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[netCDF #HYF-949395]: Error during "make"

Good morning,

NetCDF 4.1.3 is an old, outdated version of the netcdf library.  I will do my 
best to assist you with your error, however.  It appears that you do not have 
libhdf5 installed on your system.  If you intend to work with netcdf4 data 
files/data models, you will need to install hdf5 from the hdfgroup.  If you 
will not be working with netcdf4 data/models, you can turn netcdf4 off by 
passing the '--disable-netcdf4` argument when you run 'configure'.

I hope this helps,

-Ward

> Dear Sir
> 
> I am encountering the following error during "make" for netcdf-4.1.3
> Please find the attached config.log file.
> 
> checking for inttypes.h... yes
> checking for stdint.h... yes
> checking for unistd.h... yes
> checking for dlfcn.h... yes
> checking for objdir... .libs
> checking if gcc supports -fno-rtti -fno-exceptions... no
> checking for gcc option to produce PIC... -fPIC -DPIC
> checking if gcc PIC flag -fPIC -DPIC works... yes
> checking if gcc static flag -static works... yes
> checking if gcc supports -c -o file.o... yes
> checking if gcc supports -c -o file.o... (cached) yes
> checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared
> libraries... yes
> checking whether -lc should be explicitly linked in... no
> checking dynamic linker characteristics... GNU/Linux ld.so
> checking how to hardcode library paths into programs... immediate
> checking whether stripping libraries is possible... yes
> checking if libtool supports shared libraries... yes
> checking whether to build shared libraries... yes
> checking whether to build static libraries... yes
> checking how to run the C++ preprocessor... g++ -E
> checking for ld used by g++... /usr/bin/ld -m elf_x86_64
> checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
> checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared
> libraries... yes
> checking for g++ option to produce PIC... -fPIC -DPIC
> checking if g++ PIC flag -fPIC -DPIC works... yes
> checking if g++ static flag -static works... yes
> checking if g++ supports -c -o file.o... yes
> checking if g++ supports -c -o file.o... (cached) yes
> checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared
> libraries... yes
> checking dynamic linker characteristics... (cached) GNU/Linux ld.so
> checking how to hardcode library paths into programs... immediate
> checking if libtool supports shared libraries... yes
> checking whether to build shared libraries... yes
> checking whether to build static libraries... yes
> checking for /usr/bin/gfortran option to produce PIC... -fPIC
> checking if /usr/bin/gfortran PIC flag -fPIC works... yes
> checking if /usr/bin/gfortran static flag -static works... yes
> checking if /usr/bin/gfortran supports -c -o file.o... yes
> checking if /usr/bin/gfortran supports -c -o file.o... (cached) yes
> checking whether the /usr/bin/gfortran linker (/usr/bin/ld -m elf_x86_64)
> supports shared libraries... yes
> checking dynamic linker characteristics... (cached) GNU/Linux ld.so
> checking how to hardcode library paths into programs... immediate
> checking if libtool supports shared libraries... yes
> checking whether to build shared libraries... yes
> checking whether to build static libraries... yes
> checking for /usr/bin/gfortran option to produce PIC... -fPIC
> checking if /usr/bin/gfortran PIC flag -fPIC works... yes
> checking if /usr/bin/gfortran static flag -static works... yes
> checking if /usr/bin/gfortran supports -c -o file.o... yes
> checking if /usr/bin/gfortran supports -c -o file.o... (cached) yes
> checking whether the /usr/bin/gfortran linker (/usr/bin/ld -m elf_x86_64)
> supports shared libraries... yes
> checking dynamic linker characteristics... (cached) GNU/Linux ld.so
> checking how to hardcode library paths into programs... immediate
> configure: finding other utilities
> configure: trying to set fortran flags for this platform
> checking for special C compiler options needed for large files... no
> checking for _FILE_OFFSET_BITS value needed for large files... no
> configure: displaying some results
> checking CPPFLAGS...
> checking CC CFLAGS... gcc -g -O2
> checking type gcc... gcc is /usr/bin/gcc
> checking CXX... g++
> checking CXXFLAGS... -g -O2
> checking type g++... g++ is /usr/bin/g++
> checking FC... /usr/bin/gfortran
> checking FFLAGS... -g -O2
> checking type /usr/bin/gfortran... /usr/bin/gfortran is /usr/bin/gfortran
> checking F90... /usr/bin/gfortran
> checking FCFLAGS... -g -O2
> checking type /usr/bin/gfortran... /usr/bin/gfortran is /usr/bin/gfortran
> checking AR... ar
> checking AR_FLAGS... cru
> checking type ar... ar is /usr/bin/ar
> checking NM... /usr/bin/nm -B
> checking NMFLAGS...
> checking for /usr/bin/nm... /usr/bin/nm -B
> checking nm flags...
> checking for C-equivalent to Fortran routine "SUB"... sub_
> checking for Fortran "byte"... yes
> checking for Fortran "integer*2"... yes
> checking if Fortran "byte" is C "signed char"... yes
> checking if Fortran "byte" is C "short"... no
> checking if Fortran "byte" is C "int"... no
> checking if Fortran "byte" is C "long"... no
> checking if Fortran "integer*2" is C "short"... yes
> checking if Fortran "integer*2" is C "int"... no
> checking if Fortran "integer*2" is C "long"... no
> checking if Fortran "integer" is C "int"... yes
> checking if Fortran "real" is C "float"... yes
> checking if Fortran "doubleprecision" is C "double"... yes
> checking for Fortran-equivalent to netCDF "byte"... byte
> checking for Fortran-equivalent to netCDF "short"... integer*2
> checking if Fortran 90 compiler capitalizes .mod filenames... no
> configure: checking types, headers, and functions
> checking for stdlib.h... (cached) yes
> checking for sys/types.h... (cached) yes
> checking for dirent.h that defines DIR... yes
> checking for library containing opendir... none required
> checking for ANSI C header files... (cached) yes
> checking for sys/wait.h that is POSIX.1 compatible... yes
> checking whether time.h and sys/time.h may both be included... yes
> checking locale.h usability... yes
> checking locale.h presence... yes
> checking for locale.h... yes
> checking stdio.h usability... yes
> checking stdio.h presence... yes
> checking for stdio.h... yes
> checking stdarg.h usability... yes
> checking stdarg.h presence... yes
> checking for stdarg.h... yes
> checking errno.h usability... yes
> checking errno.h presence... yes
> checking for errno.h... yes
> checking ctype.h usability... yes
> checking ctype.h presence... yes
> checking for ctype.h... yes
> checking fcntl.h usability... yes
> checking fcntl.h presence... yes
> checking for fcntl.h... yes
> checking malloc.h usability... yes
> checking malloc.h presence... yes
> checking for malloc.h... yes
> checking for stdlib.h... (cached) yes
> checking for string.h... (cached) yes
> checking for strings.h... (cached) yes
> checking for unistd.h... (cached) yes
> checking for sys/stat.h... (cached) yes
> checking getopt.h usability... yes
> checking getopt.h presence... yes
> checking for getopt.h... yes
> checking sys/time.h usability... yes
> checking sys/time.h presence... yes
> checking for sys/time.h... yes
> checking sys/resource.h usability... yes
> checking sys/resource.h presence... yes
> checking for sys/resource.h... yes
> checking for vprintf... yes
> checking for _doprnt... no
> checking for stdbool.h that conforms to C99... yes
> checking for _Bool... yes
> checking for strlcat... no
> checking for strerror... yes
> checking for snprintf... yes
> checking for strchr... yes
> checking for strrchr... yes
> checking for mktemp... yes
> checking for strcat... yes
> checking for strcpy... yes
> checking for strdup... yes
> checking for strcasecmp... yes
> checking for strtod... yes
> checking for strtoll... yes
> checking for strtoull... yes
> checking for getrlimit... yes
> checking for gettimeofday... yes
> checking for fsync... yes
> checking for MPI_Comm_f2c... no
> checking for size_t... yes
> checking for working alloca.h... yes
> checking for alloca... yes
> checking whether isnan is declared... yes
> checking whether isinf is declared... yes
> checking whether isfinite is declared... yes
> checking whether signbit is declared... yes
> checking for struct stat.st_blksize... yes
> checking for IEEE floating point format... yes
> checking for size_t... (cached) yes
> checking for off_t... yes
> checking for ssize_t... yes
> checking for ptrdiff_t... yes
> checking for uchar... no
> checking for longlong... no
> checking whether char is unsigned... no
> checking whether byte ordering is bigendian... no
> checking size of short... 2
> checking size of int... 4
> checking size of long... 8
> checking size of float... 4
> checking size of double... 8
> checking size of off_t... 8
> checking size of size_t... 8
> checking for library containing deflate... -lz
> checking for floor in -lm... yes
> checking for library containing H5Fflush... no
> configure: error: Can't find or link to the hdf5 library. Use
> --disable-netcdf-4, or see config.log for errors.
> iitgn@iitgn-OptiPlex-9020:~/Downloads/netcdf-4.1.3$ FC=/usr/bin/gfortran
> F77=/usr/bin/gfortran ./configure --with-hdf5=/usr/local/bin
> --with-zlib=/usr/local/bin --prefix=/usr/local/bin/netcdf-4.1.3
> --enable-shared --enable-static --enable-fortran
> configure: netCDF 4.1.3
> checking build system type... x86_64-unknown-linux-gnu
> checking host system type... x86_64-unknown-linux-gnu
> checking target system type... x86_64-unknown-linux-gnu
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether build environment is sane... yes
> checking for a thread-safe mkdir -p... /bin/mkdir -p
> checking for gawk... no
> checking for mawk... mawk
> checking whether make sets $(MAKE)... yes
> configure: checking user options
> checking whether CXX is set to ''... no
> checking whether FC is set to ''... no
> checking whether F90 is set to ''... no
> checking whether a NCIO_MINBLOCKSIZE was specified... 256
> checking whether udunits is to be built... no
> checking if fsync support is enabled... yes
> checking whether extra valgrind tests should be run... no
> checking whether we should try to build netCDF-4... yes
> checking whether libcf is to be built... no
> checking whether reading of HDF4 SD files is to be enabled... no
> checking whether to fetch some sample HDF4 files from Unidata ftp site to
> test HDF4 reading (requires wget)... no
> checking whether parallel I/O for classic and 64-bit offset files using
> parallel-netcdf is to be enabled... no
> checking whether new netCDF-4 C++ API is to be built... no
> checking whether extra example tests should be run... no
> checking whether parallel IO tests should be run... no
> checking whether a default chunk size in bytes was specified... 4194304
> checking whether a maximum per-variable cache size for HDF5 was
> specified... 67108864
> checking whether a number of chunks for the default per-variable cache was
> specified... 10
> checking whether a default file cache size for HDF5 was specified... 4194304
> checking whether a default file cache maximum number of elements for HDF5
> was specified... 1009
> checking whether a default cache preemption for HDF5 was specified... 0.75
> checking whether netCDF-4 logging is enabled... no
> checking whether cdmremote client is to be built... no
> checking whether DAP client is to be built... yes
> checking for style of include used by make... GNU
> checking for gcc... gcc
> checking whether the C compiler works... yes
> checking for C compiler default output file name... a.out
> checking for suffix of executables...
> checking whether we are cross compiling... no
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ISO C89... none needed
> checking dependency style of gcc... gcc3
> checking for curl_easy_setopt in -lcurl... no
> configure: libcurl not found; disabling dap and cdmremote support
> checking whether dap remote testing should be enabled (default on)... no
> checking whether the time-consuming dap tests should be enabled (default
> off)... no
> checking whether netCDF extra tests should be run (developers only)... no
> checking whether FFIO will be used... no
> checking whether to skip C++, F77, or F90 APIs if compiler is broken... yes
> checking whether examples should be built... yes
> checking whether F77 API is desired... yes
> checking whether any Fortran API is desired... yes
> checking whether F90 API is desired... yes
> checking whether fortran type sizes should be checked... yes
> checking whether CXX API is desired... yes
> checking whether v2 netCDF API should be built... yes
> checking whether the ncgen/ncdump/nccopy should be built... yes
> checking whether large file (> 2GB) tests should be run... no
> checking whether benchmaks should be run (experimental)... no
> checking whether extreme numbers should be used in tests... yes
> checking where to put large temp files if large file tests are run... .
> checking whether a win32 DLL is desired... no
> configure: finding C compiler
> checking for gcc... (cached) gcc
> checking whether we are using the GNU C compiler... (cached) yes
> checking whether gcc accepts -g... (cached) yes
> checking for gcc option to accept ISO C89... (cached) none needed
> checking dependency style of gcc... (cached) gcc3
> checking whether gcc and cc understand -c and -o together... yes
> checking for an ANSI C-conforming const... yes
> checking whether a CURLOPT_KEYPASSWD is defined... no
> configure: finding Fortran compiler (will not be used if Fortran API is not
> desired)
> checking whether we are using the GNU Fortran compiler... yes
> checking whether /usr/bin/gfortran accepts -g... yes
> checking whether we are using the GNU Fortran 77 compiler... yes
> checking whether /usr/bin/gfortran accepts -g... yes
> configure: setting up Fortran 90
> checking what FC is set to... /usr/bin/gfortran
> checking for Fortran flag to compile .f90 files... none
> checking fortran 90 modules inclusion flag... -I
> configure: finding C++ compiler (will not be used if C++ API is not desired)
> checking for g++... g++
> checking whether we are using the GNU C++ compiler... yes
> checking whether g++ accepts -g... yes
> checking dependency style of g++... gcc3
> configure: setting up libtool
> checking how to print strings... printf
> checking for a sed that does not truncate output... /bin/sed
> checking for grep that handles long lines and -e... /bin/grep
> checking for egrep... /bin/grep -E
> checking for fgrep... /bin/grep -F
> checking for ld used by gcc... /usr/bin/ld
> checking if the linker (/usr/bin/ld) is GNU ld... yes
> checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
> checking the name lister (/usr/bin/nm -B) interface... BSD nm
> checking whether ln -s works... yes
> checking the maximum length of command line arguments... 1572864
> checking whether the shell understands some XSI constructs... yes
> checking whether the shell understands "+="... yes
> checking how to convert x86_64-unknown-linux-gnu file names to
> x86_64-unknown-linux-gnu format... func_convert_file_noop
> checking how to convert x86_64-unknown-linux-gnu file names to toolchain
> format... func_convert_file_noop
> checking for /usr/bin/ld option to reload object files... -r
> checking for objdump... objdump
> checking how to recognize dependent libraries... pass_all
> checking for dlltool... no
> checking how to associate runtime and link libraries... printf %s\n
> checking for ar... ar
> checking for archiver @FILE support... @
> checking for strip... strip
> checking for ranlib... ranlib
> checking command to parse /usr/bin/nm -B output from gcc object... ok
> checking for sysroot... no
> checking for mt... mt
> checking if mt is a manifest tool... no
> checking how to run the C preprocessor... gcc -E
> checking for ANSI C header files... yes
> checking for sys/types.h... yes
> checking for sys/stat.h... yes
> checking for stdlib.h... yes
> checking for string.h... yes
> checking for memory.h... yes
> checking for strings.h... yes
> checking for inttypes.h... yes
> checking for stdint.h... yes
> checking for unistd.h... yes
> checking for dlfcn.h... yes
> checking for objdir... .libs
> checking if gcc supports -fno-rtti -fno-exceptions... no
> checking for gcc option to produce PIC... -fPIC -DPIC
> checking if gcc PIC flag -fPIC -DPIC works... yes
> checking if gcc static flag -static works... yes
> checking if gcc supports -c -o file.o... yes
> checking if gcc supports -c -o file.o... (cached) yes
> checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared
> libraries... yes
> checking whether -lc should be explicitly linked in... no
> checking dynamic linker characteristics... GNU/Linux ld.so
> checking how to hardcode library paths into programs... immediate
> checking whether stripping libraries is possible... yes
> checking if libtool supports shared libraries... yes
> checking whether to build shared libraries... yes
> checking whether to build static libraries... yes
> checking how to run the C++ preprocessor... g++ -E
> checking for ld used by g++... /usr/bin/ld -m elf_x86_64
> checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
> checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared
> libraries... yes
> checking for g++ option to produce PIC... -fPIC -DPIC
> checking if g++ PIC flag -fPIC -DPIC works... yes
> checking if g++ static flag -static works... yes
> checking if g++ supports -c -o file.o... yes
> checking if g++ supports -c -o file.o... (cached) yes
> checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared
> libraries... yes
> checking dynamic linker characteristics... (cached) GNU/Linux ld.so
> checking how to hardcode library paths into programs... immediate
> checking if libtool supports shared libraries... yes
> checking whether to build shared libraries... yes
> checking whether to build static libraries... yes
> checking for /usr/bin/gfortran option to produce PIC... -fPIC
> checking if /usr/bin/gfortran PIC flag -fPIC works... yes
> checking if /usr/bin/gfortran static flag -static works... yes
> checking if /usr/bin/gfortran supports -c -o file.o... yes
> checking if /usr/bin/gfortran supports -c -o file.o... (cached) yes
> checking whether the /usr/bin/gfortran linker (/usr/bin/ld -m elf_x86_64)
> supports shared libraries... yes
> checking dynamic linker characteristics... (cached) GNU/Linux ld.so
> checking how to hardcode library paths into programs... immediate
> checking if libtool supports shared libraries... yes
> checking whether to build shared libraries... yes
> checking whether to build static libraries... yes
> checking for /usr/bin/gfortran option to produce PIC... -fPIC
> checking if /usr/bin/gfortran PIC flag -fPIC works... yes
> checking if /usr/bin/gfortran static flag -static works... yes
> checking if /usr/bin/gfortran supports -c -o file.o... yes
> checking if /usr/bin/gfortran supports -c -o file.o... (cached) yes
> checking whether the /usr/bin/gfortran linker (/usr/bin/ld -m elf_x86_64)
> supports shared libraries... yes
> checking dynamic linker characteristics... (cached) GNU/Linux ld.so
> checking how to hardcode library paths into programs... immediate
> configure: finding other utilities
> configure: trying to set fortran flags for this platform
> checking for special C compiler options needed for large files... no
> checking for _FILE_OFFSET_BITS value needed for large files... no
> configure: displaying some results
> checking CPPFLAGS...
> checking CC CFLAGS... gcc -g -O2
> checking type gcc... gcc is /usr/bin/gcc
> checking CXX... g++
> checking CXXFLAGS... -g -O2
> checking type g++... g++ is /usr/bin/g++
> checking FC... /usr/bin/gfortran
> checking FFLAGS... -g -O2
> checking type /usr/bin/gfortran... /usr/bin/gfortran is /usr/bin/gfortran
> checking F90... /usr/bin/gfortran
> checking FCFLAGS... -g -O2
> checking type /usr/bin/gfortran... /usr/bin/gfortran is /usr/bin/gfortran
> checking AR... ar
> checking AR_FLAGS... cru
> checking type ar... ar is /usr/bin/ar
> checking NM... /usr/bin/nm -B
> checking NMFLAGS...
> checking for /usr/bin/nm... /usr/bin/nm -B
> checking nm flags...
> checking for C-equivalent to Fortran routine "SUB"... sub_
> checking for Fortran "byte"... yes
> checking for Fortran "integer*2"... yes
> checking if Fortran "byte" is C "signed char"... yes
> checking if Fortran "byte" is C "short"... no
> checking if Fortran "byte" is C "int"... no
> checking if Fortran "byte" is C "long"... no
> checking if Fortran "integer*2" is C "short"... yes
> checking if Fortran "integer*2" is C "int"... no
> checking if Fortran "integer*2" is C "long"... no
> checking if Fortran "integer" is C "int"... yes
> checking if Fortran "real" is C "float"... yes
> checking if Fortran "doubleprecision" is C "double"... yes
> checking for Fortran-equivalent to netCDF "byte"... byte
> checking for Fortran-equivalent to netCDF "short"... integer*2
> checking if Fortran 90 compiler capitalizes .mod filenames... no
> configure: checking types, headers, and functions
> checking for stdlib.h... (cached) yes
> checking for sys/types.h... (cached) yes
> checking for dirent.h that defines DIR... yes
> checking for library containing opendir... none required
> checking for ANSI C header files... (cached) yes
> checking for sys/wait.h that is POSIX.1 compatible... yes
> checking whether time.h and sys/time.h may both be included... yes
> checking locale.h usability... yes
> checking locale.h presence... yes
> checking for locale.h... yes
> checking stdio.h usability... yes
> checking stdio.h presence... yes
> checking for stdio.h... yes
> checking stdarg.h usability... yes
> checking stdarg.h presence... yes
> checking for stdarg.h... yes
> checking errno.h usability... yes
> checking errno.h presence... yes
> checking for errno.h... yes
> checking ctype.h usability... yes
> checking ctype.h presence... yes
> checking for ctype.h... yes
> checking fcntl.h usability... yes
> checking fcntl.h presence... yes
> checking for fcntl.h... yes
> checking malloc.h usability... yes
> checking malloc.h presence... yes
> checking for malloc.h... yes
> checking for stdlib.h... (cached) yes
> checking for string.h... (cached) yes
> checking for strings.h... (cached) yes
> checking for unistd.h... (cached) yes
> checking for sys/stat.h... (cached) yes
> checking getopt.h usability... yes
> checking getopt.h presence... yes
> checking for getopt.h... yes
> checking sys/time.h usability... yes
> checking sys/time.h presence... yes
> checking for sys/time.h... yes
> checking sys/resource.h usability... yes
> checking sys/resource.h presence... yes
> checking for sys/resource.h... yes
> checking for vprintf... yes
> checking for _doprnt... no
> checking for stdbool.h that conforms to C99... yes
> checking for _Bool... yes
> checking for strlcat... no
> checking for strerror... yes
> checking for snprintf... yes
> checking for strchr... yes
> checking for strrchr... yes
> checking for mktemp... yes
> checking for strcat... yes
> checking for strcpy... yes
> checking for strdup... yes
> checking for strcasecmp... yes
> checking for strtod... yes
> checking for strtoll... yes
> checking for strtoull... yes
> checking for getrlimit... yes
> checking for gettimeofday... yes
> checking for fsync... yes
> checking for MPI_Comm_f2c... no
> checking for size_t... yes
> checking for working alloca.h... yes
> checking for alloca... yes
> checking whether isnan is declared... yes
> checking whether isinf is declared... yes
> checking whether isfinite is declared... yes
> checking whether signbit is declared... yes
> checking for struct stat.st_blksize... yes
> checking for IEEE floating point format... yes
> checking for size_t... (cached) yes
> checking for off_t... yes
> checking for ssize_t... yes
> checking for ptrdiff_t... yes
> checking for uchar... no
> checking for longlong... no
> checking whether char is unsigned... no
> checking whether byte ordering is bigendian... no
> checking size of short... 2
> checking size of int... 4
> checking size of long... 8
> checking size of float... 4
> checking size of double... 8
> checking size of off_t... 8
> checking size of size_t... 8
> checking for library containing deflate... -lz
> checking for floor in -lm... yes
> checking for library containing H5Fflush... no
> configure: error: Can't find or link to the hdf5 library. Use
> --disable-netcdf-4, or see config.log for errors.
> 
> 
> --
> 
> Keerthi Priya Kasturi
> PhD Research Scholar,
> Civil Engineering Department
> IIT Gandhinagar
> 
> 


Ticket Details
===================
Ticket ID: HYF-949395
Department: Support netCDF
Priority: Normal
Status: Closed