dorsal team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

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?

--
Anders