deai.II module on Stampede2

[David Montiel Taboada]

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()

[Bruno Turcksin]

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

[David Montiel Taboada]

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

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[Bruno Turcksin]

David,

I don't see many solutions here: 1) try to load metis yourself, if
you're lucky it may override the other metis (I doubt this will work
but it's easy to try) 2) you can try a different compiler and hope
that the stack was better compiled 3) send an email to the helpdesk.
It looks like there is a problem in the way they built their modules.

Best,

Bruno

Le mar. 16 févr. 2021 à 10:16, David Montiel Taboada
<dmon...@umich.edu> a écrit :

> To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/CAJdNbL-%3DafjMAaOrh-UmX%2B7GLEJ8oMUr5UDX4XS-H17jnhwjAg%40mail.gmail.com.

[David Montiel Taboada]

Thank you, Bruno

David

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