dorsal team mailing list archive

[Johannes Ring <johannr@xxxxxxxxx>]

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)?

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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