dorsal team mailing list archive

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

On 01/09/10 11:12, Anders Logg 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?
> 

It would be good if these paths could somehow be set on the code at
compile/install since CMake has already done the work of finding them.

Garth

> --
> Anders
> 
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