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On 01/09/10 10:13, Harish Narayanan wrote:
On 9/1/10 2:35 PM, Harish Narayanan wrote:On 9/1/10 2:09 PM, Johannes Ring wrote:On Wed, Sep 1, 2010 at 9:17 AM, Johannes Ring<johannr@xxxxxxxxx> wrote:On Wed, Sep 1, 2010 at 8:39 AM, Harish Narayanan <harish.mlists@xxxxxxxxx> wrote:On 9/1/10 12:02 PM, Harish Narayanan wrote:On 9/1/10 2:44 AM, Marie Rognes wrote:On 31. aug. 2010 22:56, Anders Logg wrote:On Tue, Aug 31, 2010 at 04:28:32PM +0200, Marie Rognes wrote:On 31. aug. 2010 16:22, Johannes Ring wrote:On Tue, Aug 31, 2010 at 4:13 PM, Marie Rognes<meg@xxxxxxxxx> wrote:I having some issues with PETSc (surprise) as of today. Dorsal tells me that (full log attached): [\snip] -- The following optional packages were found: -- (OK) MPI -- (OK) PETSC -- (OK) SLEPC -- (OK) UMFPACK [\snap] But:from dolfin import * has_la_backend("PETSc")FalseA = PETScMatrix()Traceback (most recent call last): File "<stdin>", line 1, in<module> NameError: name 'PETScMatrix' is not definedHelp?There is no -DHAS_PETSC in your log. Try to clean up/remove the dorsal_build_dir inside the DOLFIN source directory.Removed. Check.Then rerun Dorsal and see if the PETSc test passes.-- The following optional packages were found: -- (OK) MPI -- (OK) PETSC -- (OK) SLEPC -- (OK) UMFPACK -- (OK) PARMETIS -- (OK) GMP -- (OK) CGAL -- (OK) ZLIB -- (OK) PYTHON -- The following optional packages could not be found: -- (**) TRILINOS -- (**) MTL4 -- (**) CHOLMOD -- (**) SCOTCH -- Configuring done -- Generating done -- Build files have been written to: /home/meg/local/dorsal_downloads/dolfin make: *** No rule to make target `install'. Stop. Failure with exit status: 2 Exit message: There was a problem building dolfin.I had the same problem (I think). It turned out to be a problem with my PETSC_ARCH variable which was set to linux-gnu-c-opt instead of linux-gnu-cxx-opt.Doesn't solve the problem for me :( - My PETSC_ARCH is set to linux-gnu-cxx-opt (cf gentoo.platform) - cmake reports: -- PETSC_ARCH is linux-gnu-cxx-opt - Still get same problem.I think this changed in Dorsal at some point recently.Everything updated as of 20 seconds ago ...I too am now seeing strange things such as this: . . . -- PETSC_DIR is /Users/harish/Work/FEniCS/dev/src/petsc-3.1-p4 -- PETSC_ARCH is darwin10.0.0-cxx-opt -- Found petscconf.h -- PETSc test failed -- PETSc could not be found. Be sure to set PETSC_DIR and PETSC_ARCH. (missing: PETSC_TEST_RUNS) . . . -- (OK) MPI -- (OK) MTL4 -- (OK) UMFPACK -- (OK) CHOLMOD -- (OK) SCOTCH -- (OK) PARMETIS -- (OK) GMP -- (OK) CGAL -- (OK) ZLIB -- (OK) PYTHON -- The following optional packages could not be found: -- (**) PETSC -- (**) SLEPC -- (**) TRILINOSFollowing which (and independently), CMake fails catastrophically: Building CXX object dolfin/CMakeFiles/dolfin.dir/ale/HarmonicSmoothing.cpp.o [ 1%] cd /foo/dolfin/dorsal_build_dir/dolfin&& /opt/local/bin/c++ -Ddolfin_EXPORTS -DPACKAGE_VERSION=\"0.9.8\" -DBOOST_UBLAS_NDEBUG -DHAS_MTL4 -DMTL_HAS_BLAS -DHAS_UMFPACK -DHAS_CHOLMOD -DHAS_SCOTCH -DHAS_PARMETIS -DHAS_CGAL -DHAS_GMP -DHAS_ZLIB -DHAS_CPPUNIT -DHAS_MPI -DMPICH_IGNORE_CXX_SEEK -frounding-math;-D_REENTRANT -O2 -g -fPIC -I/foo/dolfin -I/opt/local/include/libxml2 -I/Users/harish/Work/FEniCS/dev/include -I/opt/local/include -I/Users/harish/Work/FEniCS/dev/src/mtl4 -I/opt/local/include/ufsparse -I/opt/local/include/cppunit -o CMakeFiles/dolfin.dir/ale/HarmonicSmoothing.cpp.o -c /foo/dolfin/dolfin/ale/HarmonicSmoothing.cpp i686-apple-darwin10-g++-4.2.1: no input files i686-apple-darwin10-g++-4.2.1: no input files Building CXX object dolfin/CMakeFiles/dolfin.dir/ale/TransfiniteInterpolation.cpp.o cd /foo/dolfin/dorsal_build_dir/dolfin&& /opt/local/bin/c++ -Ddolfin_EXPORTS -DPACKAGE_VERSION=\"0.9.8\" -DBOOST_UBLAS_NDEBUG -DHAS_MTL4 -DMTL_HAS_BLAS -DHAS_UMFPACK -DHAS_CHOLMOD -DHAS_SCOTCH -DHAS_PARMETIS -DHAS_CGAL -DHAS_GMP -DHAS_ZLIB -DHAS_CPPUNIT -DHAS_MPI -DMPICH_IGNORE_CXX_SEEK -frounding-math;-D_REENTRANT -O2 -g -fPIC -I/foo/dolfin -I/opt/local/include/libxml2 -I/Users/harish/Work/FEniCS/dev/include -I/opt/local/include -I/Users/harish/Work/FEniCS/dev/src/mtl4 -I/opt/local/include/ufsparse -I/opt/local/include/cppunit -o CMakeFiles/dolfin.dir/ale/TransfiniteInterpolation.cpp.o -c /foo/dolfin/dolfin/ale/TransfiniteInterpolation.cpp Building CXX object dolfin/CMakeFiles/dolfin.dir/common/real.cpp.o /bin/sh: -D_REENTRANT: command not found /bin/sh: -D_REENTRANT: command not foundI made a fix for this yesterday. Maybe you just need to clean up the CMake cache (remove the dorsal_build_dir folder)?My fix was reverted but it should be fixed again now.This problem is fixed, leaving only the petsc/slepc error.I spoke too soon. I now receive the following during the linking stage (too).
Try commenting out
list(REMOVE_DUPLICATES DOLFIN_TARGET_LINK_LIBRARIES)
in dolfin/CMakeLists.txt.
Also try disabling almost everything and see if changing the order in
which package flags and libs are added dolfin/CMakeLists.txt makes a
difference.
Garth
Undefined symbols:
"_METIS_mCPartGraphRecursive2", referenced from:
_ParMETIS_V3_PartKway in libparmetis.a(kmetis.o)
_PartitionSmallGraph__ in libparmetis.a(weird.o)
_Mc_InitPartition_RB__ in libparmetis.a(initpart.o)
_Mc_InitPartition_RB__ in libparmetis.a(initpart.o)
_Balance_Partition__ in libparmetis.a(initbalance.o)
_Balance_Partition__ in libparmetis.a(initbalance.o)
ld: symbol(s) not found
collect2: ld returned 1 exit status
make[2]: *** [dolfin/libdolfin.0.9.8.dylib] Error 1
make[1]: *** [dolfin/CMakeFiles/dolfin.dir/all] Error 2
make: *** [all] Error 2
Harish
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