dorsal team mailing list archive

[Johannes Ring <johannr@xxxxxxxxx>]

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.

Johannes

> Johannes
>
>> 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/common/real.cpp.o -c
>> /foo/dolfin/dolfin/common/real.cpp
>> make[2]: *** [dolfin/CMakeFiles/dolfin.dir/ale/HarmonicSmoothing.cpp.o]
>> Error 127
>> make[2]: *** Waiting for unfinished jobs....
>> make[2]: *** [dolfin/CMakeFiles/dolfin.dir/ale/ALE.cpp.o] Error 127
>> i686-apple-darwin10-g++-4.2.1: no input files
>> /bin/sh: -D_REENTRANT: command not found
>> make[2]: *** [dolfin/CMakeFiles/dolfin.dir/common/real.cpp.o] Error 127
>> i686-apple-darwin10-g++-4.2.1: no input files
>> /bin/sh: -D_REENTRANT: command not found
>> make[2]: ***
>> [dolfin/CMakeFiles/dolfin.dir/ale/TransfiniteInterpolation.cpp.o] Error 127
>> make[1]: *** [dolfin/CMakeFiles/dolfin.dir/all] Error 2
>> make: *** [all] Error 2
>> Failure with exit status: 2
>> Exit message: There was a problem building dolfin.
>>
>>
>> Hairsh
>>
>> _______________________________________________
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>>
>