dorsal team mailing list archive

[Harish Narayanan <harish.mlists@xxxxxxxxx>]

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.

Harish