dorsal team mailing list archive

[Johannes Ring <johannr@xxxxxxxxx>]

On Wed, Sep 1, 2010 at 1:02 PM, Garth N. Wells <gnw20@xxxxxxxxx> wrote:
>
>
> On 01/09/10 11:58, 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.
>>
>
> I changed the order a few days back to reduce the number of duplicate
> libraries, with package with the most dependencies at the top, and
> package with the fewest dependencies at the bottom.
>
> I'm still unsure if the line
>
>  list(REMOVE_DUPLICATES DOLFIN_TARGET_LINK_LIBRARIES)
>
> will mess we any carefully order libraries.

I don't see why it should, but maybe it's best to remove it just to be sure.

Johannes