Build code on new cluster (@Caltech)
Hi,
I'm at Caltech now and I'd like to run more simulations on their cluster here. I'm not able to build the code due to some boost library issue.
First, I chose:
$ module list
Currently Loaded Modulefiles:
1) gcc/9.2.0 3) boost/1_81_0_openmpi-4.1.1_gcc-9.2.0 5) hdf5/1.12.1 7) python3/3.10.7
2) openmpi/4.1.1_gcc-9.2.0 4) cmake/3.18.0 6) openssl/3.0.3
With this I get:
$ cmake -DCMAKE_BUILD_TYPE=Release -DKokkos_ENABLE_OPENMP=On ..
-- The C compiler identification is GNU 9.2.0
-- The CXX compiler identification is GNU 9.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /software/gcc/9.2.0/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /software/gcc/9.2.0/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- BUILD_HOST_ID: UNKNOWN
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Found OpenMP option -fopenmp.
-- Found MPI_C: /central/software/OpenMPI/4.1.1_gcc-9.2.0/lib/libmpi.so (found version "3.1")
-- Found MPI: TRUE (found version "3.1") found components: C
-- Will use Kokkos submodule.
-- Setting default Kokkos CXX standard to 17
-- The project name is: Kokkos
-- Using -std=gnu++17 for C++17 extensions as feature
-- Built-in Execution Spaces:
-- Device Parallel: NoTypeDefined
-- Host Parallel: Kokkos::OpenMP
-- Host Serial: NONE
--
-- Architectures:
-- Found TPLLIBDL: /usr/include
-- Using internal desul_atomics copy
-- Kokkos Devices: OPENMP, Kokkos Backends: OPENMP
-- Found HDF5: /central/software/hdf5/1.12.1/lib/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so (found version "1.12.1") found components: C
-- Found Boost: /usr/include (found version "1.53.0") found components: system serialization
CMake Warning at external/HighFive/CMakeLists.txt:84 (message):
Unit tests have been DISABLED.
-- Found Doxygen: /usr/bin/doxygen (found version "1.8.5") found components: doxygen dot
-- ENABLE_PYTHON_BINDINGS not set, python binding won't be built.
-- Run cmake with -DENABLE_PYTHON_BINDINGS=On to enable.
WARN No Python Libs found
-- Could NOT find Boost: Found unsuitable version "1.53.0", but required is at least "1.65" (found /usr/include, found components: serialization program_options chrono filesystem system regex)
CMake Deprecation Warning at CMakeLists.txt:153 (message):
Could not find the mandatory Boost libraries.
FATAL Bye.
This (Could NOT find Boost: Found unsuitable version "1.53.0", but required is at least "1.65"
) is strange because I loaded boost/1_81_0_openmpi-4.1.1_gcc-9.2.0
.
So I tried passing the variable BOOST_ROOT
:
$ cmake -DCMAKE_BUILD_TYPE=Release -DKokkos_ENABLE_OPENMP=On -DBOOST_ROOT=/central/software/boost/1_81_0_openmpi-4.1.1_gcc-9.2.0/ ..
-- The C compiler identification is GNU 9.2.0
-- The CXX compiler identification is GNU 9.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /software/gcc/9.2.0/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /software/gcc/9.2.0/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- BUILD_HOST_ID: UNKNOWN
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Found OpenMP option -fopenmp.
-- Found MPI_C: /central/software/OpenMPI/4.1.1_gcc-9.2.0/lib/libmpi.so (found version "3.1")
-- Found MPI: TRUE (found version "3.1") found components: C
-- Will use Kokkos submodule.
-- Setting default Kokkos CXX standard to 17
-- The project name is: Kokkos
-- Using -std=gnu++17 for C++17 extensions as feature
-- Built-in Execution Spaces:
-- Device Parallel: NoTypeDefined
-- Host Parallel: Kokkos::OpenMP
-- Host Serial: NONE
--
-- Architectures:
-- Found TPLLIBDL: /usr/include
-- Using internal desul_atomics copy
-- Kokkos Devices: OPENMP, Kokkos Backends: OPENMP
-- Found HDF5: /central/software/hdf5/1.12.1/lib/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so (found version "1.12.1") found components: C
CMake Warning at /central/software/cmake/3.18.0/share/cmake-3.18/Modules/FindBoost.cmake:1187 (message):
New Boost version may have incorrect or missing dependencies and imported
targets
Call Stack (most recent call first):
/central/software/cmake/3.18.0/share/cmake-3.18/Modules/FindBoost.cmake:1311 (_Boost_COMPONENT_DEPENDENCIES)
/central/software/cmake/3.18.0/share/cmake-3.18/Modules/FindBoost.cmake:1919 (_Boost_MISSING_DEPENDENCIES)
external/HighFive/CMake/HighFiveTargetDeps.cmake:26 (find_package)
external/HighFive/CMakeLists.txt:63 (include)
CMake Warning at /central/software/cmake/3.18.0/share/cmake-3.18/Modules/FindBoost.cmake:1187 (message):
New Boost version may have incorrect or missing dependencies and imported
targets
Call Stack (most recent call first):
/central/software/cmake/3.18.0/share/cmake-3.18/Modules/FindBoost.cmake:1311 (_Boost_COMPONENT_DEPENDENCIES)
/central/software/cmake/3.18.0/share/cmake-3.18/Modules/FindBoost.cmake:1919 (_Boost_MISSING_DEPENDENCIES)
external/HighFive/CMake/HighFiveTargetDeps.cmake:26 (find_package)
external/HighFive/CMakeLists.txt:63 (include)
-- Found Boost: /central/software/boost/1_81_0_openmpi-4.1.1_gcc-9.2.0/include (found version "1.81.0") found components: system serialization
CMake Warning at external/HighFive/CMakeLists.txt:84 (message):
Unit tests have been DISABLED.
-- Found Doxygen: /usr/bin/doxygen (found version "1.8.5") found components: doxygen dot
-- ENABLE_PYTHON_BINDINGS not set, python binding won't be built.
-- Run cmake with -DENABLE_PYTHON_BINDINGS=On to enable.
WARN No Python Libs found
CMake Warning at /central/software/cmake/3.18.0/share/cmake-3.18/Modules/FindBoost.cmake:1187 (message):
New Boost version may have incorrect or missing dependencies and imported
targets
Call Stack (most recent call first):
/central/software/cmake/3.18.0/share/cmake-3.18/Modules/FindBoost.cmake:1311 (_Boost_COMPONENT_DEPENDENCIES)
/central/software/cmake/3.18.0/share/cmake-3.18/Modules/FindBoost.cmake:1919 (_Boost_MISSING_DEPENDENCIES)
CMakeLists.txt:143 (find_package)
CMake Warning at /central/software/cmake/3.18.0/share/cmake-3.18/Modules/FindBoost.cmake:1187 (message):
New Boost version may have incorrect or missing dependencies and imported
targets
Call Stack (most recent call first):
/central/software/cmake/3.18.0/share/cmake-3.18/Modules/FindBoost.cmake:1311 (_Boost_COMPONENT_DEPENDENCIES)
/central/software/cmake/3.18.0/share/cmake-3.18/Modules/FindBoost.cmake:1919 (_Boost_MISSING_DEPENDENCIES)
CMakeLists.txt:143 (find_package)
CMake Warning at /central/software/cmake/3.18.0/share/cmake-3.18/Modules/FindBoost.cmake:1187 (message):
New Boost version may have incorrect or missing dependencies and imported
targets
Call Stack (most recent call first):
/central/software/cmake/3.18.0/share/cmake-3.18/Modules/FindBoost.cmake:1311 (_Boost_COMPONENT_DEPENDENCIES)
/central/software/cmake/3.18.0/share/cmake-3.18/Modules/FindBoost.cmake:1919 (_Boost_MISSING_DEPENDENCIES)
CMakeLists.txt:143 (find_package)
CMake Warning at /central/software/cmake/3.18.0/share/cmake-3.18/Modules/FindBoost.cmake:1187 (message):
New Boost version may have incorrect or missing dependencies and imported
targets
Call Stack (most recent call first):
/central/software/cmake/3.18.0/share/cmake-3.18/Modules/FindBoost.cmake:1311 (_Boost_COMPONENT_DEPENDENCIES)
/central/software/cmake/3.18.0/share/cmake-3.18/Modules/FindBoost.cmake:1919 (_Boost_MISSING_DEPENDENCIES)
CMakeLists.txt:143 (find_package)
CMake Warning at /central/software/cmake/3.18.0/share/cmake-3.18/Modules/FindBoost.cmake:1187 (message):
New Boost version may have incorrect or missing dependencies and imported
targets
Call Stack (most recent call first):
/central/software/cmake/3.18.0/share/cmake-3.18/Modules/FindBoost.cmake:1311 (_Boost_COMPONENT_DEPENDENCIES)
/central/software/cmake/3.18.0/share/cmake-3.18/Modules/FindBoost.cmake:1919 (_Boost_MISSING_DEPENDENCIES)
CMakeLists.txt:143 (find_package)
CMake Warning at /central/software/cmake/3.18.0/share/cmake-3.18/Modules/FindBoost.cmake:1187 (message):
New Boost version may have incorrect or missing dependencies and imported
targets
Call Stack (most recent call first):
/central/software/cmake/3.18.0/share/cmake-3.18/Modules/FindBoost.cmake:1311 (_Boost_COMPONENT_DEPENDENCIES)
/central/software/cmake/3.18.0/share/cmake-3.18/Modules/FindBoost.cmake:1919 (_Boost_MISSING_DEPENDENCIES)
CMakeLists.txt:143 (find_package)
CMake Warning at /central/software/cmake/3.18.0/share/cmake-3.18/Modules/FindBoost.cmake:1187 (message):
New Boost version may have incorrect or missing dependencies and imported
targets
Call Stack (most recent call first):
/central/software/cmake/3.18.0/share/cmake-3.18/Modules/FindBoost.cmake:1311 (_Boost_COMPONENT_DEPENDENCIES)
/central/software/cmake/3.18.0/share/cmake-3.18/Modules/FindBoost.cmake:1919 (_Boost_MISSING_DEPENDENCIES)
CMakeLists.txt:143 (find_package)
-- Could NOT find Boost (missing: mpi) (found suitable version "1.81.0", minimum required is "1.65")
CMake Deprecation Warning at CMakeLists.txt:153 (message):
Could not find the mandatory Boost libraries.
FATAL Bye.
So apparently there's an issue with mpi (Could NOT find Boost (missing: mpi) (found suitable version "1.81.0", minimum required is "1.65")
).
However I specifically asked IT over here to install a boost version that is compatible with the MPI implementation and C++ compiler I'm using.
It could be that something is wrong in their setup, but maybe there's something else?
Cheers,
Gabriele