It looks like HDF5 needs zlib to be compiled with the -fPIC flag (you can set
CFLAGS="-arch x86_64 -g -O2 -fPIC", or something along those lines), so I'd
start there. Also, what is the output of the following command:
file /home/ronnieleeper/prgfiles/zlib/lib/libz.a
Thanks!
Sean
> So initial tries to install HDF5 from source are not going well. I have
> attempt to configure HDF5 source with the following command line argument:
> ./configure --enable-fortran --with-zlib=/home/ronnieleeper/prgfiles/zlib
> --with-szlib=/home/ronnieleeper/prgfiles/szip
> --prefix=/home/ronnieleeper/prgfiles/hdf5
>
> The configure seems to run fine, but make errors with the following
> statement. I am not sure where ÂfPIC should be placed?
>
> H5Ztrans.c:1406: warning: will never be executed
> CCLD libhdf5.la
> /usr/bin/ld: /home/ronnieleeper/prgfiles/zlib/lib/libz.a(compress.o):
> relocation R_X86_64_32 against `a local symbol' can not be used when making
> a shared object; recompile with -fPIC
> /home/ronnieleeper/prgfiles/zlib/lib/libz.a: could not read symbols: Bad
> value
> collect2: ld returned 1 exit status
> make[2]: *** [libhdf5.la] Error 1
> make[2]: Leaving directory `/home/ronnieleeper/prgfiles/hdf5/hdf5-1.8.7/src'
> make[1]: *** [all] Error 2
> make[1]: Leaving directory `/home/ronnieleeper/prgfiles/hdf5/hdf5-1.8.7/src'
> make: *** [all-recursive] Error 1
>
> In addition, here are hundreds of warning messages stating such as this one .
> H5.c:523: warning: will never be executed
>
> However, searches from google suggest these lines indicate they are not
> issue? In addition there were other error messages such as the following:
>
> CC H5make_libsettings.o
> CCLD H5make_libsettings
> LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo | \
> sed -e 's/-L/:/g' -e 's/ //g'`"
> \
> ./H5make_libsettings > H5lib_settings.c ||
> \
> (test $HDF5_Make_Ignore && echo "*** Error ignored") ||
> \
> (rm -f H5lib_settings.c ; exit 1)
> CC H5lib_settings.lo
> CC H5MF.lo
>
> Attached are the config.log and make.log files.
>
> Any suggestions?
>
> Ronald David Leeper
> USCRN Quality Assurance Specialist, NCDC
> Research Associate, CICS-NC
> Global Climate Applications Division
> National Climatic Data Center
> 151 Patton Ave.
> Asheville, NC 28801-5001
> address@hidden
> address@hidden
> Office: (828) 257-3185
> Fax: (828) 271-4022
>
>
>
> On 8/23/11 5:37 PM, "Unidata netCDF Support"
> <address@hidden> wrote:
>
> > Greetings,
> >
> > I wonder if there is a compatibility issue between the hdf5 RMP library
> > (since
> > it's a binary distribution) and your compilers. Have you tried building hdf5
> > from source?
> >
> > Sean
> >
> >> Not much luck there. The configure crashes at the same location:
> >> <from the command line>
> >> checking for manual-page index command...
> >> checking whether we should try to build netCDF-4... yes
> >> checking for deflate in -lz... yes
> >> checking for H5Fflush in -lhdf5... yes
> >> checking for H5DSis_scale in -lhdf5_hl... no
> >> configure: error: Can't find or link to the hdf5 high-level. Configure
> >> with
> >> --with-hdf5, or use --disable-netcdf-4, or see config.log for
> >> errors.
> >>
> >> <from config.log>
> >> configure:26872: checking for H5DSis_scale in -lhdf5_hl
> >> configure:26897: cc -o conftest -g -O2 -I/usr/include
> >> -I/home/ronnieleeper/prgfiles/hdf5/include -I/usr/local/szip/include
> >> -L/usr/lib64 -L/usr/lib -L/home/ronnieleeper/prgfiles/hdf5/lib
> >> -L/usr/local/szip/lib conftest.c -lhdf5_hl -lhdf5 -lz >&5
> >> /tmp/cc6HuE8i.o: In function `main':
> >> /home/ronnieleeper/prgfiles/netcdf/netcdf-4.1.2/conftest.c:114: undefined
> >> reference to `H5DSis_scale'
> >> collect2: ld returned 1 exit status
> >> configure:26897: $? = 1
> >> configure: failed program was:
> >> | /* confdefs.h */
> >> | #define PACKAGE_NAME "netCDF"
> >> | #define PACKAGE_TARNAME "netcdf"
> >> | #define PACKAGE_VERSION "4.1.2"
> >> | #define PACKAGE_STRING "netCDF 4.1.2"
> >> | #define PACKAGE_BUGREPORT "address@hidden"
> >> | #define PACKAGE_URL ""
> >> | #define PACKAGE "netcdf"
> >> | #define VERSION "4.1.2"
> >> | #define NCIO_MINBLOCKSIZE 256
> >> | #define USE_FSYNC 1
> >> | #define DEFAULT_CHUNK_SIZE 4194304
> >> | #define MAX_DEFAULT_CACHE_SIZE 67108864
> >> | #define DEFAULT_CHUNKS_IN_CACHE 10
> >> | #define CHUNK_CACHE_SIZE 4194304
> >> | #define CHUNK_CACHE_NELEMS 1009
> >> | #define CHUNK_CACHE_PREEMPTION 0.75
> >> | #define USE_DAP 1
> >> | #define ENABLE_DAP 1
> >> | #define ENABLE_DAP_REMOTE_TESTS 1
> >> | #define USE_EXTREME_NUMBERS 1
> >> | #define TEMP_LARGE "."
> >> | #define STDC_HEADERS 1
> >> | #define HAVE_SYS_TYPES_H 1
> >> | #define HAVE_SYS_STAT_H 1
> >> | #define HAVE_STDLIB_H 1
> >> | #define HAVE_STRING_H 1
> >> | #define HAVE_MEMORY_H 1
> >> | #define HAVE_STRINGS_H 1
> >> | #define HAVE_INTTYPES_H 1
> >> | #define HAVE_STDINT_H 1
> >> | #define HAVE_UNISTD_H 1
> >> | #define HAVE_DLFCN_H 1
> >> | #define LT_OBJDIR ".libs/"
> >> | #define f2cFortran 1
> >> | #define NF_INT1_T byte
> >> | #define NF_INT2_T integer*2
> >> | #define NF_INT1_IS_C_SIGNED_CHAR 1
> >> | #define NF_INT2_IS_C_SHORT 1
> >> | #define NF_INT_IS_C_INT 1
> >> | #define NF_REAL_IS_C_FLOAT 1
> >> | #define NF_DOUBLEPRECISION_IS_C_DOUBLE 1
> >> | #define NCBYTE_T byte
> >> | #define NCSHORT_T integer*2
> >> | #define HAVE_LOCALE_H 1
> >> | #define HAVE_DIRENT_H 1
> >> | #define STDC_HEADERS 1
> >> | #define HAVE_SYS_WAIT_H 1
> >> | #define TIME_WITH_SYS_TIME 1
> >> | #define HAVE_STDIO_H 1
> >> | #define HAVE_STDARG_H 1
> >> | #define HAVE_ERRNO_H 1
> >> | #define HAVE_CTYPE_H 1
> >> | #define HAVE_FCNTL_H 1
> >> | #define HAVE_MALLOC_H 1
> >> | #define HAVE_STDLIB_H 1
> >> | #define HAVE_STRING_H 1
> >> | #define HAVE_STRINGS_H 1
> >> | #define HAVE_UNISTD_H 1
> >> | #define HAVE_SYS_STAT_H 1
> >> | #define HAVE_GETOPT_H 1
> >> | #define HAVE_SYS_TIME_H 1
> >> | #define HAVE_SYS_RESOURCE_H 1
> >> | #define HAVE_VPRINTF 1
> >> | #define HAVE__BOOL 1
> >> | #define HAVE_STDBOOL_H 1
> >> | #define HAVE_STRERROR 1
> >> | #define HAVE_SNPRINTF 1
> >> | #define HAVE_STRCHR 1
> >> | #define HAVE_STRRCHR 1
> >> | #define HAVE_MKTEMP 1
> >> | #define HAVE_STRCAT 1
> >> | #define HAVE_STRCPY 1
> >> | #define HAVE_STRDUP 1
> >> | #define HAVE_STRCASECMP 1
> >> | #define HAVE_STRTOD 1
> >> | #define HAVE_STRTOLL 1
> >> | #define HAVE_GETRLIMIT 1
> >> | #define HAVE_GETTIMEOFDAY 1
> >> | #define HAVE_FSYNC 1
> >> | #define HAVE_ALLOCA_H 1
> >> | #define HAVE_ALLOCA 1
> >> | #define HAVE_DECL_ISNAN 1
> >> | #define HAVE_DECL_ISINF 1
> >> | #define HAVE_DECL_ISFINITE 0
> >> | #define HAVE_DECL_SIGNBIT 0
> >> | #define HAVE_STRUCT_STAT_ST_BLKSIZE 1
> >> | #define HAVE_ST_BLKSIZE 1
> >> | #define HAVE_SSIZE_T 1
> >> | #define HAVE_PTRDIFF_T 1
> >> | #define SIZEOF_SHORT 2
> >> | #define SIZEOF_INT 4
> >> | #define SIZEOF_LONG 8
> >> | #define SIZEOF_FLOAT 4
> >> | #define SIZEOF_DOUBLE 8
> >> | #define SIZEOF_OFF_T 8
> >> | #define SIZEOF_SIZE_T 8
> >> | #define HAVE_LIBZ 1
> >> | #define USE_NETCDF4 1
> >> | #define H5_USE_16_API 1
> >> | #define HAVE_LIBHDF5 1
> >> | /* end confdefs.h. */
> >> |
> >> | /* Override any GCC internal prototype to avoid an error.
> >> | Use char because int might match the return type of a GCC
> >> | builtin and then its argument prototype would still apply. */
> >> | #ifdef __cplusplus
> >> | extern "C"
> >> | #endif
> >> | char H5DSis_scale ();
> >> | int
> >> | main ()
> >> | {
> >> | return H5DSis_scale ();
> >> | ;
> >> | return 0;
> >> | }
> >> configure:26906: result: no
> >> configure:26916: error: Can't find or link to the hdf5 high-level.
> >> Configure
> >> with --with-hdf5, or use --disable-netcdf-4, or see config.log for
> >> errors.
> >>
> >> I have also attached the newly config.log file.
> >>
> >> Ronald David Leeper
> >> USCRN Quality Assurance Specialist, NCDC
> >> Research Associate, CICS-NC
> >> Global Climate Applications Division
> >> National Climatic Data Center
> >> 151 Patton Ave.
> >> Asheville, NC 28801-5001
> >> address@hidden
> >> address@hidden
> >> Office: (828) 257-3185
> >> Fax: (828) 271-4022
> >>
> >>
> >>
> >> On 8/23/11 4:11 PM, "Unidata netCDF Support"
> >> <address@hidden> wrote:
> >>
> >>> > It could be. Would you mind taking that out and reconfigure / recompile
> >>> netCDF
> >>> > to see if that works?
> >>> >
> >>>> >> Yes I am. I have it set as a bash profile variable because of
> >>>> another
> >>>> >> program I am trying to install, which relies of netcdf, requires it.
> Is
> >>>> >> this what is causing the error?
> >>>> >>
> >>>> >> Thanks
> >>>> >>
> >>>> >> Ronald David Leeper
> >>>> >> USCRN Quality Assurance Specialist, NCDC
> >>>> >> Research Associate, CICS-NC
> >>>> >> Global Climate Applications Division
> >>>> >> National Climatic Data Center
> >>>> >> 151 Patton Ave.
> >>>> >> Asheville, NC 28801-5001
> >>>> >> address@hidden
> >>>> >> address@hidden
> >>>> >> Office: (828) 257-3185
> >>>> >> Fax: (828) 271-4022
> >>>> >>
> >>>> >>
> >>>> >>
> >>>> >>
> >>>> >> On 8/23/11 3:57 PM, "Unidata netCDF Support"
> >>>> >> <address@hidden> wrote:
> >>>> >>
> >>>>>> >>> >Thanks for passing that along. Are you setting the -Df2cFortran
> flag
> >>>>>> >>> >yourself in your $CFLAGS?
> >>>>>> >>> >
> >>>>>>>> >>>> >> Ok here are the results of the command: "nm
> >>>>>>>> >>>> >> /home/ronnieleeper/prgfiles/hdf5/lib64/libhdf5_hl.a | grep
> >>>>>>>> H5DSis" were
> >>>>>>>> >>>> >>
> >>>>>>>> >>>> >> 0000000000001110 T H5DSis_attached
> >>>>>>>> >>>> >> 00000000000002d0 T H5DSis_scale
> >>>>>>>> >>>> >>
> >>>>>>>> >>>> >>
> >>>>>>>> >>>> >> Ronald David Leeper
> >>>>>>>> >>>> >> USCRN Quality Assurance Specialist, NCDC
> >>>>>>>> >>>> >> Research Associate, CICS-NC
> >>>>>>>> >>>> >> Global Climate Applications Division
> >>>>>>>> >>>> >> National Climatic Data Center
> >>>>>>>> >>>> >> 151 Patton Ave.
> >>>>>>>> >>>> >> Asheville, NC 28801-5001
> >>>>>>>> >>>> >> address@hidden
> >>>>>>>> >>>> >> address@hidden
> >>>>>>>> >>>> >> Office: (828) 257-3185
> >>>>>>>> >>>> >> Fax: (828) 271-4022
> >>>>>>>> >>>> >>
> >>>>>>>> >>>> >>
> >>>>>>>> >>>> >>
> >>>>>>>> >>>> >>
> >>>>>>>> >>>> >> On 8/23/11 3:03 PM, "Unidata netCDF Support"
> >>>>>>>> >>>> >> <address@hidden> wrote:
> >>>>>>>> >>>> >>
> >>>>>>>>>> >>>>> >> >nm /path/to/hdf5_hl_library | grep H5DSis
> >>>>>>>> >>>> >>
> >>>>>>>> >>>> >>
> >>>>>>>> >>>> >>
> >>>>>> >>> >
> >>>>>> >>> >
> >>>>>> >>> >Ticket Details
> >>>>>> >>> >===================
> >>>>>> >>> >Ticket ID: XXN-487077
> >>>>>> >>> >Department: Support netCDF
> >>>>>> >>> >Priority: Normal
> >>>>>> >>> >Status: Open
> >>>>>> >>> >
> >>>> >>
> >>>> >>
> >>>> >>
> >>> >
> >>> >
> >>> > Ticket Details
> >>> > ===================
> >>> > Ticket ID: XXN-487077
> >>> > Department: Support netCDF
> >>> > Priority: Normal
> >>> > Status: Open
> >>> >
> >>> >
> >>
> >>
> >>
> >>
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: XXN-487077
> > Department: Support netCDF
> > Priority: Normal
> > Status: Open
> >
> >
>
>
>
>
Ticket Details
===================
Ticket ID: XXN-487077
Department: Support netCDF
Priority: Normal
Status: Open
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