[Dune] a problem with ALUGrid and Metis

Arya Fallahi arya.fallahi at gmail.com
Fri Jul 2 19:16:34 CEST 2021 

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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lib/CMakeFiles/dunealugrid.dir/__/dune/alugrid/impl/macrofileheader.cc.o

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lib/CMakeFiles/dunealugrid.dir/__/dune/alugrid/impl/serial/ghost_info.cc.o

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lib/CMakeFiles/dunealugrid.dir/__/dune/alugrid/impl/serial/gitter_geo.cc.o

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[ 96%] Building CXX object
lib/CMakeFiles/dunealugrid.dir/__/dune/alugrid/3d/topology.cc.o

[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
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