dorsal team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

On Wed, Sep 01, 2010 at 11:36:11AM +0200, Johannes Ring wrote:
> On Wed, Sep 1, 2010 at 11:13 AM, Harish Narayanan
> <harish.mlists@xxxxxxxxx> 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 <johannr@xxxxxxxxx> wrote:
> >>>> On Wed, Sep 1, 2010 at 8:39 AM, Harish Narayanan
> >>>> <harish.mlists@xxxxxxxxx> 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 <meg@xxxxxxxxx> 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.

--
Anders