dorsal team mailing list archive

["Garth N. Wells" <gnw20@xxxxxxxxx>]

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.

Garth


> Johannes
> 
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