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