David, It looks like you have two modules that provides metis */opt/apps/intel18/metis/5.0.2/lib and /home1/apps/intel18/impi18_0/petsc/3.11/skylake/lib *This creates a conflict because the cmake see the symbols twice Which modules are you loading? Are you loading both yourself?
Best, Bruno On Monday, February 15, 2021 at 7:57:01 PM UTC-5 [email protected] wrote: > Hello, > > I compiling PRISMS-PF, a deal.II-based framework on Stampede2 by loading > the deal.II module, e.g.: > > module load dealii/9.2.0 > I have no errors when compiling the core library. But when I do "cmake" > for any particular application I run into the following errors (which also > cause "make" to fail): > > *CMake Warning at CMakeLists.txt:60 (ADD_EXECUTABLE):* > * Cannot generate a safe runtime search path for target main because > there is* > * a cycle in the constraint graph:* > > * dir 0 is [/home1/apps/intel18/impi18_0/dealii/9.2.0/lib]* > * dir 1 is [/opt/apps/intel18/metis/5.0.2/lib]* > * dir 9 must precede it due to runtime library [libmetis.so]* > * dir 2 is [/home1/apps/intel18/impi18_0/trilinos/12.18.1/lib]* > * dir 3 is [/opt/apps/intel18/boost/1.68/lib]* > * dir 4 is > [/opt/apps/intel18/impi18_0/parallel-netcdf/4.6.2/x86_64/lib]* > * dir 5 is > [/opt/intel/compilers_and_libraries_2018.2.199/linux/mpi/intel64/lib]* > * dir 6 is [/opt/apps/intel18/gsl/2.6/lib]* > * dir 7 is [/home1/apps/intel18/impi18_0/p4est/2.0/lib]* > * dir 8 is [/home1/apps/intel18/impi18_0/slepc/3.11/skylake/lib]* > * dir 9 is [/home1/apps/intel18/impi18_0/petsc/3.11/skylake/lib]* > * dir 1 must precede it due to runtime library [libmetis.so]* > * dir 10 is [/opt/apps/intel18/impi18_0/phdf5/1.10.4/x86_64/lib]* > * dir 11 is > [/opt/intel/compilers_and_libraries_2018.2.199/linux/mpi/intel64/lib/release_mt]* > > * Some of these libraries may not be found correctly.* > > Does anyone know why this is happening and how to fix it? I also tried > including the option "-D > CMAKE_IGNORE_PATH=/home1/apps/intel18/impi18_0/petsc/3.11/skylake/lib" > > But that did not work. > > By the way, this error does not occur if I manually install and use > deal.II on my home directory. > > I've copied the contents of my CMakeLists.txt file below. > > Thank you, > > David > > *##* > *# CMake script for the PRISMS-PF applications:* > *##* > > *CMAKE_MINIMUM_REQUIRED(VERSION 2.8.8)* > > *# Find deal.II installation* > *FIND_PACKAGE(deal.II 8.3.0 REQUIRED* > * HINTS ${DEAL_II_DIR} ../ ../../ $ENV{DEAL_II_DIR})* > > *# Check to make sure deal.II is configured with p4est* > *IF(NOT ${DEAL_II_WITH_P4EST})* > * MESSAGE(FATAL_ERROR "\n"* > * "*** deal.II was not installed with p4est. ***\n\n"* > * “The p4est library is a mandatory prerequisite for PRISMS-PF. Please > consult the \n”* > * “user guide to confirm that deal.II and p4est were installed and > configured correctly.”* > * )* > *ENDIF()* > > *DEAL_II_INITIALIZE_CACHED_VARIABLES()* > > *# Set up the debug, release, and run targets* > *ADD_CUSTOM_TARGET(debug* > * COMMAND +env ${CMAKE_COMMAND} -DCMAKE_BUILD_TYPE=Debug > ${CMAKE_SOURCE_DIR}* > * COMMAND +env ${CMAKE_COMMAND} --build ${CMAKE_BINARY_DIR} --target all* > * COMMENT "Switch CMAKE_BUILD_TYPE to Debug"* > * )* > > *ADD_CUSTOM_TARGET(release* > * COMMAND +env ${CMAKE_COMMAND} -DCMAKE_BUILD_TYPE=Release > ${CMAKE_SOURCE_DIR}* > * COMMAND +env ${CMAKE_COMMAND} --build ${CMAKE_BINARY_DIR} --target all* > * COMMENT "Switch CMAKE_BUILD_TYPE to Release"* > * )* > > *ADD_CUSTOM_TARGET(run COMMAND main* > * COMMENT "Run with ${CMAKE_BUILD_TYPE} configuration"* > * )* > > *PROJECT(myapp)* > *if (${CMAKE_BUILD_TYPE} MATCHES DebugRelease)* > * SET(CMAKE_BUILD_TYPE Debug)* > *endif()* > > *# Check if postprocess.cc and nucleation.cc exist and set preprocessor > variables* > *if (EXISTS "postprocess.cc")* > * add_definitions(-DPOSTPROCESS_FILE_EXISTS)* > *endif()* > *if (EXISTS "nucleation.cc")* > * add_definitions(-DNUCLEATION_FILE_EXISTS)* > *endif()* > > *# Append extra flags for the GNU compiler to suppress some warnings* > *if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")* > * set(DEAL_II_CXX_FLAGS_DEBUG "${DEAL_II_CXX_FLAGS_DEBUG} > -Wno-maybe-uninitialized -Wno-unused-parameter -Wno-extra")* > * set(DEAL_II_CXX_FLAGS_RELEASE "${DEAL_II_CXX_FLAGS_RELEASE} > -Wno-maybe-uninitialized -Wno-unused-parameter -Wno-extra")* > * #set(DEAL_II_CXX_FLAGS_DEBUG "${DEAL_II_CXX_FLAGS_DEBUG} > -Wno-maybe-uninitialized -Wno-deprecated-declarations -Wno-comment > -Wno-unused-parameter -Wno-unused-variable -Wno-unused-but-set-variable")* > * #set(DEAL_II_CXX_FLAGS_RELEASE "${DEAL_II_CXX_FLAGS_RELEASE} > -Wno-maybe-uninitialized -Wno-deprecated-declarations -Wno-comment > -Wno-unused-parameter -Wno-unused-variable -Wno-unused-but-set-variable")* > *endif()* > > *ADD_EXECUTABLE(main main.cc )* > > *DEAL_II_SETUP_TARGET(main)* > > *set(cmd "cmake")* > *set(arg "CMakeLists.txt")* > *set(dir ${PROJECT_SOURCE_DIR}/../..)* > *EXECUTE_PROCESS(COMMAND ${cmd} ${arg}* > * WORKING_DIRECTORY ${dir})* > > *set(cmd "make")* > > *EXECUTE_PROCESS(COMMAND ${cmd}* > * WORKING_DIRECTORY ${dir})* > > *if (${CMAKE_BUILD_TYPE} STREQUAL "Release")* > * TARGET_LINK_LIBRARIES(main ${CMAKE_SOURCE_DIR}/../../libprisms_pf.a)* > *elseif(${CMAKE_BUILD_TYPE} STREQUAL "DebugRelease")* > * TARGET_LINK_LIBRARIES(main ${CMAKE_SOURCE_DIR}/../../libprisms_pf.a)* > *else()* > * TARGET_LINK_LIBRARIES(main > ${CMAKE_SOURCE_DIR}/../../libprisms_pf_debug.a)* > *endif()* > > -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. 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