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()*
--
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