[deal.II] Creating a FESystem with bulk and surface FE spaces
Hello, I need to solve a system of many PDEs (currently 18). The actual number changes since the PDEs are defined by a truncated infinite sum and some recursive equations. Anyway, the first two equations are defined on a 2D or 3D domain (call it Omega) and the rest is only defined on the boundary of Omega. My first idea was to create a FESystem object and attach to it 2 FE spaces defined on Omega and 16 FE spaces defined on the boundary. That is, I tried these options - FESystem<1, 2> fe(FE_Q<2, 2>(degree), 2, FE_Q<1, 2>(degree), 16) - FESystem<2, 2> fe(FE_Q<2, 2>(degree), 2, FE_Q<1, 2>(degree), 16) However, that produced compilation errors. What I understand is that the FESystem must be created by either FE spaces defined in Omega or FE spaces defined in the manifold, but not a combination. As a way around I tried (a very ugly hack) where I defined all FE spaces in Omega and then add constraints to all DoFs associated with the internal nodes for the variables that are defined on the manifold. This sounds like a tremendous waste of resources since most of the equations in my system live in the manifold, so I end up constraining most of the DoFs. And even worse, it produced a matrix that seems to be sometimes singular and sometimes non-singular. That is, I can solve the system and get accurate results (I have the exact solution) for some grids but in other grids the matrix is singular so I get NaNs. I suspect this problem is a consequence of constraining most of my DoFs. FYI, the solver that I am using is the MUMPS implementation in PETSc. I wonder if there is a proper or standard way to construct systems that are defined by some equations in a domain and some in a manifold of the domain. I definitely don't think constraining most of my DoFs is the way to go. Thanks and all the best, Manuel Quezada -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/92fb368a-b689-48a8-982d-b97bd6946e4bn%40googlegroups.com.
[deal.II] PETSc Vector set deprecated
Hello, I am building PETSc vectors with the set operation and I see it’s deprecated. The documentation suggests to use “import( )” but I don’t see how to use it. How can I use import( ) as a replacement for set( ) as the documentation suggests? Please provide an example. Thank you, Zachary -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/8CBCFFAA-05DE-42F3-A65A-0A5842736424%40gmail.com.
[deal.II] Boost serialization linking error
Dear All, I am trying to install deal.ii-9.0.1 using spack v.15 on our HPC cluster (Centos 7 OS). The installation works fine. Most of my code compiles without any issues, but when compiling targets using Boost serilization functionalities, I get the following linking errors: iwtm020h@emmy1:/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build$ make VERBOSE=1 /home/woody/iwtm/iwtm020h/spack-install/dealii901-spackv15-gcc/spack/opt/spack/linux-centos7-ivybridge/gcc-7.3.0/cmake-3.17.3-yp7x4tfykdwkolbguxb2nbd46ktt5e6h/bin/cmake -S/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac -B/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build --check-build-system CMakeFiles/Makefile.cmake 0 /home/woody/iwtm/iwtm020h/spack-install/dealii901-spackv15-gcc/spack/opt/spack/linux-centos7-ivybridge/gcc-7.3.0/cmake-3.17.3-yp7x4tfykdwkolbguxb2nbd46ktt5e6h/bin/cmake -E cmake_progress_start /home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build/CMakeFiles /home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[1]: Entering directory `/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build' make -f CMakeFiles/mncfrac.dir/build.make CMakeFiles/mncfrac.dir/depend make[2]: Entering directory `/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build' cd /home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build && /home/woody/iwtm/iwtm020h/spack-install/dealii901-spackv15-gcc/spack/opt/spack/linux-centos7-ivybridge/gcc-7.3.0/cmake-3.17.3-yp7x4tfykdwkolbguxb2nbd46ktt5e6h/bin/cmake -E cmake_depends "Unix Makefiles" /home/woody/iwtm/iwtm020h/trial-code/MNC-Frac /home/woody/iwtm/iwtm020h/trial-code/MNC-Frac /home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build /home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build /home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build/CMakeFiles/mncfrac.dir/DependInfo.cmake --color= make[2]: Leaving directory `/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build' make -f CMakeFiles/mncfrac.dir/build.make CMakeFiles/mncfrac.dir/build make[2]: Entering directory `/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build' make[2]: Nothing to be done for `CMakeFiles/mncfrac.dir/build'. make[2]: Leaving directory `/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build' [ 54%] Built target mncfrac make -f CMakeFiles/mncfracture.dir/build.make CMakeFiles/mncfracture.dir/depend make[2]: Entering directory `/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build' cd /home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build && /home/woody/iwtm/iwtm020h/spack-install/dealii901-spackv15-gcc/spack/opt/spack/linux-centos7-ivybridge/gcc-7.3.0/cmake-3.17.3-yp7x4tfykdwkolbguxb2nbd46ktt5e6h/bin/cmake -E cmake_depends "Unix Makefiles" /home/woody/iwtm/iwtm020h/trial-code/MNC-Frac /home/woody/iwtm/iwtm020h/trial-code/MNC-Frac /home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build /home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build /home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build/CMakeFiles/mncfracture.dir/DependInfo.cmake --color= make[2]: Leaving directory `/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build' make -f CMakeFiles/mncfracture.dir/build.make CMakeFiles/mncfracture.dir/build make[2]: Entering directory `/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build' make[2]: Nothing to be done for `CMakeFiles/mncfracture.dir/build'. make[2]: Leaving directory `/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build' [ 63%] Built target mncfracture make -f variants/CMakeFiles/cookmembranedistributed.dir/build.make variants/CMakeFiles/cookmembranedistributed.dir/depend make[2]: Entering directory `/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build' cd /home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build && /home/woody/iwtm/iwtm020h/spack-install/dealii901-spackv15-gcc/spack/opt/spack/linux-centos7-ivybridge/gcc-7.3.0/cmake-3.17.3-yp7x4tfykdwkolbguxb2nbd46ktt5e6h/bin/cmake -E cmake_depends "Unix Makefiles" /home/woody/iwtm/iwtm020h/trial-code/MNC-Frac /home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/variants /home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build /home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build/variants /home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build/variants/CMakeFiles/cookmembranedistributed.dir/DependInfo.cmake --color= make[2]: Leaving directory `/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build' make -f variants/CMakeFiles/cookmembranedistributed.dir/build.make variants/CMakeFiles/cookmembranedistributed.dir/build make[2]: Entering directory `/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build' [ 68%] Linking CXX executable cookmembranedistributed cd /home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build/variants && /home/woody/iwtm/iwtm020h/spack-install/dealii901-spackv15-gcc/spack/opt/spack/linux-centos7-ivybridge/gcc-7.3.0/cmake-3.17.3-yp7x4tfykdwkolbguxb2nbd46ktt5e6h/bin/cmake -E cmake_link_script CMakeFiles/cookmembranedistributed.dir/link.txt --verbose=1 /home/woody/iwtm/iwtm020h/spack-install/deal
Re: [deal.II] Boost serialization linking error
Paras: deal.II 9.0.1 is nearly 3 years old and it's unlikely that anyone will spend the time to figure out in detail what the issue is. I would suggest upgrading to a more recent version and seeing whether the problem persists. That said, this... cd /home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build/variants and this... /home/woody/iwtm/iwtm020h/spack-install/dealii901-spackv15-gcc/spack/opt/spack/linux-centos7-ivybridge/gcc-7.3.0/cmake-3.17.3-yp7x4tfykdwkolbguxb2nbd46ktt5e6h/bin/cmake and this... -E cmake_link_script CMakeFiles/cookmembranedistributed.dir/link.txt --verbose=1 /home/woody/iwtm/iwtm020h/spack-install/dealii901-spackv15-gcc/spack/opt/spack/linux-centos7-ivybridge/gcc-7.3.0/openmpi-3.1.6-6d7xi6tah53fltt3wtens3wt6zoaysr7/bin/mpic++ -rdynamic -rdynamic -fuse-ld=gold -ggdb CMakeFiles/cookmembranedistributed.dir/cook_membrane_distributed/CookMembraneDistributed.cc.o CMakeFiles/cookmembranedistributed.dir/cook_membrane_distributed/CookMembraneDistributedMain.cc.o -o cookmembranedistributed -Wl,-rpath,/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build /home/woody/iwtm/iwtm020h/spack-install/dealii901-spackv15-gcc/spack/opt/spack/linux-centos7-ivybridge/gcc-7.3.0/dealii-9.0.1-dealii-901-dev-mzkyyfiqp2zxw4ip4cuyx7ok6ym57bp7/lib/libdeal_II.g.so.9.0.1 ../libmncfrac.so /home/woody/iwtm/iwtm020h/spack-install/dealii901-spackv15-gcc/spack/opt/spack/linux-centos7-ivybridge/gcc-7.3.0/dealii-9.0.1-dealii-901-dev-mzkyyfiqp2zxw4ip4cuyx7ok6ym57bp7/lib/libdeal_II.g.so.9.0.1 -ltbb_debug -lboost_iostreams-mt -lboost_serialization-mt -lboost_system-mt -lboost_thread-mt -lboost_regex-mt -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -lmuelu-adapters -lmuelu-interface -lmuelu -lifpack2 -lanasazitpetra -lModeLaplace -lanasaziepetra -lanasazi -lmapvarlib -lsuplib -lsuplib_c -lsuplib_cpp -lsupes -laprepro_lib -lio_info_lib -lIonit -lIotr -lIohb -lIogs -lIogn -lIovs -lIoexo_fac -lIopx -lIofx -lIoex -lIoss -lnemesis -lexoIIv2for32 -lexodus_for -lexodus -lamesos2 -lbelosxpetra -lbelostpetra -lbelosepetra -lbelos -lml -lifpack -lzoltan2 -lamesos -lgaleri-xpetra -lgaleri-epetra -laztecoo -lxpetra-sup -lxpetra -ltrilinosss -ltpetraext -ltpetrainout -ltpetra -lkokkostsqr -ltpetraclassiclinalg -ltpetraclassicnodeapi -ltpetraclassic -lepetraext -ltriutils -lzoltan -lepetra -lsacado -lkokkoskernels -lteuchoskokkoscomm -lteuchoskokkoscompat -lteuchosremainder -lteuchosnumerics -lteuchoscomm -lteuchosparameterlist -lteuchosparser -lteuchoscore -lkokkosalgorithms -lkokkoscontainers -lkokkoscore -lgtest -lmatio -ldmumps -lmumps_common -lpord -lumfpack -lcholmod -lccolamd -lcolamd -lcamd -lsuitesparseconfig -lamd -lrt -ladolc -lparpack -larpack -lassimp -lgsl -lgslcblas -lmuparser -lnetcdf_c++ -lnetcdf -lTKBO -lTKBool -lTKBRep -lTKernel -lTKFeat -lTKFillet -lTKG2d -lTKG3d -lTKGeomAlgo -lTKGeomBase -lTKHLR -lTKIGES -lTKMath -lTKMesh -lTKOffset -lTKPrim -lTKShHealing -lTKSTEP -lTKSTEPAttr -lTKSTEPBase -lTKSTEP209 -lTKSTL -lTKTopAlgo -lTKXSBase -lp4est -lsc -lscalapack -lslepc -lpetsc -lHYPRE -lsuperlu_dist -lopenblas -lhdf5hl_fortran -lhdf5_hl -lhdf5_fortran -lhdf5 -lparmetis -lmetis -lz -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -lpthread -lquadmath -ldl -lsundials_idas -lsundials_arkode -lsundials_kinsol -lsundials_nvecserial -lsundials_nvecparallel ...are the commands that trigger the error. You can execute them by hand on the command line, and test your hypothesis about the order of libraries by switching what needs to be switched. Best W. -- Wolfgang Bangerth email: bange...@colostate.edu www: http://www.math.colostate.edu/~bangerth/ -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/86dedcca-b197-1bef-acce-bd26840b2879%40colostate.edu.
Re: [deal.II] PETSc Vector set deprecated
I am building PETSc vectors with the set operation and I see it’s deprecated. The documentation suggests to use “import( )” but I don’t see how to use it. How can I use import( ) as a replacement for set( ) as the documentation suggests? Please provide an example. I don't know the answer, but maybe David Wells does given that the deprecation was added in https://github.com/dealii/dealii/pull/10398 For sure, you could simply write into the vector elements one by one. That doesn't require 'import()' at all. Best W. -- Wolfgang Bangerth email: bange...@colostate.edu www: http://www.math.colostate.edu/~bangerth/ -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/547b180f-8666-a20d-1922-d95b7425f237%40colostate.edu.
