HDF5 error while running BuildIt

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karthickmurugan
Posts: 6
Joined: Tue Feb 19, 2019 1:17 pm America/New_York

HDF5 error while running BuildIt

by karthickmurugan » Thu Feb 20, 2020 5:08 am America/New_York

Hi,

i am getting below error while doing BuildIt.

[ 73%] Building C object tools/lib/CMakeFiles/hdf5_tools-static.dir/h5tools_ref.c.o
CMakeFiles/Makefile2:1864: recipe for target 'fortran/src/CMakeFiles/hdf5_f90cstub-shared.dir/all' failed
make[1]: *** [fortran/src/CMakeFiles/hdf5_f90cstub-shared.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 73%] Building C object hl/src/CMakeFiles/hdf5_hl-static.dir/H5PT.c.o
[ 73%] Building C object tools/lib/CMakeFiles/hdf5_tools-static.dir/h5tools_type.c.o
[ 73%] Building C object fortran/src/CMakeFiles/hdf5_f90cstub-static.dir/H5_f.c.o
/home/karthick/seadas/ocssw/opt/src/hdf5/hdf5-1.8.19/fortran/src/H5_f.c: In function ‘h5init_types_c_’:
/home/karthick/seadas/ocssw/opt/src/hdf5/hdf5-1.8.19/fortran/src/H5_f.c:117:16: error: ‘int_1_f’ undeclared (first use in this function)
     if (sizeof(int_1_f) == sizeof(char)) {
                ^
/home/karthick/seadas/ocssw/opt/src/hdf5/hdf5-1.8.19/fortran/src/H5_f.c:117:16: note: each undeclared identifier is reported only once for each function it appears in
/home/karthick/seadas/ocssw/opt/src/hdf5/hdf5-1.8.19/fortran/src/H5_f.c:132:16: error: ‘int_2_f’ undeclared (first use in this function)
     if (sizeof(int_2_f) == sizeof(char)) {
                ^
/home/karthick/seadas/ocssw/opt/src/hdf5/hdf5-1.8.19/fortran/src/H5_f.c:147:16: error: ‘int_4_f’ undeclared (first use in this function)
     if (sizeof(int_4_f) == sizeof(char)) {
                ^
/home/karthick/seadas/ocssw/opt/src/hdf5/hdf5-1.8.19/fortran/src/H5_f.c:162:16: error: ‘int_8_f’ undeclared (first use in this function)
     if (sizeof(int_8_f) == sizeof(char)) {
                ^
/home/karthick/seadas/ocssw/opt/src/hdf5/hdf5-1.8.19/fortran/src/H5_f.c:177:16: error: ‘real_4_f’ undeclared (first use in this function)
     if (sizeof(real_4_f) == sizeof(float)) {
                ^
/home/karthick/seadas/ocssw/opt/src/hdf5/hdf5-1.8.19/fortran/src/H5_f.c:191:16: error: ‘real_8_f’ undeclared (first use in this function)
     if (sizeof(real_8_f) == sizeof(float)) {
                ^
/home/karthick/seadas/ocssw/opt/src/hdf5/hdf5-1.8.19/fortran/src/H5_f.c:205:16: error: ‘real_16_f’ undeclared (first use in this function)
     if (sizeof(real_16_f) == sizeof(float)) {

                ^
fortran/src/CMakeFiles/hdf5_f90cstub-static.dir/build.make:93: recipe for target 'fortran/src/CMakeFiles/hdf5_f90cstub-static.dir/H5_f.c.o' failed
make[2]: *** [fortran/src/CMakeFiles/hdf5_f90cstub-static.dir/H5_f.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
[ 73%] Building C object fortran/src/CMakeFiles/hdf5_f90cstub-static.dir/H5Df.c.o
[ 73%] Building C object tools/lib/CMakeFiles/hdf5_tools-static.dir/h5tools_utils.c.o
[ 73%] Building C object hl/src/CMakeFiles/hdf5_hl-static.dir/H5TB.c.o
[ 73%] Building C object tools/lib/CMakeFiles/hdf5_tools-static.dir/h5trav.c.o
[ 73%] Building C object fortran/src/CMakeFiles/hdf5_f90cstub-static.dir/H5Af.c.o
[ 73%] Building C object tools/lib/CMakeFiles/hdf5_tools-static.dir/io_timer.c.o
[ 73%] Linking C shared library ../../bin/libhdf5_hl.so
[ 73%] Built target hdf5_hl-shared
CMakeFiles/Makefile2:1940: recipe for target 'fortran/src/CMakeFiles/hdf5_f90cstub-static.dir/all' failed
make[1]: *** [fortran/src/CMakeFiles/hdf5_f90cstub-static.dir/all] Error 2
[ 73%] Linking C static library ../../bin/libhdf5_hl.a
[ 73%] Built target hdf5_hl-static
[ 73%] Linking C shared library ../../bin/libhdf5_tools.so
[ 73%] Built target hdf5_tools-shared
[ 73%] Linking C static library ../../bin/libhdf5_tools.a
[ 73%] Built target hdf5_tools-static
Makefile:149: recipe for target 'all' failed
make: *** [all] Error 2
***** make failed *****
***** BuildIt (hdf5) failed *****

Also i already tried by deleting share, lib, include, bin from OCSSWROOT/opt but it is not working.

Kindly help me to rectify this problem.

Tags:

gnwiii
Posts: 606
Joined: Fri Jan 29, 2021 5:51 pm America/New_York
Answers: 1

HDF5 error while running BuildIt

by gnwiii » Thu Feb 20, 2020 10:14 am America/New_York

When a Cmake build has problems you can get more details by running "make -E" in the ""build directory, in your case:

$ cd ~/seadas/ocssw/opt/src/hdf5/hdf5-1.8.19/build
$ make VERBOSE=1


The "int_1_f" type should have been defined in the generated header, "H5f90i.h".  

If you still need help, it could be useful to post details of the platform and compiler used to build hdf5 (from the output of the "BuildIt" command).  You can
run this command in the hdf5 directory with "OCSSW_DEBUG=1" so the build directory isn't deleted and using the "tee" command to save the output to a file:
$ OCSSW_DEBUG=1 ./BuildIt |tee BuildIt.log

karthickmurugan
Posts: 6
Joined: Tue Feb 19, 2019 1:17 pm America/New_York

HDF5 error while running BuildIt

by karthickmurugan » Fri Feb 21, 2020 12:20 am America/New_York

Hi,

Again i facing the same issue. I am using Ubuntu 16.04. i have run OCSSW_DEBUG=1 ./BuildIt |tee BuildIt.log and attached the details below. Please find it (I am adding 2 replies here because of page restrictions)

Post 1

***********************************
********** Building hdf5 **********
***********************************
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/g++
-- Check for working CXX compiler: /usr/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- SOVERSION: 10.2.1
-- SOVERSION_TOOLS: 10.0.4
-- SOVERSION_CXX: 13.0.0
-- SOVERSION_F: 10.0.4
-- SOVERSION_HL: 10.1.1
-- SOVERSION_HL_CXX: 11.1.0
-- SOVERSION_HL_F: 10.0.3
-- Check for STD namespace
-- Check for STD namespace - 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
-- Check if the system is big endian
-- Searching 16 bit integer
-- 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 unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Performing Other Test STDC_HEADERS - Success
-- Looking for include file sys/resource.h
-- Looking for include file sys/resource.h - found
-- Looking for include files sys/resource.h, sys/time.h
-- Looking for include files sys/resource.h, sys/time.h - found
-- Looking for 3 include files sys/resource.h, ..., unistd.h
-- Looking for 3 include files sys/resource.h, ..., unistd.h - found
-- Looking for 4 include files sys/resource.h, ..., sys/ioctl.h
-- Looking for 4 include files sys/resource.h, ..., sys/ioctl.h - found
-- Looking for 5 include files sys/resource.h, ..., sys/stat.h
-- Looking for 5 include files sys/resource.h, ..., sys/stat.h - found
-- Looking for 6 include files sys/resource.h, ..., sys/socket.h
-- Looking for 6 include files sys/resource.h, ..., sys/socket.h - found
-- Looking for 7 include files sys/resource.h, ..., sys/types.h
-- Looking for 7 include files sys/resource.h, ..., sys/types.h - found
-- Looking for 8 include files sys/resource.h, ..., stddef.h
-- Looking for 8 include files sys/resource.h, ..., stddef.h - found
-- Looking for 9 include files sys/resource.h, ..., setjmp.h
-- Looking for 9 include files sys/resource.h, ..., setjmp.h - found
-- Looking for 10 include files sys/resource.h, ..., features.h
-- Looking for 10 include files sys/resource.h, ..., features.h - found
-- Looking for 11 include files sys/resource.h, ..., dirent.h
-- Looking for 11 include files sys/resource.h, ..., dirent.h - found
-- Looking for 12 include files sys/resource.h, ..., stdint.h
-- Looking for 12 include files sys/resource.h, ..., stdint.h - found
-- Looking for C++ include stdint.h
-- Looking for C++ include stdint.h - found
-- Looking for 13 include files sys/resource.h, ..., mach/mach_time.h
-- Looking for 13 include files sys/resource.h, ..., mach/mach_time.h - not found
-- Looking for 13 include files sys/resource.h, ..., io.h
-- Looking for 13 include files sys/resource.h, ..., io.h - not found
-- Looking for 13 include files sys/resource.h, ..., winsock2.h
-- Looking for 13 include files sys/resource.h, ..., winsock2.h - not found
-- Looking for 13 include files sys/resource.h, ..., sys/timeb.h
-- Looking for 13 include files sys/resource.h, ..., sys/timeb.h - found
-- Looking for 14 include files sys/resource.h, ..., globus/common.h
-- Looking for 14 include files sys/resource.h, ..., globus/common.h - not found
-- Looking for 14 include files sys/resource.h, ..., pdb.h
-- Looking for 14 include files sys/resource.h, ..., pdb.h - not found
-- Looking for 14 include files sys/resource.h, ..., pthread.h
-- Looking for 14 include files sys/resource.h, ..., pthread.h - found
-- Looking for 15 include files sys/resource.h, ..., srbclient.h
-- Looking for 15 include files sys/resource.h, ..., srbclient.h - not found
-- Looking for 15 include files sys/resource.h, ..., string.h
-- Looking for 15 include files sys/resource.h, ..., string.h - found
-- Looking for 16 include files sys/resource.h, ..., strings.h
-- Looking for 16 include files sys/resource.h, ..., strings.h - found
-- Looking for 17 include files sys/resource.h, ..., stdlib.h
-- Looking for 17 include files sys/resource.h, ..., stdlib.h - found
-- Looking for 18 include files sys/resource.h, ..., memory.h
-- Looking for 18 include files sys/resource.h, ..., memory.h - found
-- Looking for 19 include files sys/resource.h, ..., dlfcn.h
-- Looking for 19 include files sys/resource.h, ..., dlfcn.h - found
-- Looking for 20 include files sys/resource.h, ..., inttypes.h
-- Looking for 20 include files sys/resource.h, ..., inttypes.h - found
-- Looking for 21 include files sys/resource.h, ..., netinet/in.h
-- Looking for 21 include files sys/resource.h, ..., netinet/in.h - found
-- Performing TEST_LFS_WORKS... yes
-- Performing Other Test HAVE_OFF64_T - Success
-- Looking for lseek64
-- Looking for lseek64 - found
-- Looking for fseeko64
-- Looking for fseeko64 - found
-- Looking for ftello64
-- Looking for ftello64 - found
-- Looking for ftruncate64
-- Looking for ftruncate64 - found
-- Looking for fseeko
-- Looking for fseeko - found
-- Looking for ftello
-- Looking for ftello - found
-- Performing Other Test HAVE_STAT64_STRUCT - Success
-- Looking for fstat64
-- Looking for fstat64 - found
-- Looking for stat64
-- Looking for stat64 - 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
-- Looking for 22 include files sys/resource.h, ..., stdbool.h
-- Looking for 22 include files sys/resource.h, ..., stdbool.h - found
-- Check size of _Bool
-- Check size of _Bool - done
-- Performing Other Test DEV_T_IS_SCALAR - Success
-- Looking for CLOCK_MONOTONIC
-- Looking for CLOCK_MONOTONIC - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Performing Other Test HAVE_TM_GMTOFF - Success
-- Performing Other Test HAVE___TM_GMTOFF - Failed
-- Performing Other Test HAVE_STRUCT_TIMEZONE - Success
-- Performing Other Test GETTIMEOFDAY_GIVES_TZ - Success
-- Performing Other Test TIME_WITH_SYS_TIME - Success
-- Performing Other Test HAVE_TM_ZONE - Failed
-- Performing Other Test HAVE_STRUCT_TM_TM_ZONE - Failed
-- Performing Other Test HAVE_TIMEZONE - Success
-- Performing Other Test HAVE_STAT_ST_BLOCKS - Success
-- Looking for ioctl
-- Looking for ioctl - found
-- Performing Other Test HAVE_STRUCT_VIDEOCONFIG - Failed
-- Performing Other Test 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 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 lstat
-- Looking for lstat - found
-- Looking for rand_r
-- Looking for rand_r - found
-- Looking for random
-- Looking for random - 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 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
-- Performing Other Test VSNPRINTF_WORKS - Success
-- Looking for sigsetjmp
-- Looking for sigsetjmp - found
-- Performing Other Test HAVE_ATTRIBUTE - Success
-- Performing Other Test HAVE_C99_FUNC - Success
-- Performing Other Test HAVE_FUNCTION - Success
-- Performing Other Test HAVE_C99_DESIGNATED_INITIALIZER - Success
-- Performing Other Test SYSTEM_SCOPE_THREADS - Success
-- Performing Other Test HAVE_SOCKLEN_T - Success
-- Performing Other Test CXX_HAVE_OFFSETOF - Success
-- Performing CXX Test OLD_HEADER_FILENAME - Failed
-- Performing CXX Test H5_NO_NAMESPACE - Failed
-- Performing CXX Test H5_NO_STD - Failed
-- Performing CXX Test BOOL_NOTDEFINED - Failed
-- Performing CXX Test NO_STATIC_CAST - Failed
-- Performing Other Test HAVE_INLINE - Success
-- Performing Other Test HAVE___INLINE__ - Success
-- Performing Other Test HAVE___INLINE - Success
-- Checking for appropriate format for 64 bit long:
-- Checking for appropriate format for 64 bit long: found "l"
-- 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
-- Performing Other Test HAVE_DIRECT - Success
-- Checking IF your system converts long double to (unsigned) long values with special algorithm... no
-- Checking IF your system can convert (unsigned) long to long double values with special algorithm... no
-- Checking IF correctly converting long double to (unsigned) long long values... yes
-- Checking IF correctly converting (unsigned) long long to long double values... yes
-- Checking IF alignment restrictions are strictly enforced... yes
-- Found ZLIB: /home/karthick/anaconda2/lib/libz.so (found version "1.2.11")
-- Filter ZLIB is ON
-- The Fortran compiler identification is GNU 5.4.0
-- Check for working Fortran compiler: /usr/bin/gfortran
-- Check for working Fortran compiler: /usr/bin/gfortran  -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/bin/gfortran supports Fortran 90
-- Checking whether /usr/bin/gfortran supports Fortran 90 -- yes
-- Detecting Fortran/C Interface
-- Detecting Fortran/C Interface - Found GLOBAL and MODULE mangling
-- Testing Fortran sizeof
-- Testing Fortran sizeof - OK
-- Testing Fortran c_sizeof
-- Testing Fortran c_sizeof - OK
-- Testing Fortran storage_size
-- Testing Fortran storage_size - OK
-- Testing Fortran ISO_FORTRAN_ENV
-- Testing Fortran ISO_FORTRAN_ENV - OK
-- Testing Fortran RealIsNotDouble
-- Testing Fortran RealIsNotDouble - OK
-- Testing Fortran iso_c_binding
-- Testing Fortran iso_c_binding - OK
-- Configuring done
-- Generating done
-- Build files have been written to: /home/karthick/seadas/ocssw/opt/src/hdf5/hdf5-1.8.18/build
Scanning dependencies of target H5test_FortranHavekind-shared
Scanning dependencies of target H5test_FortranHavekind
Scanning dependencies of target zip_perf_files
Scanning dependencies of target H5make_libsettings

karthickmurugan
Posts: 6
Joined: Tue Feb 19, 2019 1:17 pm America/New_York

HDF5 error while running BuildIt

by karthickmurugan » Fri Feb 21, 2020 12:23 am America/New_York

Post 2

Scanning dependencies of target H5detect

[ 47%] Building C object src/CMakeFiles/hdf5-static.dir/H5RC.c.o
[ 47%] Building C object src/CMakeFiles/hdf5-shared.dir/H5Orefcount.c.o
[ 47%] Building C object src/CMakeFiles/hdf5-static.dir/H5S.c.o
[ 47%] Building C object src/CMakeFiles/hdf5-static.dir/H5RS.c.o
[ 48%] Building C object src/CMakeFiles/hdf5-shared.dir/H5Osdspace.c.o
[ 48%] Building C object src/CMakeFiles/hdf5-shared.dir/H5Oshared.c.o
[ 48%] Building C object src/CMakeFiles/hdf5-static.dir/H5Sdbg.c.o
[ 48%] Building C object src/CMakeFiles/hdf5-static.dir/H5Sall.c.o
[ 48%] Building C object src/CMakeFiles/hdf5-shared.dir/H5Oshmesg.c.o
[ 48%] Building C object src/CMakeFiles/hdf5-shared.dir/H5Ostab.c.o
[ 48%] Building C object src/CMakeFiles/hdf5-shared.dir/H5Otest.c.o
[ 49%] Building C object src/CMakeFiles/hdf5-static.dir/H5Shyper.c.o
[ 49%] Building C object src/CMakeFiles/hdf5-shared.dir/H5Ounknown.c.o
[ 49%] Building C object src/CMakeFiles/hdf5-static.dir/H5Smpio.c.o
[ 49%] Building C object src/CMakeFiles/hdf5-static.dir/H5Snone.c.o
[ 49%] Building C object src/CMakeFiles/hdf5-static.dir/H5Spoint.c.o
[ 49%] Building C object src/CMakeFiles/hdf5-shared.dir/H5P.c.o
[ 49%] Building C object src/CMakeFiles/hdf5-static.dir/H5Sselect.c.o
[ 50%] Building C object src/CMakeFiles/hdf5-shared.dir/H5Pacpl.c.o
[ 50%] Building C object src/CMakeFiles/hdf5-static.dir/H5Stest.c.o
[ 50%] Building C object src/CMakeFiles/hdf5-shared.dir/H5Pdeprec.c.o
[ 50%] Building C object src/CMakeFiles/hdf5-shared.dir/H5Pdapl.c.o
[ 50%] Building C object src/CMakeFiles/hdf5-shared.dir/H5Pdcpl.c.o
[ 50%] Building C object src/CMakeFiles/hdf5-static.dir/H5SM.c.o
[ 50%] Building C object src/CMakeFiles/hdf5-static.dir/H5SMbtree2.c.o
[ 50%] Building C object src/CMakeFiles/hdf5-shared.dir/H5Pdxpl.c.o
[ 50%] Building C object src/CMakeFiles/hdf5-shared.dir/H5Pfapl.c.o
[ 50%] Building C object src/CMakeFiles/hdf5-shared.dir/H5Pfcpl.c.o
[ 50%] Building C object src/CMakeFiles/hdf5-shared.dir/H5Pfmpl.c.o
[ 51%] Building C object src/CMakeFiles/hdf5-static.dir/H5SMcache.c.o
[ 51%] Building C object src/CMakeFiles/hdf5-shared.dir/H5Pint.c.o
[ 52%] Building C object src/CMakeFiles/hdf5-shared.dir/H5Pgcpl.c.o
[ 52%] Building C object src/CMakeFiles/hdf5-shared.dir/H5Plapl.c.o
[ 52%] Building C object src/CMakeFiles/hdf5-static.dir/H5SMmessage.c.o
[ 52%] Building C object src/CMakeFiles/hdf5-static.dir/H5SMtest.c.o
[ 52%] Building C object src/CMakeFiles/hdf5-static.dir/H5T.c.o
[ 52%] Building C object src/CMakeFiles/hdf5-shared.dir/H5Plcpl.c.o
[ 52%] Building C object src/CMakeFiles/hdf5-static.dir/H5Tarray.c.o
[ 52%] Building C object src/CMakeFiles/hdf5-shared.dir/H5Pocpl.c.o
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[ 69%] Linking C static library ../bin/libhdf5.a
[ 69%] Built target hdf5-static
[ 69%] Generating ../H5f90i_gen.h, ../H5fortran_types.f90
Scanning dependencies of target hdf5_hl-static
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[ 69%] Building C object hl/src/CMakeFiles/hdf5_hl-static.dir/H5LT.c.o
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[ 70%] Building C object hl/src/CMakeFiles/hdf5_hl-static.dir/H5LTanalyze.c.o
Scanning dependencies of target hdf5_f90cstub-static
[ 70%] Building C object tools/lib/CMakeFiles/hdf5_tools-static.dir/h5diff.c.o
[ 70%] Building C object hl/src/CMakeFiles/hdf5_hl-static.dir/H5PT.c.o
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[ 73%] Building C object fortran/src/CMakeFiles/hdf5_f90cstub-static.dir/H5Lf.c.o
fortran/src/CMakeFiles/hdf5_f90cstub-static.dir/build.make:93: recipe for target 'fortran/src/CMakeFiles/hdf5_f90cstub-static.dir/H5_f.c.o' failed
CMakeFiles/Makefile2:1700: recipe for target 'fortran/src/CMakeFiles/hdf5_f90cstub-static.dir/all' failed
[ 73%] Linking C static library ../../bin/libhdf5_hl.a
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[ 73%] Linking C static library ../../bin/libhdf5_tools.a
[ 73%] Built target hdf5_tools-static
Makefile:149: recipe for target 'all' failed
***** make failed *****

gnwiii
Posts: 606
Joined: Fri Jan 29, 2021 5:51 pm America/New_York
Answers: 1

HDF5 error while running BuildIt

by gnwiii » Fri Feb 21, 2020 7:33 am America/New_York

The key bits from the BuiltIt output are:

***********************************
********** Building hdf5 **********
***********************************
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/g++
-- Check for working CXX compiler: /usr/bin/g++ -- works
[...]
-- The Fortran compiler identification is GNU 5.4.0
-- Check for working Fortran compiler: /usr/bin/gfortran
-- Check for working Fortran compiler: /usr/bin/gfortran  -- works
[...]
[ 73%] Building C object fortran/src/CMakeFiles/hdf5_f90cstub-static.dir/H5Lf.c.o
fortran/src/CMakeFiles/hdf5_f90cstub-static.dir/build.make:93: recipe for target 'fortran/src/CMakeFiles/hdf5_f90cstub-static.dir/H5_f.c.o' failed
CMakeFiles/Makefile2:1700: recipe for target 'fortran/src/CMakeFiles/hdf5_f90cstub-static.dir/all' failed
[ 73%] Linking C static library ../../bin/libhdf5_hl.a
[ 73%] Built target hdf5_hl-static
[ 73%] Built target hdf5-shared
[ 73%] Linking C static library ../../bin/libhdf5_tools.a
[ 73%] Built target hdf5_tools-static
Makefile:149: recipe for target 'all' failed
***** make failed *****


The HDF5 1.8.18 Release Notes indicate that your distro and compiler combination has been tested:
Ubuntu 16.04 4.4.0-38-generic #62-Ubuntu SMP x86_64 GNU/Linux
                                  gcc (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0
                                  GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0
                                  (cmake and autotools)


The same combination has worked for me in the past, but for an older OCSSW version.  

The next step is to get the more detailed make VERBOSE=1 results (I misremembered this as make -E).

I fired up an Ubuntu 16.04 VM and ran the BuildIt script in the hdf5 directory after renaming $OCSSWROOT/opt/lib/libgfortran.so.3 (because it conflicts with the system's libgfortran.so.3.0.0).  Note that $OCSSWROOT/opt/README.md says: You may want to remove $OCSSWROOT/opt/bin, $OCSSWROOT/opt/lib, and $OCSSWROOT/opt/include.  I have attached the hdf5/BuildIt output.   Comparing this to the failing results might provide a hint to the reason the build on your system is failing.
attachment 1

gfireman
Posts: 59
Joined: Thu Jan 07, 2010 2:59 pm America/New_York

HDF5 error while running BuildIt

by gfireman » Mon Feb 24, 2020 11:10 am America/New_York

Please, PLEASE submit large files as attachments!  Including them in message text is visual clutter and makes the forum hard to read.

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