dorsal team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

On Wed, Sep 01, 2010 at 12:34:04PM +0100, Garth N. Wells wrote:
>
>
> On 01/09/10 12:30, Anders Logg wrote:
> > On Wed, Sep 01, 2010 at 12:22:27PM +0100, Garth N. Wells wrote:
> >>
> >>
> >> On 01/09/10 12:17, Anders Logg wrote:
> >>> On Wed, Sep 01, 2010 at 01:13:30PM +0200, Anders Logg wrote:
> >>>> On Wed, Sep 01, 2010 at 12:58:36PM +0200, Johannes Ring wrote:
> >>>>> On Wed, Sep 1, 2010 at 12:50 PM, Anders Logg <logg@xxxxxxxxx> wrote:
> >>>>>> On Wed, Sep 01, 2010 at 12:43:12PM +0200, Anders Logg wrote:
> >>>>>>> On Wed, Sep 01, 2010 at 12:33:40PM +0200, Johannes Ring wrote:
> >>>>>>>> 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.
> >>>>>>>
> >>>>>>> Your latest fix seems to have done the trick. It's working fine now.
> >>>>>>>
> >>>>>>> So, clean install from Dorsal on Mac OS X without any extra tweaks
> >>>>>>> seems to work perfectly now, at least for me.
> >>>>>>>
> >>>>>>> Anyone else still having trouble?
> >>>>>>>
> >>>>>>> I'll try removing some PETSc files next to see if it breaks cleanly.
> >>>>>>
> >>>>>> One thing that's still missing on OS X is SLEPc. It has worked before
> >>>>>> but the test program fails during configuration with the following message:
> >>>>>>
> >>>>>> Undefined symbols:
> >>>>>>  "_ompi_mpi_comm_self"
> >>>>>
> >>>>> I'm having a similar problem with PETSc on the Mac buildbot:
> >>>>>
> >>>>>   http://fenics.org:8080/builders/dolfin-mac-osx/builds/721/steps/dolfin%20build/logs/CMakeError.log
> >>>>>
> >>>>>> I think I remember seeing this in a discussion recently. Is there a
> >>>>>> solution for this? It has worked before.
> >>>>>
> >>>>> One solution will be to set CXX=mpic++ before running cmake. I guess
> >>>>> the reason it worked before might be that the test was not required to
> >>>>> work in order for PETSc and SLEPc to be found. This was changed a few
> >>>>> days back.
> >>>>
> >>>> Did we have CXX=mpic++ or similar in the Dorsal platform file for Snow Leopard?
> >>>
> >>> We used to have this in dolfin.package:
> >>>
> >>> package_specific_setup () {
> >>>     export CC=mpicc
> >>>     export CXX=mpic++
> >>> }
> >>>
> >>> Can we add it back? SLEPc works again for me on OS X when I add it.
> >>>
> >>
> >> Best would be to get the MPI flags right in dolfin/CMakeLists.txt. There
> >> are a few FIXME related the link flags.
> >>
> >> If we use the MPI wrappers, we should somehow test for this and then not
> >> add the MPI compiler flags in dolfin/CMakeLists.txt.
> >
> > I don't understand. That seems like a secondary issue, that we would
> > add flags we don't really need if we are using the MPI wrappers.
> >
>
> CMake might pick up a different version of MPI to what mpicxx points to.
> It's not very tidy to mix things ups.
>
> > Does anyone know which extra flag is needed to get things to run?
> > Otherwise, I suggest adding the above to dolfin.platform and also a
> > FIXME to dolfin/CMakeLists.txt about needing to figure out how to get
> > those libraries on Mac. At least that would get things working now.
> >
>
> Read the FIXME:
>
>     # FIXME: Is this linker flag required?

Those flags are now working.

--
Anders