dorsal team mailing list archive

[Johannes Ring <johannr@xxxxxxxxx>]

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.

Johannes