[Dune] problem compiling dune-grid from git repository
Edscott Wilson
edscott.wilson.garcia at gmail.com
Mon Nov 14 16:06:32 CET 2016
First of all, thank you Oliver for kind, helpful and prompt response. I
will now explain the issue in more detail and annex the requested log files.
First step, I cloned git repositories as mentioned in Oliver’s text at
http://www.math.tu-dresden.de/~osander/research/sander-getting-started-with-dune.pdf
and followed the instructions detailed in the text as follows. As you can
see towards the end, compilation hangs when reaching dunealbertagrid_1d.dir.
--- going to build dune-common dune-geometry dune-uggrid dune-grid
dune-typetree dune-istl dune-localfunctions dune-functions ---
--- calling all for dune-common ---
--- calling vcsetup for dune-common ---
--- calling configure for dune-common ---
cmake -DCMAKE_MODULE_PATH="" "/archive/src/dune-git/dune-common"
-- Performing tests specific to dune-common from file
/archive/src/dune-git/dune-common/cmake/modules/DuneCommonMacros.cmake.
-- A library with BLAS API found.
-- A library with LAPACK API found.
-- Detected Compiler: GCC 5.3.0
-- Detected CPU: haswell
-- Using scripts from /archive/src/dune-git/dune-common/cmake/scripts for
creating doxygen stuff.
-- using /archive/src/dune-git/dune-common/doc/doxygen/Doxystyle to create
doxystyle file
-- Not adding custom target for config.h generation
--
-- The following OPTIONAL packages have been found:
* MPI
* LATEX
* UnixCommands
* Sphinx
* PythonInterp
* Doxygen
* PkgConfig
* BLAS
* Threads
* LAPACK
* GMP
* Inkscape
* Vc , C++ Vectorization library , <https://github.com/VcDevel/Vc>
-- Configuring done
-- Generating done
-- Build files have been written to:
/archive/src/dune-git/dune-common/build-cmake
--- calling make for dune-common ---
build directory: build-cmake
cmake --build . --
[ 10%] Building CXX object
dune/common/CMakeFiles/dunecommon.dir/debugallocator.cc.o
[ 10%] Building CXX object
dune/common/CMakeFiles/dunecommon.dir/dynmatrixev.cc.o
[ 20%] Building CXX object
dune/common/CMakeFiles/dunecommon.dir/exceptions.cc.o
[ 20%] Building CXX object
dune/common/CMakeFiles/dunecommon.dir/fmatrixev.cc.o
[ 30%] Building CXX object
dune/common/CMakeFiles/dunecommon.dir/ios_state.cc.o
[ 30%] Building CXX object
dune/common/CMakeFiles/dunecommon.dir/parametertree.cc.o
[ 40%] Building CXX object
dune/common/CMakeFiles/dunecommon.dir/parametertreeparser.cc.o
[ 40%] Building CXX object dune/common/CMakeFiles/dunecommon.dir/path.cc.o
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dune/common/CMakeFiles/dunecommon.dir/stdstreams.cc.o
[ 50%] Building CXX object
dune/common/CMakeFiles/dunecommon.dir/stdthread.cc.o
[ 60%] Linking CXX static library ../../lib/libdunecommon.a
[ 60%] Built target dunecommon
[ 70%] Generating poosc08_test.cc
Scanning dependencies of target poosc08_test
[ 70%] Building CXX object
doc/comm/CMakeFiles/poosc08_test.dir/poosc08_test.cc.o
[ 80%] Linking CXX executable poosc08_test
[ 80%] Built target poosc08_test
[ 90%] Building CXX object doc/comm/CMakeFiles/poosc08.dir/poosc08.cc.o
[ 90%] Linking CXX executable poosc08
[ 90%] Built target poosc08
[ 90%] Building CXX object doc/comm/CMakeFiles/indexset.dir/indexset.cc.o
[100%] Linking CXX executable indexset
[100%] Built target indexset
--- dune-common done ---
--- calling all for dune-geometry ---
--- calling vcsetup for dune-geometry ---
--- calling configure for dune-geometry ---
cmake -DCMAKE_MODULE_PATH=""
"-Ddune-common_DIR=/archive/src/dune-git/dune-common/build-cmake"
"/archive/src/dune-git/dune-geometry"
-- Dependencies for dune-geometry: dune-common (>= 3.0)
-- Performing tests specific to dune-common from file
/archive/src/dune-git/dune-common/cmake/modules/DuneCommonMacros.cmake.
-- A library with BLAS API found.
-- A library with LAPACK API found.
-- Detected Compiler: GCC 5.3.0
-- Detected CPU: haswell
-- Setting dune-common_INCLUDE_DIRS=/archive/src/dune-git/dune-common
-- Setting dune-common_LIBRARIES=dunecommon
-- Using scripts from /archive/src/dune-git/dune-common/cmake/scripts for
creating doxygen stuff.
-- using /archive/src/dune-git/dune-common/doc/doxygen/Doxystyle to create
doxystyle file
-- Adding custom target for config.h generation
--
-- The following OPTIONAL packages have been found:
* MPI
* LATEX
* UnixCommands
* Sphinx
* PythonInterp
* Doxygen
* PkgConfig
* BLAS
* Threads
* LAPACK
* GMP
* Inkscape
* Vc , C++ Vectorization library , <https://github.com/VcDevel/Vc>
-- The following REQUIRED packages have been found:
* dune-common
-- Configuring done
-- Generating done
-- Build files have been written to:
/archive/src/dune-git/dune-geometry/build-cmake
--- calling make for dune-geometry ---
build directory: build-cmake
cmake --build . --
[ 10%] Building CXX object
lib/CMakeFiles/dunegeometry.dir/__/dune/geometry/referenceelements.cc.o
[ 10%] Building CXX object
lib/CMakeFiles/dunegeometry.dir/__/dune/geometry/quadraturerules/gauss.cc.o
[ 10%] Building CXX object
lib/CMakeFiles/dunegeometry.dir/__/dune/geometry/quadraturerules/jacobi_1_0.cc.o
[ 10%] Building CXX object
lib/CMakeFiles/dunegeometry.dir/__/dune/geometry/quadraturerules/jacobi_2_0.cc.o
[ 10%] Building CXX object
lib/CMakeFiles/dunegeometry.dir/__/dune/geometry/quadraturerules/quadraturerules.cc.o
[ 10%] Building CXX object
lib/CMakeFiles/dunegeometry.dir/__/dune/geometry/quadraturerules/gausslobatto.cc.o
[ 10%] Linking CXX static library libdunegeometry.a
[ 10%] Built target dunegeometry
--- dune-geometry done ---
--- calling all for dune-uggrid ---
--- calling vcsetup for dune-uggrid ---
--- calling configure for dune-uggrid ---
find: ‘dune’: No existe el fichero o el directorio
cmake -DCMAKE_MODULE_PATH=""
"-Ddune-common_DIR=/archive/src/dune-git/dune-common/build-cmake"
"/archive/src/dune-git/dune-uggrid"
-- Dependencies for dune-uggrid: dune-common
-- Performing tests specific to dune-common from file
/archive/src/dune-git/dune-common/cmake/modules/DuneCommonMacros.cmake.
-- A library with BLAS API found.
-- A library with LAPACK API found.
-- Detected Compiler: GCC 5.3.0
-- Detected CPU: haswell
-- Setting dune-common_INCLUDE_DIRS=/archive/src/dune-git/dune-common
-- Setting dune-common_LIBRARIES=dunecommon
-- Performing tests specific to dune-uggrid from file
/archive/src/dune-git/dune-uggrid/cmake/modules/DuneUggridMacros.cmake.
-- Adding custom target for config.h generation
--
-- The following OPTIONAL packages have been found:
* LATEX
* UnixCommands
* Sphinx
* PythonInterp
* Doxygen
* PkgConfig
* BLAS
* Threads
* LAPACK
* GMP
* Inkscape
* Vc , C++ Vectorization library , <https://github.com/VcDevel/Vc>
* MPI
-- The following REQUIRED packages have been found:
* dune-common
-- Configuring done
-- Generating done
-- Build files have been written to:
/archive/src/dune-git/dune-uggrid/build-cmake
--- calling make for dune-uggrid ---
build directory: build-cmake
cmake --build . --
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/archive/src/dune-git/dune-uggrid/parallel/ddd/xfer/pack.cc:545:46: aviso:
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/archive/src/dune-git/dune-uggrid/parallel/ddd/xfer/pack.cc:545:46: aviso:
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[ 81%] Building CXX object np/algebra/CMakeFiles/algebra3.dir/ugblas.cc.o
[ 81%] Building CXX object np/algebra/CMakeFiles/algebra3.dir/ugiter.cc.o
[ 82%] Building CXX object np/algebra/CMakeFiles/algebra3.dir/transgrid.cc.o
[ 82%] Building CXX object np/algebra/CMakeFiles/algebra3.dir/block.cc.o
[ 83%] Building CXX object np/algebra/CMakeFiles/algebra3.dir/npcheck.cc.o
[ 83%] Building CXX object np/algebra/CMakeFiles/algebra3.dir/sm.cc.o
[ 84%] Building CXX object np/algebra/CMakeFiles/algebra3.dir/blasm.cc.o
[ 84%] Built target algebra3
[ 84%] Building CXX object np/algebra/CMakeFiles/algebra2.dir/ugblas.cc.o
[ 85%] Building CXX object np/algebra/CMakeFiles/algebra2.dir/ugiter.cc.o
[ 85%] Building CXX object np/algebra/CMakeFiles/algebra2.dir/transgrid.cc.o
[ 86%] Building CXX object np/algebra/CMakeFiles/algebra2.dir/block.cc.o
[ 86%] Building CXX object np/algebra/CMakeFiles/algebra2.dir/npcheck.cc.o
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[ 87%] Built target algebra2
[ 88%] Building CXX object np/udm/CMakeFiles/udm3.dir/disctools.cc.o
[ 88%] Building CXX object np/udm/CMakeFiles/udm3.dir/npscan.cc.o
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[ 89%] Building CXX object np/udm/CMakeFiles/udm3.dir/formats.cc.o
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[ 90%] Building CXX object np/udm/CMakeFiles/udm2.dir/disctools.cc.o
[ 91%] Building CXX object np/udm/CMakeFiles/udm2.dir/npscan.cc.o
[ 91%] Building CXX object np/udm/CMakeFiles/udm2.dir/udm.cc.o
[ 92%] Building CXX object np/udm/CMakeFiles/udm2.dir/formats.cc.o
[ 92%] Building CXX object np/udm/CMakeFiles/udm2.dir/numproc.cc.o
[ 92%] Built target udm2
[ 92%] Building CXX object ui/CMakeFiles/ugui3.dir/initui.cc.o
[ 93%] Building CXX object ui/CMakeFiles/ugui3.dir/cmdline.cc.o
[ 93%] Building CXX object ui/CMakeFiles/ugui3.dir/commands.cc.o
[ 93%] Built target ugui3
[ 94%] Building CXX object ui/CMakeFiles/ugui2.dir/initui.cc.o
[ 94%] Building CXX object ui/CMakeFiles/ugui2.dir/cmdline.cc.o
[ 95%] Building CXX object ui/CMakeFiles/ugui2.dir/commands.cc.o
[ 95%] Built target ugui2
[ 96%] Building CXX object lib/CMakeFiles/ugS3.dir/__/initug.cc.o
[ 96%] Linking CXX static library libugS3.a
[ 96%] Built target ugS3
[ 97%] Building CXX object lib/CMakeFiles/ugS2.dir/__/initug.cc.o
[ 97%] Linking CXX static library libugS2.a
[ 97%] Built target ugS2
[ 98%] Building CXX object lib/CMakeFiles/ugL3.dir/__/initug.cc.o
[ 98%] Linking CXX static library libugL3.a
[ 98%] Built target ugL3
[100%] Building CXX object lib/CMakeFiles/ugL2.dir/__/initug.cc.o
[100%] Linking CXX static library libugL2.a
[100%] Built target ugL2
--- dune-uggrid done ---
--- calling all for dune-grid ---
--- calling vcsetup for dune-grid ---
--- calling configure for dune-grid ---
cmake -DCMAKE_MODULE_PATH=""
"-Ddune-common_DIR=/archive/src/dune-git/dune-common/build-cmake"
"-Ddune-geometry_DIR=/archive/src/dune-git/dune-geometry/build-cmake"
"-Ddune-uggrid_DIR=/archive/src/dune-git/dune-uggrid/build-cmake"
"/archive/src/dune-git/dune-grid"
-- Dependencies for dune-grid: dune-geometry (>= 3.0)
-- Suggestions for dune-grid: dune-uggrid
-- Dependencies for dune-geometry: dune-common (>= 3.0)
CMake Warning at
/archive/src/dune-git/dune-common/cmake/modules/DuneMacros.cmake:174
(find_package):
Found package configuration file:
/archive/src/dune-git/dune-uggrid/build-cmake/dune-uggrid-config.cmake
but it set dune-uggrid_FOUND to FALSE so package "dune-uggrid" is
considered to be NOT FOUND.
Call Stack (most recent call first):
/archive/src/dune-git/dune-common/cmake/modules/DuneMacros.cmake:420
(find_dune_package)
/archive/src/dune-git/dune-common/cmake/modules/DuneMacros.cmake:467
(dune_process_dependency_leafs)
/archive/src/dune-git/dune-common/cmake/modules/DuneMacros.cmake:487
(dune_create_dependency_leafs)
/archive/src/dune-git/dune-common/cmake/modules/DuneMacros.cmake:633
(dune_create_dependency_tree)
CMakeLists.txt:22 (dune_project)
-- No full CMake package configuration support available. Falling back to
pkg-config.
-- Checking for module 'dune-uggrid '
-- No package 'dune-uggrid' found
-- Performing tests specific to dune-common from file
/archive/src/dune-git/dune-common/cmake/modules/DuneCommonMacros.cmake.
-- A library with BLAS API found.
-- A library with LAPACK API found.
-- Detected Compiler: GCC 5.3.0
-- Detected CPU: haswell
-- Setting dune-common_INCLUDE_DIRS=/archive/src/dune-git/dune-common
-- Setting dune-common_LIBRARIES=dunecommon
-- Performing tests specific to dune-uggrid from file
/archive/src/dune-git/dune-uggrid/cmake/modules/DuneUggridMacros.cmake.
-- Setting dune-uggrid_INCLUDE_DIRS=/archive/src/dune-git/dune-uggrid
-- Setting dune-uggrid_LIBRARIES=ugS2;ugS3
-- Setting dune-geometry_INCLUDE_DIRS=/archive/src/dune-git/dune-geometry
-- Setting dune-geometry_LIBRARIES=dunegeometry
-- Performing tests specific to dune-grid from file
/archive/src/dune-git/dune-grid/cmake/modules/DuneGridMacros.cmake.
-- Found alberta libraries for dimensions 1;2;3
CMake Warning at cmake/modules/UseUG.cmake:79 (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):
cmake/modules/DuneGridMacros.cmake:19 (include)
/archive/src/dune-git/dune-common/cmake/modules/DuneMacros.cmake:576
(include)
/archive/src/dune-git/dune-common/cmake/modules/DuneMacros.cmake:719
(dune_process_dependency_macros)
CMakeLists.txt:22 (dune_project)
-- Could NOT find UG (missing: UG_DIR HAVE_UG)
-- Checking for one of the modules 'psurface'
-- Checking for module 'psurface'
-- No package 'psurface' found
-- Could NOT find AmiraMesh (missing: AMIRAMESH_INCLUDE_DIR
AMIRAMESH_LIBRARY)
-- Using scripts from /archive/src/dune-git/dune-common/cmake/scripts for
creating doxygen stuff.
-- using /archive/src/dune-git/dune-common/doc/doxygen/Doxystyle to create
doxystyle file
-- Adding custom target for config.h generation
--
-- The following OPTIONAL packages have been found:
* MPI
* LATEX
* UnixCommands
* Sphinx
* PythonInterp
* Doxygen
* PkgConfig
* BLAS
* Threads
* LAPACK
* GMP
* Inkscape
* Vc , C++ Vectorization library , <https://github.com/VcDevel/Vc>
* METIS
* ParMETIS
* Alberta
* Psurface
-- The following REQUIRED packages have been found:
* dune-common
* dune-geometry
-- The following features have been disabled:
* Experimental grid extensions , Enables additional grid features.
-- The following OPTIONAL packages have not been found:
* dune-uggrid
* UG (required version >= 3.11.0) , External UG grid, superseded by
dune-uggrid , <
http://www.iwr.uni-heidelberg.de/frame/iwrwikiequipment/software/ug>
* AmiraMesh
-- Configuring done
-- Generating done
-- Build files have been written to:
/archive/src/dune-git/dune-grid/build-cmake
--- calling make for dune-grid ---
build directory: build-cmake
cmake --build . --
[ 2%] Building CXX object
lib/CMakeFiles/dunealbertagrid_1d.dir/__/dune/grid/albertagrid/dgfparser.cc.o
lib/CMakeFiles/dunealbertagrid_1d.dir/build.make:62: fallo en las
instrucciones para el objetivo
'lib/CMakeFiles/dunealbertagrid_1d.dir/__/dune/grid/albertagrid/dgfparser.cc.o'
make[2]: ***
[lib/CMakeFiles/dunealbertagrid_1d.dir/__/dune/grid/albertagrid/dgfparser.cc.o]
Interrupción
CMakeFiles/Makefile2:3952: fallo en las instrucciones para el objetivo
'lib/CMakeFiles/dunealbertagrid_1d.dir/all'
make[1]: *** [lib/CMakeFiles/dunealbertagrid_1d.dir/all] Interrupción
Makefile:160: fallo en las instrucciones para el objetivo 'all'
make: *** [all] Interrupción
Terminating dunecontrol due to previous errors!
So I did some digging around and by examining the actual Makefile, I found
the problema instruction to be:
c++ -std=c++14 -DALBERTA_DIM=1 -DENABLE_ALBERTA -DHAVE_CONFIG_H
-DUG_USE_NEW_DIMENSION_DEFINES
-I/archive/src/dune-git/dune-grid/build-cmake
-I/archive/src/dune-git/dune-grid -I/archive/src/dune-git/dune-common
-I/low -I/gm -I/dev -I/dom -I/np -I/ui -I/np/algebra -I/np/udm -I/parallel
-I/parallel/ddd -I/parallel/ppif -I/parallel/dddif -I/parallel/util
-I/parallel/ddd/include -I/archive/src/dune-git/dune-uggrid
-I/archive/src/dune-git/dune-geometry -I/usr/local/include
-I/usr/local/include/alberta -o
CMakeFiles/dunealbertagrid_1d.dir/__/dune/grid/albertagrid/dgfparser.cc.o
-c /archive/src/dune-git/dune-grid/dune/grid/albertagrid/dgfparser.cc
First thing that caught my eye was the inclusion of directories which do
not exist in my system. Although this is incorrect, it should not be a
problem. But there is one directory which does exist and which really has
no reason to be considered as an include directory: /dev. If I remove /dev
from the include path, all is well and compilation will proceed with no
problem. The include flags are defined in
“dune-grid/build-cmake/lib/CMakeFiles/dunealbertagrid_1d.dir/DependInfo.cmake”
This file is generated with the command “dunecontrol all”, and can also be
generated with “dunecontrol configure” and the –I/dev is included in the
DependInfo.cmake of all modules, but **only** causes compilation to hang in
dunealbertagrid_1d.dir, dunealbertagrid_2d.dir, dunealbertagrid_3d.dir and
dunegrid.dir.
Although I am a newbie to cmake, I do have some experience with autotools
and I know that if you run autoconf and have defined your envar CXXFLAGS to
something or other, this will be included into the configure script. To get
around this issue, packages usually have a “distclean” target, which will
remove the configure script so that it must be regenerated with clean
CXXFLAGS. So I looked for a distclean target in dunecontrol, but did not
find any. Only “clean” target exists, but this does not clean out the
includes which some developer probably has defined in CXXFLAGS or some
other cmake envar and which is written somewhere in the cmake configure
step.
I have not figured out where the incorrect include files are cached or how
to regenerate the DependInfo.cmake files correctly. That is mostly due to
my current state of ignorance as to the inner workings of cmake in the dune
project, and a pointer to solve the issue is the core of my appeal to the
dune mailing list.
Other requested information:
I have not defined an opts file and 'find ./ -name "*.opts"' reveals none.
Dune version (“dunecontrol –version” is not enabled), but these are the
git revisions I worked on yesterday:
Common:
commit 01c9b3bd35f5ed32203b740d2ec2af17c1aebcb3
Date: Tue Nov 8 05:17:34 2016 +0100
Functions:
commit bcfa83346ae7c239c8851d625b86f388c61433c0
Date: Wed Nov 9 12:24:21 2016 +0100
Geometry:
commit 1019d7c0112749c41c83ad4ed9133438d31af690
Date: Thu Nov 10 13:38:10 2016 +0100
Grid:
commit f6fd64efadf00372fb2f361ca2beb78c181b40a1
Date: Tue Nov 8 11:01:13 2016 +0000
Istl:
commit 3ea2d3239a8644fe16e054cc9cde8f8f053fb7c9
Date: Thu Nov 10 16:46:39 2016 +0000
Localfunctions:
commit 6dbb17fe832e18d1ef5ae949a3317ea7da4b9470
Date: Sun Nov 6 15:48:52 2016 +0000
Typetree:
commit 10b4ad7e4302b4dfb6f11819d7ffc891548129a6
Date: Tue Oct 18 19:06:10 2016 +0000
Uggrid:
commit 9d791f5621ae974896f0d631bda46b2457019583
Date: Thu Nov 3 10:40:09 2016 +0000
I’m attaching CMakeError.log and CMakeOutput.log for dune-grid module.
Thank you in advance for your time and advice.
Kind regards,
Edscott
*De:* Dominic Kempf [mailto:dominic.r.kempf at gmail.com
<dominic.r.kempf at gmail.com>]
*Enviado el:* viernes, 11 de noviembre de 2016 03:36 a. m.
*Para:* Christoph Grüninger
*CC:* Ed Scott Wilson Garcia; DUNE Liste
*Asunto:* Re: [Dune] problem compiling dune-grid from git repository
Hey,
the CMake{Error,Output}.log from the CMakeFiles directory would also be
interesting.
Dominic
On Fri, Nov 11, 2016 at 10:03 AM, Christoph Grüninger <
christoph.grueninger at iws.uni-stuttgart.de> wrote:
Hi Ed,
can you please share your version of Dune and how you invoke
dunecontrol (opts file).
I have never looked into flags.make myself, I use make VERBOSE=ON
but that shouldn't change your diagnostics. Actually, from your
email I have no clue what's going wrong.
Bye
Christoph
--
[..] Mathematicians are like theologians: we regard
existence as the prime attribute of what we study.
But unlike theologians, we need not always rely upon
faith alone. [Lawrence Evans]
_______________________________________________
Dune mailing list
Dune at dune-project.org
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--
------------------------------------------------------------------------------------
Dr. Edscott Wilson Garcia
Reservoir Engineering
Mexican Petroleum Institute
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