On Fri, Dec 5, 2014 at 1:01 PM, Steffen Wittek <[email protected]> wrote:
> found that in the archives:
>
> Supported combinations are
>
> [...] DOLFIN dev + PETSc 3.3,3.4,3.5,dev
>
> So I have to use the DOLFIN dev instead?
Yes, set STABLE_BUILD=false in dorsal.cfg and make sure you rebuild
all FEniCS packages.
Johannes
>
>
>
>
> On 12/05/14 12:40, Steffen Wittek wrote:
>>
>> Yesterday I tried the compilation of the dolfin-source 1.4.0 . I got all
>> the dependencies installed I guess, but during the cmake of dolfin the
>> compilation stops at 62% with
>>
>> [ 62%] Building CXX object
>> dolfin/CMakeFiles/dolfin.dir/nls/PETScSNESSolver.cpp.o
>> In file included from
>> /usr/include/c++/4.9.2/x86_64-unknown-linux-gnu/bits/os_defines.h:39:0,
>> from
>> /usr/include/c++/4.9.2/x86_64-unknown-linux-gnu/bits/c++config.h:430,
>> from /usr/include/c++/4.9.2/bits/stl_algobase.h:59,
>> from /usr/include/c++/4.9.2/bits/stl_tree.h:61,
>> from /usr/include/c++/4.9.2/map:60,
>> from
>> /home/phoenix/FEniCS/dolfin-1.4.0/dolfin/nls/PETScSNESSolver.cpp:26:
>> /usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and
>> _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
>> # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use
>> _DEFAULT_SOURCE"
>> ^
>> /home/phoenix/FEniCS/dolfin-1.4.0/dolfin/nls/PETScSNESSolver.cpp: In
>> member function 'void
>> dolfin::PETScSNESSolver::init(dolfin::NonlinearProblem&,
>> dolfin::GenericVector&)':
>> /home/phoenix/FEniCS/dolfin-1.4.0/dolfin/nls/PETScSNESSolver.cpp:245:29:
>> error: invalid conversion from 'PetscErrorCode (*)(SNES, Vec, _p_Mat**,
>> _installationp_Mat**, MatStructure*, void*) {aka int (*)(_p_SNES*, _p_Vec*,
>> _p_Mat**, _p_Mat**, MatStructure*, void*)}' to 'PetscErrorCode (*)(SNES,
>> Vec, Mat, Mat, void*) {aka int (*)(_p_SNES*, _p_Vec*, _p_Mat*, _p_Mat*,
>> void*)}' [-fpermissive]
>> &_snes_ctx);
>> ^
>> In file included from
>> /home/phoenix/FEniCS/dolfin-1.4.0/dolfin/nls/PETScSNESSolver.h:29:0,
>> from
>> /home/phoenix/FEniCS/dolfin-1.4.0/dolfin/nls/PETScSNESSolver.cpp:42:
>> /opt/petsc/arch-linux2-cxx-opt/include/petscsnes.h:327:29: note:
>> initializing argument 4 of 'PetscErrorCode SNESSetJacobian(SNES, Mat, Mat,
>> PetscErrorCode (*)(SNES, Vec, Mat, Mat, void*), void*)'
>> PETSC_EXTERN PetscErrorCode SNESSetJacobian(SNES,Mat,Mat,PetscErrorCode
>> (*)(SNES,Vec,Mat,Mat,void*),void*);
>> ^
>> /home/phoenix/FEniCS/dolfin-1.4.0/dolfin/nls/PETScSNESSolver.cpp: In
>> member function 'void
>> dolfin::PETScSNESSolver::set_bounds(dolfin::GenericVector&)':
>> /home/phoenix/FEniCS/dolfin-1.4.0/dolfin/nls/PETScSNESSolver.cpp:605:20:
>> error: 'SNES_VI_INF' was not declared in this scope
>> VecSet(ub, SNES_VI_INF);
>> ^
>> /home/phoenix/FEniCS/dolfin-1.4.0/dolfin/nls/PETScSNESSolver.cpp:617:20:
>> error: 'SNES_VI_INF' was not declared in this scope
>> VecSet(lb, SNES_VI_INF);
>> ^
>> dolfin/CMakeFiles/dolfin.dir/build.make:3734: recipe for target
>> 'dolfin/CMakeFiles/dolfin.dir/nls/PETScSNESSolver.cpp.o' failed
>> make[2]: *** [dolfin/CMakeFiles/dolfin.dir/nls/PETScSNESSolver.cpp.o]
>> Error 1
>> CMakeFiles/Makefile2:201: recipe for target
>> 'dolfin/CMakeFiles/dolfin.dir/all' failed
>> make[1]: *** [dolfin/CMakeFiles/dolfin.dir/all] Error 2
>> Makefile:117: recipe for target 'all' failed
>> make: *** [all] Error 2
>>
>>
>>
>> On 12/04/14 18:26, Steffen Wittek wrote:
>>>
>>> Perfect. I will try it as soon as I have the sources compiled.
>>>
>>> Thank you both,
>>> Steffen
>>>
>>> On 12/04/14 18:20, Benjamin Kehlet wrote:
>>>>
>>>> In fact, the PolygonalMeshGenerator has been removed completely, but
>>>> equivalent functionality is in mshr. Do
>>>>
>>>> domain = Polygon(vertices)
>>>> mesh = mshr.generate_mesh(domain, resolution)
>>>>
>>>> where vertices is an oriented list of dolfin.Points and resolution is an
>>>> int.
>>>>
>>>> Regards
>>>>
>>>> Benjamin Kehlet
>>>>
>>>> 2014-12-04 18:05 GMT+01:00 Steffen Wittek <[email protected]>:
>>>>>
>>>>> Meant the additional functions like PolygonalMeshGenerator etc.. ;).
>>>>>
>>>>> Sounds great. A new Dolfin for Christmas.
>>>>>
>>>>>
>>>>>
>>>>> On 12/04/14 17:43, Jan Blechta wrote:
>>>>>>
>>>>>> On Thu, 04 Dec 2014 17:39:22 +0100
>>>>>> Steffen Wittek<[email protected]> wrote:
>>>>>>
>>>>>>> I see, great. So I use the meshing functions like UnitSquare etc.
>>>>>>
>>>>>> Basic meshes like UnitSquareMesh are still in DOLFIN. No need for mshr
>>>>>> for these.
>>>>>>
>>>>>>> from the mshr package and forget about CGAL. The config
>>>>>>> (DDOLFIN_ENABLE_CGAL:BOOL=OFF) goes directly into the platform-file?
>>>>>>
>>>>>> Into FEniCS/packages/dolfin.package to variable CONFOPTS.
>>>>>>
>>>>>> Jan
>>>>>>
>>>>>>> a
>>>>>>>
>>>>>>> Thank you a lot for your help already!
>>>>>>>
>>>>>>> Steffen
>>>>>>>
>>>>>>>
>>>>>>> On 12/04/14 17:26, Jan Blechta wrote:
>>>>>>>>
>>>>>>>> On Thu, 04 Dec 2014 15:58:38 +0000
>>>>>>>> Steffen Wittek<[email protected]> wrote:
>>>>>>>>
>>>>>>>>> thanks. I deleted the working tree and am compiling again. While
>>>>>>>>> this happens the compiler complains that CGAL cannot be found:
>>>>>>>>>
>>>>>>>>> CMake Warning at cmake/modules/FindCGAL.cmake:46 (find_package):
>>>>>>>>> Could not find a package configuration file provided by
>>>>>>>>> "CGAL"
>>>>>>>>> with any of
>>>>>>>>> the following names:
>>>>>>>>>
>>>>>>>>> CGALConfig.cmake
>>>>>>>>> cgal-config.cmake
>>>>>>>>>
>>>>>>>>> Add the installation prefix of "CGAL" to CMAKE_PREFIX_PATH or
>>>>>>>>> set "CGAL_DIR" to a directory containing one of the above files.
>>>>>>>>> If "CGAL" provides a separate development package or SDK, be sure
>>>>>>>>> it has been installed.
>>>>>>>>> Call Stack (most recent call first):
>>>>>>>>> CMakeLists.txt:512 (find_package)
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> -- CGAL could not be found. Be sure to set CGAL_DIR (missing:
>>>>>>>>> CGAL_LIBRARIES CGAL_INCLUDE_DIRS CGAL_TEST_RUNS CGAL_VERSION_OK)
>>>>>>>>> (Required is at least version "4.1")
>>>>>>>>>
>>>>>>>>> So it seems that there is something else wrong on top. Is CGAL
>>>>>>>>> just a standalone package or is it included in another one? When I
>>>>>>>>> had
>>>>>>>>
>>>>>>>> CGAL is in 1.4.0 used for CSG (constructive solid geometry) meshing.
>>>>>>>> This functionality was removed from DOLFIN and is now in a separate
>>>>>>>> packagehttps://bitbucket.org/benjamik/mshr/. So I wouldn't bother
>>>>>>>>
>>>>>>>> with compiling with CGAL as by the new year you can compile DOLFIN
>>>>>>>> 1.5.0 and mshr with CGAL separately. Disable by configuring with
>>>>>>>> -DDOLFIN_ENABLE_CGAL:BOOL=OFF
>>>>>>>>
>>>>>>>>> Dolfin installed from the tarballs the python ver. used was 2.7 .
>>>>>>>>> If I now include the FFC and UFC in dorsal it directly accesses
>>>>>>>>> python3.4 and throws around with errors (below). I guess it could
>>>>>>>>> be
>>>>>>>>
>>>>>>>> FEniCS 1.4.0 will not run with python 3 (hence the syntax errors
>>>>>>>> below). Use py2.7. Development version of FEniCS should run with
>>>>>>>> py3 in theory.
>>>>>>>>
>>>>>>>>> the mismatch as you mentioned. The way to go is to delete the whole
>>>>>>>>> working tree of FEniCS/src and let dorsal wget all packages again?
>>>>>>>>
>>>>>>>> Maybe.
>>>>>>>>
>>>>>>>> Jan
>>>>>>>>
>>>>>>>>> ####################################
>>>>>>>>> File
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> "/home/phoenix/Work/FEniCS/lib/python3.4/site-packages/ferari/sigdig.py",
>>>>>>>>> line 41
>>>>>>>>> print "%.16e" % (a,)
>>>>>>>>> ^
>>>>>>>>> SyntaxError: invalid syntax
>>>>>>>>>
>>>>>>>>> File
>>>>>>>>>
>>>>>>>>> "/home/phoenix/Work/FEniCS/lib/python3.4/site-packages/ferari/pg.py",
>>>>>>>>> line 65
>>>>>>>>> raise RuntimeError, "can't compare"
>>>>>>>>> ^
>>>>>>>>> SyntaxError: invalid syntax
>>>>>>>>>
>>>>>>>>> Fetching ufl-1.4.0
>>>>>>>>> Verifying ufl-1.4.0
>>>>>>>>> ufl-1.4.0.tar.gz: OK
>>>>>>>>> Unpacking ufl-1.4.0
>>>>>>>>> Building ufl-1.4.0
>>>>>>>>> File "setup.py", line 24
>>>>>>>>> print version
>>>>>>>>> ^
>>>>>>>>> SyntaxError: Missing parentheses in call to 'print'
>>>>>>>>>
>>>>>>>>> ####################################
>>>>>>>>>
>>>>>>>>> Steffen
>>>>>>>>>
>>>>>>>>> On 12/04/14 15:27, Jan Blechta wrote:
>>>>>>>>>>
>>>>>>>>>> Some form files in DOLFIN source tree like
>>>>>>>>>> /home/phoenix/Work/FEniCS/src/dolfin-1.4.0/dolfin/ale/Poisson3D.h
>>>>>>>>>> are generated by FFC and they may be outdated. Try cleaning DOLFIN
>>>>>>>>>> working tree or force their regeneration by
>>>>>>>>>>
>>>>>>>>>> $ ./cmake/scripts/generate-form-files
>>>>>>>>>>
>>>>>>>>>> If this does not help you may have some mismatch in DOLFIN, FFC,
>>>>>>>>>> UFC (now part of FFC) versions.
>>>>>>>>>>
>>>>>>>>>> Jan
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Thu, 04 Dec 2014 15:09:08 +0000
>>>>>>>>>> Steffen Wittek<[email protected]> wrote:
>>>>>>>>>>
>>>>>>>>>>> Dear community,
>>>>>>>>>>>
>>>>>>>>>>> I used the tarball from myles at the AUR, but unfortunately
>>>>>>>>>>> dolfin is compiled without cgal and hence I wanted to recompile
>>>>>>>>>>> the source myself. On top viper had some problems and I hope to
>>>>>>>>>>> fix that on top.
>>>>>>>>>>>
>>>>>>>>>>> I got dorsal and modified another platform-file to get my own.
>>>>>>>>>>> The tarball that was finally downloaded was dolfin-1.4.0.tar.gz
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> <https://bitbucket.org/fenics-project/dolfin/downloads/dolfin-1.4.0.tar.gz>.
>>>>>>>>>>> The compilation stops however in the file MeshDisplacement.cpp
>>>>>>>>>>> with some dozens error messages that all read similiar. The last
>>>>>>>>>>> one reads:
>>>>>>>>>>>
>>>>>>>>>>> ############################################
>>>>>>>>>>> In file included from
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> /home/phoenix/Work/FEniCS/src/dolfin-1.4.0/dolfin/ale/MeshDisplacement.cpp:25:0:
>>>>>>>>>>>
>>>>>>>>>>> /home/phoenix/Work/FEniCS/src/dolfin-1.4.0/dolfin/ale/Poisson3D.h:
>>>>>>>>>>> In constructor 'Poisson3D::Form_a::Form_a(std::shared_ptr<const
>>>>>>>>>>> dolfin::FunctionSpace>, std::shared_ptr<const
>>>>>>>>>>> dolfin::FunctionSpace>)':
>>>>>>>>>>>
>>>>>>>>>>> /home/phoenix/Work/FEniCS/src/dolfin-1.4.0/dolfin/ale/Poisson3D.h:2010:71:
>>>>>>>>>>> error: invalid new-expression of abstract class type
>>>>>>>>>>> 'poisson3d_form_0' _ufc_form = std::shared_ptr<const
>>>>>>>>>>> ufc::form>(new poisson3d_form_0()); ^
>>>>>>>>>>> dolfin/CMakeFiles/dolfin.dir/build.make:2676: recipe for target
>>>>>>>>>>> 'dolfin/CMakeFiles/dolfin.dir/ale/MeshDisplacement.cpp.o' failed
>>>>>>>>>>> ############################################
>>>>>>>>>>>
>>>>>>>>>>> I thought the pure fact that dorsal is starting with the
>>>>>>>>>>> compilation means that all other packages that were needed were
>>>>>>>>>>> indeed found and it is an internal problem in dolfin.
>>>>>>>>>>> Does anyone have some input on this? If there is any further
>>>>>>>>>>> input needed just let me know.
>>>>>>>>>>>
>>>>>>>>>>> Thank you already,
>>>>>>>>>>> Steffen
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> fenics mailing list
>>>>>>> [email protected]
>>>>>>> http://fenicsproject.org/mailman/listinfo/fenics
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> fenics mailing list
>>>>> [email protected]
>>>>> http://fenicsproject.org/mailman/listinfo/fenics
>>>
>>>
>>> _______________________________________________
>>> fenics mailing list
>>> [email protected]
>>> http://fenicsproject.org/mailman/listinfo/fenics
>>
>>
>> _______________________________________________
>> fenics mailing list
>> [email protected]
>> http://fenicsproject.org/mailman/listinfo/fenics
>
>
> _______________________________________________
> fenics mailing list
> [email protected]
> http://fenicsproject.org/mailman/listinfo/fenics
_______________________________________________
fenics mailing list
[email protected]
http://fenicsproject.org/mailman/listinfo/fenics
