[Dune] dunecontrol crash
Aleksejs Fomins
aleksejs.fomins at lspr.ch
Tue May 12 10:26:50 CEST 2015
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
Regards,
Aleksejs
---------------------------------------------------------------
-- 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/extli
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_FLAGS="
-
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
>
-------------- next part --------------
#################################################################
## 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)
-------------- next part --------------
#################################################################################################################
## 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' \
-------------- next part --------------
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-------------- next part --------------
## set(modules "VulcainMacros.cmake")
set(modules
AddBoostFlags.cmake
AddSUPERLUDISTFlags.cmake
FindBoost.cmake
)
install(FILES ${modules} DESTINATION ${DUNE_INSTALL_MODULEDIR})
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