First test file compile error in ubuntu "No rule to make target "
Hello all
I am new to Dune and I just learned about this software. I am trying to install it in ubuntu system and followed instruction in the link below.
https://dune-project.org/doc/beginners-resources-binary/
My system info is below:
System spec:Distributor ID: Ubuntu
Description: Ubuntu 18.04.4 LTS
Release: 18.04
Codename: bionic
processor : Intel® Core™ i3 CPU M 370 @ 2.40GHz × 4
GNOME : 3.28.2
OS : 64-bit
Every thing works fine except one (also texlive-math-extra not found) which is following:
(base) wonseok@wonseok:~/code/Dune_source$ dunecontrol --only=dune-grid-howto all
--- going to build dune-grid-howto ---
--- calling all for dune-grid-howto ---
--- calling vcsetup for dune-grid-howto ---
--> Installing Git pre-commit hook to enforce whitespace policy
--- calling configure for dune-grid-howto ---
ERROR: version mismatch.
dune-grid-howto requires dune-grid >= 2.8,
but only dune-grid = 2.5.1 is available.
--- Failed to build dune-grid-howto ---
Terminating dunecontrol due to previous errors!
Anyway I tried to move on. I followed instruction in this tutorial to make my first module.
http://www.math.tu-dresden.de/~osander/research/sander-getting-started-with-dune.pdf
Everything works fine. But when I tried to compile the module, I got an error message at the end of compile.
[ 50%] Building CXX object src/CMakeFiles/dune_first_test.dir/dune_first_test.cc.o
make[2]: *** No rule to make target '/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so', needed by 'src/dune_first_test'. Stop.
I attached full output below for your information.
Can you help how to fix this issue ?
Thanks, Wonseok
(base) wonseok@wonseok:~/code/Dune_project$ dunecontrol all
--- going to build dune_first_test ---
--- calling all for dune_first_test ---
--- calling vcsetup for dune_first_test ---
--- calling configure for dune_first_test ---
find: ‘dune’: No such file or directory
cmake -DCMAKE_MODULE_PATH="" "-Ddune-common_DIR=/usr/lib/x86_64-linux-gnu/cmake/dune-common" "-Ddune-istl_DIR=/usr/lib/cmake/dune-istl" "-Ddune-uggrid_DIR=/usr/lib/x86_64-linux-gnu/cmake/dune-uggrid" "-Ddune-geometry_DIR=/usr/lib/x86_64-linux-gnu/cmake/dune-geometry" "-Ddune-grid_DIR=/usr/lib/x86_64-linux-gnu/cmake/dune-grid" "/home/wonseok/code/Dune_project/dune_first_test"
-- The CXX compiler identification is GNU 7.5.0
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- The C compiler identification is GNU 7.5.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Dependencies for dune_first_test: dune-common;dune-istl;dune-uggrid;dune-geometry;dune-grid
-- Dependencies for dune-istl: dune-common (>= 2.5.0)
-- Dependencies for dune-uggrid: dune-common (>= 2.5.0)
-- Dependencies for dune-geometry: dune-common (>= 2.5.0)
-- Dependencies for dune-grid: dune-geometry (>= 2.5.0)
-- Suggestions for dune-grid: dune-uggrid
-- Dependencies for dune-geometry: dune-common (>= 2.5.0)
-- Dependencies for dune-uggrid: dune-common (>= 2.5.0)
-- The Fortran compiler identification is GNU 7.5.0
-- Check for working Fortran compiler: /usr/bin/gfortran
-- Check for working Fortran compiler: /usr/bin/gfortran -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/bin/gfortran supports Fortran 90
-- Checking whether /usr/bin/gfortran supports Fortran 90 -- yes
-- Performing Test cxx_std_flag_14
-- Performing Test cxx_std_flag_14 - Success
-- Performing Test compiler_supports_cxx14
-- Performing Test compiler_supports_cxx14 - Success
-- Performing Test HAS_ATTRIBUTE_UNUSED
-- Performing Test HAS_ATTRIBUTE_UNUSED - Success
-- Performing Test HAS_ATTRIBUTE_DEPRECATED
-- Performing Test HAS_ATTRIBUTE_DEPRECATED - Success
-- Performing Test HAS_ATTRIBUTE_DEPRECATED_MSG
-- Performing Test HAS_ATTRIBUTE_DEPRECATED_MSG - Success
-- Performing Test HAVE_IS_INDEXABLE_SUPPORT
-- Performing Test HAVE_IS_INDEXABLE_SUPPORT - Success
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Check if compiler accepts -pthread
-- Check if compiler accepts -pthread - yes
-- Found Threads: TRUE
-- Performing Test STDTHREAD_WORKS
-- Performing Test STDTHREAD_WORKS - Success
-- Performing Test HAVE_CXA_DEMANGLE
-- Performing Test HAVE_CXA_DEMANGLE - Success
-- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS)
-- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS)
-- Could NOT find MPI_Fortran (missing: MPI_Fortran_LIB_NAMES MPI_Fortran_F77_HEADER_DIR MPI_Fortran_MODULE_DIR MPI_Fortran_WORKS)
-- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND MPI_Fortran_FOUND)
-- Detecting Fortran/C Interface
-- Detecting Fortran/C Interface - Found GLOBAL and MODULE mangling
-- Verifying Fortran/CXX Compiler Compatibility
-- Verifying Fortran/CXX Compiler Compatibility - Success
-- Found LATEX: /usr/bin/latex
-- Found UnixCommands: /bin/bash
-- I could not find the biber command.
-- Found Sphinx: /home/wonseok/anaconda3/bin/sphinx-build
-- Found PythonInterp: /home/wonseok/anaconda3/bin/python (found version "3.7.6")
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1")
-- Performing tests specific to dune-common from file /usr/share/dune/cmake/modules/DuneCommonMacros.cmake.
-- Looking for Fortran sgemm
-- Looking for Fortran sgemm - found
-- A library with BLAS API found.
-- Looking for Fortran cheev
-- Looking for Fortran cheev - found
-- A library with LAPACK API found.
-- Looking for C++ include gmpxx.h
-- Looking for C++ include gmpxx.h - not found
-- Could NOT find GMP (missing: GMP_INCLUDE_DIR GMP_LIB GMPXX_LIB GMP_HEADER_WORKS GMPXX_LIB_WORKS)
-- Looking for sys/mman.h
-- Looking for sys/mman.h - found
-- Performing Test HAVE_MPROTECT
-- Performing Test HAVE_MPROTECT - Success
CMake Warning at /usr/share/dune/cmake/modules/DuneCommonMacros.cmake:32 (find_package):
By not providing "FindVc.cmake" in CMAKE_MODULE_PATH this project has asked
CMake to find a package configuration file provided by "Vc", but CMake did
not find one.
Could not find a package configuration file provided by "Vc" with any of
the following names:
VcConfig.cmake
vc-config.cmake
Add the installation prefix of "Vc" to CMAKE_PREFIX_PATH or set "Vc_DIR" to
a directory containing one of the above files. If "Vc" provides a separate
development package or SDK, be sure it has been installed.
Call Stack (most recent call first):
/usr/share/dune/cmake/modules/DuneMacros.cmake:576 (include)
/usr/share/dune/cmake/modules/DuneMacros.cmake:727 (dune_process_dependency_macros)
CMakeLists.txt:19 (dune_project)
CMake Deprecation Warning at /usr/share/cmake-3.10/Modules/FeatureSummary.cmake:671 (message):
SET_PACKAGE_INFO is deprecated. Use SET_PACKAGE_PROPERTIES instead.
Call Stack (most recent call first):
/usr/share/dune/cmake/modules/DuneCommonMacros.cmake:34 (set_package_info)
/usr/share/dune/cmake/modules/DuneMacros.cmake:576 (include)
/usr/share/dune/cmake/modules/DuneMacros.cmake:727 (dune_process_dependency_macros)
CMakeLists.txt:19 (dune_project)
-- Setting dune-common_INCLUDE_DIRS=/usr/include
-- Setting dune-common_LIBRARIES=dunecommon
-- Performing tests specific to dune-uggrid from file /usr/share/dune/cmake/modules/DuneUggridMacros.cmake.
-- Setting dune-uggrid_INCLUDE_DIRS=/usr/include
-- Setting dune-uggrid_LIBRARIES=ugL2;ugL3;ugS2;ugS3
-- Setting dune-geometry_INCLUDE_DIRS=/usr/include
-- Setting dune-geometry_LIBRARIES=dunegeometry
-- Performing tests specific to dune-grid from file /usr/share/dune/cmake/modules/DuneGridMacros.cmake.
-- Looking for mkstemp
-- Looking for mkstemp - found
-- Looking for metis.h
-- Looking for metis.h - not found
-- Could NOT find METIS (missing: METIS_INCLUDE_DIR METIS_LIBRARY HAVE_METIS_PARTGRAPHKWAY)
-- Looking for parmetis.h
-- Looking for parmetis.h - not found
-- Could NOT find ParMETIS (missing: PARMETIS_INCLUDE_DIR PARMETIS_LIBRARY HAVE_PARMETIS)
-- Looking for include file alberta/alberta.h
-- Looking for include file alberta/alberta.h - found
-- Performing Test ALBERTA_IS_VERSION_3
-- Performing Test ALBERTA_IS_VERSION_3 - Success
-- Looking for alberta_calloc in /usr/lib/x86_64-linux-gnu/libalberta_utilities.so
-- Looking for alberta_calloc in /usr/lib/x86_64-linux-gnu/libalberta_utilities.so - found
-- Looking for mesh_traverse in /usr/lib/x86_64-linux-gnu/libalberta_1d.so
-- Looking for mesh_traverse in /usr/lib/x86_64-linux-gnu/libalberta_1d.so - found
-- Looking for mesh_traverse in /usr/lib/x86_64-linux-gnu/libalberta_2d.so
-- Looking for mesh_traverse in /usr/lib/x86_64-linux-gnu/libalberta_2d.so - found
-- Looking for mesh_traverse in /usr/lib/x86_64-linux-gnu/libalberta_3d.so
-- Looking for mesh_traverse in /usr/lib/x86_64-linux-gnu/libalberta_3d.so - found
-- Found alberta libraries for dimensions 1;2;3
CMake Deprecation Warning at /usr/share/cmake-3.10/Modules/FeatureSummary.cmake:671 (message):
SET_PACKAGE_INFO is deprecated. Use SET_PACKAGE_PROPERTIES instead.
Call Stack (most recent call first):
/usr/share/dune/cmake/modules/UseUG.cmake:62 (set_package_info)
/usr/share/dune/cmake/modules/DuneGridMacros.cmake:19 (include)
/usr/share/dune/cmake/modules/DuneMacros.cmake:576 (include)
/usr/share/dune/cmake/modules/DuneMacros.cmake:727 (dune_process_dependency_macros)
CMakeLists.txt:19 (dune_project)
CMake Warning at /usr/share/dune/cmake/modules/UseUG.cmake:155 (message):
The support of UG as an external library is deprecated in Dune 2.5. Use
dune-uggrid instead.
Call Stack (most recent call first):
/usr/share/dune/cmake/modules/DuneGridMacros.cmake:19 (include)
/usr/share/dune/cmake/modules/DuneMacros.cmake:576 (include)
/usr/share/dune/cmake/modules/DuneMacros.cmake:727 (dune_process_dependency_macros)
CMakeLists.txt:19 (dune_project)
-- Checking for one of the modules 'psurface'
-- Checking for module 'psurface'
-- No package 'psurface' found
-- Could NOT find psurface (missing: PSURFACE_INCLUDE_DIR PSURFACE_LIBRARY)
-- Could NOT find AmiraMesh (missing: AMIRAMESH_INCLUDE_DIR AMIRAMESH_LIBRARY)
-- Setting dune-grid_INCLUDE_DIRS=/usr/include
-- Setting dune-grid_LIBRARIES=dunegrid;dunealbertagrid_1d;dunealbertagrid_2d;dunealbertagrid_3d
-- Performing tests specific to dune-istl from file /usr/share/dune/cmake/modules/DuneIstlMacros.cmake.
-- Could NOT find METIS (missing: METIS_INCLUDE_DIR METIS_LIBRARY HAVE_METIS_PARTGRAPHKWAY)
-- Could NOT find ParMETIS (missing: PARMETIS_INCLUDE_DIR PARMETIS_LIBRARY HAVE_PARMETIS)
-- Performing Test SUPERLU_MIN_VERSION_4
-- Performing Test SUPERLU_MIN_VERSION_4 - Failed
-- Performing Test SUPERLU_MIN_VERSION_4_3
-- Performing Test SUPERLU_MIN_VERSION_4_3 - Failed
-- Performing Test SUPERLU_MIN_VERSION_5
-- Performing Test SUPERLU_MIN_VERSION_5 - Failed
-- Could NOT find SuperLU (missing: SUPERLU_INCLUDE_DIR SUPERLU_LIBRARY SUPERLU_MIN_VERSION_4)
CMake Deprecation Warning at /usr/share/cmake-3.10/Modules/FeatureSummary.cmake:671 (message):
SET_PACKAGE_INFO is deprecated. Use SET_PACKAGE_PROPERTIES instead.
Call Stack (most recent call first):
/usr/share/dune/cmake/modules/FindSuperLU.cmake:159 (set_package_info)
/usr/share/dune/cmake/modules/DuneIstlMacros.cmake:9 (find_package)
/usr/share/dune/cmake/modules/DuneMacros.cmake:576 (include)
/usr/share/dune/cmake/modules/DuneMacros.cmake:727 (dune_process_dependency_macros)
CMakeLists.txt:19 (dune_project)
-- Could NOT find ARPACK (missing: ARPACK_LIBRARY)
-- Could NOT find ARPACKPP (missing: ARPACK_FOUND ARPACKPP_INCLUDE_DIR)
-- Performing Test SUITESPARSE_MIN_VERSION_4_3
-- Performing Test SUITESPARSE_MIN_VERSION_4_3 - Success
-- Found SuiteSparse: TRUE found components: LDL SPQR UMFPACK
-- Setting dune-istl_INCLUDE_DIRS=/usr/include
-- Performing tests specific to dune_first_test from file /home/wonseok/code/Dune_project/dune_first_test/cmake/modules/Dune_first_testMacros.cmake.
-- Using scripts from /usr/share/dune/cmake/scripts for creating doxygen stuff.
-- Adding custom target for config.h generation
-- The following OPTIONAL packages have been found:
* LATEX
* UnixCommands
* Sphinx
* PythonInterp
* PkgConfig
* LAPACK
* Alberta
* Threads
* SuiteSparse
-- The following REQUIRED packages have been found:
* dune-common
* dune-istl
* dune-uggrid
* dune-geometry
* dune-grid
-- The following features have been disabled:
* Experimental grid extensions, Enables additional grid features.
-- The following OPTIONAL packages have not been found:
* MPI
* Doxygen
* GMP
* Inkscape
* Vc, C++ Vectorization library, <https://github.com/VcDevel/Vc>
* Psurface
* AmiraMesh
* METIS
* ParMETIS
* SuperLU, Direct linear solver library
* ARPACK
* ARPACKPP
-- Configuring done
-- Generating done
-- Build files have been written to: /home/wonseok/code/Dune_project/dune_first_test/build-cmake
--- calling make for dune_first_test ---
build directory: build-cmake
cmake --build . --
Scanning dependencies of target dune_first_test
[ 50%] Building CXX object src/CMakeFiles/dune_first_test.dir/dune_first_test.cc.o
make[2]: *** No rule to make target '/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so', needed by 'src/dune_first_test'. Stop.
CMakeFiles/Makefile2:1333: recipe for target 'src/CMakeFiles/dune_first_test.dir/all' failed
make[1]: *** [src/CMakeFiles/dune_first_test.dir/all] Error 2
Makefile:162: recipe for target 'all' failed
make: *** [all] Error 2
--- Failed to build dune_first_test ---
Terminating dunecontrol due to previous errors!
(base) wonseok@wonseok:~/code/Dune_project$