On Wed, Sep 01, 2010 at 12:43:12PM +0200, Anders Logg wrote: > On Wed, Sep 01, 2010 at 12:33:40PM +0200, Johannes Ring wrote: > > On Wed, Sep 1, 2010 at 12:12 PM, Anders Logg <[email protected]> wrote: > > > 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? > > > > Yes, that might be a good idea, however, it might not always be defined. > > Your latest fix seems to have done the trick. It's working fine now. > > So, clean install from Dorsal on Mac OS X without any extra tweaks > seems to work perfectly now, at least for me. > > Anyone else still having trouble? > > I'll try removing some PETSc files next to see if it breaks cleanly.
One thing that's still missing on OS X is SLEPc. It has worked before but the test program fails during configuration with the following message: Undefined symbols: "_ompi_mpi_comm_self" I think I remember seeing this in a discussion recently. Is there a solution for this? It has worked before. -- Anders _______________________________________________ Mailing list: https://launchpad.net/~dorsal Post to : [email protected] Unsubscribe : https://launchpad.net/~dorsal More help : https://help.launchpad.net/ListHelp
