On Wed, Sep 01, 2010 at 11:36:11AM +0200, Johannes Ring wrote: > On Wed, Sep 1, 2010 at 11:13 AM, Harish Narayanan > <[email protected]> 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 <[email protected]> wrote: > >>>> On Wed, Sep 1, 2010 at 8:39 AM, Harish Narayanan > >>>> <[email protected]> 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 <[email protected]> > >>>>>>>>>> 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") > >>>>>>>>>>>>>> > >>>>>>>>>>>>>> > >>>>>>>>>>> False > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>>>>> A = PETScMatrix() > >>>>>>>>>>>>>> > >>>>>>>>>>>>>> > >>>>>>>>>>> Traceback (most recent call last): > >>>>>>>>>>> File "<stdin>", line 1, in <module> > >>>>>>>>>>> NameError: name 'PETScMatrix' is not defined > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>>>>> > >>>>>>>>>>> Help? > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>> 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 > >>>>>> -- (**) TRILINOS > >>>>> > >>>>> Following 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 found > >>>> > >>>> I 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). > > > > 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 > > I also got this on the Mac buildbot. The problem is that there is a > file /opt/local/lib/libmetis.dylib that is used instead of the one > that comes with ParMETIS (that Dorsal builds). I worked around this by > configuring DOLFIN with > -DMETIS_LIBRARY=/Users/fenicsslave2/Work/FEniCS/lib/libmetis.a (the > one that Dorsal installed with ParMETIS). > > This problem only shows up when PETSc is not found because > PETSC_LIBRARIES contains the correct link flags (-L/path/to/libmetis.a > -lmetis). > > Johannes
Everything seems to work fine except BOOST_DIR is missing when I run the demos. -- Anders _______________________________________________ Mailing list: https://launchpad.net/~dorsal Post to : [email protected] Unsubscribe : https://launchpad.net/~dorsal More help : https://help.launchpad.net/ListHelp
