On Fri, Dec 5, 2014 at 1:11 PM, Steffen Wittek <[email protected]> wrote: > with all you mean the whole list > > petsc > slepc > FFC > UFL > ...
No, with all FEniCS packages I mean fiat ufl ffc instant dolfin You can add skip: in front of the other packages. Johannes PS: Please use [email protected] next time for installation related questions. > > On 12/05/14 13:02, Johannes Ring wrote: > >> On Fri, Dec 5, 2014 at 1:01 P M, 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
