dorsal team mailing list archive

[Johannes Ring <johannr@xxxxxxxxx>]

On Wed, Sep 1, 2010 at 1:30 PM, Anders Logg <logg@xxxxxxxxx> 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.
>
> Does anyone know which extra flag is needed to get things to run?

I guess that these should do it: -lmpi -lopen-rte -lopen-pal

The problem (in my case with PETSc) is that these are missing from
PETSC_LIBRARIES so the test program in FindPETSc.cmake fails.

Johannes

> 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.
>
> --
> Anders
>