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geospace-code / nc4fortran

Object-oriented Fortran NetCDF4 interface
MIT License
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Autobuild with Intel oneAPI on Ubuntu20.04 not working (linker error for netcdf-fortran) #4

Closed MuellerSeb closed 2 years ago

MuellerSeb commented 2 years ago

Describe the bug

When compiling this (from commit 6ee7c58) with Intel oneAPI with auto-building dependencies, I run into a linker error for libnetcdff:

source /opt/intel/oneapi/setvars.sh
export FC=ifort
export CC=icc
cmake -B build
cmake --build build

results in:

...
[100%] Linking Fortran shared library libnetcdff.so
ld: CMakeFiles/netcdff_c.dir/nf_v2compat.c.o: relocation R_X86_64_32S against `.rodata' can not be used when making a shared object; recompile with -fPIC
ld: CMakeFiles/netcdff_c.dir/nf_lib.c.o: relocation R_X86_64_PC32 against symbol `nc_inq_varids' can not be used when making a shared object; recompile with -fPIC
ld: final link failed: bad value

Did I do something wrong?

Thanks for this package! Sebastian

System details

MuellerSeb commented 2 years ago

I was able to compile with adding this to the netcdf_fortran_cmake_args in netcdf.cmake:

-DCMAKE_C_FLAGS:STRING="-fPIC"

So the problem is upstream in netcdf-fortran. There -fPIC is only added when on APPLE or compiling with GNUCC as C compiler. They should add the POSITION_INDEPENDENT_CODE ON property to the netcdff_c instead of adding compiler flags by hand here: https://github.com/Unidata/netcdf-fortran/blob/43e3308bba4b6139c12bed53f10fd2dea9f55014/fortran/CMakeLists.txt#L142

MuellerSeb commented 2 years ago

Adding this also worked:

-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON

But afterwards two tests are failing:

      Start 10: string
10/11 Test #10: string ...........................***Failed    0.02 sec
      Start 11: version
11/11 Test #11: version ..........................***Failed    0.02 sec

I don't know if this is crucial.

MuellerSeb commented 2 years ago

I created a PR at netcdf-fortran: https://github.com/Unidata/netcdf-fortran/pull/334

For the sake of completeness, this is the TestLog for test 10:

"string" start time: Mar 07 22:41 CET
Output:
----------------------------------------------------------
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC                Routine            Line        Source             
test_string        0000000000432D6A  for__signal_handl     Unknown  Unknown
libpthread-2.31.s  00007F93ED93F3C0  Unknown               Unknown  Unknown
test_string        00000000004CA3C8  __intel_avx_memmo     Unknown  Unknown
test_string        0000000000464E9C  for_cpystr            Unknown  Unknown
libnetcdff.so.7.1  00007F93EDFEF278  nf_get_vars_text_     Unknown  Unknown
test_string        000000000041290E  Unknown               Unknown  Unknown
test_string        000000000040D2C1  Unknown               Unknown  Unknown
test_string        000000000040CE22  Unknown               Unknown  Unknown
libc-2.31.so       00007F93ED6080B3  __libc_start_main     Unknown  Unknown
test_string        000000000040CD2E  Unknown               Unknown  Unknown
<end of output>
Test time =   0.02 sec
----------------------------------------------------------
Test Failed.
"string" end time: Mar 07 22:41 CET
"string" time elapsed: 00:00:00
----------------------------------------------------------

The version test seem to be just a missmatch, since I am using the development version of this library.

MuellerSeb commented 2 years ago

Or maybe the version test is also hinting a problem:

"version" start time: Mar 08 13:11 CET
Output:
----------------------------------------------------------
4.8.1 of Mar  8 2022 13:
version mismatch: 4.7.3 /= 4.8.1
<end of output>
Test time =   0.02 sec
----------------------------------------------------------
Test Failed.
"version" end time: Mar 08 13:11 CET
"version" time elapsed: 00:00:00
----------------------------------------------------------

Where 4.8.1 is the version of the netcdf-c package given in libraries.json and 4.7.3 is my systems netcdf version.

MuellerSeb commented 2 years ago
Full cmake log. Click to expand! ``` $ cmake -B build -- The C compiler identification is Intel 2021.5.0.20211109 -- The Fortran compiler identification is Intel 2021.5.0.20211109 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /opt/intel/oneapi/compiler/2022.0.2/linux/bin/intel64/icc - 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: /opt/intel/oneapi/compiler/2022.0.2/linux/bin/intel64/ifort - skipped -- checking that C and Fortran compilers can link -- checking that C and Fortran compilers can link - OK -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1") -- Checking for one of the modules 'hdf5-serial;hdf5' -- Looking for H5_HAVE_FILTER_SZIP -- Looking for H5_HAVE_FILTER_SZIP - found -- Looking for H5_HAVE_FILTER_DEFLATE -- Looking for H5_HAVE_FILTER_DEFLATE - found -- Looking for H5_HAVE_PARALLEL -- Looking for H5_HAVE_PARALLEL - not found -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- Found SZIP: /usr/lib/x86_64-linux-gnu/libsz.so -- 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 HDF5_C_links -- Performing Test HDF5_C_links - Success -- Performing Test HDF5_Fortran_links -- Performing Test HDF5_Fortran_links - Failed -- Could NOT find HDF5 (missing: HDF5_links) (found version "1.10.4") -- Checking for one of the modules 'netcdf-fortran;netcdf' -- Performing Test NetCDF_Fortran_links -- Performing Test NetCDF_Fortran_links - Failed -- Could NOT find NetCDF (missing: Fortran) (found version "4.7.3") -- * BuildNetCDF, build NetCDF libraries -- Configuring done -- Generating done -- Build files have been written to: nc4fortran/build $ cmake --build build/ --parallel [ 2%] Creating directories for 'HDF5' [ 4%] Performing download step (download, verify and extract) for 'HDF5' -- Downloading... dst='/home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/HDF5-prefix/src/hdf5-1_12_1.tar.gz' timeout='none' inactivity timeout='15 seconds' -- Using src='https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5-1_12_1.tar.gz' -- [download 100% complete] -- verifying file... file='/home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/HDF5-prefix/src/hdf5-1_12_1.tar.gz' -- Downloading... done -- extracting... src='/home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/HDF5-prefix/src/hdf5-1_12_1.tar.gz' dst='/home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/HDF5-prefix/src/HDF5' -- extracting... [tar xfz] -- extracting... [analysis] -- extracting... [rename] -- extracting... [clean up] -- extracting... done [ 6%] No patch step for 'HDF5' [ 8%] Performing configure step for 'HDF5' -- The C compiler identification is Intel 2021.5.0.20211109 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /opt/intel/oneapi/compiler/2022.0.2/linux/bin/intel64/icc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Looking for include file sys/file.h -- Looking for include file sys/file.h - found -- Looking for include files sys/file.h, sys/ioctl.h -- Looking for include files sys/file.h, sys/ioctl.h - found -- Looking for 3 include files sys/file.h, ..., sys/resource.h -- Looking for 3 include files sys/file.h, ..., sys/resource.h - found -- Looking for 4 include files sys/file.h, ..., sys/socket.h -- Looking for 4 include files sys/file.h, ..., sys/socket.h - found -- Looking for 5 include files sys/file.h, ..., sys/stat.h -- Looking for 5 include files sys/file.h, ..., sys/stat.h - found -- Looking for 6 include files sys/file.h, ..., sys/time.h -- Looking for 6 include files sys/file.h, ..., sys/time.h - found -- Looking for 7 include files sys/file.h, ..., sys/types.h -- Looking for 7 include files sys/file.h, ..., sys/types.h - found -- Looking for 8 include files sys/file.h, ..., features.h -- Looking for 8 include files sys/file.h, ..., features.h - found -- Looking for 9 include files sys/file.h, ..., dirent.h -- Looking for 9 include files sys/file.h, ..., dirent.h - found -- Looking for 10 include files sys/file.h, ..., setjmp.h -- Looking for 10 include files sys/file.h, ..., setjmp.h - found -- Looking for 11 include files sys/file.h, ..., stddef.h -- Looking for 11 include files sys/file.h, ..., stddef.h - found -- Looking for 12 include files sys/file.h, ..., stdint.h -- Looking for 12 include files sys/file.h, ..., stdint.h - found -- Looking for 13 include files sys/file.h, ..., unistd.h -- Looking for 13 include files sys/file.h, ..., unistd.h - found -- Looking for 14 include files sys/file.h, ..., io.h -- Looking for 14 include files sys/file.h, ..., io.h - not found -- Looking for 14 include files sys/file.h, ..., winsock2.h -- Looking for 14 include files sys/file.h, ..., winsock2.h - not found -- Looking for 14 include files sys/file.h, ..., globus/common.h -- Looking for 14 include files sys/file.h, ..., globus/common.h - not found -- Looking for 14 include files sys/file.h, ..., pdb.h -- Looking for 14 include files sys/file.h, ..., pdb.h - not found -- Looking for 14 include files sys/file.h, ..., pthread.h -- Looking for 14 include files sys/file.h, ..., pthread.h - found -- Looking for 15 include files sys/file.h, ..., srbclient.h -- Looking for 15 include files sys/file.h, ..., srbclient.h - not found -- Looking for 15 include files sys/file.h, ..., string.h -- Looking for 15 include files sys/file.h, ..., string.h - found -- Looking for 16 include files sys/file.h, ..., strings.h -- Looking for 16 include files sys/file.h, ..., strings.h - found -- Looking for 17 include files sys/file.h, ..., stdlib.h -- Looking for 17 include files sys/file.h, ..., stdlib.h - found -- Looking for 18 include files sys/file.h, ..., memory.h -- Looking for 18 include files sys/file.h, ..., memory.h - found -- Looking for 19 include files sys/file.h, ..., dlfcn.h -- Looking for 19 include files sys/file.h, ..., dlfcn.h - found -- Looking for 20 include files sys/file.h, ..., inttypes.h -- Looking for 20 include files sys/file.h, ..., inttypes.h - found -- Looking for 21 include files sys/file.h, ..., netinet/in.h -- Looking for 21 include files sys/file.h, ..., netinet/in.h - found -- Looking for 22 include files sys/file.h, ..., netdb.h -- Looking for 22 include files sys/file.h, ..., netdb.h - found -- Looking for 23 include files sys/file.h, ..., arpa/inet.h -- Looking for 23 include files sys/file.h, ..., arpa/inet.h - found -- Looking for 24 include files sys/file.h, ..., stdbool.h -- Looking for 24 include files sys/file.h, ..., stdbool.h - found -- Looking for include file quadmath.h -- Looking for include file quadmath.h - found -- Looking for ceil in m; -- Looking for ceil in m; - found -- Looking for dlopen in dl;m -- Looking for dlopen in dl;m - found -- Looking for WSAStartup in ws2_32;m;dl -- Looking for WSAStartup in ws2_32;m;dl - not found -- Looking for gethostbyname in wsock32;m;dl -- Looking for gethostbyname in wsock32;m;dl - not found -- Looking for gethostname in ucb;m;dl -- Looking for gethostname in ucb;m;dl - not found -- Looking for lseek64 -- Looking for lseek64 - found -- Looking for fseeko -- Looking for fseeko - found -- Performing Test HAVE_STAT64_STRUCT -- Performing Test HAVE_STAT64_STRUCT - Success -- Looking for stat64 -- Looking for stat64 - found -- 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 char -- Check size of char - done -- Check size of short -- Check size of short - done -- Check size of int -- Check size of int - done -- Check size of unsigned -- Check size of unsigned - done -- Check size of long -- Check size of long - done -- Check size of long long -- Check size of long long - done -- Check size of __int64 -- Check size of __int64 - done -- Check size of float -- Check size of float - done -- Check size of double -- Check size of double - done -- Check size of long double -- Check size of long double - done -- Check size of int8_t -- Check size of int8_t - done -- Check size of uint8_t -- Check size of uint8_t - done -- Check size of int_least8_t -- Check size of int_least8_t - done -- Check size of uint_least8_t -- Check size of uint_least8_t - done -- Check size of int_fast8_t -- Check size of int_fast8_t - done -- Check size of uint_fast8_t -- Check size of uint_fast8_t - done -- Check size of int16_t -- Check size of int16_t - done -- Check size of uint16_t -- Check size of uint16_t - done -- Check size of int_least16_t -- Check size of int_least16_t - done -- Check size of uint_least16_t -- Check size of uint_least16_t - done -- Check size of int_fast16_t -- Check size of int_fast16_t - done -- Check size of uint_fast16_t -- Check size of uint_fast16_t - done -- Check size of int32_t -- Check size of int32_t - done -- Check size of uint32_t -- Check size of uint32_t - done -- Check size of int_least32_t -- Check size of int_least32_t - done -- Check size of uint_least32_t -- Check size of uint_least32_t - done -- Check size of int_fast32_t -- Check size of int_fast32_t - done -- Check size of uint_fast32_t -- Check size of uint_fast32_t - done -- Check size of int64_t -- Check size of int64_t - done -- Check size of uint64_t -- Check size of uint64_t - done -- Check size of int_least64_t -- Check size of int_least64_t - done -- Check size of uint_least64_t -- Check size of uint_least64_t - done -- Check size of int_fast64_t -- Check size of int_fast64_t - done -- Check size of uint_fast64_t -- Check size of uint_fast64_t - 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 ptrdiff_t -- Check size of ptrdiff_t - done -- Check size of off_t -- Check size of off_t - done -- Check size of off64_t -- Check size of off64_t - done -- Check size of time_t -- Check size of time_t - done -- Check size of _Bool -- Check size of _Bool - done -- Looking for CLOCK_MONOTONIC -- Looking for CLOCK_MONOTONIC - not found -- Performing Test H5_HAVE_TM_GMTOFF -- Performing Test H5_HAVE_TM_GMTOFF - Success -- Performing Test H5_HAVE___TM_GMTOFF -- Performing Test H5_HAVE___TM_GMTOFF - Failed -- Performing Test H5_TIME_WITH_SYS_TIME -- Performing Test H5_TIME_WITH_SYS_TIME - Success -- Performing Test H5_HAVE_STRUCT_TIMEZONE -- Performing Test H5_HAVE_STRUCT_TIMEZONE - Failed -- Looking for gettimeofday -- Looking for gettimeofday - found -- Performing Test H5_HAVE_STAT_ST_BLOCKS -- Performing Test H5_HAVE_STAT_ST_BLOCKS - Success -- Looking for ioctl -- Looking for ioctl - found -- Performing Test H5_HAVE_STRUCT_VIDEOCONFIG -- Performing Test H5_HAVE_STRUCT_VIDEOCONFIG - Failed -- Performing Test H5_HAVE_STRUCT_TEXT_INFO -- Performing Test H5_HAVE_STRUCT_TEXT_INFO - Failed -- Looking for _getvideoconfig -- Looking for _getvideoconfig - not found -- Looking for gettextinfo -- Looking for gettextinfo - not found -- Looking for _scrsize -- Looking for _scrsize - not found -- Looking for GetConsoleScreenBufferInfo -- Looking for GetConsoleScreenBufferInfo - not found -- Looking for TIOCGWINSZ -- Looking for TIOCGWINSZ - found -- Looking for TIOCGETD -- Looking for TIOCGETD - found -- Looking for getpwuid -- Looking for getpwuid - found -- Looking for alarm -- Looking for alarm - found -- Looking for fcntl -- Looking for fcntl - found -- Looking for flock -- Looking for flock - found -- Looking for fork -- Looking for fork - found -- Looking for frexpf -- Looking for frexpf - found -- Looking for frexpl -- Looking for frexpl - found -- Looking for gethostname -- Looking for gethostname - found -- Looking for getrusage -- Looking for getrusage - found -- Looking for llround -- Looking for llround - found -- Looking for llroundf -- Looking for llroundf - found -- Looking for lround -- Looking for lround - found -- Looking for lroundf -- Looking for lroundf - found -- Looking for lstat -- Looking for lstat - found -- Looking for pread -- Looking for pread - found -- Looking for pwrite -- Looking for pwrite - found -- Looking for rand_r -- Looking for rand_r - found -- Looking for random -- Looking for random - found -- Looking for round -- Looking for round - found -- Looking for roundf -- Looking for roundf - found -- Looking for setsysinfo -- Looking for setsysinfo - not found -- Looking for signal -- Looking for signal - found -- Looking for longjmp -- Looking for longjmp - found -- Looking for setjmp -- Looking for setjmp - found -- Looking for siglongjmp -- Looking for siglongjmp - found -- Looking for sigsetjmp -- Looking for sigsetjmp - not found -- Looking for sigprocmask -- Looking for sigprocmask - found -- Looking for snprintf -- Looking for snprintf - found -- Looking for srandom -- Looking for srandom - found -- Looking for strdup -- Looking for strdup - found -- Looking for strtoll -- Looking for strtoll - found -- Looking for strtoull -- Looking for strtoull - found -- Looking for symlink -- Looking for symlink - found -- Looking for system -- Looking for system - found -- Looking for tmpfile -- Looking for tmpfile - found -- Looking for asprintf -- Looking for asprintf - found -- Looking for vasprintf -- Looking for vasprintf - found -- Looking for waitpid -- Looking for waitpid - found -- Looking for vsnprintf -- Looking for vsnprintf - found -- Looking for sigsetjmp -- Looking for sigsetjmp - found -- Looking for difftime -- Looking for difftime - found -- Looking for clock_gettime -- Looking for clock_gettime - found -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for clock_gettime in posix4 -- Looking for clock_gettime in posix4 - not found -- Check size of __float128 -- Check size of __float128 - done -- Check size of _Quad -- Check size of _Quad - failed -- Testing maximum decimal precision for C - 21;33; -- maximum decimal precision for C var - 33 -- Found Perl: /usr/bin/perl (found version "5.30.0") -- ....Compiler warnings are suppressed -- ....All Warnings are enabled -- Could NOT find ZLIB (missing: ZLIB_DIR) -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- The Fortran compiler identification is Intel 2021.5.0.20211109 -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Check for working Fortran compiler: /opt/intel/oneapi/compiler/2022.0.2/linux/bin/intel64/ifort - skipped -- Detecting Fortran/C Interface -- Detecting Fortran/C Interface - Found GLOBAL and MODULE mangling -- Performing Test H5_FORTRAN_HAVE_SIZEOF -- Performing Test H5_FORTRAN_HAVE_SIZEOF - Success -- Performing Test H5_FORTRAN_HAVE_C_SIZEOF -- Performing Test H5_FORTRAN_HAVE_C_SIZEOF - Success -- Performing Test H5_FORTRAN_HAVE_STORAGE_SIZE -- Performing Test H5_FORTRAN_HAVE_STORAGE_SIZE - Success -- Performing Test H5_HAVE_ISO_FORTRAN_ENV -- Performing Test H5_HAVE_ISO_FORTRAN_ENV - Success -- Performing Test H5_FORTRAN_DEFAULT_REAL_NOT_DOUBLE -- Performing Test H5_FORTRAN_DEFAULT_REAL_NOT_DOUBLE - Success -- Performing Test H5_FORTRAN_HAVE_ISO_C_BINDING -- Performing Test H5_FORTRAN_HAVE_ISO_C_BINDING - Success -- ....Compiler warnings are suppressed -- Performing Test FORTRAN_HAVE_C_LONG_DOUBLE -- Performing Test FORTRAN_HAVE_C_LONG_DOUBLE - Success -- Performing Test FORTRAN_C_LONG_DOUBLE_IS_UNIQUE -- Performing Test FORTRAN_C_LONG_DOUBLE_IS_UNIQUE - Success -- Performing Test FC_AVAIL_KINDS_RESULT -- Performing Test FC_AVAIL_KINDS_RESULT - Failed -- ....NUMBER OF INTEGER KINDS FOUND 4 -- ....REAL KINDS FOUND {4,8,16} -- ....INTEGER KINDS FOUND {1,2,4,8} -- ....MAX DECIMAL PRECISION 33 -- Performing Test VALIDINTKINDS_RESULT_1 -- Performing Test VALIDINTKINDS_RESULT_1 - Failed -- Performing Test VALIDINTKINDS_RESULT_2 -- Performing Test VALIDINTKINDS_RESULT_2 - Failed -- Performing Test VALIDINTKINDS_RESULT_4 -- Performing Test VALIDINTKINDS_RESULT_4 - Failed -- Performing Test VALIDINTKINDS_RESULT_8 -- Performing Test VALIDINTKINDS_RESULT_8 - Failed -- Performing Test VALIDREALKINDS_RESULT_4 -- Performing Test VALIDREALKINDS_RESULT_4 - Failed -- Performing Test VALIDREALKINDS_RESULT_8 -- Performing Test VALIDREALKINDS_RESULT_8 - Failed -- Performing Test VALIDREALKINDS_RESULT_16 -- Performing Test VALIDREALKINDS_RESULT_16 - Failed -- ....FOUND SIZEOF for REAL KINDs {4,8,16} -- Performing Test PAC_SIZEOF_NATIVE_KINDS_RESULT -- Performing Test PAC_SIZEOF_NATIVE_KINDS_RESULT - Failed -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: USE_LIBAEC -- Build files have been written to: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/HDF5-prefix/src/HDF5-build [ 10%] Performing build step for 'HDF5' Scanning dependencies of target H5_buildiface Scanning dependencies of target H5HL_buildiface [ 0%] Building Fortran object hl/fortran/src/CMakeFiles/H5HL_buildiface.dir/H5HL_buildiface.F90.o [ 0%] Building C object fortran/src/CMakeFiles/H5match_types.dir/H5match_types.c.o [ 1%] Building C object src/CMakeFiles/H5detect.dir/H5detect.c.o [ 1%] Building Fortran object fortran/src/CMakeFiles/H5_buildiface.dir/H5_buildiface.F90.o [ 1%] Building C object src/CMakeFiles/H5make_libsettings.dir/H5make_libsettings.c.o [ 2%] Linking C executable ../../bin/H5match_types [ 2%] Linking C executable ../bin/H5make_libsettings Create H5lib_settings.c [ 2%] Built target H5make_libsettings [ 2%] Built target H5match_types [ 2%] Built target H5gen_i [ 2%] Linking C 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Built target h5import [ 92%] Built target h5jam Consolidate compiler generated dependencies of target h5unjam Consolidate compiler generated dependencies of target h5copy Consolidate compiler generated dependencies of target h5stat Consolidate compiler generated dependencies of target h5dump Consolidate compiler generated dependencies of target h5format_convert Consolidate compiler generated dependencies of target gif2h5 [ 94%] Built target h5repack Consolidate compiler generated dependencies of target h52gif [ 95%] Built target h5unjam Consolidate compiler generated dependencies of target h5watch [ 96%] Built target h5copy [ 96%] Built target h5stat [ 97%] Built target h5format_convert [ 97%] Built target h5dump [ 98%] Built target gif2h5 [ 99%] Built target h52gif [ 99%] Built target h5watch [100%] Built target hdf5_hl_fortran-static Install the project... -- Install configuration: "Release" -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/share/cmake/hdf5/hdf5-targets.cmake -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/share/cmake/hdf5/hdf5-targets-release.cmake -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/share/cmake/hdf5/hdf5-config.cmake -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/share/cmake/hdf5/hdf5-config-version.cmake -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libhdf5.settings -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/share/COPYING -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/share/USING_HDF5_CMake.txt -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/share/RELEASE.txt -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libchkp.so -- Installing: 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-- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/h5global.mod -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/h5a.mod -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/h5d.mod -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/h5e.mod -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/h5f.mod -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/h5g.mod -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/h5i.mod -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/h5l.mod -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/h5lib.mod -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/h5o.mod -- Installing: 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/home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/bin/h5fc -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/static/h5ds.mod -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/static/h5tb.mod -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/static/h5tb_const.mod -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/static/h5lt.mod -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/static/h5lt_const.mod -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/static/h5im.mod -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/h5ds.mod -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/h5tb.mod -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/h5tb_const.mod -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/h5lt.mod -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/h5lt_const.mod -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/h5im.mod -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libhdf5_hl_f90cstub.a -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libhdf5_hl_fortran.a -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/pkgconfig/hdf5_hl_fortran.pc -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/bin/h5hlfc [ 14%] Completed 'HDF5' [ 14%] Built target HDF5 [ 16%] Creating directories for 'NETCDF_C' [ 18%] Performing download step (download, verify and extract) for 'NETCDF_C' -- Downloading... dst='/home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/NETCDF_C-prefix/src/v4.8.1.tar.gz' timeout='none' inactivity timeout='30 seconds' -- Using src='https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.8.1.tar.gz' -- [download 100% complete] -- verifying file... file='/home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/NETCDF_C-prefix/src/v4.8.1.tar.gz' -- Downloading... done -- extracting... src='/home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/NETCDF_C-prefix/src/v4.8.1.tar.gz' dst='/home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/NETCDF_C-prefix/src/NETCDF_C' -- extracting... [tar xfz] -- extracting... [analysis] -- extracting... [rename] -- extracting... [clean up] -- extracting... done [ 20%] No patch step for 'NETCDF_C' [ 22%] Performing configure step for 'NETCDF_C' -- The C compiler identification is Intel 2021.5.0.20211109 -- The CXX compiler identification is GNU 9.4.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /opt/intel/oneapi/compiler/2022.0.2/linux/bin/intel64/icc - 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: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test CC_SUPPORTS_NO_STRICT_ALIASING -- Performing Test CC_SUPPORTS_NO_STRICT_ALIASING - Success -- HDF5 C compiler wrapper is unable to compile a minimal HDF5 program. -- Found HDF5: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libhdf5.a (found version "1.12.1") found components: C HL -- Found HDF5 libraries version 1.12.1 -- Using HDF5 include dir: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include -- 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 USE_SZIP -- Performing Test USE_SZIP - Failed -- Looking for H5Pget_fapl_mpio in /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libhdf5.a -- Looking for H5Pget_fapl_mpio in /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libhdf5.a - not found -- Looking for H5Pset_all_coll_metadata_ops in /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libhdf5.a -- Looking for H5Pset_all_coll_metadata_ops in /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libhdf5.a - not found -- Looking for H5free_memory in /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libhdf5.a -- Looking for H5free_memory in /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libhdf5.a - not found -- Looking for H5allocate_memory in /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libhdf5.a -- Looking for H5allocate_memory in /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libhdf5.a - not found -- Looking for H5resize_memory in /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libhdf5.a -- Looking for H5resize_memory in /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libhdf5.a - not found -- Looking for H5Dread_chunk in /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libhdf5.a -- Looking for H5Dread_chunk in /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libhdf5.a - not found -- Looking for H5Pset_fapl_ros3 in /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libhdf5.a -- Looking for H5Pset_fapl_ros3 in /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libhdf5.a - not found -- Checking for HDF5 version 1.10.6 or later: ON -- Performing Test HAVE_HDF5_ZLIB -- Performing Test HAVE_HDF5_ZLIB - Success -- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version "7.68.0") -- Performing Test HAVE_LIBCURL_766 -- Performing Test HAVE_LIBCURL_766 - Success -- Found Math library: /usr/lib/x86_64-linux-gnu/libm.so -- Enabling use of fill value when NC_ERANGE -- Enabling a more relaxed check for NC_EINVALCOORDS -- Looking for math.h -- Looking for math.h - found -- Looking for unistd.h -- Looking for unistd.h - found -- Looking for alloca.h -- Looking for alloca.h - found -- Looking for malloc.h -- Looking for malloc.h - found -- Looking for fcntl.h -- Looking for fcntl.h - found -- Looking for getopt.h -- Looking for getopt.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/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/mman.h -- Looking for sys/mman.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 string.h -- Looking for string.h - found -- Looking for winsock2.h -- Looking for winsock2.h - not found -- Looking for ftw.h -- Looking for ftw.h - found -- Looking for libgen.h -- Looking for libgen.h - found -- Looking for execinfo.h -- Looking for execinfo.h - found -- Looking for dirent.h -- Looking for dirent.h - found -- Looking for time.h -- Looking for time.h - found -- Looking for isfinite -- Looking for isfinite - found -- Looking for isnan -- Looking for isnan - found -- Looking for isinf -- Looking for isinf - found -- Looking for st_blksize -- Looking for st_blksize - not found -- Looking for alloca -- Looking for alloca - found -- Looking for snprintf -- Looking for snprintf - found -- 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 uint -- Check size of uint - done -- Check size of schar -- Check size of schar - failed -- Check size of long -- Check size of long - done -- Check size of long long -- Check size of long long - done -- Check size of unsigned long long -- Check size of unsigned long long - done -- Check size of off_t -- Check size of off_t - done -- Check size of off64_t -- Check size of off64_t - done -- Check size of short -- Check size of short - done -- Check size of ushort -- Check size of ushort - done -- Check size of _Bool -- Check size of _Bool - 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 ptrdiff_t -- Check size of ptrdiff_t - done -- Check size of uintptr_t -- Check size of uintptr_t - done -- Check size of __int64 -- Check size of __int64 - done -- Check size of int64_t -- Check size of int64_t - done -- Check size of uint64 -- Check size of uint64 - failed -- Check size of unsigned char -- Check size of unsigned char - done -- Check size of unsigned short int -- Check size of unsigned short int - done -- Check size of unsigned int -- Check size of unsigned int - done -- Check size of long long -- Check size of long long - done -- Check size of unsigned long long -- Check size of unsigned long long - done -- Check size of uint64_t -- Check size of uint64_t - done -- Looking for fsync -- Looking for fsync - found -- Looking for strlcat -- Looking for strlcat - not found -- Looking for strdup -- Looking for strdup - found -- Looking for strndup -- Looking for strndup - found -- Looking for strtoll -- Looking for strtoll - found -- Looking for strtoull -- Looking for strtoull - found -- Looking for mkstemp -- Looking for mkstemp - found -- Looking for mktemp -- Looking for mktemp - found -- Looking for random -- Looking for random - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for MPI_Comm_f2c -- Looking for MPI_Comm_f2c - not found -- Looking for MPI_Info_f2c -- Looking for MPI_Info_f2c - not found -- Looking for memmove -- Looking for memmove - found -- Looking for getpagesize -- Looking for getpagesize - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for getrlimit -- Looking for getrlimit - found -- Looking for _filelengthi64 -- Looking for _filelengthi64 - not found -- Looking for mmap -- Looking for mmap - found -- Looking for mremap -- Looking for mremap - found -- Looking for fileno -- Looking for fileno - found -- Looking for clock_gettime -- Looking for clock_gettime - found -- Looking for struct timespec -- Looking for struct timespec - not found -- Performing Test HAVE_MAPANON -- Performing Test HAVE_MAPANON - Success -- Found m4: /usr/bin/m4 -- Found bash: /usr/bin/bash CMake Warning at /usr/share/cmake-3.22/Modules/InstallRequiredSystemLibraries.cmake:732 (message): system runtime library file does not exist: '/opt/intel/oneapi/compiler/2022.0.2/linux/bin/intel64/../../compiler/lib/intel64_lin/liboffload.so' Call Stack (most recent call first): CMakeLists.txt:2048 (INCLUDE) CMake Warning at /usr/share/cmake-3.22/Modules/InstallRequiredSystemLibraries.cmake:732 (message): system runtime library file does not exist: '/opt/intel/oneapi/compiler/2022.0.2/linux/bin/intel64/../../compiler/lib/intel64_lin/liboffload.so.5' Call Stack (most recent call first): CMakeLists.txt:2048 (INCLUDE) CMake Warning at /usr/share/cmake-3.22/Modules/InstallRequiredSystemLibraries.cmake:732 (message): system runtime library file does not exist: '/opt/intel/oneapi/compiler/2022.0.2/linux/bin/intel64/../../compiler/lib/intel64_lin/libgfxoffload.so' Call Stack (most recent call first): CMakeLists.txt:2048 (INCLUDE) CMake Warning at /usr/share/cmake-3.22/Modules/InstallRequiredSystemLibraries.cmake:732 (message): system runtime library file does not exist: '/opt/intel/oneapi/compiler/2022.0.2/linux/bin/intel64/../../compiler/lib/intel64_lin/libioffload_host.so' Call Stack (most recent call first): CMakeLists.txt:2048 (INCLUDE) CMake Warning at /usr/share/cmake-3.22/Modules/InstallRequiredSystemLibraries.cmake:732 (message): system runtime library file does not exist: '/opt/intel/oneapi/compiler/2022.0.2/linux/bin/intel64/../../compiler/lib/intel64_lin/libioffload_host.so.5' Call Stack (most recent call first): CMakeLists.txt:2048 (INCLUDE) CMake Warning at /usr/share/cmake-3.22/Modules/InstallRequiredSystemLibraries.cmake:732 (message): system runtime library file does not exist: '/opt/intel/oneapi/compiler/2022.0.2/linux/bin/intel64/../../compiler/lib/intel64_lin/libioffload_target.so' Call Stack (most recent call first): CMakeLists.txt:2048 (INCLUDE) CMake Warning at /usr/share/cmake-3.22/Modules/InstallRequiredSystemLibraries.cmake:732 (message): system runtime library file does not exist: '/opt/intel/oneapi/compiler/2022.0.2/linux/bin/intel64/../../compiler/lib/intel64_lin/libioffload_target.so.5' Call Stack (most recent call first): CMakeLists.txt:2048 (INCLUDE) CMake Warning at /usr/share/cmake-3.22/Modules/InstallRequiredSystemLibraries.cmake:732 (message): system runtime library file does not exist: '/opt/intel/oneapi/compiler/2022.0.2/linux/bin/intel64/../../compiler/lib/intel64_lin/libmpx.so' Call Stack (most recent call first): CMakeLists.txt:2048 (INCLUDE) CMake Warning at /usr/share/cmake-3.22/Modules/InstallRequiredSystemLibraries.cmake:732 (message): system runtime library file does not exist: '/opt/intel/oneapi/compiler/2022.0.2/linux/bin/intel64/../../compiler/lib/intel64_lin/offload_main' Call Stack (most recent call first): CMakeLists.txt:2048 (INCLUDE) CMake Warning at /usr/share/cmake-3.22/Modules/InstallRequiredSystemLibraries.cmake:742 (message): system runtime library file does not exist: '/opt/intel/oneapi/compiler/2022.0.2/linux/bin/intel64/../../compiler/lib/intel64_lin/irml' Call Stack (most recent call first): CMakeLists.txt:2048 (INCLUDE) Configuration Summary: -- Building Shared Libraries: ON -- Building netCDF-4: ON -- Building DAP2 Support: OFF -- Building DAP4 Support: OFF -- Building Byte-range Support: OFF -- Building Utilities: OFF -- CMake Prefix Path: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build Tests Enabled: off Compiler: -- Build Type: RELEASE -- CMAKE_C_COMPILER: /opt/intel/oneapi/compiler/2022.0.2/linux/bin/intel64/icc -- CMAKE_C_FLAGS: -fno-strict-aliasing -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -- CMAKE_C_FLAGS_RELEASE: -O3 -DNDEBUG -- Linking against: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libhdf5_hl.a;/home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libhdf5.a;/usr/lib/x86_64-linux-gnu/libm.so;/usr/lib/x86_64-linux-gnu/libcurl.so -- # NetCDF C Configuration Summary ============================== # General ------- NetCDF Version: 4.8.1 Dispatch Version: 3 Configured On: Di 8. Mär 13:09:36 CET 2022 Host System: x86_64-Linux-5.13.0-30-generic Build Directory: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/NETCDF_C-prefix/src/NETCDF_C-build Install Prefix: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build # Compiling Options ----------------- C Compiler: /opt/intel/oneapi/compiler/2022.0.2/linux/bin/intel64/icc CFLAGS: -fno-strict-aliasing -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG CPPFLAGS: LDFLAGS: AM_CFLAGS: AM_CPPFLAGS: AM_LDFLAGS: Shared Library: yes Static Library: no Extra libraries: -lhdf5_hl -lhdf5 -lm -lcurl # Features -------- NetCDF-2 API: yes HDF4 Support: no HDF5 Support: yes NetCDF-4 API: yes NC-4 Parallel Support: no PnetCDF Support: no DAP2 Support: no DAP4 Support: no Byte-Range Support: no Diskless Support: yes MMap Support: yes JNA Support: no CDF5 Support: yes ERANGE Fill Support: yes Relaxed Boundary Check: yes SZIP Support: no SZIP Write Support: no Parallel Filters: no NCZarr Support: yes Multi-Filter Support: yes -- Configuring done -- Generating done -- Build files have been written to: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/NETCDF_C-prefix/src/NETCDF_C-build [ 24%] Performing build step for 'NETCDF_C' [ 1%] Generating /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/NETCDF_C-prefix/src/NETCDF_C/libsrc/attr.c [ 2%] Generating /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/NETCDF_C-prefix/src/NETCDF_C/libsrc/putget.c [ 3%] Generating /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/NETCDF_C-prefix/src/NETCDF_C/libsrc/ncx.c [ 3%] Building C object libsrc4/CMakeFiles/netcdf4.dir/nc4dispatch.c.o [ 5%] Building C object libhdf5/CMakeFiles/netcdfhdf5.dir/nc4hdf.c.o [ 5%] Building C object libsrc4/CMakeFiles/netcdf4.dir/nc4attr.c.o [ 5%] Building C object libhdf5/CMakeFiles/netcdfhdf5.dir/hdf5file.c.o [ 6%] Building C object libsrc4/CMakeFiles/netcdf4.dir/nc4dim.c.o [ 8%] Building C object libhdf5/CMakeFiles/netcdfhdf5.dir/nc4info.c.o [ 8%] Building C object libhdf5/CMakeFiles/netcdfhdf5.dir/hdf5grp.c.o [ 9%] Building C object libhdf5/CMakeFiles/netcdfhdf5.dir/hdf5attr.c.o [ 10%] Building C object libnczarr/CMakeFiles/nczarr.dir/zarr.c.o [ 11%] Building C object libdispatch/CMakeFiles/dispatch.dir/dcopy.c.o [ 12%] Building C object libnczarr/CMakeFiles/nczarr.dir/zxcache.c.o [ 14%] Building C object libdispatch/CMakeFiles/dispatch.dir/dfile.c.o [ 14%] Building C object libhdf5/CMakeFiles/netcdfhdf5.dir/hdf5dim.c.o [ 14%] Building C object libdispatch/CMakeFiles/dispatch.dir/dparallel.c.o [ 15%] Building C object libnczarr/CMakeFiles/nczarr.dir/zattr.c.o [ 16%] Building C object libsrc4/CMakeFiles/netcdf4.dir/nc4grp.c.o [ 17%] Building C object libhdf5/CMakeFiles/netcdfhdf5.dir/hdf5type.c.o [ 18%] Building C object libdispatch/CMakeFiles/dispatch.dir/ddim.c.o [ 18%] Building C object libnczarr/CMakeFiles/nczarr.dir/zchunking.c.o [ 19%] Building C object libsrc4/CMakeFiles/netcdf4.dir/nc4internal.c.o [ 20%] Building C object libsrc4/CMakeFiles/netcdf4.dir/nc4type.c.o [ 21%] Building C object libhdf5/CMakeFiles/netcdfhdf5.dir/hdf5internal.c.o [ 21%] Building C object libsrc4/CMakeFiles/netcdf4.dir/ncfunc.c.o [ 22%] Building C object libsrc4/CMakeFiles/netcdf4.dir/error4.c.o [ 22%] Building C object libhdf5/CMakeFiles/netcdfhdf5.dir/hdf5open.c.o [ 23%] Building C object libhdf5/CMakeFiles/netcdfhdf5.dir/hdf5create.c.o [ 24%] Building C object libsrc4/CMakeFiles/netcdf4.dir/ncindex.c.o [ 25%] Building C object libsrc4/CMakeFiles/netcdf4.dir/nc4var.c.o [ 27%] Building C object libnczarr/CMakeFiles/nczarr.dir/zcreate.c.o [ 28%] Building C object libhdf5/CMakeFiles/netcdfhdf5.dir/nc4mem.c.o [ 28%] Building C object libnczarr/CMakeFiles/nczarr.dir/zclose.c.o [ 29%] Building C object libdispatch/CMakeFiles/dispatch.dir/datt.c.o [ 30%] Building C object libhdf5/CMakeFiles/netcdfhdf5.dir/hdf5var.c.o [ 31%] Building C object libnczarr/CMakeFiles/nczarr.dir/zcvt.c.o [ 32%] Building C object libdispatch/CMakeFiles/dispatch.dir/dattinq.c.o [ 32%] Built target manpage [ 33%] Building C object libnczarr/CMakeFiles/nczarr.dir/zdim.c.o [ 33%] Building C object libdispatch/CMakeFiles/dispatch.dir/dattput.c.o [ 34%] Building C object libhdf5/CMakeFiles/netcdfhdf5.dir/nc4memcb.c.o [ 36%] Building C object libdispatch/CMakeFiles/dispatch.dir/dattget.c.o [ 35%] Building C object libnczarr/CMakeFiles/nczarr.dir/zfile.c.o [ 37%] Building C object libsrc4/CMakeFiles/netcdf4.dir/nc4cache.c.o [ 38%] Building C object libdispatch/CMakeFiles/dispatch.dir/derror.c.o [ 39%] Building C object libnczarr/CMakeFiles/nczarr.dir/zdispatch.c.o [ 39%] Building C object libsrc/CMakeFiles/netcdf3.dir/v1hpg.c.o [ 40%] Building C object libhdf5/CMakeFiles/netcdfhdf5.dir/hdf5dispatch.c.o [ 40%] Building C object libnczarr/CMakeFiles/nczarr.dir/zfilter.c.o [ 41%] Building C object libnczarr/CMakeFiles/nczarr.dir/zgrp.c.o [ 42%] Building C object libhdf5/CMakeFiles/netcdfhdf5.dir/hdf5filter.c.o [ 43%] Building C object libnczarr/CMakeFiles/nczarr.dir/zinternal.c.o [ 44%] Building C object libsrc/CMakeFiles/netcdf3.dir/putget.c.o [ 45%] Building C object libhdf5/CMakeFiles/netcdfhdf5.dir/hdf5debug.c.o [ 46%] Building C object libdispatch/CMakeFiles/dispatch.dir/dvarget.c.o [ 47%] Building C object libsrc/CMakeFiles/netcdf3.dir/attr.c.o [ 49%] Building C object libdispatch/CMakeFiles/dispatch.dir/dvarput.c.o [ 51%] Building C object libdispatch/CMakeFiles/dispatch.dir/dvar.c.o [ 51%] Building C object libdispatch/CMakeFiles/dispatch.dir/dvarinq.c.o [ 51%] Building C object libsrc/CMakeFiles/netcdf3.dir/nc3dispatch.c.o [ 51%] Building C object libdispatch/CMakeFiles/dispatch.dir/ddispatch.c.o [ 53%] Building C object libnczarr/CMakeFiles/nczarr.dir/zmap.c.o [ 54%] Building C object libsrc/CMakeFiles/netcdf3.dir/nc3internal.c.o [ 54%] Building C object libsrc/CMakeFiles/netcdf3.dir/var.c.o [ 55%] Building C object libnczarr/CMakeFiles/nczarr.dir/zodom.c.o [ 56%] Building C object libnczarr/CMakeFiles/nczarr.dir/zmap_file.c.o [ 56%] Building C object libnczarr/CMakeFiles/nczarr.dir/zopen.c.o [ 56%] Building C object libsrc/CMakeFiles/netcdf3.dir/ncx.c.o [ 57%] Building C object libsrc/CMakeFiles/netcdf3.dir/dim.c.o [ 58%] Building C object libdispatch/CMakeFiles/dispatch.dir/nclog.c.o [ 59%] Building C object libsrc/CMakeFiles/netcdf3.dir/ncio.c.o [ 60%] Building C object libsrc/CMakeFiles/netcdf3.dir/lookup3.c.o [ 61%] Building C object libnczarr/CMakeFiles/nczarr.dir/zprov.c.o [ 62%] Building C object libdispatch/CMakeFiles/dispatch.dir/dutf8.c.o [ 63%] Building C object libsrc/CMakeFiles/netcdf3.dir/memio.c.o [ 64%] Building C object libdispatch/CMakeFiles/dispatch.dir/dstring.c.o [ 65%] Building C object libnczarr/CMakeFiles/nczarr.dir/ztype.c.o [ 66%] Building C object libnczarr/CMakeFiles/nczarr.dir/zsync.c.o [ 67%] Building C object libnczarr/CMakeFiles/nczarr.dir/zvar.c.o [ 69%] Building C object libnczarr/CMakeFiles/nczarr.dir/zwalk.c.o [ 69%] Building C object libdispatch/CMakeFiles/dispatch.dir/dinternal.c.o [ 70%] Building C object libnczarr/CMakeFiles/nczarr.dir/zutil.c.o [ 71%] Building C object libsrc/CMakeFiles/netcdf3.dir/mmapio.c.o [ 71%] Building C object libnczarr/CMakeFiles/nczarr.dir/zdebug.c.o [ 72%] Building C object libsrc/CMakeFiles/netcdf3.dir/posixio.c.o [ 73%] Building C object libdispatch/CMakeFiles/dispatch.dir/doffsets.c.o [ 73%] Building C object libdispatch/CMakeFiles/dispatch.dir/ncuri.c.o [ 74%] Building C object libdispatch/CMakeFiles/dispatch.dir/ncbytes.c.o [ 75%] Building C object libdispatch/CMakeFiles/dispatch.dir/nclist.c.o [ 76%] Building C object libdispatch/CMakeFiles/dispatch.dir/nchashmap.c.o [ 77%] Building C object libdispatch/CMakeFiles/dispatch.dir/nctime.c.o [ 78%] Building C object libdispatch/CMakeFiles/dispatch.dir/nc.c.o [ 79%] Building C object libdispatch/CMakeFiles/dispatch.dir/nclistmgr.c.o [ 79%] Building C object libdispatch/CMakeFiles/dispatch.dir/utf8proc.c.o [ 80%] Building C object libdispatch/CMakeFiles/dispatch.dir/dutil.c.o [ 81%] Building C object libdispatch/CMakeFiles/dispatch.dir/dpathmgr.c.o [ 82%] Building C object libdispatch/CMakeFiles/dispatch.dir/dauth.c.o [ 83%] Building C object libdispatch/CMakeFiles/dispatch.dir/drc.c.o [ 83%] Building C object libdispatch/CMakeFiles/dispatch.dir/dnotnc4.c.o [ 84%] Building C object libdispatch/CMakeFiles/dispatch.dir/dreadonly.c.o [ 85%] Building C object libdispatch/CMakeFiles/dispatch.dir/daux.c.o [ 86%] Building C object libdispatch/CMakeFiles/dispatch.dir/dinfermodel.c.o [ 87%] Building C object libdispatch/CMakeFiles/dispatch.dir/dcrc32.c.o [ 88%] Building C object libdispatch/CMakeFiles/dispatch.dir/dnotnc3.c.o [ 89%] Building C object libdispatch/CMakeFiles/dispatch.dir/dcrc64.c.o [ 90%] Building C object libdispatch/CMakeFiles/dispatch.dir/ncexhash.c.o [ 90%] Building C object libdispatch/CMakeFiles/dispatch.dir/ncxcache.c.o [ 91%] Building C object libdispatch/CMakeFiles/dispatch.dir/ncjson.c.o [ 92%] Building C object libdispatch/CMakeFiles/dispatch.dir/dgroup.c.o [ 93%] Building C object libdispatch/CMakeFiles/dispatch.dir/dvlen.c.o [ 94%] Building C object libdispatch/CMakeFiles/dispatch.dir/dcompound.c.o [ 95%] Building C object libdispatch/CMakeFiles/dispatch.dir/dtype.c.o [ 95%] Building C object libdispatch/CMakeFiles/dispatch.dir/denum.c.o [ 96%] Building C object libdispatch/CMakeFiles/dispatch.dir/dfilter.c.o [ 97%] Building C object libdispatch/CMakeFiles/dispatch.dir/dopaque.c.o [ 98%] Building C object libdispatch/CMakeFiles/dispatch.dir/dv2i.c.o /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/NETCDF_C-prefix/src/NETCDF_C/libdispatch/dcrc32.c(303): warning #180: argument is incompatible with formal parameter value = crc32_z(value, cbuf, len); ^ [ 98%] Built target dispatch [ 98%] Built target netcdfhdf5 [ 98%] Built target nczarr [ 98%] Built target netcdf4 [ 98%] Built target netcdf3 [ 99%] Building C object liblib/CMakeFiles/netcdf.dir/nc_initialize.c.o [100%] Linking C shared library libnetcdf.so [100%] Built target netcdf [ 26%] Performing install step for 'NETCDF_C' Consolidate compiler generated dependencies of target netcdf3 Consolidate compiler generated dependencies of target netcdf4 Consolidate compiler generated dependencies of target nczarr Consolidate compiler generated dependencies of target netcdfhdf5 Consolidate compiler generated dependencies of target dispatch [ 9%] Built target netcdf4 [ 23%] Built target netcdf3 [ 43%] Built target nczarr [ 57%] Built target netcdfhdf5 [ 98%] Built target dispatch Consolidate compiler generated dependencies of target netcdf [100%] Built target netcdf [100%] Built target manpage Install the project... -- Install configuration: "RELEASE" -- Up-to-date: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libchkp.so -- Up-to-date: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libcilkrts.so -- Up-to-date: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libcilkrts.so.5 -- Up-to-date: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libimf.so -- Up-to-date: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libintlc.so -- Up-to-date: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libintlc.so.5 -- Up-to-date: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libirc.so -- Up-to-date: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libpdbx.so -- Up-to-date: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libpdbx.so.5 -- Up-to-date: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libsvml.so -- Up-to-date: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libirng.so -- Up-to-date: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/cilk_db.so -- Up-to-date: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libistrconv.so -- Up-to-date: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/pkgconfig/netcdf.pc -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/bin/nc-config -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libnetcdf.settings -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/cmake/netCDF/netCDFTargets.cmake -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/cmake/netCDF/netCDFTargets-release.cmake -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/cmake/netCDF/netCDFConfig.cmake -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/cmake/netCDF/netCDFConfigVersion.cmake -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/netcdf.h -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/netcdf_mem.h -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/netcdf_aux.h -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/netcdf_meta.h -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/netcdf_filter.h -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/netcdf_filter_build.h -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/netcdf_dispatch.h -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/share/man/man3/netcdf.3 -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libnetcdf.so.19 -- Set runtime path of "/home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libnetcdf.so.19" to "/home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib" -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libnetcdf.so [ 28%] Completed 'NETCDF_C' [ 28%] Built target NETCDF_C [ 30%] Creating directories for 'NETCDF_FORTRAN' [ 32%] Performing download step (download, verify and extract) for 'NETCDF_FORTRAN' -- Downloading... dst='/home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/NETCDF_FORTRAN-prefix/src/v4.5.4.tar.gz' timeout='none' inactivity timeout='30 seconds' -- Using src='https://github.com/Unidata/netcdf-fortran/archive/refs/tags/v4.5.4.tar.gz' -- [download 100% complete] -- verifying file... file='/home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/NETCDF_FORTRAN-prefix/src/v4.5.4.tar.gz' -- Downloading... done -- extracting... src='/home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/NETCDF_FORTRAN-prefix/src/v4.5.4.tar.gz' dst='/home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/NETCDF_FORTRAN-prefix/src/NETCDF_FORTRAN' -- extracting... [tar xfz] -- extracting... [analysis] -- extracting... [rename] -- extracting... [clean up] -- extracting... done [ 34%] No patch step for 'NETCDF_FORTRAN' [ 36%] Performing configure step for 'NETCDF_FORTRAN' -- The Fortran compiler identification is Intel 2021.5.0.20211109 -- The C compiler identification is Intel 2021.5.0.20211109 -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Check for working Fortran compiler: /opt/intel/oneapi/compiler/2022.0.2/linux/bin/intel64/ifort - skipped -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /opt/intel/oneapi/compiler/2022.0.2/linux/bin/intel64/icc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Found m4: /usr/bin/m4 -- Found netCDF CMake package: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libnetcdf.so -- 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 - done -- 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 nc_get_chunk_cache_ints in /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libnetcdf.so -- Looking for nc_get_chunk_cache_ints in /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libnetcdf.so - found -- Looking for nccreate in /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libnetcdf.so -- Looking for nccreate in /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libnetcdf.so - found -- Looking for nc_set_log_level in /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libnetcdf.so -- Looking for nc_set_log_level in /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libnetcdf.so - found -- Looking for oc_open in /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libnetcdf.so -- Looking for oc_open in /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libnetcdf.so - not found -- Performing Test HAVE_SZIP_WRITE -- Performing Test HAVE_SZIP_WRITE - Failed -- Looking for nc_def_var_szip in /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libnetcdf.so -- Looking for nc_def_var_szip in /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libnetcdf.so - found -- Check size of signed char -- Check size of signed char - done Matching Fortran types to C types Matching Fortran types to C types - done CMake Deprecation Warning at fortran/CMakeLists.txt:1 (CMAKE_MINIMUM_REQUIRED): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Looking for nc_create_par -- Looking for nc_create_par - not found -- found netcdf-c parallel support: CMake Warning (dev) in fortran/CMakeLists.txt: A logical block opening on the line /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/NETCDF_FORTRAN-prefix/src/NETCDF_FORTRAN/fortran/CMakeLists.txt:18 (IF) closes on the line /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/NETCDF_FORTRAN-prefix/src/NETCDF_FORTRAN/fortran/CMakeLists.txt:26 (ENDIF) with mis-matching arguments. This warning is for project developers. Use -Wno-dev to suppress it. -- no netcdf-f parallel support CMake Deprecation Warning at libsrc/CMakeLists.txt:1 (CMAKE_MINIMUM_REQUIRED): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- CMake Summary: -- Build Type: Release -- Building Shared Libraries: ON -- Building netCDF-4: ON -- Building DAP Support: OFF -- Logging Support: ON -- Enabling CDF5: TRUE -- Relaxed check NC_EINVALCOORDS: TRUE -- Building Parallel IO: OFF -- Using NetCDF4 Parallel IO: FALSE -- Using PnetCDF Parallel IO: FALSE -- Testing Parallel IO: OFF -- CMake Prefix Path: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build -- Linking against: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libnetcdf.so; # NetCDF Fortran Configuration Summary ============================== # General ------- Library Version: 4.5.4 Configured On: Host System: x86_64-Linux-5.13.0-30-generic Build Directory: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/NETCDF_FORTRAN-prefix/src/NETCDF_FORTRAN-build Install Prefix: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build # Compiling Options ----------------- Fortran Compiler: /opt/intel/oneapi/compiler/2022.0.2/linux/bin/intel64/ifort FFLAGS: LDFLAGS: C Compiler: /opt/intel/oneapi/compiler/2022.0.2/linux/bin/intel64/icc CPPFLAGS: CFLAGS: "-fPIC" -O2 Shared Library: yes Static Library: no Extra libraries: -lnetcdf -lnetcdf -lnetcdff_c # Features -------- F03: yes Dap Support: no Logging Support: yes NetCDF-2 API: yes NetCDF-4 API: yes CDF5 Support: yes Parallel IO: no NetCDF4 Parallel IO: no PnetCDF Parallel IO: no SZIP Write Support: no -- Configuring done -- Generating done -- Build files have been written to: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/NETCDF_FORTRAN-prefix/src/NETCDF_FORTRAN-build [ 38%] Performing build step for 'NETCDF_FORTRAN' [ 3%] Building C object fortran/CMakeFiles/netcdff_c.dir/nf_lib.c.o [ 6%] Building C object fortran/CMakeFiles/netcdff_c.dir/nf_v2compat.c.o [ 6%] Built target manpage [ 6%] Built target netcdff_c Scanning dependencies of target netcdff [ 10%] Building Fortran object fortran/CMakeFiles/netcdff.dir/module_netcdf_nc_data.F90.o [ 13%] Building Fortran object fortran/CMakeFiles/netcdff.dir/nf_logging.F90.o [ 16%] Building Fortran object fortran/CMakeFiles/netcdff.dir/typeSizes.f90.o [ 20%] Building Fortran object fortran/CMakeFiles/netcdff.dir/netcdf4.f90.o [ 23%] Building Fortran object fortran/CMakeFiles/netcdff.dir/module_netcdf_nc_interfaces.f90.o [ 26%] Building Fortran object fortran/CMakeFiles/netcdff.dir/module_netcdf_nf_data.F90.o [ 30%] Building Fortran object fortran/CMakeFiles/netcdff.dir/module_netcdf_nf_interfaces.F90.o [ 33%] Building Fortran object fortran/CMakeFiles/netcdff.dir/nf_attio.F90.o [ 36%] Building Fortran object fortran/CMakeFiles/netcdff.dir/nf_control.F90.o [ 43%] Building Fortran object fortran/CMakeFiles/netcdff.dir/module_netcdf4_nc_interfaces.f90.o [ 40%] Building Fortran object fortran/CMakeFiles/netcdff.dir/module_netcdf_fortv2_c_interfaces.f90.o [ 46%] Building Fortran object fortran/CMakeFiles/netcdff.dir/nf_dim.f90.o [ 53%] Building Fortran object fortran/CMakeFiles/netcdff.dir/nf_genvar.f90.o [ 53%] Building Fortran object fortran/CMakeFiles/netcdff.dir/nf_misc.f90.o [ 56%] Building Fortran object fortran/CMakeFiles/netcdff.dir/nf_geninq.f90.o [ 60%] Building Fortran object fortran/CMakeFiles/netcdff.dir/nf_genatt.f90.o [ 63%] Building Fortran object fortran/CMakeFiles/netcdff.dir/nf_vario.F90.o [ 66%] Building Fortran object fortran/CMakeFiles/netcdff.dir/nf_var1io.F90.o [ 70%] Building Fortran object fortran/CMakeFiles/netcdff.dir/nf_varaio.F90.o [ 73%] Building Fortran object fortran/CMakeFiles/netcdff.dir/nf_varmio.F90.o [ 76%] Building Fortran object fortran/CMakeFiles/netcdff.dir/nf_varsio.F90.o [ 80%] Building Fortran object fortran/CMakeFiles/netcdff.dir/nf_nc_noparallel.f90.o [ 83%] Building Fortran object fortran/CMakeFiles/netcdff.dir/module_netcdf_f03.f90.o [ 86%] Building Fortran object fortran/CMakeFiles/netcdff.dir/module_netcdf4_nf_interfaces.F90.o [ 90%] Building Fortran object fortran/CMakeFiles/netcdff.dir/nf_nc4.f90.o [ 93%] Building Fortran object fortran/CMakeFiles/netcdff.dir/nf_fortv2.f90.o [ 96%] Building Fortran object fortran/CMakeFiles/netcdff.dir/module_netcdf4_f03.f90.o [100%] Linking Fortran shared library libnetcdff.so [100%] Built target netcdff [ 40%] Performing install step for 'NETCDF_FORTRAN' Consolidate compiler generated dependencies of target netcdff_c [ 6%] Built target netcdff_c [ 10%] Built target manpage [100%] Built target netcdff Install the project... -- Install configuration: "Release" -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/pkgconfig/netcdf-fortran.pc -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/bin/nf-config -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libnetcdff.settings -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/cmake/netCDF/netcdffTargets.cmake -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/cmake/netCDF/netcdffTargets-release.cmake -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/cmake/netCDF/netCDF-FortranConfig.cmake -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/cmake/netCDF/netCDF-FortranConfigVersion.cmake -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/objects-Release/netcdff_c/nf_lib.c.o -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/objects-Release/netcdff_c/nf_v2compat.c.o -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libnetcdff.so.7.1.0 -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libnetcdff.so.7 -- Set runtime path of "/home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libnetcdff.so.7.1.0" to "/home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib" -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/lib/libnetcdff.so -- Up-to-date: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/netcdf4_f03.mod -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/CMakeFiles -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/CMakeFiles/netcdff.dir -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/CMakeFiles/netcdff_c.dir -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/netcdf_nf_data.mod -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/netcdf4_nc_interfaces.mod -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/netcdf_f03.mod -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/netcdf_fortv2_c_interfaces.mod -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/netcdf_nf_interfaces.mod -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/netcdf.mod -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/typesizes.mod -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/netcdf_nc_interfaces.mod -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/netcdf.inc -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/netcdf_nc_data.mod -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/include/netcdf4_nf_interfaces.mod -- Installing: /home/muellese/AtWork/Cloud/GIT/GitHub/Tests/nc4fortran/build/share/man/man3/netcdf_fortran.3 [ 42%] Completed 'NETCDF_FORTRAN' [ 42%] Built target NETCDF_FORTRAN Scanning dependencies of target nc4fortran [ 44%] Building Fortran object CMakeFiles/nc4fortran.dir/src/interface.f90.o [ 46%] Building Fortran object CMakeFiles/nc4fortran.dir/src/attributes.f90.o [ 50%] Building Fortran object CMakeFiles/nc4fortran.dir/src/write.f90.o [ 48%] Building Fortran object CMakeFiles/nc4fortran.dir/src/read.f90.o [ 52%] Building Fortran object CMakeFiles/nc4fortran.dir/src/writer.f90.o [ 54%] Building Fortran object CMakeFiles/nc4fortran.dir/src/reader.f90.o [ 56%] Linking Fortran static library libnc4fortran.a [ 56%] Built target nc4fortran Scanning dependencies of target test_attributes Scanning dependencies of target test_deflate Scanning dependencies of target test_minimal Scanning dependencies of target test_exist Scanning dependencies of target test_destructor Scanning dependencies of target test_array Scanning dependencies of target test_shape Scanning dependencies of target test_error Scanning dependencies of target test_version Scanning dependencies of target test_string Scanning dependencies of target test_scalar [ 60%] Building Fortran object tests/CMakeFiles/test_attributes.dir/test_attributes.f90.o [ 60%] Building Fortran object tests/CMakeFiles/test_deflate.dir/test_deflate.f90.o [ 62%] Building Fortran object tests/CMakeFiles/test_array.dir/test_array.f90.o [ 66%] Building Fortran object tests/CMakeFiles/test_exist.dir/test_exist.f90.o [ 66%] Building Fortran object tests/CMakeFiles/test_minimal.dir/test_minimal.f90.o [ 68%] Building Fortran object tests/CMakeFiles/test_destructor.dir/test_destructor.f90.o [ 70%] Building Fortran object tests/CMakeFiles/test_scalar.dir/test_scalar.f90.o [ 72%] Building Fortran object tests/CMakeFiles/test_error.dir/test_error.f90.o [ 74%] Building Fortran object tests/CMakeFiles/test_shape.dir/test_shape.f90.o [ 76%] Building Fortran object tests/CMakeFiles/test_version.dir/test_version.f90.o [ 78%] Building Fortran object tests/CMakeFiles/test_string.dir/test_string.f90.o [ 80%] Linking Fortran executable test_destructor [ 82%] Linking Fortran executable test_minimal [ 84%] Linking Fortran executable test_attributes [ 86%] Linking Fortran executable test_version [ 88%] Linking Fortran executable test_exist [ 90%] Linking Fortran executable test_error [ 92%] Linking Fortran executable test_string [ 94%] Linking Fortran executable test_shape [ 96%] Linking Fortran executable test_deflate [ 98%] Linking Fortran executable test_array [100%] Linking Fortran executable test_scalar [100%] Built target test_attributes [100%] Built target test_minimal [100%] Built target test_error [100%] Built target test_destructor [100%] Built target test_version [100%] Built target test_string [100%] Built target test_shape [100%] Built target test_exist [100%] Built target test_scalar [100%] Built target test_deflate [100%] Built target test_array ```
scivision commented 2 years ago

Thanks after this update I still notice failures on Intel oneAPI on Linux on two different machines, whether with icc/ifort or icx/ifx for NetCDF-Fortran.

Checking with nm the symbols are in that libnetcdf.so file, so maybe a NetCDF package problem

-- 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 nc_get_chunk_cache_ints in /tmp/nci/lib/libnetcdf.so
-- Looking for nc_get_chunk_cache_ints in /tmp/nci/lib/libnetcdf.so - not found
-- Looking for nccreate in /tmp/nci/lib/libnetcdf.so
-- Looking for nccreate in /tmp/nci/lib/libnetcdf.so - not found
-- Looking for nc_set_log_level in /tmp/nci/lib/libnetcdf.so
-- Looking for nc_set_log_level in /tmp/nci/lib/libnetcdf.so - not found
-- Looking for oc_open in /tmp/nci/lib/libnetcdf.so
-- Looking for oc_open in /tmp/nci/lib/libnetcdf.so - not found
-- Performing Test HAVE_SZIP_WRITE
-- Performing Test HAVE_SZIP_WRITE - Failed
-- Looking for nc_def_var_szip in /tmp/nci/lib/libnetcdf.so
-- Looking for nc_def_var_szip in /tmp/nci/lib/libnetcdf.so - not found
CMake Error at CMakeLists.txt:643 (message):
  netcdf-c version 4.7.4 or greater is required
MuellerSeb commented 2 years ago

Do you have any idea how to solve this?

scivision commented 2 years ago

I would ask NetCDF project. I am simply providing a script that executes their CMake script

scivision commented 2 years ago

Hello, I believe I fixed this issue with nc4fortran v1.6.1. Please reopen if still an issue. I worked around the bugs in the netcdf-fortran/CMakeLists.txt upstream by sending additional hints from nc4fortran/cmake/netcdf.cmake.