Thank you, Bruno
I figured that was going on, that is why I attempted including the
option to ignore one of the paths but it did not seem to have any effect.
Here is a list of my loaded modules:
1) intel/18.0.2 3) impi/18.0.2 5) autotools/1.1 7) cmake/3.16.1
9) TACC 11) phdf5/1.10.4*
2) libfabric/1.7.0 4) git/2.24.1 6) python2/2.7.15 8) xalt/2.8
10) boost/1.68* 12) dealii/9.2.0*
Out of those modules, the ones I marked with an asterisk are automatically
added when I load the dealii module. The rest are the default modules that
are loaded when I login.
David
On Tue, Feb 16, 2021 at 8:32 AM Bruno Turcksin <bruno.turck...@gmail.com>
wrote:
> 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 dmon...@umich.edu 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()*
>>
>> --
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