Hi again,
Thanks for your help! By "rebuild UFC", do you mean I should just run
python setup.py install
in the FFC source directory? I have done this, but I have my doubts that
this is what you really mean. I'm not sure on how else to do a rebuild. In
other packages I could do ./configure, cmake, make and make install. But
there are no cmake or make-files in FFC. I tried running
debuild -us -uc
which I've found is the way to rebuild packages from source in Debian, but
it just complains that it "cannot find readable debian/changelog anywhere!"
When using Dorsal, I tried the sid.platform-file but got an error when it
was configuring trilinos. Since no CMakeError.log file was produced, and I
don't know how much of the terminal output I should include, here is the
last 60 lines of output:
failed to compile a simple test project using both languages. The output
was:
Change Dir:
/home/wensby/Work/FEniCS/src/trilinos-11.4.1-Source/dorsal_build_dir/CMakeFiles/FortranCInterface/VerifyCXX
Run Build Command:/usr/bin/make
/usr/bin/cmake -H/usr/share/cmake-2.8/Modules/FortranCInterface/Verify
-B/home/wensby/Work/FEniCS/src/trilinos-11.4.1-Source/dorsal_build_dir/CMakeFiles/FortranCInterface/VerifyCXX
--check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start
/home/wensby/Work/FEniCS/src/trilinos-11.4.1-Source/dorsal_build_dir/CMakeFiles/FortranCInterface/VerifyCXX/CMakeFiles
/home/wensby/Work/FEniCS/src/trilinos-11.4.1-Source/dorsal_build_dir/CMakeFiles/FortranCInterface/VerifyCXX/CMakeFiles/progress.marks
/usr/bin/make -f CMakeFiles/Makefile2 all
make[1]: Entering directory
'/home/wensby/Work/FEniCS/src/trilinos-11.4.1-Source/dorsal_build_dir/CMakeFiles/FortranCInterface/VerifyCXX'
/usr/bin/make -f CMakeFiles/VerifyFortran.dir/build.make
CMakeFiles/VerifyFortran.dir/depend
make[2]: Entering directory
'/home/wensby/Work/FEniCS/src/trilinos-11.4.1-Source/dorsal_build_dir/CMakeFiles/FortranCInterface/VerifyCXX'
cd
/home/wensby/Work/FEniCS/src/trilinos-11.4.1-Source/dorsal_build_dir/CMakeFiles/FortranCInterface/VerifyCXX
&& /usr/bin/cmake -E cmake_depends "Unix Makefiles"
/usr/share/cmake-2.8/Modules/FortranCInterface/Verify
/usr/share/cmake-2.8/Modules/FortranCInterface/Verify
/home/wensby/Work/FEniCS/src/trilinos-11.4.1-Source/dorsal_build_dir/CMakeFiles/FortranCInterface/VerifyCXX
/home/wensby/Work/FEniCS/src/trilinos-11.4.1-Source/dorsal_build_dir/CMakeFiles/FortranCInterface/VerifyCXX
/home/wensby/Work/FEniCS/src/trilinos-11.4.1-Source/dorsal_build_dir/CMakeFiles/FortranCInterface/VerifyCXX/CMakeFiles/VerifyFortran.dir/DependInfo.cmake
make[2]: Leaving directory
'/home/wensby/Work/FEniCS/src/trilinos-11.4.1-Source/dorsal_build_dir/CMakeFiles/FortranCInterface/VerifyCXX'
/usr/bin/make -f CMakeFiles/VerifyFortran.dir/build.make
CMakeFiles/VerifyFortran.dir/requires
make[2]: Entering directory
'/home/wensby/Work/FEniCS/src/trilinos-11.4.1-Source/dorsal_build_dir/CMakeFiles/FortranCInterface/VerifyCXX'
make[2]: Nothing to be done for 'CMakeFiles/VerifyFortran.dir/requires'.
make[2]: Leaving directory
'/home/wensby/Work/FEniCS/src/trilinos-11.4.1-Source/dorsal_build_dir/CMakeFiles/FortranCInterface/VerifyCXX'
/usr/bin/make -f CMakeFiles/VerifyFortran.dir/build.make
CMakeFiles/VerifyFortran.dir/build
make[2]: Entering directory
'/home/wensby/Work/FEniCS/src/trilinos-11.4.1-Source/dorsal_build_dir/CMakeFiles/FortranCInterface/VerifyCXX'
Linking Fortran static library libVerifyFortran.a
/usr/bin/cmake -P CMakeFiles/VerifyFortran.dir/cmake_clean_target.cmake
/usr/bin/cmake -E cmake_link_script
CMakeFiles/VerifyFortran.dir/link.txt --verbose=1
"" cr libVerifyFortran.a CMakeFiles/VerifyFortran.dir/VerifyFortran.f.o
Error running link command: No such file or directory
CMakeFiles/VerifyFortran.dir/build.make:83: recipe for target
'libVerifyFortran.a' failed
make[2]: *** [libVerifyFortran.a] Error 2
make[2]: Leaving directory
'/home/wensby/Work/FEniCS/src/trilinos-11.4.1-Source/dorsal_build_dir/CMakeFiles/FortranCInterface/VerifyCXX'
CMakeFiles/Makefile2:66: recipe for target
'CMakeFiles/VerifyFortran.dir/all' failed
make[1]: *** [CMakeFiles/VerifyFortran.dir/all] Error 2
make[1]: Leaving directory
'/home/wensby/Work/FEniCS/src/trilinos-11.4.1-Source/dorsal_build_dir/CMakeFiles/FortranCInterface/VerifyCXX'
Makefile:78: recipe for target 'all' failed
make: *** [all] Error 2
Call Stack (most recent call first):
cmake/tribits/package_arch/TribitsFortranMangling.cmake:50
(FortranCInterface_VERIFY)
cmake/tribits/package_arch/TribitsGlobalMacros.cmake:1260 (INCLUDE)
cmake/tribits/package_arch/TribitsProjectImpl.cmake:226
(TRIBITS_SETUP_ENV)
cmake/tribits/package_arch/TribitsProject.cmake:75 (TRIBITS_PROJECT_IMPL)
CMakeLists.txt:88 (TRIBITS_PROJECT)
-- Configuring incomplete, errors occurred!
See also
"/home/wensby/Work/FEniCS/src/trilinos-11.4.1-Source/dorsal_build_dir/CMakeFiles/CMakeOutput.log".
See also
"/home/wensby/Work/FEniCS/src/trilinos-11.4.1-Source/dorsal_build_dir/CMakeFiles/CMakeError.log".
You have changed variables that require your cache to be deleted.
Configure will be re-run and you may have to reset some variables.
The following variables have changed:
CMAKE_C_COMPILER= mpicc
CMAKE_CXX_COMPILER= mpicxx
CMAKE_Fortran_COMPILER= mpif90
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
Trilinos_INSTALL_INCLUDE_DIR
UMFPACK_INCLUDE_DIRS
-- Build files have been written to:
/home/wensby/Work/FEniCS/src/trilinos-11.4.1-Source/dorsal_build_dir
*Failure with exit status: 1Exit message: There was a problem configuring
trilinos-11.4.1-Source.*
Will I have to delete my cache, and reset some variables like it says
above? And if so, how do I go about doing this?
Best regards,
Lukas
On 11 June 2014 16:25, Johannes Ring <[email protected]> wrote:
> On Tue, Jun 10, 2014 at 5:02 PM, Lukas Wensby <[email protected]> wrote:
> > I'm sitting on a Debian / Jessie system and I've had a working
> installation
> > of FEniCS for some months now but a few days ago it suddenly stopped
> > working. I try to remember what the initial error message said but I have
> > forgotten. I think it complained on the FFC or something. Anyway, so I
> > thought I needed a refresh of my packages and saw that FEniCS was marked
> as
> > to be removed. "No problem", I thought, as I just figured I'd reinstall
> it
> > right after the updates. But of course now I can't locate FEniCS
> anywhere in
> > aptitude.
>
> The problem is that I uploaded version 1.4.0 of FFC, FIAT, Instant and
> UFL last week but I'm still waiting on my sponsor to upload DOLFIN
> 1.4.0, so the packages are currently in a broken state in Debian.
>
> > Instead I've tried installing it manually from source, manually
> > adding some FEniCS PPA to my APT sources,
>
> The FEniCS PPA is not usable on Debian.
>
> > as well as using Dorsal. All
> > attempts have showed very little success.
> >
> > When trying to install DOLFIN manually, I first downloaded the source
> code
> > for FFC, FIAT, Instant and UFL and followed the given instructions. Then,
> > for DOLFIN, I downloaded the source and as instructed did cmake into a
> build
> > directory like so:
> >
> > mkdir build
> > cd build
> > cmake-gui ..
> >
> > This results in:
> >
> > CMake Warning at dolfin/CMakeLists.txt:318 (message):
> > UFC compiled with different version of SWIG. Please install SWIG version
> > 2.0.11 or recompile UFC with present SWIG.
> >
> > After some hassle I finally managed to install SWIG version 2.0.11,
>
> It would probably be easier to recompile UFC with the present SWIG.
>
> > so I
> > removed the build directory of DOLFIN, created a new one and ran cmake
> only
> > to find:
> >
> > CMake Warning at dolfin/CMakeLists.txt:318 (message):
> > UFC compiled with different version of SWIG. Please install SWIG version
> > 2.0.7 or recompile UFC with present SWIG.
> >
> > So downloading yet another SWIG version and running ./configure (with the
> > option --without-octave to get it to work) I ran both make and make
> install
> > successfully. Then once again I removed the DOLFIN build directory and
> > repeated the steps above, but still got the same warning message. Now I
> > didn't know if this warning message was important or not, so I decided to
> > press on with the hope that it would work anyway. The cmake did after all
> > create a make-file so why not try it?
>
> The Python extension modules will not be built in this case and you
> will end up with the problem below.
>
> > Running make, that beautiful list started to appear in the console:
> >
> > Scanning dependencies of target dolfin
> > [ 0%] Building CXX object
> > dolfin/CMakeFiles/dolfin.dir/nls/TAOLinearBoundSolver.cpp.o
> > [ 1%] Building CXX object
> > dolfin/CMakeFiles/dolfin.dir/nls/PETScSNESSolver.cpp.o
> > [ 1%] Building CXX object
> > dolfin/CMakeFiles/dolfin.dir/nls/NewtonSolver.cpp.o
> >
> > and so on... until after some tens of minutes it ended with:
> >
> > [ 98%] Building CXX object
> > dolfin/CMakeFiles/dolfin.dir/fem/CCFEMAssembler.cpp.o
> > [100%] Building CXX object dolfin/CMakeFiles/dolfin.dir/fem/Form.cpp.o
> > [100%] Building CXX object dolfin/CMakeFiles/dolfin.dir/fem/UFC.cpp.o
> > Linking CXX shared library libdolfin.so
> > /usr/bin/ld: /usr/local/lib/vtk-5.10/libvtkCommon.a(vtkDataArray.cxx.o):
> > relocation R_X86_64_32 against `.bss' can not be used when making a
> shared
> > object; recompile with -fPIC
> > /usr/local/lib/vtk-5.10/libvtkCommon.a: error adding symbols: Bad value
> > collect2: error: ld returned 1 exit status
> > dolfin/CMakeFiles/dolfin.dir/build.make:6366: recipe for target
> > 'dolfin/libdolfin.so.1.4.0' failed
> > make[2]: *** [dolfin/libdolfin.so.1.4.0] Error 1
> > CMakeFiles/Makefile2:202: recipe for target
> > 'dolfin/CMakeFiles/dolfin.dir/all' failed
> > make[1]: *** [dolfin/CMakeFiles/dolfin.dir/all] Error 2
> > Makefile:116: recipe for target 'all' failed
> > make: *** [all] Error 2
> >
> > I don't know how to solve this. Is it some problem with VTK?
>
> Yes. I see you have manually installed VTK in /usr/local. You will
> need to rebuild this with either shared libs enabled or with the -fPIC
> flag. Or use the packages in Debian.
>
> > When trying to run the demo_poisson.py code I get:
> >
> > Traceback (most recent call last):
> > File "demo_poisson.py", line 37, in <module>
> > from dolfin import *
> > File "/usr/lib/python2.7/dist-packages/dolfin/__init__.py", line 16, in
> > <module>
> > import cpp
> > File "/usr/lib/python2.7/dist-packages/dolfin/cpp/__init__.py", line
> 42,
> > in <module>
> > exec("import %s" % module_name)
> > File "<string>", line 1, in <module>
> > ImportError: No module named common
> >
> > In another FEniCS support thread, Johannes Ring's says that this problem
> of
> > "No module named common" comes from DOLFIN and UFC not being built with
> the
> > same version of SWIG, or that DOLFIN is not built with support for CGAL.
> He
> > recommends building FEniCS from source to get DOLFIN with CGAL support.
>
> No, that is not related to the problem with "No module named common".
> You will need to rebuild UFC (now part of FFC) and DOLFIN with the
> same version of SWIG.
>
> > But
> > I am building DOLFIN from source, and I don't know what to do with that
> SWIG
> > problem. Is there anything blatantly wrong with my attempts here? To be
> > fair, it is recommended to use Dorsal, but there is no supported
> > platform-file for the system I am on (Debain / Jessie). I am going to
> try to
> > tailor my own platform-file for but I don't have high hopes of that
> working
> > since I'm fairly new to all of this.
>
> You can use the platform file for Debian sid.
>
> Johannes
>
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