CMake: HDF5 1.12.1 Does Error in ConfigureChecks

[ax3l]

On Ubuntu 20.04 (x86_64):

git clone -b hdf5-1_12_1 https://github.com/HDFGroup/hdf5.git src/hdf5
cmake -S src/hdf5 -B src/hdf5-build

$ cmake -S src/hdf5 -B src/hdf5-build -- The C compiler identification is GNU 9.4.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - 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 - failed -- 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 - not found -- Looking for llroundf -- Looking for llroundf - not found -- Looking for lround -- Looking for lround - not found -- Looking for lroundf -- Looking for lroundf - not 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 - not found -- Looking for roundf -- Looking for roundf - not 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 CMake Error at config/cmake/ConfigureChecks.cmake:334 (file): file failed to open for reading (No such file or directory):

/home/axel/tmp/tmp/src/hdf5-build/pac_Cconftest.out

Call Stack (most recent call first):
CMakeLists.txt:464 (include)

-- Testing maximum decimal precision for C -
-- maximum decimal precision for C var - 0
-- Found Perl: /usr/bin/perl (found version "5.30.0")
-- ....All Warnings are enabled
-- Configuring incomplete, errors occurred!
See also "/home/axel/tmp/tmp/src/hdf5-build/CMakeFiles/CMakeOutput.log".
See also "/home/axel/tmp/tmp/src/hdf5-build/CMakeFiles/CMakeError.log".

...
-- Check size of __float128
-- Check size of __float128 - done
-- Check size of _Quad
-- Check size of _Quad - failed
CMake Error at config/cmake/ConfigureChecks.cmake:334 (file):
  file failed to open for reading (No such file or directory):

    /home/axel/tmp/tmp/src/hdf5-build/pac_Cconftest.out
Call Stack (most recent call first):
  CMakeLists.txt:464 (include)


-- Testing maximum decimal precision for C - 
-- maximum decimal precision for C var - 0
-- Found Perl: /usr/bin/perl (found version "5.30.0") 
-- ....All Warnings are enabled
-- Configuring incomplete, errors occurred!
See also "/home/axel/tmp/tmp/src/hdf5-build/CMakeFiles/CMakeOutput.log".
See also "/home/axel/tmp/tmp/src/hdf5-build/CMakeFiles/CMakeError.log".

• CMakeOutput.log
• CMakeError.log

[byrnHDF]

Yes that was fixed in development code and will be in the next 1.12.2 release next month.

[scivision]

great, this or similar "pac*.out" error has been a long-standing problem on several platforms and compilers

[sdebionne]

On origin/1.12/master

git cherry-pick aa2f6735fb7b0dbeae52e9478890e81216c63744

works for me (IBM Power9)