dorsal team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

On Wed, Sep 01, 2010 at 11:43:41AM +0100, Garth N. Wells wrote:
>
>
> On 01/09/10 11:12, Anders Logg 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?
> >
>
> It would be good if these paths could somehow be set on the code at
> compile/install since CMake has already done the work of finding them.
>
> Garth

Looks like it's not needed.

--
Anders