex2.c:152: error: template argument 1 is invalid
> ex2.c:152: error: template argument 2 is invalid
> ex2.c:152: error: invalid type in declaration before ‘=’ token
> ex2.c:152: error: expected type-specifier
> ex2.c:152: error: invalid conversion from ‘int*’ to ‘int’
> ex2.c:152: error: expected ‘,’ or ‘;’
> ex2.c:153: error: template argument 1 is invalid
> ex2.c:153: error: template argument 2 is invalid
> ex2.c:153: error: invalid type in declaration before ‘=’ token
> ex2.c:153: error: expected type-specifier
> ex2.c:153: error: invalid conversion from ‘int*’ to ‘int’
> ex2.c:153: error: expected ‘,’ or ‘;’
> ex2.c:156: error: base operand of ‘->’ is not a pointer
> ex2.c:157: error: ‘template<class IndexType, class ScalarType> class
> ALE::Mesh’ used without template parameters
> ex2.c:157: error: expected `;' before ‘edge’
> ex2.c:161: error: ‘vertices’ was not declared in this scope
> ex2.c:161: error: ‘template<class IndexType, class ScalarType> class
> ALE::Mesh’ used without template parameters
> ex2.c:164: error: ‘edge’ was not declared in this scope
> ex2.c:164: error: ‘template<class IndexType, class ScalarType> class
> ALE::Mesh’ used without template parameters
> ex2.c:165: error: base operand of ‘->’ is not a pointer
> ex2.c:165: error: ‘vertices’ was not declared in this scope
> ex2.c:166: error: base operand of ‘->’ is not a pointer
> ex2.c:168: error: ‘edge’ was not declared in this scope
> ex2.c:168: error: ‘template<class IndexType, class ScalarType> class
> ALE::Mesh’ used without template parameters
> ex2.c:169: error: base operand of ‘->’ is not a pointer
> ex2.c:169: error: ‘vertices’ was not declared in this scope
> ex2.c:170: error: base operand of ‘->’ is not a pointer
> ex2.c:171: error: ‘template<class IndexType, class ScalarType> class
> ALE::Mesh’ used without template parameters
> ex2.c:172: error: base operand of ‘->’ is not a pointer
> ex2.c:173: error: base operand of ‘->’ is not a pointer
> ex2.c:174: error: ‘template<class IndexType, class ScalarType> class
> ALE::Mesh’ used without template parameters
> ex2.c:175: error: base operand of ‘->’ is not a pointer
> ex2.c:176: error: base operand of ‘->’ is not a pointer
> ex2.c:177: error: ‘template<class IndexType, class ScalarType> class
> ALE::Mesh’ used without template parameters
> ex2.c:178: error: base operand of ‘->’ is not a pointer
> ex2.c:179: error: base operand of ‘->’ is not a pointer
> ex2.c:181: error: base operand of ‘->’ is not a pointer
> ex2.c:182: error: base operand of ‘->’ is not a pointer
> ex2.c:182: error: ‘patch’ was not declared in this scope
> ex2.c:183: error: base operand of ‘->’ is not a pointer
> ex2.c:184: error: base operand of ‘->’ is not a pointer
> ex2.c:185: error: ‘SieveBuilder’ is not a member of ‘ALE::New’
> ex2.c:185: error: ‘template<class IndexType, class ScalarType> class
> ALE::Mesh’ used without template parameters
> ex2.c:185: error: ‘::buildCoordinates’ has not been declared
> ex2.c:185: error: base operand of ‘->’ is not a pointer
> ex2.c:187: error: template argument 1 is invalid
> ex2.c:187: error: template argument 2 is invalid
> ex2.c:187: error: invalid type in declaration before ‘=’ token
> ex2.c:187: error: base operand of ‘->’ is not a pointer
> ex2.c:189: error: base operand of ‘->’ is not a pointer
> ex2.c:191: error: base operand of ‘->’ is not a pointer
> ex2.c:194: error: base operand of ‘->’ is not a pointer
> ex2.c: At global scope:
> ex2.c:213: error: type/value mismatch at argument 1 in template parameter
> list for ‘template<class X, class A> class ALE::Obj’
> ex2.c:213: error:   expected a type, got ‘Mesh’
> ex2.c:213: error: template argument 2 is invalid
> ex2.c:345: error: ‘Mesh’ has not been declared
> ex2.c: In function ‘PetscErrorCode CreateMeshBoundary(MPI_Comm, int*,
> Options*)’:
> ex2.c:347: error: type/value mismatch at argument 1 in template parameter
> list for ‘template<class X, class A> class ALE::Obj’
> ex2.c:347: error:   expected a type, got ‘Mesh’
> ex2.c:347: error: template argument 2 is invalid
> ex2.c:347: error: invalid type in declaration before ‘;’ token
> ex2.c:351: error: ‘MeshCreate’ was not declared in this scope
> ex2.c:354: error: base operand of ‘->’ is not a pointer
> ex2.c:355: error: template argument 1 is invalid
> ex2.c:355: error: template argument 2 is invalid
> ex2.c:355: error: invalid type in declaration before ‘=’ token
> ex2.c:355: error: base operand of ‘->’ is not a pointer
> ex2.c:356: error: template argument 1 is invalid
> ex2.c:356: error: template argument 2 is invalid
> ex2.c:356: error: invalid type in declaration before ‘=’ token
> ex2.c:356: error: base operand of ‘->’ is not a pointer
> ex2.c:357: error: template argument 1 is invalid
> ex2.c:357: error: template argument 2 is invalid
> ex2.c:357: error: invalid type in declaration before ‘=’ token
> ex2.c:357: error: base operand of ‘->’ is not a pointer
> ex2.c:358: error: template argument 1 is invalid
> ex2.c:358: error: template argument 2 is invalid
> ex2.c:358: error: invalid type in declaration before ‘=’ token
> ex2.c:358: error: base operand of ‘->’ is not a pointer
> ex2.c:360: error: ‘template<class IndexType, class ScalarType> class
> ALE::Mesh’ used without template parameters
> ex2.c:360: error: expected `;' before ‘v_iter’
> ex2.c:360: error: ‘v_iter’ was not declared in this scope
> ex2.c:360: error: base operand of ‘->’ is not a pointer
> ex2.c:361: error: base operand of ‘->’ is not a pointer
> ex2.c:363: error: ‘template<class IndexType, class ScalarType> class
> ALE::Mesh’ used without template parameters
> ex2.c:363: error: expected `;' before ‘e_iter’
> ex2.c:363: error: ‘e_iter’ was not declared in this scope
> ex2.c:363: error: base operand of ‘->’ is not a pointer
> ex2.c:364: error: base operand of ‘->’ is not a pointer
> ex2.c:373: error: ‘template<class Mesh> class ALE::MeshBuilder’ used
> without template parameters
> ex2.c:375: error: expected type-specifier
> ex2.c:375: error: invalid conversion from ‘int*’ to ‘int’
> ex2.c:375: error: expected `;'
> ex2.c:382: error: base operand of ‘->’ is not a pointer
> ex2.c:384: error: ‘MeshSetMesh’ was not declared in this scope
> ex2.c: At global scope:
> ex2.c:390: error: redefinition of ‘PetscErrorCode CreateMesh’
> ex2.c:46: error: ‘PetscErrorCode CreateMesh’ previously defined here
> ex2.c:390: error: ‘Mesh’ was not declared in this scope
> ex2.c:390: error: ‘Mesh’ was not declared in this scope
> ex2.c:390: error: ‘mesh’ was not declared in this scope
> ex2.c:390: error: expected primary-expression before ‘*’ token
> ex2.c:390: error: ‘options’ was not declared in this scope
> make[1]: [ex2.o] Error 1 (ignored)
> /Users/barrysmith/Src/petsc-dev/arch-sieve/bin/mpicxx
> -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   -Wall -Wwrite-strings
> -Wno-strict-aliasing -Wno-unknown-pragmas -g  -o ex2 ex2.o
>  -L/Users/barrysmith/Src/petsc-dev/arch-sieve/lib  -lpetsc -L/usr/X11R6/lib
> -lX11 -llapack -lblas -L/usr/lib/gcc/i686-apple-darwin10/4.2.1/x86_64
> -L/usr/lib/i686-apple-darwin10/4.2.1
> -L/usr/lib/gcc/i686-apple-darwin10/4.2.1 -ldl -lpmpich -lmpich -lopa -lmpl
> -lpthread -lSystem -lmpichf90 -lgfortran
> -L/usr/local/lib/gcc/x86_64-apple-darwin10.4.0/4.6.0 -L/usr/local/lib
> -lgfortran -lgcc_ext.10.5 -lmpichcxx -lstdc++ -lmpichcxx -lstdc++ -ldl
> -lpmpich -lmpich -lopa -lmpl -lpthread -lSystem -ldl
> i686-apple-darwin10-g++-4.2.1: ex2.o: No such file or directory
> make[1]: [ex2] Error 1 (ignored)
> /bin/rm -f -f ex2.o
> /usr/bin/diff: data/ex2_1.vtk: No such file or directory
> /usr/bin/diff: testMesh.vtk: No such file or directory
> Possible problem with ex2_1, diffs above
> /usr/bin/diff: data/ex2_1.vtk: No such file or directory
> /usr/bin/diff: testMesh.vtk: No such file or directory
> Possible problem with ex2_1, diffs above
> /usr/bin/diff: data/ex2_1.vtk: No such file or directory
> /usr/bin/diff: testMesh.vtk: No such file or directory
> Possible problem with ex2_1, diffs above
> make: *** No rule to make target `ex10.PETSc', needed by
> `testexamples_SIEVE'.  Stop.
> barry-smiths-macbook-pro:tutorials barrysmith$
>
>

-- 
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-dev/attachments/20110525/e28eb5d9/attachment.html>