dorsal team mailing list archive

[Harish Narayanan <harish.mlists@xxxxxxxxx>]

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
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