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