dorsal team mailing list archive

[Harish Narayanan <harish.mlists@xxxxxxxxx>]

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

Harish