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Adios2 Summit logs
-- The C compiler identification is GNU 6.4.0
-- The CXX compiler identification is GNU 6.4.0
-- Check for working C compiler: /sw/summit/gcc/6.4.0/bin/gcc
-- Check for working C compiler: /sw/summit/gcc/6.4.0/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /sw/summit/gcc/6.4.0/bin/g++
-- Check for working CXX compiler: /sw/summit/gcc/6.4.0/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Could NOT find BZip2 (missing: BZIP2_LIBRARIES BZIP2_INCLUDE_DIR)
-- Could NOT find ZFP (missing: ZFP_LIBRARY ZFP_INCLUDE_DIR)
-- Could NOT find SZ (missing: SZ_LIBRARY ZLIB_LIBRARY ZSTD_LIBRARY SZ_INCLUDE_DIR)
-- Could NOT find MGARD (missing: MGARD_LIBRARY ZLIB_LIBRARY MGARD_INCLUDE_DIR)
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.7")
-- Could NOT find PNG: Found unsuitable version "1.5.13", but required is at least "1.6.0" (found /usr/lib64/libpng.so)
-- Found MPI_C: /autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/gcc-6.4.0/spectrum-mpi-10.3.0.0-20190419-4um5hjogm3tepg4xe23hrptlrs2y7ez6/lib/libmpiprofilesupport.so (found version "3.1")
-- Found MPI_CXX: /autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/gcc-6.4.0/spectrum-mpi-10.3.0.0-20190419-4um5hjogm3tepg4xe23hrptlrs2y7ez6/lib/libmpiprofilesupport.so (found version "3.1")
-- Found MPI: TRUE (found version "3.1") found components: C CXX
-- HDF5: Using hdf5 compiler wrapper to determine C configuration
-- Found HDF5: /sw/summit/python/3.6/anaconda3/5.3.0/lib/libhdf5.so;/usr/lib64/libpthread.so;/sw/summit/python/3.6/anaconda3/5.3.0/lib/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so (found version "1.10.2") found components: C
-- Found PythonInterp: /sw/summit/python/3.6/anaconda3/5.3.0/bin/python3 (found version "3.6.7")
-- Found PythonLibs: /sw/summit/python/3.6/anaconda3/5.3.0/lib/libpython3.6m.so (found version "3.6.7")
-- Found PythonModule_numpy: /sw/summit/python/3.6/anaconda3/5.3.0/lib/python3.6/site-packages/numpy
-- Found PythonModule_mpi4py: /sw/summit/python/3.6/anaconda3/5.3.0/lib/python3.6/site-packages/mpi4py
-- Found PythonFull: /sw/summit/python/3.6/anaconda3/5.3.0/bin/python3 found components: Interp Libs numpy mpi4py
-- Looking for shmget
-- Looking for shmget - found
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- 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
-- ADIOS2 ThirdParty: Configuring KWSys
-- Checking whether header cstdio is available
-- Checking whether header cstdio is available - yes
-- Checking for Large File Support
-- Checking for Large File Support - yes
-- Checking whether C++ compiler has 'long long'
-- Checking whether C++ compiler has 'long long' - yes
-- Checking whether C++ compiler has '__int64'
-- Checking whether C++ compiler has '__int64' - no
-- 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 GTest
-- Check if compiler accepts -pthread
-- Check if compiler accepts -pthread - yes
-- ADIOS2 ThirdParty: Configuring pybind11
-- Found PythonLibs: /sw/summit/python/3.6/anaconda3/5.3.0/lib/libpython3.6m.so
-- pybind11 v2.2.4
-- ADIOS2 ThirdParty: Configuring pugixml
-- ADIOS2 ThirdParty: Configuring nlohmann_json
-- Performing Test HAS_FLTO
-- Performing Test HAS_FLTO - Success
-- LTO enabled
CMake Warning at testing/utils/iotest/CMakeLists.txt:228 (message):
We don't have enough (2) processes to run insitu test fwith adios_iotest
-- Found MPI: TRUE (found version "3.1") found components: C
ADIOS2 build configuration:
ADIOS Version: 2.3.1
C++ Compiler : GNU 6.4.0
/sw/summit/gcc/6.4.0/bin/g++
Installation prefix: /gpfs/alpine/syb105/proj-shared/piet/software/adios2
bin: bin
lib: lib64
include: include
cmake: lib64/cmake/adios2
python: lib64/python3.6/site-packages
Features:
Library Type: shared
Build Type: Release
Testing: ON
Build Options:
BZip2 : OFF
ZFP : OFF
SZ : OFF
MGARD : OFF
PNG : OFF
MPI : ON
DataMan : OFF
SSC : OFF
SST : OFF
ZeroMQ : OFF
HDF5 : OFF
Python : ON
Fortran : OFF
SysVShMem: ON
Profiling: ON
Endian_Reverse: OFF
-- Configuring done
-- Generating done
-- Build files have been written to: /gpfs/alpine/syb105/proj-shared/piet/git/adios2-source/adios2-build
Scanning dependencies of target adios2sys_objects
[ 0%] Building C object thirdparty/KWSys/adios2sys/CMakeFiles/adios2sys_objects.dir/EncodingC.c.o
[ 0%] Building CXX object thirdparty/KWSys/adios2sys/CMakeFiles/adios2sys_objects.dir/Directory.cxx.o
[ 1%] Building CXX object thirdparty/KWSys/adios2sys/CMakeFiles/adios2sys_objects.dir/DynamicLoader.cxx.o
[ 1%] Building CXX object thirdparty/KWSys/adios2sys/CMakeFiles/adios2sys_objects.dir/EncodingCXX.cxx.o
[ 2%] Building CXX object thirdparty/KWSys/adios2sys/CMakeFiles/adios2sys_objects.dir/RegularExpression.cxx.o
[ 2%] Building CXX object thirdparty/KWSys/adios2sys/CMakeFiles/adios2sys_objects.dir/SystemTools.cxx.o
[ 2%] Building CXX object thirdparty/KWSys/adios2sys/CMakeFiles/adios2sys_objects.dir/CommandLineArguments.cxx.o
[ 3%] Building CXX object thirdparty/KWSys/adios2sys/CMakeFiles/adios2sys_objects.dir/FStream.cxx.o
[ 3%] Built target adios2sys_objects
Scanning dependencies of target taustubs
[ 3%] Building CXX object source/adios2/CMakeFiles/taustubs.dir/toolkit/profiling/taustubs/tautimer.cpp.o
[ 4%] Linking CXX shared library ../../lib64/libtaustubs.so
[ 4%] Built target taustubs
Scanning dependencies of target adios2
[ 4%] Building CXX object source/adios2/CMakeFiles/adios2.dir/common/ADIOSTypes.cpp.o
[ 5%] Building CXX object source/adios2/CMakeFiles/adios2.dir/core/Attribute.cpp.o
[ 5%] Building CXX object source/adios2/CMakeFiles/adios2.dir/core/AttributeBase.cpp.o
[ 5%] Building CXX object source/adios2/CMakeFiles/adios2.dir/core/ADIOS.cpp.o
[ 6%] Building CXX object source/adios2/CMakeFiles/adios2.dir/core/Engine.cpp.o
[ 6%] Building CXX object source/adios2/CMakeFiles/adios2.dir/core/IO.cpp.o
[ 7%] Building CXX object source/adios2/CMakeFiles/adios2.dir/core/Operator.cpp.o
[ 7%] Building CXX object source/adios2/CMakeFiles/adios2.dir/core/Stream.cpp.o
[ 7%] Building CXX object source/adios2/CMakeFiles/adios2.dir/core/Variable.cpp.o
[ 8%] Building CXX object source/adios2/CMakeFiles/adios2.dir/core/VariableBase.cpp.o
[ 8%] Building CXX object source/adios2/CMakeFiles/adios2.dir/core/VariableCompound.cpp.o
[ 8%] Building CXX object source/adios2/CMakeFiles/adios2.dir/operator/callback/Signature1.cpp.o
[ 9%] Building CXX object source/adios2/CMakeFiles/adios2.dir/operator/callback/Signature2.cpp.o
[ 9%] Building CXX object source/adios2/CMakeFiles/adios2.dir/helper/adiosDynamicBinder.cpp.o
[ 9%] Building CXX object source/adios2/CMakeFiles/adios2.dir/helper/adiosMath.cpp.o
[ 10%] Building CXX object source/adios2/CMakeFiles/adios2.dir/helper/adiosMemory.cpp.o
[ 10%] Building CXX object source/adios2/CMakeFiles/adios2.dir/helper/adiosMPIFunctions.cpp.o
[ 10%] Building CXX object source/adios2/CMakeFiles/adios2.dir/helper/adiosNetwork.cpp.o
[ 11%] Building CXX object source/adios2/CMakeFiles/adios2.dir/helper/adiosString.cpp.o
[ 11%] Building CXX object source/adios2/CMakeFiles/adios2.dir/helper/adiosSystem.cpp.o
[ 11%] Building CXX object source/adios2/CMakeFiles/adios2.dir/helper/adiosType.cpp.o
[ 12%] Building CXX object source/adios2/CMakeFiles/adios2.dir/helper/adiosXML.cpp.o
[ 12%] Building CXX object source/adios2/CMakeFiles/adios2.dir/engine/bp3/BP3Reader.cpp.o
[ 13%] Building CXX object source/adios2/CMakeFiles/adios2.dir/engine/bp3/BP3Writer.cpp.o
[ 13%] Building CXX object source/adios2/CMakeFiles/adios2.dir/engine/bp4/BP4Reader.cpp.o
[ 13%] Building CXX object source/adios2/CMakeFiles/adios2.dir/engine/bp4/BP4Writer.cpp.o
[ 14%] Building CXX object source/adios2/CMakeFiles/adios2.dir/engine/skeleton/SkeletonReader.cpp.o
[ 14%] Building CXX object source/adios2/CMakeFiles/adios2.dir/engine/skeleton/SkeletonWriter.cpp.o
[ 14%] Building CXX object source/adios2/CMakeFiles/adios2.dir/engine/inline/InlineReader.cpp.o
[ 15%] Building CXX object source/adios2/CMakeFiles/adios2.dir/engine/inline/InlineWriter.cpp.o
[ 15%] Building CXX object source/adios2/CMakeFiles/adios2.dir/engine/null/NullEngine.cpp.o
[ 15%] Building CXX object source/adios2/CMakeFiles/adios2.dir/toolkit/format/BufferSTL.cpp.o
[ 16%] Building CXX object source/adios2/CMakeFiles/adios2.dir/toolkit/format/bp3/BP3Base.cpp.o
[ 16%] Building CXX object source/adios2/CMakeFiles/adios2.dir/toolkit/format/bp3/BP3Serializer.cpp.o
[ 16%] Building CXX object source/adios2/CMakeFiles/adios2.dir/toolkit/format/bp3/BP3Deserializer.cpp.o
[ 17%] Building CXX object source/adios2/CMakeFiles/adios2.dir/toolkit/format/bp4/BP4Base.cpp.o
[ 17%] Building CXX object source/adios2/CMakeFiles/adios2.dir/toolkit/format/bp4/BP4Serializer.cpp.o
[ 18%] Building CXX object source/adios2/CMakeFiles/adios2.dir/toolkit/format/bp4/BP4Deserializer.cpp.o
[ 18%] Building CXX object source/adios2/CMakeFiles/adios2.dir/toolkit/format/bpOperation/BPOperation.cpp.o
[ 18%] Building CXX object source/adios2/CMakeFiles/adios2.dir/toolkit/format/bpOperation/compress/BPZFP.cpp.o
[ 19%] Building CXX object source/adios2/CMakeFiles/adios2.dir/toolkit/format/bpOperation/compress/BPSZ.cpp.o
[ 19%] Building CXX object source/adios2/CMakeFiles/adios2.dir/toolkit/format/bpOperation/compress/BPMGARD.cpp.o
[ 19%] Building CXX object source/adios2/CMakeFiles/adios2.dir/toolkit/format/bpOperation/compress/BPPNG.cpp.o
[ 20%] Building CXX object source/adios2/CMakeFiles/adios2.dir/toolkit/format/bpOperation/compress/BPBZIP2.cpp.o
[ 20%] Building CXX object source/adios2/CMakeFiles/adios2.dir/toolkit/profiling/iochrono/Timer.cpp.o
[ 20%] Building CXX object source/adios2/CMakeFiles/adios2.dir/toolkit/transport/Transport.cpp.o
[ 21%] Building CXX object source/adios2/CMakeFiles/adios2.dir/toolkit/transport/file/FileStdio.cpp.o
[ 21%] Building CXX object source/adios2/CMakeFiles/adios2.dir/toolkit/transport/file/FileFStream.cpp.o
[ 21%] Building CXX object source/adios2/CMakeFiles/adios2.dir/toolkit/transportman/TransportMan.cpp.o
[ 22%] Building CXX object source/adios2/CMakeFiles/adios2.dir/toolkit/aggregator/mpi/MPIAggregator.cpp.o
[ 22%] Building CXX object source/adios2/CMakeFiles/adios2.dir/toolkit/aggregator/mpi/MPIChain.cpp.o
[ 22%] Building CXX object source/adios2/CMakeFiles/adios2.dir/toolkit/transport/file/FilePOSIX.cpp.o
[ 23%] Building CXX object source/adios2/CMakeFiles/adios2.dir/toolkit/transport/shm/ShmSystemV.cpp.o
[ 23%] Building CXX object source/adios2/CMakeFiles/adios2.dir/engine/insitumpi/InSituMPIWriter.cpp.o
[ 24%] Building CXX object source/adios2/CMakeFiles/adios2.dir/engine/insitumpi/InSituMPIReader.cpp.o
[ 24%] Building CXX object source/adios2/CMakeFiles/adios2.dir/engine/insitumpi/InSituMPIFunctions.cpp.o
[ 24%] Building CXX object source/adios2/CMakeFiles/adios2.dir/engine/insitumpi/InSituMPISchedules.cpp.o
[ 25%] Building CXX object source/adios2/CMakeFiles/adios2.dir/helper/mpidummy.cpp.o
[ 25%] Building CXX object source/adios2/CMakeFiles/adios2.dir/helper/mpiwrap.cpp.o
[ 25%] Building CXX object source/adios2/CMakeFiles/adios2.dir/__/__/bindings/C/adios2/c/adios2_c_adios.cpp.o
[ 26%] Building CXX object source/adios2/CMakeFiles/adios2.dir/__/__/bindings/C/adios2/c/adios2_c_io.cpp.o
[ 26%] Building CXX object source/adios2/CMakeFiles/adios2.dir/__/__/bindings/C/adios2/c/adios2_c_engine.cpp.o
[ 26%] Building CXX object source/adios2/CMakeFiles/adios2.dir/__/__/bindings/C/adios2/c/adios2_c_variable.cpp.o
[ 27%] Building CXX object source/adios2/CMakeFiles/adios2.dir/__/__/bindings/C/adios2/c/adios2_c_attribute.cpp.o
[ 27%] Building CXX object source/adios2/CMakeFiles/adios2.dir/__/__/bindings/C/adios2/c/adios2_c_operator.cpp.o
[ 27%] Building CXX object source/adios2/CMakeFiles/adios2.dir/__/__/bindings/CXX11/adios2/cxx11/ADIOS.cpp.o
[ 28%] Building CXX object source/adios2/CMakeFiles/adios2.dir/__/__/bindings/CXX11/adios2/cxx11/Attribute.cpp.o
[ 28%] Building CXX object source/adios2/CMakeFiles/adios2.dir/__/__/bindings/CXX11/adios2/cxx11/Engine.cpp.o
[ 28%] Building CXX object source/adios2/CMakeFiles/adios2.dir/__/__/bindings/CXX11/adios2/cxx11/IO.cpp.o
[ 29%] Building CXX object source/adios2/CMakeFiles/adios2.dir/__/__/bindings/CXX11/adios2/cxx11/Operator.cpp.o
[ 29%] Building CXX object source/adios2/CMakeFiles/adios2.dir/__/__/bindings/CXX11/adios2/cxx11/Types.cpp.o
[ 30%] Building CXX object source/adios2/CMakeFiles/adios2.dir/__/__/bindings/CXX11/adios2/cxx11/Variable.cpp.o
[ 30%] Building CXX object source/adios2/CMakeFiles/adios2.dir/__/__/bindings/CXX11/adios2/cxx11/fstream/ADIOS2fstream.cpp.o
[ 30%] Building CXX object source/adios2/CMakeFiles/adios2.dir/__/__/thirdparty/pugixml/pugixml/src/pugixml.cpp.o
[ 31%] Linking CXX shared library ../../lib64/libadios2.so
[ 31%] Built target adios2
Scanning dependencies of target adios_reorganize
[ 32%] Building CXX object source/utils/CMakeFiles/adios_reorganize.dir/adios_reorganize/main.cpp.o
[ 32%] Building CXX object source/utils/CMakeFiles/adios_reorganize.dir/adios_reorganize/Reorganize.cpp.o
[ 32%] Building CXX object source/utils/CMakeFiles/adios_reorganize.dir/Utils.cpp.o
[ 33%] Linking CXX executable ../../bin/adios_reorganize
[ 33%] Built target adios_reorganize
Scanning dependencies of target bpls
[ 33%] Building CXX object source/utils/CMakeFiles/bpls.dir/bpls/bpls.cpp.o
[ 34%] Building CXX object source/utils/CMakeFiles/bpls.dir/__/__/thirdparty/pugixml/pugixml/src/pugixml.cpp.o
[ 34%] Linking CXX executable ../../bin/bpls
[ 34%] Built target bpls
Scanning dependencies of target adios_iotest
[ 34%] Building CXX object source/utils/adios_iotest/CMakeFiles/adios_iotest.dir/settings.cpp.o
[ 34%] Building CXX object source/utils/adios_iotest/CMakeFiles/adios_iotest.dir/decomp.cpp.o
[ 35%] Building CXX object source/utils/adios_iotest/CMakeFiles/adios_iotest.dir/processConfig.cpp.o
[ 35%] Building CXX object source/utils/adios_iotest/CMakeFiles/adios_iotest.dir/ioGroup.cpp.o
[ 35%] Building CXX object source/utils/adios_iotest/CMakeFiles/adios_iotest.dir/stream.cpp.o
[ 36%] Building CXX object source/utils/adios_iotest/CMakeFiles/adios_iotest.dir/adiosStream.cpp.o
[ 36%] Building CXX object source/utils/adios_iotest/CMakeFiles/adios_iotest.dir/adios_iotest.cpp.o
[ 36%] Linking CXX executable ../../../bin/adios_iotest
[ 36%] Built target adios_iotest
Scanning dependencies of target adios2py
[ 36%] Building CXX object bindings/Python/CMakeFiles/adios2py.dir/py11ADIOS.cpp.o
[ 36%] Building CXX object bindings/Python/CMakeFiles/adios2py.dir/py11IO.cpp.o
[ 37%] Building CXX object bindings/Python/CMakeFiles/adios2py.dir/py11Variable.cpp.o
[ 37%] Building CXX object bindings/Python/CMakeFiles/adios2py.dir/py11Attribute.cpp.o
[ 37%] Building CXX object bindings/Python/CMakeFiles/adios2py.dir/py11Engine.cpp.o
[ 38%] Building CXX object bindings/Python/CMakeFiles/adios2py.dir/py11Operator.cpp.o
[ 38%] Building CXX object bindings/Python/CMakeFiles/adios2py.dir/py11File.cpp.o
[ 38%] Building CXX object bindings/Python/CMakeFiles/adios2py.dir/py11glue.cpp.o
[ 39%] Linking CXX shared module ../../lib64/python3.6/site-packages/adios2.cpython-36m-powerpc64le-linux-gnu.so
lto1: internal compiler error: invalid line in the resolution file
0x101d225b lto_resolution_read
/sw/summit/gcc/6.4.0/src/gcc-6.4.0/gcc/lto/lto.c:1912
0x101d225b lto_file_read
/sw/summit/gcc/6.4.0/src/gcc-6.4.0/gcc/lto/lto.c:2092
0x101d225b read_cgraph_and_symbols
/sw/summit/gcc/6.4.0/src/gcc-6.4.0/gcc/lto/lto.c:2806
0x101d225b lto_main()
/sw/summit/gcc/6.4.0/src/gcc-6.4.0/gcc/lto/lto.c:3310
Please submit a full bug report,
with preprocessed source if appropriate.
Please include the complete backtrace with any bug report.
See <http://gcc.gnu.org/bugs.html> for instructions.
lto-wrapper: fatal error: /sw/summit/gcc/6.4.0/bin/g++ returned 1 exit status
compilation terminated.
/usr/bin/ld: error: lto-wrapper failed
/usr/bin/sha1sum: ../../lib64/python3.6/site-packages/adios2.cpython-36m-powerpc64le-linux-gnu.so: No such file or directory
collect2: error: ld returned 1 exit status
make[2]: *** [lib64/python3.6/site-packages/adios2.cpython-36m-powerpc64le-linux-gnu.so] Error 1
make[1]: *** [bindings/Python/CMakeFiles/adios2py.dir/all] Error 2
make: *** [all] Error 2
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