dolfin team mailing list archive

[Johannes Ring <johannr@xxxxxxxxx>]

On Wed, Sep 1, 2010 at 8:32 AM, Harish Narayanan
<harish.mlists@xxxxxxxxx> 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)

A few days ago I made the PETSc CMake module fail if the test program
didn't run. Look in CMakeFiles/CMakeError.log in the build directory.
Does it look similar to what the Mac buildbot slave reports:

  http://fenics.org:8080/builders/dolfin-mac-osx/builds/721/steps/dolfin%20build/logs/CMakeError.log

?

PETSC_LIBRARIES in FindPETSc.cmake seems to be missing some of the
required OpenMPI libraries

  fenicsslave2@buildbotmac:dolfin$ mpic++ --showme:link
  -Wl,-u,_munmap -Wl,-multiply_defined,suppress -lmpi_cxx -lmpi
-lopen-rte -lopen-pal
  fenicsslave2@buildbotmac:dolfin$

The latter three does not appear in PETSC_LIBRARIES on OS X.

I'm not sure what the best fix is but it should work if CXX=mpic++ is
specified before running cmake. Note that the CMake cache must be
cleaned up first.

Johannes

> .
> .
> .
>
> -- (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
>
> Harish
>
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