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ornladios / ADIOS2

Next generation of ADIOS developed in the Exascale Computing Program
https://adios2.readthedocs.io/en/latest/index.html
Apache License 2.0
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Installation error on the JLSE system (Argone) #3012

Open jychoi-hpc opened 2 years ago

jychoi-hpc commented 2 years ago

A collaborator reported me this installation problem on the JLSE system in Argone. He got the following error during "make install":

...
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found MPI_C: /soft/restricted/CNDA/mpich/drop41.1/mpich-ofi-sockets-icc-default-gen9-drop41/bin/mpicc (found version "3.1")
-- Found MPI_CXX: /soft/restricted/CNDA/mpich/drop41.1/mpich-ofi-sockets-icc-default-gen9-drop41/bin/mpicxx (found version "3.1")
-- Found MPI: TRUE (found version "3.1")
-- Found adios2: /home/zippy/xgc/foof/XGC-Devel-jlse/dependencies/x86_64/ADIOS2/lib64/cmake/adios2/adios2-config.cmake (found version "2.7.1.1049") found components: C CXX MPI
CMake Error at CMakeLists.txt:9 (find_package):
  Found package configuration file:

    /home/zippy/xgc/foof/XGC-Devel-jlse/dependencies/x86_64/ADIOS2/lib64/cmake/adios2/adios2-config.cmake

  but it set adios2_FOUND to FALSE so package "adios2" is considered to be
  NOT FOUND.  Reason given by package:

  The following imported targets are referenced, but are missing: ffs::ffs

-- Configuring incomplete, errors occurred!
See also "/tmp/tmp.7fr5O9vNmP/CMakeFiles/CMakeOutput.log".
Failed
CMake Error at cmake/install/post/cmake_install.cmake:49 (message):
  generate-adios2-config.sh returned 1, should be 0
Call Stack (most recent call first):
  cmake_install.cmake:57 (include)

make: *** [Makefile:110: install] Error 1
(base) jlselogin6(jbuild)>

I recommended to turn off SST to remove any complicated dependencies but he is still getting the error. We appreciate any help and advice.

Here is the full configure output:

(base) jlselogin6(jbuild)> CC=mpicc FC=mpifort CXX=mpicxx cmake -DCMAKE_INSTALL_PREFIX=/home/zippy/xgc/foof/XGC-Devel-jlse/dependencies/x86_64/ADIOS2 -DBUILD_SHARED_LIBS=OFF -DCMAKE_BUILD_TYPE="RelWithDebInfo" -DADIOS2_USE_MPI=ON -DADIOS2_BUILD_EXAMPLES=OFF -DADIOS2_USE_Fortran=ON -DADIOS2_USE_Python=ON -DADIOS2_USE_BZip2=OFF -DADIOS2_USE_Blosc=OFF -DADIOS2_USE_HDF5=OFF -DADIOS2_USE_IME=OFF -DADIOS2_USE_MGARD=OFF -DADIOS2_USE_PNG=OFF -DADIOS2_USE_SSC=OFF -DADIOS2_USE_SST=OFF -DADIOS2_USE_SZ=OFF -DADIOS2_USE_ZFP=OFF -DADIOS2_USE_ZeroMQ=OFF -DCMAKE_CXX_FLAGS="-std=gnu++14" ..;
-- The C compiler identification is IntelLLVM 2022.1.0
-- The CXX compiler identification is IntelLLVM 2022.1.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /soft/restricted/CNDA/mpich/drop41.1/mpich-ofi-sockets-icc-default-gen9-drop41/bin/mpicc - 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: /soft/restricted/CNDA/mpich/drop41.1/mpich-ofi-sockets-icc-default-gen9-drop41/bin/mpicxx - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Could not find nvcc, please set CUDAToolkit_ROOT.
-- The Fortran compiler identification is Intel 2021.5.0.20211026
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Check for working Fortran compiler: /soft/restricted/CNDA/mpich/drop41.1/mpich-ofi-sockets-icc-default-gen9-drop41/bin/mpifort - skipped
-- Performing Test ADIOS2_HAVE_FORTRAN_F03_ARGS
-- Performing Test ADIOS2_HAVE_FORTRAN_F03_ARGS - Success
-- Performing Test ADIOS2_HAVE_FORTRAN_GNU_ARGS
-- Performing Test ADIOS2_HAVE_FORTRAN_GNU_ARGS - Success
-- Found MPI_C: /soft/restricted/CNDA/mpich/drop41.1/mpich-ofi-sockets-icc-default-gen9-drop41/bin/mpicc (found version "3.1")
-- Found MPI_CXX: /soft/restricted/CNDA/mpich/drop41.1/mpich-ofi-sockets-icc-default-gen9-drop41/bin/mpicxx (found version "3.1")
-- Found MPI_Fortran: /soft/restricted/CNDA/mpich/drop41.1/mpich-ofi-sockets-icc-default-gen9-drop41/bin/mpifort (found version "3.1")
-- Found MPI: TRUE (found version "3.1") found components: C Fortran CXX
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2")
-- Checking for module 'dspaces'
--   No package 'dspaces' found
-- Could NOT find DataSpaces (missing: DATASPACES_VERSION DATASPACES_INCLUDE_DIR DATASPACES_LIBRARIES) (Required is at least version "2.1.1")
-- Found Python: /home/zippy/miniconda3/bin/python3.8 (found suitable version "3.8.3", minimum required is "3") found components: Interpreter Development NumPy Development.Module Development.Embed
-- Found PythonModule_mpi4py: /home/zippy/miniconda3/lib/python3.8/site-packages/mpi4py
-- DAOS_ROOT is :
-- Could NOT find DAOS (missing: DAOS_LIBRARY DAOS_INCLUDE_DIR)
-- Looking for shmget
-- Looking for shmget - found
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Performing Test ADIOS2_USE_Fortran_flag_argument_mismatch
-- Performing Test ADIOS2_USE_Fortran_flag_argument_mismatch - Failed

-- ADIOS2 ThirdParty: Configuring KWSys
-- Checking whether wstring is available
-- Checking whether wstring is available - yes
-- Checking whether C compiler has ptrdiff_t in stddef.h
-- Checking whether C compiler has ptrdiff_t in stddef.h - yes
-- Checking whether C compiler has ssize_t in unistd.h
-- Checking whether C compiler has ssize_t in unistd.h - yes
-- Checking whether CXX compiler has setenv
-- Checking whether CXX compiler has setenv - yes
-- Checking whether CXX compiler has unsetenv
-- Checking whether CXX compiler has unsetenv - yes
-- Checking whether CXX compiler has environ in stdlib.h
-- Checking whether CXX compiler has environ in stdlib.h - no
-- Checking whether CXX compiler has utimes
-- Checking whether CXX compiler has utimes - yes
-- Checking whether CXX compiler has utimensat
-- Checking whether CXX compiler has utimensat - yes
-- Checking whether CXX compiler struct stat has st_mtim member
-- Checking whether CXX compiler struct stat has st_mtim member - yes
-- Checking whether CXX compiler struct stat has st_mtimespec member
-- Checking whether CXX compiler struct stat has st_mtimespec member - no
-- Checking whether <ext/stdio_filebuf.h> is available
-- Checking whether <ext/stdio_filebuf.h> is available - yes

-- ADIOS2 ThirdParty: Configuring perfstubs

-- ADIOS2 ThirdParty: Configuring GTest
CMake Deprecation Warning at thirdparty/GTest/googletest/CMakeLists.txt:4 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.

CMake Deprecation Warning at thirdparty/GTest/googletest/googletest/CMakeLists.txt:56 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.

-- Found PythonInterp: /home/zippy/miniconda3/bin/python3.8 (found version "3.8.3")

-- ADIOS2 ThirdParty: Configuring pybind11

-- ADIOS2 ThirdParty: Configuring pugixml

-- ADIOS2 ThirdParty: Configuring nlohmann_json

-- ADIOS2 ThirdParty: Configuring yaml-cpp

-- ADIOS2 ThirdParty: Configuring atl
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of double
-- Check size of double - done
-- Check size of float
-- Check size of float - done
-- Check size of int
-- Check size of int - done
-- Check size of short
-- Check size of short - done
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file stdlib.h
-- Looking for include file stdlib.h - found
-- Looking for include file string.h
-- Looking for include file string.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file windows.h
-- Looking for include file windows.h - not found
-- Looking for fork
-- Looking for fork - found
-- Found atl: /home/zippy/xgc/foof/XGC-Devel-jlse/dependencies/src/ADIOS2/jbuild/thirdparty/atl/atl/atl-config.cmake (found version "2.2.1")

-- ADIOS2 ThirdParty: Configuring dill
-- Check size of void*
-- Check size of void* - done
-- Check size of long
-- Check size of long - done
-- Checking for module 'libffi'
--   Found libffi, version 3.99999
-- Found LibFFI: -L/usr/lib64/../lib64;-lffi
-- Enabling emulation
-- Looking for include file stdarg.h
-- Looking for include file stdarg.h - found
-- Looking for include file memory.h
-- Looking for include file memory.h - found
-- Looking for __clear_cache
-- Looking for __clear_cache - not found
-- Clear cache defined is
-- Found dill: /home/zippy/xgc/foof/XGC-Devel-jlse/dependencies/src/ADIOS2/jbuild/thirdparty/dill/dill/dill-config.cmake (found version "2.4.1")

-- ADIOS2 ThirdParty: Configuring ffs
-- Check size of off_t
-- Check size of off_t - done
-- Check size of long double
-- Check size of long double - done
-- Check size of long long
-- Check size of long long - done
-- Check size of size_t
-- Check size of size_t - done
-- Looking for socket
-- Looking for socket - found
-- Found BISON: /usr/bin/bison (found version "3.0.4")
-- Found FLEX: /usr/bin/flex (found version "2.6.4")
-- Found Perl: /usr/bin/perl (found version "5.26.1")
-- Found dill: /home/zippy/xgc/foof/XGC-Devel-jlse/dependencies/src/ADIOS2/jbuild/thirdparty/dill/dill/dill-config.cmake (found suitable version "2.4.1", minimum required is "2.3.1")
-- Found atl: /home/zippy/xgc/foof/XGC-Devel-jlse/dependencies/src/ADIOS2/jbuild/thirdparty/atl/atl/atl-config.cmake (found suitable version "2.2.1", minimum required is "2.2.1")
-- Looking for netdb.h
-- Looking for netdb.h - found
-- Looking for sockLib.h
-- Looking for sockLib.h - not found
-- Looking for sys/select.h
-- Looking for sys/select.h - found
-- Looking for sys/socket.h
-- Looking for sys/socket.h - found
-- Looking for sys/times.h
-- Looking for sys/times.h - found
-- Looking for sys/uio.h
-- Looking for sys/uio.h - found
-- Looking for sys/un.h
-- Looking for sys/un.h - found
-- Looking for winsock.h
-- Looking for winsock.h - not found
-- Looking for strtof
-- Looking for strtof - found
-- Looking for strtod
-- Looking for strtod - found
-- Looking for strtold
-- Looking for strtold - found
-- Looking for getdomainname
-- Looking for getdomainname - found
-- Check size of struct iovec
-- Check size of struct iovec - done
-- Performing Test HAS_IOV_BASE_IOVEC
-- Performing Test HAS_IOV_BASE_IOVEC - Success
-- Found atl: /home/zippy/xgc/foof/XGC-Devel-jlse/dependencies/src/ADIOS2/jbuild/thirdparty/atl/atl/atl-config.cmake (found version "2.2.1")
-- Found dill: /home/zippy/xgc/foof/XGC-Devel-jlse/dependencies/src/ADIOS2/jbuild/thirdparty/dill/dill/dill-config.cmake (found version "2.4.1")
-- Found ffs: /home/zippy/xgc/foof/XGC-Devel-jlse/dependencies/src/ADIOS2/jbuild/thirdparty/ffs/ffs/ffs-config.cmake (found version "1.6.0")

-- ADIOS2 ThirdParty: Configuring enet
-- Looking for getaddrinfo
-- Looking for getaddrinfo - found
-- Looking for getnameinfo
-- Looking for getnameinfo - found
-- Looking for gethostbyaddr_r
-- Looking for gethostbyaddr_r - found
-- Looking for gethostbyname_r
-- Looking for gethostbyname_r - found
-- Looking for poll
-- Looking for poll - found
-- Looking for fcntl
-- Looking for fcntl - found
-- Looking for inet_pton
-- Looking for inet_pton - found
-- Looking for inet_ntop
-- Looking for inet_ntop - found
-- Performing Test HAS_MSGHDR_FLAGS
-- Performing Test HAS_MSGHDR_FLAGS - Success
-- Performing Test HAS_SOCKLEN_T
-- Performing Test HAS_SOCKLEN_T - Success
-- Found enet: /home/zippy/xgc/foof/XGC-Devel-jlse/dependencies/src/ADIOS2/jbuild/thirdparty/enet/enet/enet-config.cmake (found version "1.3.14")

-- ADIOS2 ThirdParty: Configuring EVPath
-- Performing Test HAVE_MATH
-- Performing Test HAVE_MATH - Success
-- Found atl: /home/zippy/xgc/foof/XGC-Devel-jlse/dependencies/src/ADIOS2/jbuild/thirdparty/atl/atl/atl-config.cmake (found suitable version "2.2.1", minimum required is "2.2.1")
-- Found atl: /home/zippy/xgc/foof/XGC-Devel-jlse/dependencies/src/ADIOS2/jbuild/thirdparty/atl/atl/atl-config.cmake (found version "2.2.1")
-- Found ffs: /home/zippy/xgc/foof/XGC-Devel-jlse/dependencies/src/ADIOS2/jbuild/thirdparty/ffs/ffs/ffs-config.cmake (found suitable version "1.6.0", minimum required is "1.5.1")
-- Found dill: /home/zippy/xgc/foof/XGC-Devel-jlse/dependencies/src/ADIOS2/jbuild/thirdparty/dill/dill/dill-config.cmake (found suitable version "2.4.1", minimum required is "2.3.1")
-- Looking for clock_gettime
-- Looking for clock_gettime - found
-- Looking for sys/epoll.h
-- Looking for sys/epoll.h - found
-- Looking for hostlib.h
-- Looking for hostlib.h - not found
-- Looking for sys/sockio.h
-- Looking for sys/sockio.h - not found
-- Performing Test HAVE_FDS_BITS
-- Performing Test HAVE_FDS_BITS - Failed
-- Looking for writev
-- Looking for writev - found
-- Looking for uname
-- Looking for uname - found
-- Looking for getloadavg
-- Looking for getloadavg - found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for getifaddrs
-- Looking for getifaddrs - found
-- Found atl: /home/zippy/xgc/foof/XGC-Devel-jlse/dependencies/src/ADIOS2/jbuild/thirdparty/atl/atl/atl-config.cmake (found suitable version "2.2.1", minimum required is "2.2.1")
-- Found atl: /home/zippy/xgc/foof/XGC-Devel-jlse/dependencies/src/ADIOS2/jbuild/thirdparty/atl/atl/atl-config.cmake (found version "2.2.1")
-- Found dill: /home/zippy/xgc/foof/XGC-Devel-jlse/dependencies/src/ADIOS2/jbuild/thirdparty/dill/dill/dill-config.cmake (found version "2.4.1")
-- Found ffs: /home/zippy/xgc/foof/XGC-Devel-jlse/dependencies/src/ADIOS2/jbuild/thirdparty/ffs/ffs/ffs-config.cmake (found suitable version "1.6.0", minimum required is "1.6.0")
-- Found dill: /home/zippy/xgc/foof/XGC-Devel-jlse/dependencies/src/ADIOS2/jbuild/thirdparty/dill/dill/dill-config.cmake (found suitable version "2.4.1", minimum required is "2.4.1")
-- Found enet: /home/zippy/xgc/foof/XGC-Devel-jlse/dependencies/src/ADIOS2/jbuild/thirdparty/enet/enet/enet-config.cmake (found suitable version "1.3.14", minimum required is "1.3.14")
-- Found EVPath: /home/zippy/xgc/foof/XGC-Devel-jlse/dependencies/src/ADIOS2/jbuild/thirdparty/EVPath/EVPath/EVPathConfigCommon.cmake (found version "4.5.0")

-- Detecting Fortran/C Interface
-- Detecting Fortran/C Interface - Found GLOBAL and MODULE mangling
-- Verifying Fortran/CXX Compiler Compatibility
-- Verifying Fortran/CXX Compiler Compatibility - Success
-- Performing Test ADIOS2_HAVE_FORTRAN_SUBMODULES
-- Performing Test ADIOS2_HAVE_FORTRAN_SUBMODULES - Success

ADIOS2 build configuration:
  ADIOS Version: 2.7.1.1049
  C++ Compiler : IntelLLVM 2022.1.0
    /soft/restricted/CNDA/mpich/drop41.1/mpich-ofi-sockets-icc-default-gen9-drop41/bin/mpicxx

  Fortran Compiler : Intel 2021.5.0.20211026
    /soft/restricted/CNDA/mpich/drop41.1/mpich-ofi-sockets-icc-default-gen9-drop41/bin/mpifort

  Installation prefix: /home/zippy/xgc/foof/XGC-Devel-jlse/dependencies/x86_64/ADIOS2
        bin: bin
        lib: lib64
    include: include
      cmake: lib64/cmake/adios2
     python: lib/python3.8/site-packages

  Features:
    Library Type: static (with PIC)
    Build Type:   RelWithDebInfo
    Testing: ON
    Examples: OFF
    Build Options:
      BP5       : ON
      DataMan   : OFF
      DataSpaces: OFF
      HDF5      : OFF
      HDF5_VOL  : OFF
      MHS       : ON
      SST       : OFF
      CUDA      : OFF
      Fortran   : ON
      MPI       : ON
      Python    : ON
      Blosc     : OFF
      BZip2     : OFF
      LIBPRESSIO: OFF
      MGARD     : OFF
      PNG       : OFF
      SZ        : OFF
      ZFP       : OFF
      DAOS      : OFF
      IME       : OFF
      SysVShMem : ON
      ZeroMQ    : OFF
      Profiling : OFF
      Endian_Reverse: OFF
    RDMA Transport for Staging: Unconfigured
-- Configuring done
-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:

    ADIOS2_USE_SSC

-- Build files have been written to: /home/zippy/xgc/foof/XGC-Devel-jlse/dependencies/src/ADIOS2/jbuild
(base) jlselogin6(jbuild)>
JasonRuonanWang commented 2 years ago

_I recommended to turn off SST to remove any complicated dependencies but he is still getting the error.
Manually-specified variables were not used by the project:

ADIOS2_USE_SSC_

This looks like it turned off SSC rather than SST.

What cmake version was used? I would try the latest cmake release.

vicentebolea commented 1 year ago

This might have been resolved in https://github.com/ornladios/ADIOS2/pull/3760