Re: [deal.II] Loading solution in step 6
On 2/23/19 7:16 PM, Yangshuai Wang wrote: > Thanks so much! I delete const, and the error says: > > An error occurred in line <1105> of file > > in function > Number ::Vector::operator()(const > dealii::Vector::size_type) [number = double] > The violated condition was: > i Additional information: > Index 289 is not in the half-open range [0,289). So you sized the vector to have 289 elements (0...288) but then you try to write into element 289 as you continue to read from a file. Apparently, your file has more than 289 double precision numbers. (You also have to pay attention that you could have been reading the first 289 elements already and the 289th read fails -- but you only find out about it after the fact because the statement 'while(!File.eof())' might only stop the iteration once the last read failed. This could happen if, for example, you have a space or a newline after the 289th element: in that case, after reading the 289th element, you are not yet at the end of the file, and so you attempt to read and write into the 290th element, even though the read will have failed.) > By the way, I can read my "solution-txt" file to an array, but how to > transfer the array to Vector type since the solution in > KellyErrorEstimator::estimate must be a Vector. You could create a Vector of the correct size and simply copy the elements one by one from your array into the vector. 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. For more options, visit https://groups.google.com/d/optout.
Re: [deal.II] Position of a given node
On 2/23/19 7:31 PM, yswang2...@sjtu.edu.cn wrote: > > I have printed the constraints, it reads: > ... > 24 = 0 > 25 5: 0.5 > 25 10: 0.5 > 26 5: 0.5 > ... > which means No.25 node is a hanging node, right? Yes, assuming that you are using Q1 elements, this very much looks like a hanging node. > But how to obtain the > position of No.25 node? I'm writing this from a plane and so don't have the URL, but this is a question you can find on the website among the Frequently Asked Questions (FAQ). > Moreover, I want to know the index numbering rules. You should probably treat the numbering rules as arbitrary and unpredictable. If you need a specific numbering, you can always use the ones in DoFRenumbering. (The rules are basically that we traverse all cells in the order in which the triangulation presents them to us, and enumerate all degrees of freedom on them that have not previously been numbered on a different cell. So it all depends on the order in which you visit cells.) 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. For more options, visit https://groups.google.com/d/optout.
Re: [deal.II] Re: Install error when compile with Trilinos
Jaekwang, This is the problem: Le dim. 24 févr. 2019 à 22:10, Jaekwang Kim a écrit : > -- Include > /Users/jaekwangkim/Program/dealii-9.0.1/cmake/configure/configure_2_trilinos.cmake > > CMake Warning at /usr/local/lib/cmake/Trilinos/TrilinosConfig.cmake:156 > (MESSAGE): > > Component "Pike" NOT found. > > Call Stack (most recent call first): > > cmake/macros/macro_find_package.cmake:27 (_FIND_PACKAGE) > > cmake/modules/FindTRILINOS.cmake:41 (FIND_PACKAGE) > > cmake/macros/macro_find_package.cmake:27 (_FIND_PACKAGE) > > cmake/configure/configure_2_trilinos.cmake:22 (FIND_PACKAGE) > > > /Users/jaekwangkim/Program/dealii/CMakeFiles/CMakeTmp/evaluate_expression.tmp:1 > (FEATURE_TRILINOS_FIND_EXTERNAL) > > cmake/macros/macro_evaluate_expression.cmake:30 (INCLUDE) > > cmake/macros/macro_configure_feature.cmake:237 (EVALUATE_EXPRESSION) > > cmake/configure/configure_2_trilinos.cmake:219 (CONFIGURE_FEATURE) > > cmake/macros/macro_verbose_include.cmake:19 (INCLUDE) > > CMakeLists.txt:124 (VERBOSE_INCLUDE) > > > > CMake Error at /usr/local/lib/cmake/Trilinos/TrilinosConfig.cmake:219 > (include): > > include could not find load file: > > > /usr/local/lib/cmake/Trilinos/../Pike/PikeConfig.cmake Basically what happens is that Trilinos says that Pike is installed but when deal.II is trying to find the configuration file for Pike, it can't find it. These kind of errors used to happen for the old versions of Trilinos but I haven't seen that in a while. Try to install a newer version of Trilinos and if you don't need Pike, don't enable it. Best, Bruno -- 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. For more options, visit https://groups.google.com/d/optout.
[deal.II] Re: Install error when compile with Trilinos
I resummarized screen messages that seems to be a problem ...~~ *-- Performing Test DEAL_II_HAVE_AVX* *-- Performing Test DEAL_II_HAVE_AVX - Failed* *-- Performing Test DEAL_II_HAVE_AVX512* *-- Performing Test DEAL_II_HAVE_AVX512 - Failed* *DEAL_II_COMPILER_DEFAULTS_TO_CXX11_OR_NEWER - Failed* *DEAL_II_HAVE_COMPLEX_OPERATOR_OVERLOADS - Failed* *-- Performing Test gfortran_LIBRARY* *-- Performing Test gfortran_LIBRARY - Failed* *-- Performing Test gcc_ext.10.5_LIBRARY* *-- Performing Test gcc_ext.10.5_LIBRARY - Failed* *-- Performing Test gcc_LIBRARY* *-- Performing Test gcc_LIBRARY - Failed* *-- Performing Test quadmath_LIBRARY* *-- Performing Test quadmath_LIBRARY - Failed* *-- Include /Users/jaekwangkim/Program/dealii-* *-- Performing Test DEAL_II_HAVE_MT_POSIX_BARRIERS* *-- Performing Test DEAL_II_HAVE_MT_POSIX_BARRIERS - Failed* -- Performing Test DEAL_II_HAVE_FLAG_Wno_parentheses -- Performing Test DEAL_II_HAVE_FLAG_Wno_parentheses - Success -- DEAL_II_WITH_THREADS successfully set up with bundled packages. -- -- Performing Test DEAL_II_HAS_AUTO_PTR -- Performing Test DEAL_II_HAS_AUTO_PTR - Failed CMake Error at /usr/local/lib/cmake/Trilinos/TrilinosConfig.cmake:219 (include): include could not find load file: /usr/local/lib/cmake/Trilinos/../Pike/PikeConfig.cmake -- Found EPETRA_CONFIG_H -- Found SACADO_CONFIG_H -- Found SACADO_CMATH_HPP -- Performing Test TRILINOS_SUPPORTS_CPP11 -- Performing Test TRILINOS_SUPPORTS_CPP11 - Success -- Performing Test TRILINOS_HAS_C99_TR1_WORKAROUND -- Performing Test TRILINOS_HAS_C99_TR1_WORKAROUND - Success -- Found SACADO_TRAD_HPP -- Performing Test TRILINOS_CXX_SUPPORTS_SACADO_COMPLEX_RAD -- Performing Test TRILINOS_CXX_SUPPORTS_SACADO_COMPLEX_RAD - Failed -- Found TRILINOS_LIBRARY_trilinoscouplings -- Found TRILINOS_LIBRARY_msqutil -- Found TRILINOS_LIBRARY_mesquite -- Found TRILINOS_LIBRARY_ctrilinos -- Found TRILINOS_LIBRARY_rol -- Found TRILINOS_LIBRARY_moochothyra -- Found TRILINOS_LIBRARY_moocho -- Found TRILINOS_LIBRARY_rythmos -- Found TRILINOS_LIBRARY_muelu-adapters -- Found TRILINOS_LIBRARY_muelu-interface -- Found TRILINOS_LIBRARY_muelu -- Found TRILINOS_LIBRARY_moertel -- Found TRILINOS_LIBRARY_phalanx -- Found TRILINOS_LIBRARY_intrepid -- Found TRILINOS_LIBRARY_ifpack2-adapters -- Found TRILINOS_LIBRARY_ifpack2 -- Found TRILINOS_LIBRARY_anasazitpetra -- Found TRILINOS_LIBRARY_ModeLaplace -- Found TRILINOS_LIBRARY_anasaziepetra -- Found TRILINOS_LIBRARY_anasazi -- Found TRILINOS_LIBRARY_komplex -- Found TRILINOS_LIBRARY_suplib_cpp -- Found TRILINOS_LIBRARY_suplib_c -- Found TRILINOS_LIBRARY_suplib -- Found TRILINOS_LIBRARY_supes -- Found TRILINOS_LIBRARY_aprepro_lib -- Found TRILINOS_LIBRARY_chaco -- Found TRILINOS_LIBRARY_io_info_lib -- Found TRILINOS_LIBRARY_Ionit -- Found TRILINOS_LIBRARY_Iotr -- Found TRILINOS_LIBRARY_Iohb -- Found TRILINOS_LIBRARY_Iogn -- Found TRILINOS_LIBRARY_Iovs -- Found TRILINOS_LIBRARY_Iopg -- Found TRILINOS_LIBRARY_Ioss -- Found TRILINOS_LIBRARY_amesos2 -- Found TRILINOS_LIBRARY_shylu -- Found TRILINOS_LIBRARY_belostpetra -- Found TRILINOS_LIBRARY_belosepetra -- Found TRILINOS_LIBRARY_belos -- Found TRILINOS_LIBRARY_ml -- Found TRILINOS_LIBRARY_ifpack -- Found TRILINOS_LIBRARY_zoltan2 -- Found TRILINOS_LIBRARY_pamgen_extras -- Found TRILINOS_LIBRARY_pamgen -- Found TRILINOS_LIBRARY_amesos -- Found TRILINOS_LIBRARY_galeri-xpetra -- Found TRILINOS_LIBRARY_galeri-epetra -- Found TRILINOS_LIBRARY_aztecoo -- Found TRILINOS_LIBRARY_dpliris -- Found TRILINOS_LIBRARY_isorropia -- Found TRILINOS_LIBRARY_optipack -- Found TRILINOS_LIBRARY_xpetra-sup -- Found TRILINOS_LIBRARY_xpetra -- Found TRILINOS_LIBRARY_thyratpetra -- Found TRILINOS_LIBRARY_thyraepetraext -- Found TRILINOS_LIBRARY_thyraepetra -- Found TRILINOS_LIBRARY_thyracore -- Found TRILINOS_LIBRARY_domi -- Found TRILINOS_LIBRARY_epetraext -- Found TRILINOS_LIBRARY_trilinosss -- Found TRILINOS_LIBRARY_tpetraext -- Found TRILINOS_LIBRARY_tpetrainout -- Found TRILINOS_LIBRARY_tpetra -- Found TRILINOS_LIBRARY_kokkostsqr -- Found TRILINOS_LIBRARY_tpetraclassiclinalg -- Found TRILINOS_LIBRARY_tpetraclassicnodeapi -- Found TRILINOS_LIBRARY_tpetraclassic -- Found TRILINOS_LIBRARY_triutils -- Found TRILINOS_LIBRARY_globipack -- Found TRILINOS_LIBRARY_shards -- Found TRILINOS_LIBRARY_zoltan -- Found TRILINOS_LIBRARY_simpi -- Found TRILINOS_LIBRARY_epetra -- Found TRILINOS_LIBRARY_minitensor -- Found TRILINOS_LIBRARY_sacado -- Found TRILINOS_LIBRARY_rtop -- Found TRILINOS_LIBRARY_kokkoskernels -- Found TRILINOS_LIBRARY_teuchoskokkoscomm -- Found TRILINOS_LIBRARY_teuchoskokkoscompat -- Found TRILINOS_LIBRARY_teuchosremainder -- Found TRILINOS_LIBRARY_teuchosnumerics -- Found TRILINOS_LIBRARY_teuchoscomm -- Found TRILINOS_LIBRARY_teuchosparameterlist -- Found TRILINOS_LIBRARY_teuchoscore -- Found TRILINOS_LIBRARY_kokkosalgorithms
[deal.II] Re: Install error when compile with Trilinos
Jaekwang, Unfortunately, I don't see anything wrong in the log. I found that the best way to understand what is wrong when you get a Configuring incomplete error is to carefully read the messages printed on the screen. If possible, can you post the messages you get during configuration. Best, Bruno On Sunday, February 24, 2019 at 5:25:31 PM UTC-5, Jaekwang Kim wrote: > > Hi, all. > > I have used deal.ii for year, and recently I need to compiled deal.ii with > Trilinos > > I installed Trilinos on my local enabling only serial (non MPI) > > However, after the installation, when I tried to reinstall with deal.ii > enabling Trilinos packages, > > I got error so that I cannot 'make install' > > My configuration is as follow and I also attach my 'CMakeError.log' file. > > I would appreciate any idea to resolve present issue > > Thanks! > > Jaekwang > > ### > > # > > # deal.II configuration: > > #CMAKE_BUILD_TYPE: DebugRelease > > #BUILD_SHARED_LIBS: ON > > #CMAKE_INSTALL_PREFIX: /Users/jaekwangkim/Program/dealii > > #CMAKE_SOURCE_DIR: /Users/jaekwangkim/Program/dealii-9.0.1 > > #(version 9.0.1) > > #CMAKE_BINARY_DIR: /Users/jaekwangkim/Program/dealii > > #CMAKE_CXX_COMPILER: AppleClang 10.0.0.10001044 on platform > Darwin x86_64 > > # > /Library/Developer/CommandLineTools/usr/bin/c++ > > # > > # Configured Features (DEAL_II_ALLOW_BUNDLED = ON, > DEAL_II_ALLOW_AUTODETECTION = ON): > > # ( DEAL_II_WITH_64BIT_INDICES = OFF ) > > # ( DEAL_II_WITH_ADOLC = OFF ) > > # ( DEAL_II_WITH_ARPACK = OFF ) > > # ( DEAL_II_WITH_ASSIMP = OFF ) > > #DEAL_II_WITH_BOOST set up with external dependencies > > # ( DEAL_II_WITH_CUDA = OFF ) > > #DEAL_II_WITH_CXX14 = ON > > #DEAL_II_WITH_CXX17 = ON > > # ( DEAL_II_WITH_GMSH = OFF ) > > # ( DEAL_II_WITH_GSL = OFF ) > > # ( DEAL_II_WITH_HDF5 = OFF ) > > #DEAL_II_WITH_LAPACK set up with external dependencies > > # ( DEAL_II_WITH_METIS = OFF ) > > # ( DEAL_II_WITH_MPI = OFF ) > > #DEAL_II_WITH_MUPARSER set up with bundled packages > > # ( DEAL_II_WITH_NANOFLANN = OFF ) > > # ( DEAL_II_WITH_NETCDF = OFF ) > > # ( DEAL_II_WITH_OPENCASCADE = OFF ) > > # ( DEAL_II_WITH_P4EST = OFF ) > > # ( DEAL_II_WITH_PETSC = OFF ) > > # ( DEAL_II_WITH_SCALAPACK = OFF ) > > # ( DEAL_II_WITH_SLEPC = OFF ) > > # ( DEAL_II_WITH_SUNDIALS = OFF ) > > #DEAL_II_WITH_THREADS set up with bundled packages > > #DEAL_II_WITH_TRILINOS set up with external dependencies > > #DEAL_II_WITH_UMFPACK set up with external dependencies > > #DEAL_II_WITH_ZLIB set up with external dependencies > > # > > # Component configuration: > > # ( DEAL_II_COMPONENT_DOCUMENTATION = OFF ) > > #DEAL_II_COMPONENT_EXAMPLES > > # ( DEAL_II_COMPONENT_PACKAGE = OFF ) > > # ( DEAL_II_COMPONENT_PYTHON_BINDINGS = OFF ) > > # > > # Detailed information (compiler flags, feature configuration) can be > found in detailed.log > > # > > # Run $ make info to print a help message with a list of top level > targets > > # > > ### > > *-- Configuring incomplete, errors occurred!* > > > > > -- 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. For more options, visit https://groups.google.com/d/optout.
[deal.II] Install error when compile with Trilinos
Hi, all.
I have used deal.ii for year, and recently I need to compiled deal.ii with
Trilinos
I installed Trilinos on my local enabling only serial (non MPI)
However, after the installation, when I tried to reinstall with deal.ii
enabling Trilinos packages,
I got error so that I cannot 'make install'
My configuration is as follow and I also attach my 'CMakeError.log' file.
I would appreciate any idea to resolve present issue
Thanks!
Jaekwang
###
#
# deal.II configuration:
#CMAKE_BUILD_TYPE: DebugRelease
#BUILD_SHARED_LIBS: ON
#CMAKE_INSTALL_PREFIX: /Users/jaekwangkim/Program/dealii
#CMAKE_SOURCE_DIR: /Users/jaekwangkim/Program/dealii-9.0.1
#(version 9.0.1)
#CMAKE_BINARY_DIR: /Users/jaekwangkim/Program/dealii
#CMAKE_CXX_COMPILER: AppleClang 10.0.0.10001044 on platform
Darwin x86_64
#
/Library/Developer/CommandLineTools/usr/bin/c++
#
# Configured Features (DEAL_II_ALLOW_BUNDLED = ON,
DEAL_II_ALLOW_AUTODETECTION = ON):
# ( DEAL_II_WITH_64BIT_INDICES = OFF )
# ( DEAL_II_WITH_ADOLC = OFF )
# ( DEAL_II_WITH_ARPACK = OFF )
# ( DEAL_II_WITH_ASSIMP = OFF )
#DEAL_II_WITH_BOOST set up with external dependencies
# ( DEAL_II_WITH_CUDA = OFF )
#DEAL_II_WITH_CXX14 = ON
#DEAL_II_WITH_CXX17 = ON
# ( DEAL_II_WITH_GMSH = OFF )
# ( DEAL_II_WITH_GSL = OFF )
# ( DEAL_II_WITH_HDF5 = OFF )
#DEAL_II_WITH_LAPACK set up with external dependencies
# ( DEAL_II_WITH_METIS = OFF )
# ( DEAL_II_WITH_MPI = OFF )
#DEAL_II_WITH_MUPARSER set up with bundled packages
# ( DEAL_II_WITH_NANOFLANN = OFF )
# ( DEAL_II_WITH_NETCDF = OFF )
# ( DEAL_II_WITH_OPENCASCADE = OFF )
# ( DEAL_II_WITH_P4EST = OFF )
# ( DEAL_II_WITH_PETSC = OFF )
# ( DEAL_II_WITH_SCALAPACK = OFF )
# ( DEAL_II_WITH_SLEPC = OFF )
# ( DEAL_II_WITH_SUNDIALS = OFF )
#DEAL_II_WITH_THREADS set up with bundled packages
#DEAL_II_WITH_TRILINOS set up with external dependencies
#DEAL_II_WITH_UMFPACK set up with external dependencies
#DEAL_II_WITH_ZLIB set up with external dependencies
#
# Component configuration:
# ( DEAL_II_COMPONENT_DOCUMENTATION = OFF )
#DEAL_II_COMPONENT_EXAMPLES
# ( DEAL_II_COMPONENT_PACKAGE = OFF )
# ( DEAL_II_COMPONENT_PYTHON_BINDINGS = OFF )
#
# Detailed information (compiler flags, feature configuration) can be
found in detailed.log
#
# Run $ make info to print a help message with a list of top level
targets
#
###
*-- Configuring incomplete, errors occurred!*
--
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
---
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Performing C++ SOURCE FILE Test DEAL_II_HAVE_FLAG_Wl__as_needed failed with the
following output:
Change Dir: /Users/jaekwangkim/Program/dealii/CMakeFiles/CMakeTmp
Run Build Command:"/usr/bin/make" "cmTC_76208/fast"
/Library/Developer/CommandLineTools/usr/bin/make -f
CMakeFiles/cmTC_76208.dir/build.make CMakeFiles/cmTC_76208.dir/build
Building CXX object CMakeFiles/cmTC_76208.dir/src.cxx.o
/Library/Developer/CommandLineTools/usr/bin/c++
-DDEAL_II_HAVE_FLAG_Wl__as_needed -isysroot
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk -o
CMakeFiles/cmTC_76208.dir/src.cxx.o -c
/Users/jaekwangkim/Program/dealii/CMakeFiles/CMakeTmp/src.cxx
Linking CXX executable cmTC_76208
/usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmTC_76208.dir/link.txt
--verbose=1
/Library/Developer/CommandLineTools/usr/bin/c++
-DDEAL_II_HAVE_FLAG_Wl__as_needed -isysroot
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk
-Wl,-search_paths_first -Wl,-headerpad_max_install_names
CMakeFiles/cmTC_76208.dir/src.cxx.o -o cmTC_76208 -Wl,--as-needed
ld: unknown option: --as-needed
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[1]: *** [cmTC_76208] Error 1
make: *** [cmTC_76208/fast] Error 2
Source file was:
int main() { return 0; }
Performing C++ SOURCE FILE Test DEAL_II_HAVE_FLAG_Wno_placement_new failed with
the following output:
Change Dir: /Users/jaekwangkim/Program/dealii/CMakeFiles/CMakeTmp
Run Build Command:"/usr/bin/make" "cmTC_6a621/fast"
/Library/Developer/CommandLineTools/usr/bin/make -f
CMakeFiles/cmTC_6a621.dir/build.make CMakeFiles/cmTC_6a621.dir/build
Building CXX object CMakeFiles/cmTC_6a621.dir/src.cxx.o
/Library/Developer/CommandLineTools/usr/bin/c++
-DDEAL_II_HAVE_FLAG_Wno_placement_new -isysroot
