==> Synchronizing chroot copy [/home/alhp/workspace/chroot/root] -> [build_326ecc4f-3cc0-497a-b57d-95f96ca14aaf]...done ==> Making package: netcdf-fortran-openmpi 4.6.1-1.1 (Sun Mar 31 01:39:15 2024) ==> Retrieving sources... -> Downloading netcdf-fortran-4.6.1.tar.gz... % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 1998k 0 1998k 0 0 3131k 0 --:--:-- --:--:-- --:--:-- 3131k ==> Validating source files with sha256sums... netcdf-fortran-4.6.1.tar.gz ... Passed ==> Making package: netcdf-fortran-openmpi 4.6.1-1.1 (Sun Mar 31 01:39:18 2024) ==> Checking runtime dependencies... ==> Installing missing dependencies... [?25lresolving dependencies... looking for conflicting packages... warning: dependency cycle detected: warning: pnetcdf-openmpi will be installed before its netcdf-openmpi dependency Package (14) New Version Net Change extra/hdf5-openmpi 1.14.3-2 11.83 MiB extra/hwloc 2.10.0-1 1.61 MiB extra/libaec 1.1.3-1 0.10 MiB extra/libfabric 1.21.0-1 3.76 MiB core/libnl 3.9.0-1 2.11 MiB extra/libpciaccess 0.18.1-1 0.06 MiB extra/libzip 1.10.1-1 0.46 MiB extra/numactl 2.0.18-1 0.23 MiB extra/openmpi 5.0.2-7 10.14 MiB extra/openpmix 4.2.9-1 3.47 MiB extra/openucx 1.15.0-2 6.11 MiB extra/pnetcdf-openmpi 1.12.3-4 15.76 MiB extra/prrte 3.0.5-1 1.83 MiB extra/netcdf-openmpi 4.9.2-4 2.25 MiB Total Installed Size: 59.71 MiB :: Proceed with installation? [Y/n] checking keyring... checking package integrity... loading package files... checking for file conflicts... :: Processing package changes... installing libaec... installing libpciaccess... installing hwloc... Optional dependencies for hwloc cairo libxml2 [installed] pciutils libx11 installing numactl... installing libfabric... installing libnl... installing openpmix... Optional dependencies for openpmix openpmix-docs: for documentation installing openucx... Optional dependencies for openucx rdma-core: for InfiniBand and RDMA support cuda: for CUDA support rocm-language-runtime: for ROCm support installing prrte... Optional dependencies for prrte openssh: for execution on remote hosts via plm_ssh_agent prrte-docs: for documentation installing openmpi... Optional dependencies for openmpi cuda: cuda support hip-runtime-amd: ROCm support gcc-fortran: fortran support openssh: for execution on remote hosts via plm_ssh_agent openucc: for UCC accelerated collectives installing hdf5-openmpi... installing pnetcdf-openmpi... installing libzip... installing netcdf-openmpi... Optional dependencies for netcdf-openmpi netcdf-fortran: fortran bindings netcdf-cxx: c++ bindings [?25h==> Checking buildtime dependencies... ==> Installing missing dependencies... [?25lresolving dependencies... looking for conflicting packages... Package (18) New Version Net Change extra/clang 17.0.6-1 198.12 MiB extra/compiler-rt 17.0.6-1 39.72 MiB extra/cppdap 1.58.0-1 1.62 MiB core/debuginfod 0.191-1 0.33 MiB extra/fmt 10.2.0-1 1.58 MiB extra/hicolor-icon-theme 0.17-3 0.05 MiB extra/jsoncpp 1.9.5-2 0.73 MiB core/libedit 20230828_3.1-1 0.28 MiB core/libmicrohttpd 1.0.1-1 0.59 MiB core/libnsl 2.0.1-1 0.07 MiB extra/libuv 1.48.0-1 0.58 MiB extra/llvm-libs 17.0.6-2 128.48 MiB extra/rhash 1.4.4-1 0.32 MiB extra/cmake 3.29.0-1 72.94 MiB extra/doxygen 1.10.0-3 17.20 MiB core/gcc-fortran 13.2.1-5 39.87 MiB core/inetutils 2.5-1 1.07 MiB extra/valgrind 3.22.0-3 68.87 MiB Total Installed Size: 572.40 MiB :: Proceed with installation? [Y/n] checking keyring... checking package integrity... loading package files... checking for file conflicts... :: Processing package changes... installing hicolor-icon-theme... installing jsoncpp... Optional dependencies for jsoncpp jsoncpp-doc: documentation installing libnsl... installing libuv... installing rhash... installing cppdap... installing cmake... Optional dependencies for cmake make: for unix Makefile generator [installed] ninja: for ninja generator qt6-base: cmake-gui installing gcc-fortran... installing libedit... installing llvm-libs... installing compiler-rt... installing clang... Optional dependencies for clang openmp: OpenMP support in clang with -fopenmp python: for scan-view and git-clang-format llvm: referenced by some clang headers installing fmt... installing doxygen... Optional dependencies for doxygen graphviz: for caller/callee graph generation qt6-base: for doxywizard texlive-fontsrecommended: for generating LaTeX, Postscript and PDF output texlive-fontutils: for generating LaTeX, Postscript and PDF output texlive-latexextra: for generating LaTeX, Postscript and PDF output texlive-plaingeneric: for generating LaTeX, Postscript and PDF output installing libmicrohttpd... installing debuginfod... Optional dependencies for debuginfod elfutils=0.191: for translations installing valgrind... Optional dependencies for valgrind lib32-glibc: 32-bit ABI support [installed] python: cg_* scripts installing inetutils... :: Running post-transaction hooks... (1/1) Updating the info directory file... [?25h==> Retrieving sources... -> Found netcdf-fortran-4.6.1.tar.gz ==> WARNING: Skipping all source file integrity checks. ==> Extracting sources... -> Extracting netcdf-fortran-4.6.1.tar.gz with bsdtar ==> Starting build()... -- The C compiler identification is GNU 13.2.1 -- The Fortran compiler identification is GNU 13.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/mpicc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Check for working Fortran compiler: /usr/bin/mpifort - skipped CMake Warning (dev) at CMakeLists.txt:41 (exec_program): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): CMakeLists.txt:43 (getuname) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at CMakeLists.txt:41 (exec_program): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): CMakeLists.txt:44 (getuname) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at CMakeLists.txt:41 (exec_program): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): CMakeLists.txt:45 (getuname) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Doxygen: /usr/bin/doxygen (found version "1.10.0") found components: doxygen missing components: dot -- Found m4: /usr/bin/m4 -- Found netCDF CMake package: netCDF::netcdf -- Whether NetCDF-C built with HDF5 enabled: yes -- Looking for alloca.h -- Looking for alloca.h - found -- Looking for malloc.h -- Looking for malloc.h - found -- Looking for ctype.h -- Looking for ctype.h - found -- Looking for dirent.h -- Looking for dirent.h - found -- Looking for dlfcn.h -- Looking for dlfcn.h - found -- Looking for errno.h -- Looking for errno.h - found -- Looking for fcntl.h -- Looking for fcntl.h - found -- Looking for getopt.h -- Looking for getopt.h - found -- Looking for stdbool.h -- Looking for stdbool.h - found -- Looking for locale.h -- Looking for locale.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stdio.h -- Looking for stdio.h - found -- Looking for stdlib.h -- Looking for stdlib.h - found -- Looking for stdarg.h -- Looking for stdarg.h - found -- Looking for strings.h -- Looking for strings.h - found -- Looking for signal.h -- Looking for signal.h - found -- Looking for sys/dir.h -- Looking for sys/dir.h - found -- Looking for sys/ndir.h -- Looking for sys/ndir.h - not found -- Looking for sys/param.h -- Looking for sys/param.h - found -- Looking for sys/stat.h -- Looking for sys/stat.h - found -- Looking for sys/time.h -- Looking for sys/time.h - found -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for sys/wait.h -- Looking for sys/wait.h - found -- Looking for sys/resource.h -- Looking for sys/resource.h - found -- Looking for inttypes.h -- Looking for inttypes.h - found -- Looking for pstdint.h -- Looking for pstdint.h - not found -- Looking for endian.h -- Looking for endian.h - found -- Looking for BaseTsd.h -- Looking for BaseTsd.h - not found -- Looking for stddef.h -- Looking for stddef.h - found -- Looking for memory.h -- Looking for memory.h - found -- Looking for netcdf.h -- Looking for netcdf.h - found -- Check size of void* -- Check size of void* - done -- Check size of char -- Check size of char - done -- 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 long -- Check size of long - done -- Check size of long long -- Check size of long long - done -- Check size of off_t -- Check size of off_t - done -- Check size of off64_t -- Check size of off64_t - failed -- Check size of short -- Check size of short - done -- Check size of size_t -- Check size of size_t - done -- Check size of ssize_t -- Check size of ssize_t - done -- Check size of __int64 -- Check size of __int64 - failed -- Check size of uchar -- Check size of uchar - failed -- Check size of int64_t -- Check size of int64_t - done -- Check size of uint64_t -- Check size of uint64_t - done -- Performing Test COMPILER_HAS_ALLOW_ARGUMENT_MISMATCH -- Performing Test COMPILER_HAS_ALLOW_ARGUMENT_MISMATCH - Failed -- Performing Test COMPILER_HAS_MISMATCH_ALL -- Performing Test COMPILER_HAS_MISMATCH_ALL - Failed -- Looking for alloca -- Looking for alloca - not found -- Looking for nccreate in netCDF::netcdf -- Looking for nccreate in netCDF::netcdf - found -- Looking for nc_set_log_level in netCDF::netcdf -- Looking for nc_set_log_level in netCDF::netcdf - found -- Looking for oc_open in netCDF::netcdf -- Looking for oc_open in netCDF::netcdf - found -- Performing Test HAVE_SZIP_WRITE -- Performing Test HAVE_SZIP_WRITE - Success -- Performing Test HAVE_QUANTIZE -- Performing Test HAVE_QUANTIZE - Success -- Looking for nc_def_var_szip in netCDF::netcdf -- Looking for nc_def_var_szip in netCDF::netcdf - found -- Performing Test NC_HAVE_ZSTD -- Performing Test NC_HAVE_ZSTD - Success CMake Warning at CMakeLists.txt:692 (MESSAGE): libnetcdf was built with zstd support, but HDF5_PLUGIN_PATH is not set. Please set the HDF5_PLUGIN_PATH environmental variable if zstandard tests fail, or pass -DDISABLE_ZSTANDARD_PLUGIN=TRUE when running cmake. -- Found MPI_C: /usr/bin/mpicc (found version "3.1") -- Found MPI_Fortran: /usr/bin/mpifort (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- Check size of signed char -- Check size of signed char - done Matching Fortran types to C types Matching Fortran types to C types - done -- Whether NetCDF-C built with paralle I/O enabled: yes Create pre-compiled tests. nf_test C_SOURCES: f03lib.c Adding C code for Test nf_test to Library tst_int64 C_SOURCES: tst_f77_v2 C_SOURCES: ftest C_SOURCES: f03lib.c Adding C code for Test ftest to Library -- CMake Summary: -- Build Type: Release -- Building Shared Libraries: ON -- Building netCDF-4: ON -- Building DAP Support: ON -- Logging Support: ON -- Enabling CDF5: TRUE -- Relaxed check NC_EINVALCOORDS: TRUE -- Building Parallel IO: ON -- Using NetCDF4 Parallel IO: TRUE -- Using PnetCDF Parallel IO: TRUE -- Testing Parallel IO: ON -- Linking against: netCDF::netcdf; # NetCDF Fortran Configuration Summary ============================== # General ------- Library Version: 4.6.1 Configured On: Host System: x86_64-Linux-6.1.83-1-lts61 Build Directory: /startdir/src/build Install Prefix: /usr # Compiling Options ----------------- Fortran Compiler: /usr/bin/mpifort FFLAGS: -march=x86-64-v2 -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -mpclmul LDFLAGS: -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,-z,pack-relative-relocs -flto=auto -falign-functions=32 C Compiler: /usr/bin/mpicc CPPFLAGS: CFLAGS: -march=x86-64-v2 -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -mpclmul -g -ffile-prefix-map=/startdir/src=/usr/src/debug/netcdf-fortran-openmpi -flto=auto -falign-functions=32 -g -Wall -Wno-unused-variable -Wno-unused-parameter -O2 Shared Library: yes Static Library: no Extra libraries: -lnetcdf -lnetcdf # Features -------- F03: yes Dap Support: yes Logging Support: yes NetCDF-2 API: yes NetCDF-4 API: yes CDF5 Support: yes Parallel IO: yes NetCDF4 Parallel IO: yes PnetCDF Parallel IO: yes SZIP Write Support: yes Zstandard Support: no Quantize: yes -- ATTENTION: NO HDF5_PLUGIN_PATH SET CMake Warning at CMakeLists.txt:1158 (MESSAGE): libnetcdf was built with zstd support, but HDF5_PLUGIN_PATH is not set. Please set the HDF5_PLUGIN_PATH environmental variable if zstandard tests fail. CMake Warning at CMakeLists.txt:1159 (MESSAGE): You can use `nc-config --plugindir` to determine the appropriate value for HDF5_PLUGIN_PATH -- Configuring done (29.9s) -- Generating done (0.1s) -- Build files have been written to: /startdir/src/build make: Entering directory '/startdir/src/build' [ 0%] Building C object fortran/CMakeFiles/netcdff_c.dir/nf_lib.c.o [ 1%] Building C object fortran/CMakeFiles/netcdff_c.dir/nf_v2compat.c.o [ 1%] Built target netcdff_c [ 2%] Building Fortran object fortran/CMakeFiles/netcdff.dir/module_netcdf_nc_data.F90.o f951: Warning: command-line option ‘-Wformat=1’ is valid for C/C++/ObjC/ObjC++ but not for Fortran f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran [ 3%] Building Fortran object fortran/CMakeFiles/netcdff.dir/module_netcdf_nc_interfaces.F90.o f951: Warning: command-line option ‘-Wformat=1’ is valid for C/C++/ObjC/ObjC++ but not for Fortran f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran [ 4%] Building Fortran object fortran/CMakeFiles/netcdff.dir/module_netcdf4_nc_interfaces.F90.o f951: Warning: command-line option ‘-Wformat=1’ is valid for C/C++/ObjC/ObjC++ but not for Fortran f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran [ 4%] Building Fortran object fortran/CMakeFiles/netcdff.dir/module_netcdf_nf_data.F90.o f951: Warning: command-line option ‘-Wformat=1’ is valid for C/C++/ObjC/ObjC++ but not for Fortran f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran [ 5%] Building Fortran object fortran/CMakeFiles/netcdff.dir/module_netcdf4_nf_interfaces.F90.o f951: Warning: command-line option ‘-Wformat=1’ is valid for C/C++/ObjC/ObjC++ but not for Fortran f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran [ 6%] Building Fortran object fortran/CMakeFiles/netcdff.dir/module_netcdf_nf_interfaces.F90.o f951: Warning: command-line option ‘-Wformat=1’ is valid for C/C++/ObjC/ObjC++ but not for Fortran f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran [ 6%] Building Fortran object fortran/CMakeFiles/netcdff.dir/module_netcdf4_f03.F90.o f951: Warning: command-line option ‘-Wformat=1’ is valid for C/C++/ObjC/ObjC++ but not for Fortran f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran [ 6%] Building Fortran object fortran/CMakeFiles/netcdff.dir/module_netcdf_f03.F90.o f951: Warning: command-line option ‘-Wformat=1’ is valid for C/C++/ObjC/ObjC++ but not for Fortran f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran [ 7%] Building Fortran object fortran/CMakeFiles/netcdff.dir/module_netcdf_fortv2_c_interfaces.F90.o f951: Warning: command-line option ‘-Wformat=1’ is valid for C/C++/ObjC/ObjC++ but not for Fortran f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran [ 7%] Building Fortran object fortran/CMakeFiles/netcdff.dir/typeSizes.F90.o f951: Warning: command-line option ‘-Wformat=1’ is valid for C/C++/ObjC/ObjC++ but not for Fortran f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran [ 8%] Building Fortran object fortran/CMakeFiles/netcdff.dir/netcdf4.F90.o f951: Warning: command-line option ‘-Wformat=1’ is valid for C/C++/ObjC/ObjC++ but not for Fortran f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran /startdir/src/netcdf-fortran-4.6.1/fortran/netcdf4_func.F90:797:75: 797 | nf90_inq_var_fill_FourByteReal = nf_inq_var_fill(ncid, varid, no_fill, fill) | 1 ...... 807 | nf90_inq_var_fill_EightByteReal = nf_inq_var_fill(ncid, varid, no_fill, fill) | 2 Error: Type mismatch between actual argument at (1) and actual argument at (2) (REAL(4)/REAL(8)). /startdir/src/netcdf-fortran-4.6.1/fortran/netcdf4_func.F90:787:75: 787 | nf90_inq_var_fill_EightByteInt = nf_inq_var_fill(ncid, varid, no_fill, fill) | 1 ...... 807 | nf90_inq_var_fill_EightByteReal = nf_inq_var_fill(ncid, varid, no_fill, fill) | 2 Error: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(8)/REAL(8)). /startdir/src/netcdf-fortran-4.6.1/fortran/netcdf4_func.F90:777:74: 777 | nf90_inq_var_fill_FourByteInt = nf_inq_var_fill(ncid, varid, no_fill, fill) | 1 ...... 807 | nf90_inq_var_fill_EightByteReal = nf_inq_var_fill(ncid, varid, no_fill, fill) | 2 Error: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(4)/REAL(8)). /startdir/src/netcdf-fortran-4.6.1/fortran/netcdf4_func.F90:767:73: 767 | nf90_inq_var_fill_TwoByteInt = nf_inq_var_fill(ncid, varid, no_fill, fill) | 1 ...... 807 | nf90_inq_var_fill_EightByteReal = nf_inq_var_fill(ncid, varid, no_fill, fill) | 2 Error: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(2)/REAL(8)). /startdir/src/netcdf-fortran-4.6.1/fortran/netcdf4_func.F90:757:73: 757 | nf90_inq_var_fill_OneByteInt = nf_inq_var_fill(ncid, varid, no_fill, fill) | 1 ...... 807 | nf90_inq_var_fill_EightByteReal = nf_inq_var_fill(ncid, varid, no_fill, fill) | 2 Error: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(1)/REAL(8)). /startdir/src/netcdf-fortran-4.6.1/fortran/netcdf4_func.F90:737:75: 737 | nf90_def_var_fill_FourByteReal = nf_def_var_fill(ncid, varid, no_fill, fill) | 1 ...... 747 | nf90_def_var_fill_EightByteReal = nf_def_var_fill(ncid, varid, no_fill, fill) | 2 Error: Type mismatch between actual argument at (1) and actual argument at (2) (REAL(4)/REAL(8)). /startdir/src/netcdf-fortran-4.6.1/fortran/netcdf4_func.F90:727:75: 727 | nf90_def_var_fill_EightByteInt = nf_def_var_fill(ncid, varid, no_fill, fill) | 1 ...... 747 | nf90_def_var_fill_EightByteReal = nf_def_var_fill(ncid, varid, no_fill, fill) | 2 Error: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(8)/REAL(8)). /startdir/src/netcdf-fortran-4.6.1/fortran/netcdf4_func.F90:717:74: 717 | nf90_def_var_fill_FourByteInt = nf_def_var_fill(ncid, varid, no_fill, fill) | 1 ...... 747 | nf90_def_var_fill_EightByteReal = nf_def_var_fill(ncid, varid, no_fill, fill) | 2 Error: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(4)/REAL(8)). /startdir/src/netcdf-fortran-4.6.1/fortran/netcdf4_func.F90:707:73: 707 | nf90_def_var_fill_TwoByteInt = nf_def_var_fill(ncid, varid, no_fill, fill) | 1 ...... 747 | nf90_def_var_fill_EightByteReal = nf_def_var_fill(ncid, varid, no_fill, fill) | 2 Error: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(2)/REAL(8)). /startdir/src/netcdf-fortran-4.6.1/fortran/netcdf4_func.F90:697:73: 697 | nf90_def_var_fill_OneByteInt = nf_def_var_fill(ncid, varid, no_fill, fill) | 1 ...... 747 | nf90_def_var_fill_EightByteReal = nf_def_var_fill(ncid, varid, no_fill, fill) | 2 Error: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(1)/REAL(8)). make[2]: *** [fortran/CMakeFiles/netcdff.dir/build.make:387: fortran/CMakeFiles/netcdff.dir/netcdf4.F90.o] Error 1 make[1]: *** [CMakeFiles/Makefile2:1159: fortran/CMakeFiles/netcdff.dir/all] Error 2 make: *** [Makefile:146: all] Error 2 make: Leaving directory '/startdir/src/build' ==> ERROR: A failure occurred in build(). Aborting... ==> ERROR: Build failed, check /home/alhp/workspace/chroot/build_326ecc4f-3cc0-497a-b57d-95f96ca14aaf/build