dorsal team mailing list archive

[Johannes Ring <johannr@xxxxxxxxx>]

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