On Wed, Sep 01, 2010 at 12:09:20PM +0200, Johannes Ring wrote: > On Wed, Sep 1, 2010 at 12:03 PM, Anders Logg <[email protected]> wrote: > > 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. > > /sw (Fink) was the default BOOST_DIR. I have changed this to > /opt/local (MacPorts) now.
It works fine when I set BOOST_DIR to /opt/local Should we write BOOST_DIR to dolfin.conf? -- Anders _______________________________________________ Mailing list: https://launchpad.net/~dorsal Post to : [email protected] Unsubscribe : https://launchpad.net/~dorsal More help : https://help.launchpad.net/ListHelp
