dorsal team mailing list archive

[Johannes Ring <johannr@xxxxxxxxx>]

On Wed, Sep 1, 2010 at 12:03 PM, Anders Logg <logg@xxxxxxxxx> 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
>> <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.

/sw (Fink) was the default BOOST_DIR. I have changed this to
/opt/local (MacPorts) now.

Johannes