On Wed, Sep 01, 2010 at 11:43:41AM +0100, Garth N. Wells wrote: > > > On 01/09/10 11:12, Anders Logg 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? > > > > It would be good if these paths could somehow be set on the code at > compile/install since CMake has already done the work of finding them. > > Garth
Looks like it's not needed. -- Anders _______________________________________________ Mailing list: https://launchpad.net/~dorsal Post to : [email protected] Unsubscribe : https://launchpad.net/~dorsal More help : https://help.launchpad.net/ListHelp
