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? -- Anders _______________________________________________ Mailing list: https://launchpad.net/~dorsal Post to : [email protected] Unsubscribe : https://launchpad.net/~dorsal More help : https://help.launchpad.net/ListHelp
