[Dune] a problem with ALUGrid and Metis
Arya Fallahi
arya.fallahi at gmail.com
Mon Jul 5 15:26:13 CEST 2021
Hi Simon,
I already see the METIS Found when dune-common is configured. In the log
file, I see the following lines during configuring dune-common:
-- Found METIS: /Users/afallahi/Documents/library/metis-5.1/lib/libmetis.a
(found version "5.1")
-- The following OPTIONAL packages have been found:
* LATEX
* LatexMk
* BLAS, fast linear algebra routines
* LAPACK, fast linear algebra routines
* QuadMath, GCC Quad-Precision Math Library, <
https://gcc.gnu.org/onlinedocs/libquadmath>
* Inkscape, converts SVG images, <www.inkscape.org>
To generate the documentation with LaTeX
* Threads, Multi-threading library
* PkgConfig, Unified interface for querying installed libraries
To find Dune module dependencies
* METIS, Serial Graph Partitioning
* MPI, Message Passing Interface library
Parallel programming on multiple processors
* Python3
Things go fine until dune-alugrid is being configured where I suddenly see
the following message:
Could NOT find METIS (missing: METIS_LIBRARY METIS_INCLUDE_DIR
METIS_API_VERSION)
I am using dune-common, dune-grid, dune-geometry and of course dune-alugrid.
I did a search and I have only one FindMetis.cmake which is in the
dune-common folder.
Actually I was firstly using -DMETIS_DIR but later saw that in dune website
using -DMETIS_ROOT is advised and I changed to that and the correct one is
metis-5.1.
I always run dunecontrol from scratch.
My guess is that I should somehow give the above three variables manually
but I do not know how to do that.
I just cloned the dune modules from git repository and I am running the
code on a mac.
I hope it helps.
Regards,
Arya
On Mon, Jul 5, 2021 at 1:52 PM Simon Praetorius <
simon.praetorius at tu-dresden.de> wrote:
> ok, I think I need more information about your setup, to find the error.
> In your first cmake output log, it says: METIS Found (see the section "The
> following OPTIONAL packages have been found:...").
>
> - You should see this METIS Found output already when you configure
> dune-common.
> - If in the same cmake output it first says "Found" and then "Not found",
> then something is wrong.
> - Which dune modules are you using? The `FindMETIS.cmake` file comes from
> dune-common. Maybe there is another module conflicting with this?
> - In your first mail, you wrote something like
> "-DMETIS_DIR=/usr/local/Cellar/metis/5.1.0", in your last mail
> "-DMETIS_ROOT=/Users/afallahi/Documents/library/metis-5.1". Maybe something
> got mixed up?
> - You could try to make a clean rebuild, i.e., remove all build
> directories and run dunecontrol from the start:
>
> dunecontrol exec rm -rf build-cmake # to delete in ALL found dune modules
> the folder build-cmake (the default cmake build folder)
>
> Best, Simon
> Am 05.07.21 um 11:13 schrieb Arya Fallahi:
>
> Dear Simon,
>
> thank you very much for your email and answer to my question.
>
> I checked your branch and did exactly the same thing as your changes in my
> alugrid but it still does not work.
>
> The strange thing I see now is that during compilation, first metis is
> found:
>
> Found METIS: /Users/afallahi/Documents/library/metis-5.1/lib/libmetis.a
> (found version "5.1")
>
> but afterward I see the following message:
>
> -- Could NOT find METIS (missing: METIS_LIBRARY METIS_INCLUDE_DIR
> METIS_API_VERSION)
>
> I am now enabling the metis support in my opts file using
>
> -DMETIS_ROOT=/Users/afallahi/Documents/library/metis-5.1
>
> Is there anything else I should do?
>
> Again thanks a lot for your help and best regards,
>
> Arya
>
> On Sat, Jul 3, 2021 at 8:49 PM Simon Praetorius <
> simon.praetorius at tu-dresden.de> wrote:
>
>> Dear Arya,
>>
>> in ALUGrid, METIS is disabled additionally by a variable ALUGRID_DISABLE_METIS
>> that is set to true by default (I don't know why, maybe the developers can
>> answer) and also you have to set METIS flags on your cmake target to get it
>> properly enabled, by using `dune_add_mets_flags(<target>)`with `<target`
>> your cmake target name (e.g. an executable).
>>
>> I suggest, you try out the branch bugfix/cmake-add-metis-flags that I
>> have uploaded quiet recently, so solve these shortcoming with METIS in
>> ALUGrid.
>>
>> Best regards,
>> Simon
>>
>>
>> Am 02.07.21 um 19:16 schrieb Arya Fallahi:
>>
>> Dear Dune,
>>
>> I am having a trouble with installing ALUGrid with support metis. In my
>> opts file I write the following to tell ALUGrid the location of metis:
>>
>> CMAKE_FLAGS="
>>
>> -DCMAKE_CXX_COMPILER=/Users/afallahi/Documents/library/gcc-9.2/bin/g++
>> \
>>
>> -DCMAKE_CXX_FLAGS='-O3' \
>>
>> -DCMAKE_C_COMPILER=/Users/afallahi/Documents/library/gcc-9.2/bin/gcc \
>>
>> -DCMAKE_C_FLAGS='-O3' \
>>
>> -DDUNE_GRID_GRIDTYPE_SELECTOR=ON \
>>
>> -DMETIS_DIR=/usr/local/Cellar/metis/5.1.0
>>
>> "
>>
>> then, during the compilation it seems metis is found:
>>
>> --- calling all for dune-alugrid ---
>>
>> --- calling vcsetup for dune-alugrid ---
>>
>> --- calling cmake for dune-alugrid ---
>>
>> ----- using default flags $CMAKE_FLAGS from
>> /Users/afallahi/Documents/codes/leist.opts -----
>>
>> WARNING: could not find module 'dune-uggrid',
>>
>> module is also unknown to pkg-config.
>>
>> Maybe you need to adjust PKG_CONFIG_PATH!
>>
>> 'dune-uggrid' is suggested by dune-grid
>>
>> Skipping 'dune-uggrid'!
>>
>> cmake -DCMAKE_CXX_COMPILER=/Users/afallahi/Documents/library/gcc-9.2/bin/g++
>> -DCMAKE_CXX_FLAGS='-O3'
>> -DCMAKE_C_COMPILER=/Users/afallahi/Documents/library/gcc-9.2/bin/gcc
>> -DCMAKE_C_FLAGS='-O3' -DDUNE_GRID_GRIDTYPE_SELECTOR=ON
>> -DMETIS_DIR=/usr/local/Cellar/metis/5.1.0
>> "-Ddune-common_DIR=/Users/afallahi/Documents/codes/dune-common/build-cmake"
>> "-Ddune-geometry_DIR=/Users/afallahi/Documents/codes/dune-geometry/build-cmake"
>> "-Ddune-grid_DIR=/Users/afallahi/Documents/codes/dune-grid/build-cmake"
>> -DCMAKE_CXX_COMPILER=/Users/afallahi/Documents/library/gcc-9.2/bin/g++
>> -DCMAKE_CXX_FLAGS='-O3'
>> -DCMAKE_C_COMPILER=/Users/afallahi/Documents/library/gcc-9.2/bin/gcc
>> -DCMAKE_C_FLAGS='-O3' -DDUNE_GRID_GRIDTYPE_SELECTOR=ON
>> -DMETIS_DIR=/usr/local/Cellar/metis/5.1.0
>> "/Users/afallahi/Documents/codes/dune-alugrid"
>>
>> -- Dependencies for dune-alugrid: dune-grid (>= 2.8)
>>
>> -- Dependencies for dune-grid: dune-geometry (>= 2.8)
>>
>> -- Suggestions for dune-grid: dune-uggrid (>=2.8)
>>
>> -- Dependencies for dune-geometry: dune-common (>= 2.8)
>>
>> -- Could NOT find dune-uggrid (missing: dune-uggrid_DIR)
>>
>> -- No full CMake package configuration support available. Falling back to
>> pkg-config.
>>
>> -- Checking for module 'dune-uggrid>=2.8'
>>
>> -- No package 'dune-uggrid' found
>>
>> -- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE)
>>
>> -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
>>
>> -- Searching for macro file 'DuneCommonMacros' for module 'dune-common'.
>>
>> -- Performing tests specific to dune-common from file
>> /Users/afallahi/Documents/codes/dune-common/cmake/modules/DuneCommonMacros.cmake.
>>
>> -- Set Minimal Debug Level to 4
>>
>> -- Could NOT find GMP (missing: GMPXX_LIB GMPXX_INCLUDE_DIR
>> GMP_INCLUDE_DIR GMP_LIB)
>>
>> -- Found MPI_C:
>> /Users/afallahi/Documents/library/openmpi-4.0/lib/libmpi.dylib (found
>> suitable version "3.1", minimum required is "3.0")
>>
>> -- Found MPI: TRUE (found suitable version "3.1", minimum required is
>> "3.0") found components: C
>>
>> -- Could NOT find TBB (set TBB_DIR to path containing TBBConfig.cmake or
>> set PKG_CONFIG_PATH to include the location of the tbb.pc file) (missing:
>> PkgConfigTBB_LINK_LIBRARIES PkgConfigTBB_FOUND) (found version "")
>>
>> -- Could NOT find PTScotch (missing: SCOTCH_LIBRARY SCOTCHERR_LIBRARY
>> SCOTCH_INCLUDE_DIR)
>>
>> -- Found MPI_C:
>> /Users/afallahi/Documents/library/openmpi-4.0/lib/libmpi.dylib (found
>> version "3.1")
>>
>> -- Found MPI: TRUE (found version "3.1") found components: C
>>
>> -- Could NOT find ParMETIS (missing: PARMETIS_LIBRARY
>> PARMETIS_INCLUDE_DIR) (Required is at least version "4.0")
>>
>> -- Could NOT find Vc (missing: Vc_DIR)
>>
>> -- Setting
>> dune-common_INCLUDE_DIRS=/Users/afallahi/Documents/codes/dune-common
>>
>> -- Setting dune-common_LIBRARIES=dunecommon
>>
>> -- Searching for macro file 'DuneUggridMacros' for module 'dune-uggrid'.
>>
>> -- No module specific tests performed for module 'dune-uggrid' because
>> macro file 'DuneUggridMacros.cmake' not found in
>> /Users/afallahi/Documents/codes/dune-alugrid/cmake/modules;/Users/afallahi/Documents/codes/dune-grid/cmake/modules;/Users/afallahi/Documents/codes/dune-geometry/cmake/modules;/Users/afallahi/Documents/codes/dune-common/cmake/modules.
>>
>> -- Searching for macro file 'DuneGeometryMacros' for module
>> 'dune-geometry'.
>>
>> -- No module specific tests performed for module 'dune-geometry' because
>> macro file 'DuneGeometryMacros.cmake' not found in
>> /Users/afallahi/Documents/codes/dune-alugrid/cmake/modules;/Users/afallahi/Documents/codes/dune-grid/cmake/modules;/Users/afallahi/Documents/codes/dune-geometry/cmake/modules;/Users/afallahi/Documents/codes/dune-common/cmake/modules.
>>
>> -- Setting
>> dune-geometry_INCLUDE_DIRS=/Users/afallahi/Documents/codes/dune-geometry
>>
>> -- Setting dune-geometry_LIBRARIES=dunegeometry
>>
>> -- Searching for macro file 'DuneGridMacros' for module 'dune-grid'.
>>
>> -- Performing tests specific to dune-grid from file
>> /Users/afallahi/Documents/codes/dune-grid/cmake/modules/DuneGridMacros.cmake.
>>
>> -- Could NOT find ParMETIS (missing: PARMETIS_LIBRARY
>> PARMETIS_INCLUDE_DIR)
>>
>> -- Checking for module 'alberta-grid_1d>=3.0'
>>
>> -- No package 'alberta-grid_1d' found
>>
>> -- Checking for module 'alberta-grid_2d>=3.0'
>>
>> -- No package 'alberta-grid_2d' found
>>
>> -- Checking for module 'alberta-grid_3d>=3.0'
>>
>> -- No package 'alberta-grid_3d' found
>>
>> -- Checking for module 'alberta-grid_4d>=3.0'
>>
>> -- No package 'alberta-grid_4d' found
>>
>> -- Checking for module 'alberta-grid_5d>=3.0'
>>
>> -- No package 'alberta-grid_5d' found
>>
>> -- Checking for module 'alberta-grid_6d>=3.0'
>>
>> -- No package 'alberta-grid_6d' found
>>
>> -- Checking for module 'alberta-grid_7d>=3.0'
>>
>> -- No package 'alberta-grid_7d' found
>>
>> -- Checking for module 'alberta-grid_8d>=3.0'
>>
>> -- No package 'alberta-grid_8d' found
>>
>> -- Checking for module 'alberta-grid_9d>=3.0'
>>
>> -- No package 'alberta-grid_9d' found
>>
>> -- Could NOT find Alberta (set PKG_CONFIG_PATH to include the location of
>> the alberta-grid_[n]d.pc files) (missing: ALBERTA_GRID_PREFIX) (Required is
>> at least version "3.0")
>>
>> CMake Warning (dev) at
>> /Applications/CMake.app/Contents/share/cmake-3.20/Modules/FindPackageHandleStandardArgs.cmake:438
>> (message):
>>
>> The package name passed to `find_package_handle_standard_args`
>> (PkgConfig)
>>
>> does not match the name of the calling package (Psurface). This can
>> lead
>>
>> to problems in calling code that expects `find_package` result
>> variables
>>
>> (e.g., `_FOUND`) to follow a certain pattern.
>>
>> Call Stack (most recent call first):
>>
>> /Applications/CMake.app/Contents/share/cmake-3.20/Modules/FindPkgConfig.cmake:70
>> (find_package_handle_standard_args)
>>
>> /Users/afallahi/Documents/codes/dune-grid/cmake/modules/FindPsurface.cmake:63
>> (include)
>>
>> /Users/afallahi/Documents/codes/dune-grid/cmake/modules/DuneGridMacros.cmake:20
>> (find_package)
>>
>> /Users/afallahi/Documents/codes/dune-common/cmake/modules/DuneMacros.cmake:614
>> (include)
>>
>> /Users/afallahi/Documents/codes/dune-common/cmake/modules/DuneMacros.cmake:704
>> (dune_process_dependency_macros)
>>
>> CMakeLists.txt:48 (dune_project)
>>
>> This warning is for project developers. Use -Wno-dev to suppress it.
>>
>>
>> -- 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=/Users/afallahi/Documents/codes/dune-grid
>>
>> -- Setting dune-grid_LIBRARIES=dunegrid
>>
>> -- Searching for macro file 'DuneAlugridMacros' for module 'dune-alugrid'.
>>
>> -- Performing tests specific to dune-alugrid from file
>> /Users/afallahi/Documents/codes/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_INCLUDE)
>>
>> -- Could NOT find PTScotch (missing: SCOTCH_LIBRARY SCOTCHERR_LIBRARY
>> SCOTCH_INCLUDE_DIR)
>>
>> Found ZOLTAN_INCLUDE_DIRS-NOTFOUND
>>
>> Found ZOLTAN_LIBRARIES-NOTFOUND
>>
>> -- Not enabling torture-tests
>>
>> -- Using scripts from
>> /Users/afallahi/Documents/codes/dune-common/cmake/scripts for creating
>> doxygen stuff.
>>
>> CMake Deprecation Warning at
>> /Users/afallahi/Documents/codes/dune-common/cmake/modules/DuneMacros.cmake:168
>> (message):
>>
>> Calling target_link_libraries without the <scope> argument is
>> deprecated.
>>
>> Call Stack (most recent call first):
>>
>> /Users/afallahi/Documents/codes/dune-common/cmake/modules/DuneMacros.cmake:159
>> (target_link_libraries_helper)
>>
>> lib/CMakeLists.txt:28 (target_link_libraries)
>>
>>
>>
>> CMake Deprecation Warning at
>> /Users/afallahi/Documents/codes/dune-common/cmake/modules/DuneMacros.cmake:168
>> (message):
>>
>> Calling target_link_libraries without the <scope> argument is
>> deprecated.
>>
>> Call Stack (most recent call first):
>>
>> /Users/afallahi/Documents/codes/dune-common/cmake/modules/DuneMacros.cmake:159
>> (target_link_libraries_helper)
>>
>> lib/CMakeLists.txt:32 (target_link_libraries)
>>
>>
>>
>> CMake Deprecation Warning at
>> /Users/afallahi/Documents/codes/dune-common/cmake/modules/DuneMacros.cmake:168
>> (message):
>>
>> Calling target_link_libraries without the <scope> argument is
>> deprecated.
>>
>> Call Stack (most recent call first):
>>
>> /Users/afallahi/Documents/codes/dune-common/cmake/modules/DuneMacros.cmake:159
>> (target_link_libraries_helper)
>>
>> lib/CMakeLists.txt:44 (target_link_libraries)
>>
>>
>>
>> -- Adding custom target for config.h generation
>>
>> -- The following OPTIONAL packages have been found:
>>
>>
>> * LATEX
>>
>> * LatexMk
>>
>> * BLAS, fast linear algebra routines
>>
>> * LAPACK, fast linear algebra routines
>>
>> * QuadMath, GCC Quad-Precision Math Library, <
>> https://gcc.gnu.org/onlinedocs/libquadmath>
>>
>> * Inkscape, converts SVG images, <www.inkscape.org>
>>
>> To generate the documentation with LaTeX
>>
>> * Threads, Multi-threading library
>>
>> * Python3
>>
>> * PkgConfig, Unified interface for querying installed libraries
>>
>> To find Dune module dependencies
>>
>> * ZLIB
>>
>> * METIS, Serial Graph Partitioning
>>
>>
>> -- The following REQUIRED packages have been found:
>>
>>
>> * dune-common
>>
>> * dune-grid
>>
>> * dune-geometry
>>
>>
>> -- The following OPTIONAL packages have not been found:
>>
>>
>> * dune-uggrid
>>
>> * Sphinx, Documentation generator, <www.sphinx-doc.org>
>>
>> To generate the documentation from CMake and Python sources
>>
>> * Doxygen, Class documentation generator, <www.doxygen.org>
>>
>> To generate the class documentation from C++ sources
>>
>> * GMP, GNU multi-precision library, <https://gmplib.org>
>>
>> * TBB, Intel's Threading Building Blocks
>>
>> * Vc, C++ Vectorization library, <https://github.com/VcDevel/Vc>
>>
>> For use of SIMD instructions
>>
>> * ParMETIS, Parallel Graph Partitioning
>>
>> * Alberta (required version >= 3.0), An adaptive hierarchical finite
>> element toolbox and grid manager
>>
>> * Psurface, Piecewise linear bijections between triangulated surfaces
>>
>> * AmiraMesh
>>
>> * SIONlib
>>
>> * DLMalloc
>>
>> * PTScotch, Sequential and Parallel Graph Partitioning
>>
>> * ZOLTAN
>>
>>
>> -- Configuring done
>>
>> CMake Warning (dev) in CMakeLists.txt:
>>
>> Policy CMP0087 is not set: Install CODE|SCRIPT allow the use of
>> generator
>>
>> expressions. Run "cmake --help-policy CMP0087" for policy details.
>> Use
>>
>> the cmake_policy command to set the policy and suppress this warning.
>>
>> This warning is for project developers. Use -Wno-dev to suppress it.
>>
>>
>> -- Generating done
>>
>> -- Build files have been written to:
>> /Users/afallahi/Documents/codes/dune-alugrid/build-cmake
>>
>> --- calling make for dune-alugrid ---
>>
>> build directory: build-cmake
>>
>> cmake --build . --
>>
>> Consolidate compiler generated dependencies of target dunealugrid
>>
>> [ 4%] Building CXX object
>> lib/CMakeFiles/dunealugrid.dir/__/dune/alugrid/impl/binaryio.cc.o
>>
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>> [ 96%] Building CXX object
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>> [100%] Linking CXX static library libdunealugrid.a
>>
>> [100%] Built target dunealugrid
>>
>> --- dune-alugrid done ---
>>
>> but when I run my code at the point I call loadBalance(), I still get the
>> following error message:
>>
>> **ERROR The use of METIS_PartGraphRecursive is not supported, when the
>> METIS library is missing! in:
>> /Users/afallahi/Documents/codes/dune-alugrid/dune/alugrid/impl/parallel/alumetis.hh
>> line: 137
>>
>> **INFO Due to license reasons the library METIS is
>>
>> not part of the ALUGrid library distribution.
>>
>> To use this feature get a copy of the METIS library
>>
>> (see http://www-users.cs.umn.edu/~karypis/metis/metis/ )
>>
>> and re-configure the ALUGrid library with the
>>
>> --with-metis=PATH_TO_METIS option,
>>
>> or choose another Graph partitioning method.
>>
>> Exiting program, bye!
>>
>> I am stuck since several days in the problem, I will be thankful if you
>> give me a hint how to resolve the issue.
>>
>> Best regards
>>
>> _______________________________________________
>> Dune mailing listDune at lists.dune-project.orghttps://lists.dune-project.org/mailman/listinfo/dune
>>
>> --
>> Dr. Simon Praetorius
>> Technische Universität Dresden
>> Institute of Scientific Computing
>> phone: +49 351 463-34432
>> mail: simon.praetorius at tu-dresden.de
>> web: https://tu-dresden.de/mn/math/wir/das-institut/beschaeftigte/simon-praetorius
>>
>> _______________________________________________
>> Dune mailing list
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>
> --
> Dr. Simon Praetorius
> Technische Universität Dresden
> Institute of Scientific Computing
> phone: +49 351 463-34432
> mail: simon.praetorius at tu-dresden.de
> web: https://tu-dresden.de/mn/math/wir/das-institut/beschaeftigte/simon-praetorius
>
>
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