[Dune] dunecontrol crash

Aleksejs Fomins aleksejs.fomins at lspr.ch
Tue May 12 13:07:03 CEST 2015 

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I got it. Thank you all :)
I was totally not aware of this functionality, so now I have removed the dead loop and it works :)

On 12/05/15 12:20, Jö Fahlke wrote:
> Am Tue, 12. May 2015, 10:26:50 +0200 schrieb Aleksejs Fomins:
>> Date: Tue, 12 May 2015 10:26:50 +0200
>> From: Aleksejs Fomins <aleksejs.fomins at lspr.ch>
>> To: dune at dune-project.org
>> Subject: Re: [Dune] dunecontrol crash
>>
>> Dear All,
>>
>> I think I have narrowed the problem as much as I could, but I still can not solve it.
>>
>> So here is the problem:
>>
>> I have a file in my project called cmake/modules/FindBoost.cmake
>> This file has exactly 1 uncommented line
>>   find_package(Boost)
>>
>> Currently this line crashes dune-control (see crash log below)
>>
>> However, if I comment this line, and write the line
>>   find_package(Boost)
>> explicitly in the root CMakeLists.txt file of my project, the code does not crash.
>>
>>
>> Could you please tell me what is the problem. I really have the feeling it is something stupid
> 
> It is indeed (but we've all been there ;))
> 
> "find_package(Boost)" tells cmake to look for a file FindBoost.cmake and
> execute it[1].  However, since you say that file contains a line
> "find_package(Boost)", cmake will recursively look for the file
> FindBoost.cmake and execute it.  So you have an infinite recursion, which is
> likely to overflow the stack, which on many architectures results in a
> segmentation fault.
> 
> So, FindBoost.cmake should not contain "find_package(Boost)".
> 
> [1] Probably in some special way that is different from "include(FindBoost)".
>>
>>
>>
>> ---------------------------------------------------------------
>> -- 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.
>> ./dune-common/bin/dunecontrol: line 723: 146086 Segmentation fault      CXX=mpicxx CC=mpicc cmake -DCMAKE_MODULE_PATH="" "-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" -DENABLE_EXPERIMENTAL_GRID_EXTENSIONS:BOOL=TRUE "-Ddune-grid_DIR=/home/fomins/gitwork/hades-github-lspr-ag/dune-grid/build-cmake" "-Ddune-istl_DIR=/home/fomins/gitwork/hades-github-lspr-ag/dune-istl/build-cmake" "-Ddune-localfunctions_DIR=/home/fomins/gitwork/hades-github-lspr-ag/dune-localfunctions/build-cmake" "-Ddune-alugrid_DIR=/home/fomins/gitwork/hades-github-lspr-ag/dune-alugrid/build-cmake" "-Ddune-curvilineargeometry_DIR=/home/fomins/gitwork/hades-github-lspr-ag/dune-curvilineargeometry/build-cmake" "-Ddune-curvilineargrid_DIR=/home/fomins/gitwork/hades-github-lspr-ag/dune-curvilineargrid/build-cmake" -DHADES_FLAGS="-DHAVE_DEBUG" -DCMAKE_CXXFLAGS="-Wall -pedantic -O0 -g3 -I/opt/ex
 t
li
>>  b
>> /parmetis/4.0.3/openmpi/1.8.1/gcc/4.9.0 -I/opt/extlib/metis/5.1.0/gcc/4.9.0/include -I/opt/extlib/superludist/3.3/openmpi/1.8.1/gcc/4.9.0/SRC " -DMETIS_ROOT="/opt/extlib/metis/5.1.0/gcc/4.9.0" -DPARMETIS_ROOT="/opt/extlib/parmetis/4.0.3/openmpi/1.8.1/gcc/4.9.0" -DSUPERLUDIST_ROOT="/opt/extlib/superludist/3.3/openmpi/1.8.1/gcc/4.9.0" -DCMAKE_LIBRARY_PATH:RELEASE="/opt/extlib/boost/1.58.0/gcc/4.9.0/lib" -DCMAKE_LIBRARY_PATH:DEBUG="/opt/extlib/boost/1.58.0/gcc/4.9.0/lib" -DCMAKE_STANDARD_LIBRARIES:RELEASE="-lboost_system -lprogram_options" -DCMAKE_STANDARD_LIBRARIES:DEBUG="-lboost_system -lprogram_options" -DCMAKE_PREFIX_PATH="/opt/extlib/boost/1.58.0/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;/opt/extlib/superludist/3.3/openmpi/1.8.1/gcc/4.9.0;/opt/extlib/superludist/3.3/openmpi/1.8.1/gcc/4.9.0/SRC;/opt/extlib/superludist/3.3/openmpi/1.8.1/gcc/4.9.0/lib;" -DDUNE_GRID_EXPERIMENTAL_GRID_EXTENSIONS:BOOL=TRUE -DCMAKE_SHARED_LINKER_FLAG
 S
="
>>  -
>> lzlib" "/home/fomins/gitwork/hades-github-lspr-ag/hades"
>> --- Failed to build hades ---
>> Terminating dunecontrol due to previous errors!
>> ---------------------------------------------------------------
>>
>>
>> On 11/05/15 17:44, Aleksejs Fomins wrote:
>>> Dear Jö,
>>>
>>> I have taken a look at that line, and there was nothing special there, just a bunch of libraries.
>>> Anyway, I moved the CMake script initializing SuperLUDist away without modifying the job file, and this particular error went away.
>>> So I am almost certain that the bug is not with the wrong parameters.
>>>
>>> My conclusion is that CMake came across some sort of bug in the script I just wrote and simply crashed. I will try to re-read the script
>>>
>>> Kind regards,
>>> Aleksejs
>>>
>>>
>>>
>>> On 11/05/15 17:04, Jö Fahlke wrote:
>>>> Am Mon, 11. May 2015, 13:58:15 +0200 schrieb Aleksejs Fomins:
>>>>> Date: Mon, 11 May 2015 13:58:15 +0200
>>>>> From: Aleksejs Fomins <aleksejs.fomins at lspr.ch>
>>>>> To: Dune <dune at dune-project.org>
>>>>> Subject: [Dune] dunecontrol crash
>>>>> X-No-Auth: unauthenticated sender
>>>>> X-No-Relay: not in my network
>>>>> User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:31.0) Gecko/20100101
>>>>>  Icedove/31.5.0
>>>>> X-Envelope-From: <aleksejs.fomins at lspr.ch>
>>>>>
>>>>> Dear All,
>>>>>
>>>>> I wrote a little CMake script to locate SuperLUDist, so I tried to compile my project with it.
>>>>> So, the only things that were changed was the .opts file and the extra CMake routines. 
>>>>>
>>>>> The compilation went well for all libraries, except our code Hades3d, which crashed 
>>>>> ./dune-common/bin/dunecontrol: line 723: 84478 Segmentation fault 
>>>
>>>> line 723 of dunecontrol (current master) is
>>>
>>>>       eval $PREPARAMS $CMAKE "-DCMAKE_MODULE_PATH=\"$CMAKE_MODULE_PATH\" $CMAKE_PARAMS $CMAKE_FLAGS \"$SRCDIR\"" || exit 1
>>>
>>>> <https://cgit.dune-project.org/repositories/dune-common/tree/bin/dunecontrol?id=87b0e08a4f0f8369906fd9a79d2678461ecf04b7#n723>
>>>
>>>> This probably means that it is cmake that is segfaulting.  Could you give us
>>>> the output emitted by dunecontrol and cmake leading up to the segfault?  in
>>>> particular, in the line before the one above dunecontrol prints the command it
>>>> is going to run.
>>>
>>>> Regards,
>>>> Jö.
>>>
>>>
>>>
>>> _______________________________________________
>>> Dune mailing list
>>> Dune at dune-project.org
>>> http://lists.dune-project.org/mailman/listinfo/dune
>>>
> 
>> #################################################################
>> ## HADES3D. All rights reserved for and by Benedikt Oswald, 2002-
>> #################################################################
>> # set up project
>> project("hades" C CXX)
>>
>> #circumvent not building docs
>> set(BUILD_DOCS 1)
>>
>> # general stuff
>> cmake_minimum_required(VERSION 2.8.6)
>>
>> # guess build tree of dune-common
>> if(NOT (dune-common_DIR OR dune-common_ROOT OR
>>         "${CMAKE_PREFIX_PATH}" MATCHES ".*dune-common.*"))
>>     string(REPLACE  ${CMAKE_PROJECT_NAME} dune-common dune-common_DIR
>>       ${PROJECT_BINARY_DIR})
>>
>> endif()
>>
>> #find dune-common and set the module path
>> find_package(dune-common REQUIRED)
>> #find_package(Boost COMPONENTS regex filesystem system thread date_time program_options log_setup log REQUIRED regex filesystem system thread date_time program_options log_setup log)
>>
>> list(APPEND CMAKE_MODULE_PATH ${dune-common_MODULE_PATH} "${PROJECT_SOURCE_DIR}/cmake/modules")
>>
>>
>> #include the dune macros and hades macros
>> include(DuneMacros)
>>
>> #include(FindBoost)
>> #include(HadesMacros)
>>
>> # start a dune project with information from dune.module
>> dune_project()
>>
>>
>> # make sure our own modules are found
>> #set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${PROJECT_SOURCE_DIR}/cmake/modules")
>> add_subdirectory("cmake/modules")
>>
>>
>>
>>
>>
>> ########################################################
>> # retrieve HADES repository information through querying
>> ########################################################
>> execute_process (
>>     COMMAND git show -s --format=%H
>>     WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
>>     OUTPUT_VARIABLE HADES_REPOSITORY_VERSION
>>     OUTPUT_STRIP_TRAILING_WHITESPACE
>> )
>>
>> execute_process (
>>     COMMAND git show -s --format=%cn
>>     WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
>>     OUTPUT_VARIABLE HADES_REPOSITORY_COMMITTER
>>     OUTPUT_STRIP_TRAILING_WHITESPACE
>> )
>>
>> execute_process (
>>     COMMAND git show -s --format=%cd
>>     WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
>>     OUTPUT_VARIABLE HADES_REPOSITORY_COMMIT_DATE
>>     OUTPUT_STRIP_TRAILING_WHITESPACE
>> )
>>
>> execute_process (
>>     COMMAND git show -s --format=%ce
>>     WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
>>     OUTPUT_VARIABLE HADES_REPOSITORY_COMMITTER_EMAIL
>>     OUTPUT_STRIP_TRAILING_WHITESPACE
>> )
>>
>>
>>
>>
>>
>>
>>
>> #########################################
>> ## define header to pass version settings
>> #########################################
>> configure_file (
>>     "${PROJECT_SOURCE_DIR}/version/version.hh.in"
>>     "${PROJECT_BINARY_DIR}/version/version.hh"
>> )
>>
>>
>>
>> ###########################################################################
>> ## add global paths that are searched by the linker 
>> ###########################################################################
>> link_directories(${PROJECT_BINARY_DIR}/hadesgeo/parser)
>> link_directories(${PROJECT_BINARY_DIR}/hadesgeo/exporter)
>>
>>
>>
>>
>> #########################################
>> ## define header to pass version settings
>> #########################################
>> configure_file (
>>     "${PROJECT_SOURCE_DIR}/stdincl/version.hh.in"
>>     "${PROJECT_BINARY_DIR}/stdincl/version.hh"
>> )
>>
>>
>>
>> ###########################################################################
>> ## add subdirectories of the HADES3D solve family
>> ###########################################################################
>>
>>
>> # add directory that contains the core solver executables
>> add_subdirectory("hades")
>> add_subdirectory("hadesx")
>> add_subdirectory("hadesgeo")
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> # finalize the dune project, e.g. generating config.h etc.
>> finalize_dune_project(GENERATE_CONFIG_H_CMAKE)
> 
>> #################################################################################################################
>> ## objective - opts file for building curvilineargrid, 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/1.58.0/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;\
>> /opt/extlib/superludist/3.3/openmpi/1.8.1/gcc/4.9.0;\
>> /opt/extlib/superludist/3.3/openmpi/1.8.1/gcc/4.9.0/SRC;\
>> /opt/extlib/superludist/3.3/openmpi/1.8.1/gcc/4.9.0/lib;\
>> "
>>
>> GXX_WARNING_OPTS="-Wall -pedantic" 
>> GXX_OPTS="-O0 -g3" 
>>
>> ## define superludist paths & library
>> SUPERLU_DIST_OPTS="-DHAVE_SUPERLU_DIST"
>> SUPERLU_DIST_INCLUDE_PATH="-I/opt/extlib/parmetis/4.0.3/openmpi/1.8.1/gcc/4.9.0 -I/opt/extlib/metis/5.1.0/gcc/4.9.0/include -I/opt/extlib/superludist/3.3/openmpi/1.8.1/gcc/4.9.0/SRC"
>> SUPERLU_DIST_LIBRARY="-L/opt/extlib/superludist/3.3/openmpi/1.8.1/gcc/4.9.0/lib -L/opt/extlib/parmetis/4.0.3/openmpi/1.8.1/gcc/4.9.0/lib -L/opt/extlib/metis/5.1.0/gcc/4.9.0/lib -framework Accelerate"
>>
>>
>> CMAKE_FLAGS=" \
>> -DHADES_FLAGS=\"-DHAVE_DEBUG\" \
>> -DCMAKE_CXXFLAGS=\"$GXX_WARNING_OPTS $GXX_OPTS $SUPERLU_DIST_INCLUDE_PATH \" \
>> -DMETIS_ROOT=\"/opt/extlib/metis/5.1.0/gcc/4.9.0\" \
>> -DPARMETIS_ROOT=\"/opt/extlib/parmetis/4.0.3/openmpi/1.8.1/gcc/4.9.0\" \
>> -DSUPERLUDIST_ROOT=\"/opt/extlib/superludist/3.3/openmpi/1.8.1/gcc/4.9.0\" \
>> -DCMAKE_LIBRARY_PATH:RELEASE=\"/opt/extlib/boost/1.58.0/gcc/4.9.0/lib\" \
>> -DCMAKE_LIBRARY_PATH:DEBUG=\"/opt/extlib/boost/1.58.0/gcc/4.9.0/lib\" \
>> -DCMAKE_STANDARD_LIBRARIES:RELEASE=\"-lboost_system -lprogram_options\" \
>> -DCMAKE_STANDARD_LIBRARIES:DEBUG=\"-lboost_system -lprogram_options\" \
>> -DCMAKE_PREFIX_PATH=\"$CMAKE_PREFIX_PATH\" \
>> -DDUNE_GRID_EXPERIMENTAL_GRID_EXTENSIONS:BOOL=TRUE \
>> -DCMAKE_SHARED_LINKER_FLAGS=\"-lzlib\" \
>> " 
>>
>>
>>
>> # -DMY_WEIRD_FLAGS='-DHAVE_SUPERLU_DIST -DBOOST_LOG_DYN_LINK -DHAVE_DEBUG' \
>> # -DMY_WEIRD_LIB_PATH='-L/opt/extlib/superludist/3.3/openmpi/1.8.1/gcc/4.9.0/lib -L/opt/extlib/parmetis/4.0.3/openmpi/1.8.1/gcc/4.9.0/lib -L/opt/extlib/metis/5.1.0/gcc/4.9.0/lib' \
> 
>> ################################################################
>> # Using CMake-automatic routine to find Boost and its packages
>> ################################################################
>>
>>
>> # Avoid using deprecated boost filesystem code
>> #set (BOOST_FILESYSTEM_NO_DEPRECATED)
>> #set (BOOST_ERROR_CODE_HEADER_ONLY)
>>
>> # search for boost
>> find_package(Boost)
>> #if(Boost_FOUND)
>>     # check for all boost libraries
>> #    find_package(Boost COMPONENTS regex filesystem system thread date_time program_options log_setup log REQUIRED regex filesystem system thread date_time program_options log_setup log)
>> #    include_directories(${Boost_INCLUDE_DIRS})
>> #else(Boost_FOUND)
>> #  message(STATUS "HADES requires boost, and will not be compiled without it.")
>> #endif(Boost_FOUND)
> 
>> ## set(modules "VulcainMacros.cmake")
>>
>> set(modules
>>   AddBoostFlags.cmake
>>   AddSUPERLUDISTFlags.cmake
>>   FindBoost.cmake
>> )
>>
>> install(FILES ${modules} DESTINATION ${DUNE_INSTALL_MODULEDIR})
> 
>> _______________________________________________
>> Dune mailing list
>> Dune at dune-project.org
>> http://lists.dune-project.org/mailman/listinfo/dune
> 
> 
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