On Wed, Sep 01, 2010 at 12:34:04PM +0100, Garth N. Wells wrote: > > > On 01/09/10 12:30, Anders Logg wrote: > > On Wed, Sep 01, 2010 at 12:22:27PM +0100, Garth N. Wells wrote: > >> > >> > >> On 01/09/10 12:17, Anders Logg wrote: > >>> On Wed, Sep 01, 2010 at 01:13:30PM +0200, Anders Logg wrote: > >>>> On Wed, Sep 01, 2010 at 12:58:36PM +0200, Johannes Ring wrote: > >>>>> On Wed, Sep 1, 2010 at 12:50 PM, Anders Logg <[email protected]> wrote: > >>>>>> 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'm having a similar problem with PETSc on the Mac buildbot: > >>>>> > >>>>> > >>>>> http://fenics.org:8080/builders/dolfin-mac-osx/builds/721/steps/dolfin%20build/logs/CMakeError.log > >>>>> > >>>>>> I think I remember seeing this in a discussion recently. Is there a > >>>>>> solution for this? It has worked before. > >>>>> > >>>>> One solution will be to set CXX=mpic++ before running cmake. I guess > >>>>> the reason it worked before might be that the test was not required to > >>>>> work in order for PETSc and SLEPc to be found. This was changed a few > >>>>> days back. > >>>> > >>>> Did we have CXX=mpic++ or similar in the Dorsal platform file for Snow > >>>> Leopard? > >>> > >>> We used to have this in dolfin.package: > >>> > >>> package_specific_setup () { > >>> export CC=mpicc > >>> export CXX=mpic++ > >>> } > >>> > >>> Can we add it back? SLEPc works again for me on OS X when I add it. > >>> > >> > >> Best would be to get the MPI flags right in dolfin/CMakeLists.txt. There > >> are a few FIXME related the link flags. > >> > >> If we use the MPI wrappers, we should somehow test for this and then not > >> add the MPI compiler flags in dolfin/CMakeLists.txt. > > > > I don't understand. That seems like a secondary issue, that we would > > add flags we don't really need if we are using the MPI wrappers. > > > > CMake might pick up a different version of MPI to what mpicxx points to. > It's not very tidy to mix things ups. > > > Does anyone know which extra flag is needed to get things to run? > > Otherwise, I suggest adding the above to dolfin.platform and also a > > FIXME to dolfin/CMakeLists.txt about needing to figure out how to get > > those libraries on Mac. At least that would get things working now. > > > > Read the FIXME: > > # FIXME: Is this linker flag required?
Those flags are now working. -- Anders _______________________________________________ Mailing list: https://launchpad.net/~dorsal Post to : [email protected] Unsubscribe : https://launchpad.net/~dorsal More help : https://help.launchpad.net/ListHelp
