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