[Dune] Problem linking parmetis with cmake
Aleksejs Fomins
aleksejs.fomins at lspr.ch
Wed Nov 26 11:11:09 CET 2014
Dear Dune,
I am having a little problem linking parmetis. I have specified a path
to it in the opts file, but it seems not to be enough
fatal error: parmetis.h: No such file or directory
#include <parmetis.h>
Do I need to specify it additionally somewhere?
Greetings,
Aleksejs
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----- using default flags $CONFIGURE_FLAGS from /home/fomins/gitwork/hades-github-lspr-ag/af.debian7.lsprag.cmakebuild.minimalistic.opts -----
--- going to build dune-curvilineargrid ---
--- calling all for dune-curvilineargrid ---
--- calling vcsetup for dune-curvilineargrid ---
--- calling autogen for dune-curvilineargrid ---
Skipping dune-autogen because of CMake
--- calling configure for dune-curvilineargrid ---
----- using default flags $CONFIGURE_FLAGS from /home/fomins/gitwork/hades-github-lspr-ag/af.debian7.lsprag.cmakebuild.minimalistic.opts -----
/home/fomins/gitwork/hades-github-lspr-ag/dune-geometry/lib/dunegeometryam2cmake.lib for converting options does not exist
/home/fomins/gitwork/hades-github-lspr-ag/dune-curvilineargeometry/lib/dunecurvilineargeometryam2cmake.lib for converting options does not exist
/home/fomins/gitwork/hades-github-lspr-ag/dune-curvilineargrid/lib/dunecurvilineargridam2cmake.lib for converting options does not exist
CXX=mpicxx CC=mpicc cmake -DCMAKE_MODULE_PATH="" -DUSE_MPI=ON "-Ddune-common_DIR=/home/fomins/gitwork/hades-github-lspr-ag/dune-common/build-cmake" "-Ddune-geometry_DIR=/home/fomins/gitwork/hades-github-lspr-ag/dune-geometry/build-cmake" "-Ddune-curvilineargeometry_DIR=/home/fomins/gitwork/hades-github-lspr-ag/dune-curvilineargeometry/build-cmake" -DENABLE_EXPERIMENTAL_GRID_EXTENSIONS:BOOL=TRUE "-Ddune-grid_DIR=/home/fomins/gitwork/hades-github-lspr-ag/dune-grid/build-cmake" "-Ddune-alugrid_DIR=/home/fomins/gitwork/hades-github-lspr-ag/dune-alugrid/build-cmake" -DCXXFLAGS="-O2 -Wall" -DCMAKE_PREFIX_PATH="/opt/extlib/boost/1.55.0/gcc/4.9.0;/opt/extlib/parmetis/4.0.3/openmpi/1.8.1/gcc/4.9.0;/opt/extlib/metis/5.1.0/gcc/4.9.0;" -DDUNE_GRID_EXPERIMENTAL_GRID_EXTENSIONS:BOOL=TRUE "/home/fomins/gitwork/hades-github-lspr-ag/dune-curvilineargrid"
-- Dependencies for dune-curvilineargrid: dune-common;dune-geometry;dune-curvilineargeometry;dune-grid;dune-alugrid
-- Dependencies for dune-geometry: dune-common (>= 2.4)
-- Dependencies for dune-curvilineargeometry: dune-common;dune-geometry
-- Dependencies for dune-grid: dune-common (>= 2.4);dune-geometry (>= 2.4)
-- Dependencies for dune-alugrid: dune-grid (>= 2.3)
-- Dependencies for dune-grid: dune-common (>= 2.4);dune-geometry (>= 2.4)
-- Dependencies for dune-geometry: dune-common (>= 2.4)
-- Dependencies for dune-geometry: dune-common (>= 2.4)
-- Dependencies for dune-geometry: dune-common (>= 2.4)
-- I could not find the latex2html command.
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
-- Performing tests specific to dune-common from file /home/fomins/gitwork/hades-github-lspr-ag/dune-common/cmake/modules/DuneCommonMacros.cmake.
-- A library with BLAS API found.
-- A library with LAPACK API found.
-- Could NOT find GMP (missing: GMP_INCLUDE_DIR GMP_LIB GMPXX_LIB GMP_HEADER_WORKS GMPXX_LIB_WORKS)
-- Setting dune-common_INCLUDE_DIRS=/home/fomins/gitwork/hades-github-lspr-ag/dune-common
-- Setting dune-common_LIBRARIES=dunecommon
-- Setting dune-geometry_INCLUDE_DIRS=/home/fomins/gitwork/hades-github-lspr-ag/dune-geometry
-- Setting dune-geometry_LIBRARIES=dunegeometry
-- Performing tests specific to dune-grid from file /home/fomins/gitwork/hades-github-lspr-ag/dune-grid/cmake/modules/DuneGridMacros.cmake.
-- checking for module 'alugrid'
-- package 'alugrid' not found
-- checking for module 'alugrid'
-- package 'alugrid' not found
-- Could NOT find ALUGrid (missing: ALUGRID_VERSION ALUGRID_INCLUDE_PATH ALUGRID_LIB ALUGRID_LIB_PATH ALULIB_FUNCTIONAL HAVE_ALUGRID_SERIAL_H)
CMake Warning at /home/fomins/gitwork/hades-github-lspr-ag/dune-grid/cmake/modules/UseUG.cmake:27 (find_package):
Could not find a package configuration file provided by "UG" (requested
version 3.11.0) with any of the following names:
UGConfig.cmake
ug-config.cmake
Add the installation prefix of "UG" to CMAKE_PREFIX_PATH or set "UG_DIR" to
a directory containing one of the above files. If "UG" provides a separate
development package or SDK, be sure it has been installed.
Call Stack (most recent call first):
/home/fomins/gitwork/hades-github-lspr-ag/dune-grid/cmake/modules/DuneGridMacros.cmake:11 (include)
/home/fomins/gitwork/hades-github-lspr-ag/dune-common/cmake/modules/DuneMacros.cmake:505 (include)
/home/fomins/gitwork/hades-github-lspr-ag/dune-common/cmake/modules/DuneMacros.cmake:634 (dune_process_dependency_macros)
CMakeLists.txt:19 (dune_project)
-- Could NOT find UG (missing: UG_DIR HAVE_UG)
-- Could NOT find Grape (missing: GRAPE_INCLUDE_DIR GRAPE_LIBRARY _GRAPE_LIB_FUNCTIONAL _GRAPE_HEADER_USABLE)
-- checking for one of the modules 'psurface'
-- checking for module 'psurface'
-- package 'psurface' not 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=/home/fomins/gitwork/hades-github-lspr-ag/dune-grid
-- Setting dune-grid_LIBRARIES=dunegrid
-- Performing tests specific to dune-alugrid from file /home/fomins/gitwork/hades-github-lspr-ag/dune-alugrid/cmake/modules/DuneAlugridMacros.cmake.
-- Could NOT find SIONlib (missing: SIONLIB_INCLUDE_DIR SIONLIB_LIBRARY SIONLIB_HEADER_USABLE SIONLIB_LIB_WORKS SIONLIB_LIB_SIONSER_WORKS)
-- Could NOT find DLMalloc (missing: DLMALLOC_INCLUDE_DIR DLMALLOC_SOURCE_USABLE)
Zoltan Dir: ZOLTAN_INCLUDE_DIR-NOTFOUND
-- Could NOT find ZOLTAN (missing: ZOLTAN_INCLUDE_DIR ZOLTAN_LIBRARY ZOLTAN_HEADER_USABLE)
CMake Warning (dev) at /home/fomins/gitwork/hades-github-lspr-ag/dune-alugrid/cmake/modules/DuneAlugridMacros.cmake:49 (message):
TODO: Improve module test.
Call Stack (most recent call first):
/home/fomins/gitwork/hades-github-lspr-ag/dune-common/cmake/modules/DuneMacros.cmake:505 (include)
/home/fomins/gitwork/hades-github-lspr-ag/dune-common/cmake/modules/DuneMacros.cmake:634 (dune_process_dependency_macros)
CMakeLists.txt:19 (dune_project)
This warning is for project developers. Use -Wno-dev to suppress it.
-- Setting dune-alugrid_INCLUDE_DIRS=/home/fomins/gitwork/hades-github-lspr-ag/dune-alugrid
-- Setting dune-alugrid_LIBRARIES=dunealugrid
-- Performing tests specific to dune-curvilineargeometry from file /home/fomins/gitwork/hades-github-lspr-ag/dune-curvilineargeometry/cmake/modules/DuneCurvilineargeometryMacros.cmake.
-- Setting dune-curvilineargeometry_INCLUDE_DIRS=/home/fomins/gitwork/hades-github-lspr-ag/dune-curvilineargeometry
-- Performing tests specific to dune-curvilineargrid from file /home/fomins/gitwork/hades-github-lspr-ag/dune-curvilineargrid/cmake/modules/DuneCurvilineargridMacros.cmake.
-- Using scripts from /home/fomins/gitwork/hades-github-lspr-ag/dune-common/cmake/scripts for creating doxygen stuff.
-- Adding custom target for config.h generation
--
-- The following features have been enabled:
* Experimental grid extensions , Enables additional grid features.
-- The following OPTIONAL packages have been found:
* MPI
* PkgConfig
* BLAS
* Threads
* LAPACK
* Inkscape
* X11
* OpenGL
* ZLIB
-- The following REQUIRED packages have been found:
* dune-common
* dune-geometry
* dune-curvilineargeometry
* dune-grid
* dune-alugrid
-- The following OPTIONAL packages have not been found:
* LATEX
* UnixCommands
* Doxygen
* GMP
* ALUGrid
* Alberta
* UG (required version >= 3.11.0)
* Grape
* Psurface
* AmiraMesh
* SIONlib
* DLMalloc
* ZOLTAN
-- Configuring done
-- Generating done
-- Build files have been written to: /home/fomins/gitwork/hades-github-lspr-ag/dune-curvilineargrid/build-cmake
--- calling make for dune-curvilineargrid ---
build directory: build-cmake
make
[ 50%] Built target dune_curvilineargrid
[100%] Building CXX object dune/curvilineargrid/io/file/test/CMakeFiles/curvilineargmshtest.dir/curvilineargmshtest.cc.o
In file included from /home/fomins/gitwork/hades-github-lspr-ag/dune-curvilineargrid/dune/curvilineargrid/io/file/curvilineargmshreader.hh:42:0,
from /home/fomins/gitwork/hades-github-lspr-ag/dune-curvilineargrid/dune/curvilineargrid/io/file/test/curvilineargmshtest.cc:43:
/home/fomins/gitwork/hades-github-lspr-ag/dune-curvilineargrid/dune/curvilineargrid/curvilineargrid/gridfactory.hh:45:22: fatal error: parmetis.h: No such file or directory
#include <parmetis.h>
^
compilation terminated.
make[2]: *** [dune/curvilineargrid/io/file/test/CMakeFiles/curvilineargmshtest.dir/curvilineargmshtest.cc.o] Error 1
make[1]: *** [dune/curvilineargrid/io/file/test/CMakeFiles/curvilineargmshtest.dir/all] Error 2
make: *** [all] Error 2
--- Failed to build dune-curvilineargrid ---
Terminating dunecontrol due to previous errors!
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#################################################################################################################
## objective - opts file for building vulcain, based on Dune, with cmake
##
## history - 2014 apr 16, created
##
## usage - time ./dune-common/bin/dunecontrol --use-cmake --opts=af.debian7.lsprag.cmakebuild.minimalistic.opts all
##
##################################################################################################################
USE_CMAKE=yes
CONFIGURE_FLAGS="--enable-parallel --enable-experimental-grid-extensions CC=mpicc CXX=mpicxx"
CMAKE_PREFIX_PATH="\
/opt/extlib/boost/1.55.0/gcc/4.9.0;\
/opt/extlib/parmetis/4.0.3/openmpi/1.8.1/gcc/4.9.0;\
/opt/extlib/metis/5.1.0/gcc/4.9.0;\
"
CMAKE_FLAGS="\
-DCXXFLAGS=\"-O2 -Wall\" \
-DCMAKE_PREFIX_PATH=\"$CMAKE_PREFIX_PATH\" \
-DDUNE_GRID_EXPERIMENTAL_GRID_EXTENSIONS:BOOL=TRUE \
"
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