Issues with HDF5 when compiling sparta

[Marccg1]

Hi,
I am having issues with hdf5 when trying to build Sparta.

When using cmake, I am getting the following message:

"HDF5 C compiler wrapper is unable to compile a minimal HDF5 program."

and 98 warnings like the following one:

"WARNING: Target "SIMDB_CoreDatabase_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item."

Despite these issues, the Makefile is generated.

However, when trying to compile Sparta I get a large number of errors like the following one:

"/scratch/tmp/ccp74VIU.s:5804: Error: unknown .loc sub-directive `view'".

I am using hdf5 1.10.4.

What am I doing wrong?

Thanks!

[ghost]

Couple of questions:

1. What machine are you building this on?
2. Can you run this command and post the output?

cmake -DSparta_VERBOSE=On -DCMAKE_BUILD_TYPE=Release ..  |& grep HDF5

[Marccg1]

Thanks for your help.

Question 1: I am building this on a Skylake Intel system that uses SuSE Linux.

Question 2: Output below.

/apps/HDF5/1.10.4/INTEL/IMPI
/apps/HDF5/1.10.4/INTEL/IMPI/BoostConfig.cmake
/apps/HDF5/1.10.4/INTEL/IMPI/boost-config.cmake

CMake Debug Log at /gpfs/apps/MN4/PYTHON/3.6.1/INTEL/lib/python3.6/site-packages/cmake/data/share/cmake-3.18/Modules/FindHDF5.cmake:484 (find_package):
Env variable HDF5_DIR [CMAKE_FIND_USE_CMAKE_ENVIRONMENT_PATH].
/apps/HDF5/1.10.4/INTEL/IMPI
/apps/HDF5/1.10.4/INTEL/IMPI/HDF5Config.cmake
/apps/HDF5/1.10.4/INTEL/IMPI/hdf5-config.cmake
/apps/HDF5/1.10.4/INTEL/IMPI/share/hdf5_examples/HDF5Config.cmake
/apps/HDF5/1.10.4/INTEL/IMPI/share/hdf5_examples/hdf5-config.cmake
/apps/CPPCHECK/2.9/HDF5Config.cmake
/apps/SQLITE/2017.07.10/INTEL/HDF5Config.cmake
/apps/PYTHON/3.6.1/INTEL/HDF5Config.cmake
/apps/CLANG/3.4/GCC/HDF5Config.cmake
/apps/LLVM/3.4/GCC/HDF5Config.cmake
/apps/GCC/11.2.0/HDF5Config.cmake
/apps/CMAKE/3.15.4/HDF5Config.cmake
/apps/modules/bsc/HDF5Config.cmake
/apps/INTEL/2017.4/impi/2017.3.196/bin64/HDF5Config.cmake
/apps/INTEL/2017.4/HDF5Config.cmake
/usr/local/HDF5Config.cmake
/usr/HDF5Config.cmake
/HDF5Config.cmake
/usr/games/HDF5Config.cmake
/usr/lpp/mmfs/HDF5Config.cmake
/home/bsc28/bsc28069/HDF5Config.cmake
/gpfs/apps/MN4/PYTHON/3.6.1/INTEL/lib/python3.6/site-packages/cmake/data/HDF5Config.cmake
/usr/X11R6/HDF5Config.cmake
/opt/HDF5Config.cmake
-- HDF5 C compiler wrapper is unable to compile a minimal HDF5 program.
-- CMAKE_CXX_FLAGS=-I/apps/HDF5/1.10.4/INTEL/IMPI/include
-- CMAKE_CXX_FLAGS_INIT=-I/apps/HDF5/1.10.4/INTEL/IMPI/include
-- CMAKE_CXX_IMPLICIT_INCLUDE_DIRECTORIES=/apps/HDF5/1.10.1/INTEL/IMPI/include;/apps/RAPIDJSON/1.1.0/INTEL/include;/apps/YAML-CPP/0.7.0/GCC/include;/apps/BOOST/1.66.0_py3/GCC/IMPI/include;/apps/PYTHON/3.6.1/INTEL/include/python3.6m;/apps/PYTHON/3.6.1/INTEL/include;/apps/CLANG/3.4/GCC/include;/apps/LLVM/3.4/GCC/include;/gpfs/apps/MN4/GCC/11.2.0/include/c++/11.2.0;/gpfs/apps/MN4/GCC/11.2.0/include/c++/11.2.0/x86_64-suse-linux;/gpfs/apps/MN4/GCC/11.2.0/include/c++/11.2.0/backward;/gpfs/apps/MN4/GCC/11.2.0/lib/gcc/x86_64-suse-linux/11.2.0/include;/gpfs/apps/MN4/GCC/11.2.0/lib/gcc/x86_64-suse-linux/11.2.0/include-fixed;/usr/local/include;/gpfs/apps/MN4/GCC/11.2.0/include;/usr/include
-- CMAKE_CXX_IMPLICIT_LINK_DIRECTORIES=/apps/HDF5/1.10.1/INTEL/IMPI/lib;/gpfs/apps/MN4/GCC/11.2.0/lib/gcc/x86_64-suse-linux/11.2.0;/gpfs/apps/MN4/GCC/11.2.0/lib/gcc;/apps/YAML-CPP/0.7.0/GCC/lib64;/apps/GCC/11.2.0/lib64;/gpfs/apps/MN4/GCC/11.2.0/lib64;/lib64;/usr/lib64;/apps/BOOST/1.66.0_py3/GCC/IMPI/lib;/apps/PYTHON/3.6.1/INTEL/lib;/apps/LLVM/3.4/GCC/lib;/apps/GCC/11.2.0/libexec/gcc/x86_64-suse-linux/11.2.0;/apps/GCC/11.2.0/lib/gcc/x86_64-suse-linux/11.2.0;/apps/GCC/11.2.0/lib;/gpfs/apps/MN4/GCC/11.2.0/lib
-- CMAKE_C_FLAGS=-I/apps/HDF5/1.10.4/INTEL/IMPI/include
-- CMAKE_C_FLAGS_INIT=-I/apps/HDF5/1.10.4/INTEL/IMPI/include
-- CMAKE_C_IMPLICIT_INCLUDE_DIRECTORIES=/apps/HDF5/1.10.1/INTEL/IMPI/include;/apps/SQLITE/2017.07.10/INTEL/include;/apps/RAPIDJSON/1.1.0/INTEL/include;/apps/YAML-CPP/0.7.0/GCC/include;/apps/BOOST/1.66.0_py3/GCC/IMPI/include;/apps/PYTHON/3.6.1/INTEL/include/python3.6m;/apps/PYTHON/3.6.1/INTEL/include;/apps/CLANG/3.4/GCC/include;/apps/LLVM/3.4/GCC/include;/apps/INTEL/2017.4/mkl/include;/gpfs/apps/MN4/GCC/11.2.0/lib/gcc/x86_64-suse-linux/11.2.0/include;/gpfs/apps/MN4/GCC/11.2.0/lib/gcc/x86_64-suse-linux/11.2.0/include-fixed;/usr/local/include;/gpfs/apps/MN4/GCC/11.2.0/include;/usr/include
-- CMAKE_C_IMPLICIT_LINK_DIRECTORIES=/apps/HDF5/1.10.1/INTEL/IMPI/lib;/gpfs/apps/MN4/GCC/11.2.0/lib/gcc/x86_64-suse-linux/11.2.0;/gpfs/apps/MN4/GCC/11.2.0/lib/gcc;/apps/YAML-CPP/0.7.0/GCC/lib64;/apps/GCC/11.2.0/lib64;/gpfs/apps/MN4/GCC/11.2.0/lib64;/lib64;/usr/lib64;/apps/BOOST/1.66.0_py3/GCC/IMPI/lib;/apps/PYTHON/3.6.1/INTEL/lib;/apps/LLVM/3.4/GCC/lib;/apps/GCC/11.2.0/libexec/gcc/x86_64-suse-linux/11.2.0;/apps/GCC/11.2.0/lib/gcc/x86_64-suse-linux/11.2.0;/apps/GCC/11.2.0/lib;/gpfs/apps/MN4/GCC/11.2.0/lib
-- CMAKE_EXE_LINKER_FLAGS=-L/apps/HDF5/1.10.4/INTEL/IMPI/lib -lhdf5 -lhdf5_hl
-- CMAKE_EXE_LINKER_FLAGS_INIT= -L/apps/HDF5/1.10.4/INTEL/IMPI/lib -lhdf5 -lhdf5_hl -L/apps/HDF5/1.10.4/INTEL/IMPI/lib -lhdf5 -lhdf5_hl
-- CMAKE_MODULE_LINKER_FLAGS=-L/apps/HDF5/1.10.4/INTEL/IMPI/lib -lhdf5 -lhdf5_hl
-- CMAKE_MODULE_LINKER_FLAGS_INIT= -L/apps/HDF5/1.10.4/INTEL/IMPI/lib -lhdf5 -lhdf5_hl -L/apps/HDF5/1.10.4/INTEL/IMPI/lib -lhdf5 -lhdf5_hl
-- CMAKE_SHARED_LINKER_FLAGS=-L/apps/HDF5/1.10.4/INTEL/IMPI/lib -lhdf5 -lhdf5_hl
-- CMAKE_SHARED_LINKER_FLAGS_INIT= -L/apps/HDF5/1.10.4/INTEL/IMPI/lib -lhdf5 -lhdf5_hl -L/apps/HDF5/1.10.4/INTEL/IMPI/lib -lhdf5 -lhdf5_hl
-- FIND_PACKAGE_MESSAGE_DETAILS_HDF5=[/apps/HDF5/1.10.4/INTEL/IMPI/lib][/apps/HDF5/1.10.4/INTEL/IMPI/include][c ][v1.10.4(1.10)]
-- HDF5_COMPILER_NO_INTERROGATE=FALSE
-- HDF5_CONSIDERED_CONFIGS=
-- HDF5_CONSIDERED_VERSIONS=
-- HDF5_CXX_COMPILER_NAMES=h5c++;h5pc++
-- HDF5_CXX_HL_LIBRARY_NAMES=hdf5_hl_cpp;hdf5_hl;hdf5;hdf5_cpp;hdf5
-- HDF5_CXX_LIBRARY_NAMES=hdf5_cpp;hdf5
-- HDF5_C_COMPILER_EXECUTABLE=/apps/HDF5/1.10.4/INTEL/IMPI/bin/h5pcc
-- HDF5_C_COMPILER_NO_INTERROGATE=FALSE
-- HDF5_C_FOUND=TRUE
-- HDF5_C_HL_LIBRARY_NAMES=hdf5_hl;hdf5
-- HDF5_C_INCLUDE_DIR=/apps/HDF5/1.10.4/INTEL/IMPI/include
-- HDF5_C_INCLUDE_DIRS=/apps/HDF5/1.10.4/INTEL/IMPI/include
-- HDF5_C_IS_PARALLEL=FALSE
-- HDF5_C_LIBRARIES=/apps/HDF5/1.10.4/INTEL/IMPI/lib
-- HDF5_C_LIBRARY_NAMES=hdf5
-- HDF5_C_RETURN_VALUE=1
-- HDF5_DIFF_EXECUTABLE=/apps/HDF5/1.10.4/INTEL/IMPI/bin/h5diff
-- HDF5_DIR=HDF5_DIR-NOTFOUND
-- HDF5_FOUND=TRUE
-- HDF5_Fortran_COMPILER_NAMES=h5fc;h5pfc
-- HDF5_Fortran_HL_LIBRARY_NAMES=hdf5hl_fortran;hdf5_hl;hdf5;hdf5_fortran;hdf5
-- HDF5_Fortran_LIBRARY_NAMES=hdf5_fortran;hdf5
-- HDF5_INCLUDE_DIR=/apps/HDF5/1.10.4/INTEL/IMPI/include
-- HDF5_INCLUDE_DIRS=/apps/HDF5/1.10.4/INTEL/IMPI/include
-- HDF5_INCLUDE_FILENAME=hdf5.h
-- HDF5_IS_PARALLEL=TRUE
-- HDF5_IS_PARALLEL=TRUE
-- HDF5_LANGUAGE_BINDINGS=C
-- HDF5_LIBRARIES=/apps/HDF5/1.10.4/INTEL/IMPI/lib
-- HDF5_REQUIRED_VARS=HDF5_LIBRARIES;HDF5_INCLUDE_DIRS
-- HDF5_VALID_LANGUAGE_BINDINGS=C;CXX;Fortran
-- HDF5_VERSION=1.10.4
-- HDF5_hdf5_FOUND=TRUE
-- HDF5_hdf5_LIBRARIES=/apps/HDF5/1.10.4/INTEL/IMPI/lib
-- HDF5_hdf5_LIBRARY=/apps/HDF5/1.10.4/INTEL/IMPI/lib
-- HDF5_hdf5_LIBRARY_DEBUG=/apps/HDF5/1.10.4/INTEL/IMPI/lib
-- HDF5_hdf5_LIBRARY_RELEASE=/apps/HDF5/1.10.4/INTEL/IMPI/lib
-- SIMDB_HDF5Database_test_BINARY_DIR=/home/bsc28/bsc28069/map/sparta/release/simdb/test/HDF5Database
-- SIMDB_HDF5Database_test_SOURCE_DIR=/home/bsc28/bsc28069/map/sparta/simdb/test/HDF5Database
-- Sparta_LIBS=sparta;simdb;/apps/HDF5/1.10.4/INTEL/IMPI/lib;sqlite3;yaml-cpp;z;pthread;Boost::date_time;Boost::filesystem;Boost::iostreams;Boost::serialization;Boost::timer;Boost::program_options;rt
-- _CMAKE_CXX_IMPLICIT_INCLUDE_DIRECTORIES_INIT=/apps/HDF5/1.10.1/INTEL/IMPI/include;/apps/RAPIDJSON/1.1.0/INTEL/include;/apps/YAML-CPP/0.7.0/GCC/include;/apps/BOOST/1.66.0_py3/GCC/IMPI/include;/apps/PYTHON/3.6.1/INTEL/include/python3.6m;/apps/PYTHON/3.6.1/INTEL/include;/apps/CLANG/3.4/GCC/include;/apps/LLVM/3.4/GCC/include;/gpfs/apps/MN4/GCC/11.2.0/include/c++/11.2.0;/gpfs/apps/MN4/GCC/11.2.0/include/c++/11.2.0/x86_64-suse-linux;/gpfs/apps/MN4/GCC/11.2.0/include/c++/11.2.0/backward;/gpfs/apps/MN4/GCC/11.2.0/lib/gcc/x86_64-suse-linux/11.2.0/include;/gpfs/apps/MN4/GCC/11.2.0/lib/gcc/x86_64-suse-linux/11.2.0/include-fixed;/usr/local/include;/gpfs/apps/MN4/GCC/11.2.0/include;/usr/include;/usr/include
/apps/HDF5/1.10.4/INTEL/IMPI/bin/ccache
/apps/HDF5/1.10.4/INTEL/IMPI/bin/cppcheck-htmlreport
/apps/HDF5/1.10.4/INTEL/IMPI/bin/bzr
/apps/HDF5/1.10.4/INTEL/IMPI/bin/p4
/apps/HDF5/1.10.4/INTEL/IMPI/bin/bzr
/apps/HDF5/1.10.4/INTEL/IMPI/bin/p4
/apps/HDF5/1.10.4/INTEL/IMPI/bin/bzr
/apps/HDF5/1.10.4/INTEL/IMPI/bin/p4
/apps/HDF5/1.10.4/INTEL/IMPI/bin/bzr
/apps/HDF5/1.10.4/INTEL/IMPI/bin/p4
/apps/HDF5/1.10.4/INTEL/IMPI
/apps/HDF5/1.10.4/INTEL/IMPI/BoostConfig.cmake
/apps/HDF5/1.10.4/INTEL/IMPI/boost-config.cmake
-- CMAKE_CXX_FLAGS=-I/apps/HDF5/1.10.4/INTEL/IMPI/include
-- CMAKE_CXX_FLAGS_INIT=-I/apps/HDF5/1.10.4/INTEL/IMPI/include
-- CMAKE_CXX_IMPLICIT_INCLUDE_DIRECTORIES=/apps/HDF5/1.10.1/INTEL/IMPI/include;/apps/RAPIDJSON/1.1.0/INTEL/include;/apps/YAML-CPP/0.7.0/GCC/include;/apps/BOOST/1.66.0_py3/GCC/IMPI/include;/apps/PYTHON/3.6.1/INTEL/include/python3.6m;/apps/PYTHON/3.6.1/INTEL/include;/apps/CLANG/3.4/GCC/include;/apps/LLVM/3.4/GCC/include;/gpfs/apps/MN4/GCC/11.2.0/include/c++/11.2.0;/gpfs/apps/MN4/GCC/11.2.0/include/c++/11.2.0/x86_64-suse-linux;/gpfs/apps/MN4/GCC/11.2.0/include/c++/11.2.0/backward;/gpfs/apps/MN4/GCC/11.2.0/lib/gcc/x86_64-suse-linux/11.2.0/include;/gpfs/apps/MN4/GCC/11.2.0/lib/gcc/x86_64-suse-linux/11.2.0/include-fixed;/usr/local/include;/gpfs/apps/MN4/GCC/11.2.0/include;/usr/include
-- CMAKE_CXX_IMPLICIT_LINK_DIRECTORIES=/apps/HDF5/1.10.1/INTEL/IMPI/lib;/gpfs/apps/MN4/GCC/11.2.0/lib/gcc/x86_64-suse-linux/11.2.0;/gpfs/apps/MN4/GCC/11.2.0/lib/gcc;/apps/YAML-CPP/0.7.0/GCC/lib64;/apps/GCC/11.2.0/lib64;/gpfs/apps/MN4/GCC/11.2.0/lib64;/lib64;/usr/lib64;/apps/BOOST/1.66.0_py3/GCC/IMPI/lib;/apps/PYTHON/3.6.1/INTEL/lib;/apps/LLVM/3.4/GCC/lib;/apps/GCC/11.2.0/libexec/gcc/x86_64-suse-linux/11.2.0;/apps/GCC/11.2.0/lib/gcc/x86_64-suse-linux/11.2.0;/apps/GCC/11.2.0/lib;/gpfs/apps/MN4/GCC/11.2.0/lib
-- CMAKE_C_FLAGS=-I/apps/HDF5/1.10.4/INTEL/IMPI/include
-- CMAKE_C_FLAGS_INIT=-I/apps/HDF5/1.10.4/INTEL/IMPI/include
-- CMAKE_C_IMPLICIT_INCLUDE_DIRECTORIES=/apps/HDF5/1.10.1/INTEL/IMPI/include;/apps/SQLITE/2017.07.10/INTEL/include;/apps/RAPIDJSON/1.1.0/INTEL/include;/apps/YAML-CPP/0.7.0/GCC/include;/apps/BOOST/1.66.0_py3/GCC/IMPI/include;/apps/PYTHON/3.6.1/INTEL/include/python3.6m;/apps/PYTHON/3.6.1/INTEL/include;/apps/CLANG/3.4/GCC/include;/apps/LLVM/3.4/GCC/include;/apps/INTEL/2017.4/mkl/include;/gpfs/apps/MN4/GCC/11.2.0/lib/gcc/x86_64-suse-linux/11.2.0/include;/gpfs/apps/MN4/GCC/11.2.0/lib/gcc/x86_64-suse-linux/11.2.0/include-fixed;/usr/local/include;/gpfs/apps/MN4/GCC/11.2.0/include;/usr/include
-- CMAKE_C_IMPLICIT_LINK_DIRECTORIES=/apps/HDF5/1.10.1/INTEL/IMPI/lib;/gpfs/apps/MN4/GCC/11.2.0/lib/gcc/x86_64-suse-linux/11.2.0;/gpfs/apps/MN4/GCC/11.2.0/lib/gcc;/apps/YAML-CPP/0.7.0/GCC/lib64;/apps/GCC/11.2.0/lib64;/gpfs/apps/MN4/GCC/11.2.0/lib64;/lib64;/usr/lib64;/apps/BOOST/1.66.0_py3/GCC/IMPI/lib;/apps/PYTHON/3.6.1/INTEL/lib;/apps/LLVM/3.4/GCC/lib;/apps/GCC/11.2.0/libexec/gcc/x86_64-suse-linux/11.2.0;/apps/GCC/11.2.0/lib/gcc/x86_64-suse-linux/11.2.0;/apps/GCC/11.2.0/lib;/gpfs/apps/MN4/GCC/11.2.0/lib
-- CMAKE_EXE_LINKER_FLAGS=-L/apps/HDF5/1.10.4/INTEL/IMPI/lib -lhdf5 -lhdf5_hl
-- CMAKE_EXE_LINKER_FLAGS_INIT= -L/apps/HDF5/1.10.4/INTEL/IMPI/lib -lhdf5 -lhdf5_hl -L/apps/HDF5/1.10.4/INTEL/IMPI/lib -lhdf5 -lhdf5_hl
-- CMAKE_MODULE_LINKER_FLAGS=-L/apps/HDF5/1.10.4/INTEL/IMPI/lib -lhdf5 -lhdf5_hl
-- CMAKE_MODULE_LINKER_FLAGS_INIT= -L/apps/HDF5/1.10.4/INTEL/IMPI/lib -lhdf5 -lhdf5_hl -L/apps/HDF5/1.10.4/INTEL/IMPI/lib -lhdf5 -lhdf5_hl
-- CMAKE_SHARED_LINKER_FLAGS=-L/apps/HDF5/1.10.4/INTEL/IMPI/lib -lhdf5 -lhdf5_hl
-- CMAKE_SHARED_LINKER_FLAGS_INIT= -L/apps/HDF5/1.10.4/INTEL/IMPI/lib -lhdf5 -lhdf5_hl -L/apps/HDF5/1.10.4/INTEL/IMPI/lib -lhdf5 -lhdf5_hl
-- FIND_PACKAGE_MESSAGE_DETAILS_HDF5=[/apps/HDF5/1.10.4/INTEL/IMPI/lib][/apps/HDF5/1.10.4/INTEL/IMPI/include][c ][v1.10.4(1.10)]
-- HDF5_COMPILER_NO_INTERROGATE=FALSE
-- HDF5_CONSIDERED_CONFIGS=
-- HDF5_CONSIDERED_VERSIONS=
-- HDF5_CXX_COMPILER_NAMES=h5c++;h5pc++
-- HDF5_CXX_HL_LIBRARY_NAMES=hdf5_hl_cpp;hdf5_hl;hdf5;hdf5_cpp;hdf5
-- HDF5_CXX_LIBRARY_NAMES=hdf5_cpp;hdf5
-- HDF5_C_COMPILER_EXECUTABLE=/apps/HDF5/1.10.4/INTEL/IMPI/bin/h5pcc
-- HDF5_C_COMPILER_NAMES=h5cc;h5pcc
-- HDF5_C_COMPILER_NO_INTERROGATE=FALSE
-- HDF5_C_FOUND=TRUE
-- HDF5_C_HL_LIBRARY_NAMES=hdf5_hl;hdf5
-- HDF5_C_INCLUDE_DIR=/apps/HDF5/1.10.4/INTEL/IMPI/include
-- HDF5_C_INCLUDE_DIRS=/apps/HDF5/1.10.4/INTEL/IMPI/include
-- HDF5_C_IS_PARALLEL=FALSE
-- HDF5_C_LIBRARIES=/apps/HDF5/1.10.4/INTEL/IMPI/lib
-- HDF5_C_LIBRARY_NAMES=hdf5
-- HDF5_C_RETURN_VALUE=1
-- HDF5_DIFF_EXECUTABLE=/apps/HDF5/1.10.4/INTEL/IMPI/bin/h5diff
-- HDF5_DIR=HDF5_DIR-NOTFOUND
-- HDF5_FOUND=TRUE
-- HDF5_Fortran_COMPILER_NAMES=h5fc;h5pfc
-- HDF5_Fortran_HL_LIBRARY_NAMES=hdf5hl_fortran;hdf5_hl;hdf5;hdf5_fortran;hdf5
-- HDF5_Fortran_LIBRARY_NAMES=hdf5_fortran;hdf5
-- HDF5_INCLUDE_DIR=/apps/HDF5/1.10.4/INTEL/IMPI/include
-- HDF5_INCLUDE_DIRS=/apps/HDF5/1.10.4/INTEL/IMPI/include
-- HDF5_INCLUDE_FILENAME=hdf5.h
-- HDF5_IS_PARALLEL=TRUE
-- HDF5_IS_PARALLEL=TRUE
-- HDF5_LANGUAGE_BINDINGS=C
-- HDF5_LIBRARIES=/apps/HDF5/1.10.4/INTEL/IMPI/lib
-- HDF5_REQUIRED_VARS=HDF5_LIBRARIES;HDF5_INCLUDE_DIRS
-- HDF5_VALID_LANGUAGE_BINDINGS=C;CXX;Fortran
-- HDF5_VERSION=1.10.4
-- HDF5_hdf5_FOUND=TRUE
-- HDF5_hdf5_LIBRARIES=/apps/HDF5/1.10.4/INTEL/IMPI/lib
-- HDF5_hdf5_LIBRARY=/apps/HDF5/1.10.4/INTEL/IMPI/lib
-- HDF5_hdf5_LIBRARY_DEBUG=/apps/HDF5/1.10.4/INTEL/IMPI/lib
-- HDF5_hdf5_LIBRARY_RELEASE=/apps/HDF5/1.10.4/INTEL/IMPI/lib
-- SIMDB_HDF5Database_test_BINARY_DIR=/home/bsc28/bsc28069/map/sparta/release/simdb/test/HDF5Database
-- SIMDB_HDF5Database_test_SOURCE_DIR=/home/bsc28/bsc28069/map/sparta/simdb/test/HDF5Database
-- Sparta_LIBS=sparta;simdb;/apps/HDF5/1.10.4/INTEL/IMPI/lib;sqlite3;yaml-cpp;z;pthread;Boost::date_time;Boost::filesystem;Boost::iostreams;Boost::serialization;Boost::timer;Boost::program_options;rt
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-- 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WARNING: Target "SIMDB_CoreDatabase_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "SIMDB_HDF5Database_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "SIMDB_SharedDB_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "SIMDB_SQLiteDatabase_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "SIMDB_Thread_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "SIMDB_StandaloneThread_test1" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "SIMDB_Utils_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "Array_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "Audience_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "BasicHistogram_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "Buffer_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "Bus_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "simple_cache" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "Clock_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "CircularBuffer_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "Color_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "Collection_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "CommandLineSimulator_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "CommandLineSimulatorArgs_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "Counter_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "ContextCounter_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "CycleHistogram_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "DAG_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "DAG_ordering" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "DataView_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "Enum_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "AsyncEvent_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "EventsPerfTest_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "SingleCycleUniqueEvent_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "Events_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "GlobalEvent_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "ExportedPort_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "FastCheckpoint_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "FILEStream_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "PersistentFastCheckpoint_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "KeyPairCollect" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "KeyValue_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "Log_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "LogAll_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "Memory_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "MemoryMap_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "MethodDelegate_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "monitor_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "Parameter_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "PEventHelper" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "Pipe_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "Preloading_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "Pipeline_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "Port_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "Queue_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "Rational_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "SpartaSharedPointer_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "Register_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "Report_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "Report_triggers_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "ReportVerifier_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "ResourceAssert_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "SpartaException_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "Scheduler_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "Scheduler_noloop_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "SchedulerCatchLoop_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "SchedulerTimeout_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "SharedData_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "SimDB_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "SmartLexCast_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "State_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "StaticInit_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "Statistic_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "StatisticExpression_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "SyncPort_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "Tag_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "TreeFilter_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "TreeNode_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "TreeNodePrivacy_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "TreeNodeScope_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "TreeNodeDebug_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "Trigger_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "VPT_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "HierarchicalBuilding_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "Notification_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "MirrorNotifications_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "Utils_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "BitArray_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "StateTimer_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "ValidValue_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "Collectable_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "NestedPEventHelper" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "StateResidencyTracker_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "MetaTypeList" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "LockedValue_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "EnumCycleHistogram_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "sparta_core_example" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "dynamic_model_pipeline" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "sparta_skeleton" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "simple_annotation_writer" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "Ports_example_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "Events_dual_example_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "Events_example_test" requests linking to directory "/apps/HDF5/1.10.4/INTEL/IMPI/lib". Targets may link only to libraries. CMake is dropping the item.

[klingaard]

Ok, this is weird. I have no experience with SUSE Linux, but the constructed Sparta_LIBS line is odd:

Sparta_LIBS=sparta;simdb;/apps/HDF5/1.10.4/INTEL/IMPI/lib;sqlite3;yaml-cpp;z;pthread;Boost::date_time;Boost::filesystem;Boost::iostreams;Boost::serialization;Boost::timer;Boost::program_options;rt

Specifically, the HDF5 addition is a directory and not a file. I don't know why cmake is doing that. I'll continue looking at it, but I can't immediately reproduce it without building a SUSE machine and running it myself.

[ghost]

Ok, so this is what's different on ubunutu/RH8 compared to SuSE:

SuSE:

 -- HDF5_LIBRARIES=/apps/HDF5/1.10.4/INTEL/IMPI/lib

Ubuntu (and others)

-- HDF5_LIBRARIES=/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so

I'm afraid you'll have to figure this one out on your own (unless someone else does and posts here). This is the cmake documentation for finding HDF5:
https://cmake.org/cmake/help/latest/module/FindHDF5.html

If you figure it out, please post your resolution.