Re: relocation against dynamic symbol

OK. After Cleaning out the PyNIO directory and untarring and logging out
and back in.

I set ENV variables:
export HAS_NETCDF4=1
export NETCDF4_PREFIX=/usr/local/netcdf-4.0_gcc
export HDF_PREFIX=/usr/local/hdf4
export NCARG_ROOT=/usr/local/ncarg5.0
and tried again. The hdf5 libraries did show up, but so did
the same error messages.

gcc -pthread -shared build/temp.linux-ia64-2.5/niomodule.o
-L/usr/local/ncarg5.0/lib -L/usr/local/hdf4/lib
-L/usr/local/netcdf-4.0_gcc/lib -lnio -lmfhdf -ldf -ljpeg -lpng -lz
-lnetcdf -lhdf5_hl -lhdf5 -lsz -o build/lib.linux-ia64-2.5/PyNIO/nio.so
/usr/lib/gcc/ia64-suse-linux/4.1.2/../../../../ia64-suse-linux/bin/ld:
/usr/local/hdf4/lib/libdf.a(herr.o): @gprel relocation against dynamic
symbol error_top
/usr/lib/gcc/ia64-suse-linux/4.1.2/../../../../ia64-suse-linux/bin/ld:
/usr/local/hdf4/lib/libdf.a(herr.o): @gprel relocation against dynamic
symbol error_top
/usr/lib/gcc/ia64-suse-linux/4.1.2/../../../../ia64-suse-linux/bin/ld:
/usr/local/hdf4/lib/libdf.a(herr.o): @gprel relocation against dynamic
symbol error_top

Mary Haley wrote:
> Steve,
>
> One thing that I noticed is that you enabled NetCDF-4 support when you
> built NetCDF. This means that when you compile PyNIO, the HDF5
> libraries must get included on the final load line. I didn't see the
> libraries listed on your compile line:
>
> gcc -pthread -shared build/temp.linux-ia64-2.5/niomodule.o
> -L/usr/local/ncarg5.0/lib -L/usr/local/hdf4/lib -lnio -lmfhdf -ldf
> -ljpeg -lpng -lz -lnetcdf -o build/lib.linux-ia64-2.5/PyNIO/nio.so
> /usr/lib/gcc/ia64-suse-linux/4.1.2/../../../../ia64-suse-linux/bin/ld:
> /usr/local/hdf4/lib/libdf.a(herr.o): @gprel relocation against dynamic
>
>
> The libraries you should see are "-lhdf5_hl -lhdf5 -lsz". These only
> get loaded if the HAS_NETCDF4 environment variable is set to something
> greater than 0.
>
> So, we need to find out why setting HAS_NETCDF4 to 1 is not working in
> your case. I assume you are building version 1.3.0b1?
>
> --Mary
>
>
> On Mon, 6 Apr 2009, David Brown wrote:
>
>> OK, we will have to look into this further. Thanks for the report. We
>> make have some more questions shortly.
>> -dave
>>
>> On Apr 6, 2009, at 3:21 PM, Steve Fletcher wrote:
>>
>>> OK. I had it both ways for the HAS_NETCDF4 since I typed it in
>>> wrong the first time.
>>> I copied the HDF5 libraries and includes into the netcdf4 directory,
>>> but it dies in exactly
>>> the same place with the same error.
>>> Steve
>>>
>>> David Brown wrote:
>>>> Hi Steve,
>>>>
>>>> We have noticed a couple of issues that might be affecting your build:
>>>> 1) The environment variable for NetCDF4 should be HAS_NETCDF4
>>>> rather than HAVE_NETCDF4.
>>>> 2) The current build process expects that the HDF5 libraries live
>>>> in the same location that the NetCDF4 library is installed.
>>>> You could either move your HDF5 libraries or create appropriate
>>>> symbolic links.
>>>> Hopefully this will get you further along. Let us know if you have
>>>> further problems.
>>>> -dave
>>>>
>>>>
>>>>
>>>>
>>>> On Apr 6, 2009, at 2:35 PM, Steve Fletcher wrote:
>>>>
>>>>> I'm trying to build PyNIO and running into problems. These are the
>>>>> messages I got.
>>>>> gcc -pthread -shared build/temp.linux-ia64-2.5/niomodule.o
>>>>> -L/usr/local/ncarg5.0/lib -L/usr/local/hdf4/lib -lnio -lmfhdf -ldf
>>>>> -ljpeg -lpng -lz -lnetcdf -o build/lib.linux-ia64-2.5/PyNIO/nio.so
>>>>> /usr/lib/gcc/ia64-suse-linux/4.1.2/../../../../ia64-suse-linux/bin/ld:
>>>>>
>>>>> /usr/local/hdf4/lib/libdf.a(herr.o): @gprel relocation against
>>>>> dynamic
>>>>> symbol error_top
>>>>>
>>>>> Most of the google pages I saw suggested some version of
>>>>> CFLAGS=-fpic or
>>>>> -fPIC. Tried both without success.
>>>>>
>>>>> I was able to compile the older version of ncl_ncarg for the
>>>>> libnio.a,
>>>>> but haven't yet found a way around the shared library problem. Any
>>>>> suggestions
>>>>> would be appreciated.
>>>>>
>>>>> Below is how the other tools were built.
>>>>> ARCH:
>>>>> IA64
>>>>>
>>>>> OS:
>>>>> SUSE Linux Enterprise Server 10 (ia64)
>>>>> VERSION = 10
>>>>> PATCHLEVEL = 2
>>>>>
>>>>> relevant ENV:
>>>>> NCARG_ROOT=/usr/local/ncarg5.0
>>>>> HAVE_NETCDF4=1
>>>>> NETCDF4_PREFIX=/usr/local/netcdf-4.0_gcc
>>>>> HDF_PREFIX=/usr/local/hdf4
>>>>>
>>>>> HDF4 build:
>>>>> It was created by HDF configure 4.2r4, which was
>>>>> generated by GNU Autoconf 2.61. Invocation command line was
>>>>>
>>>>> $ ./configure --prefix=/usr/local/hdf4 --enable-fortran --enable-cxx
>>>>> --include
>>>>> dir=/usr/local/hdf4/include/hdf --disable-netcdf CC=gcc CXX=g++
>>>>> FC=gfortran
>>>>> F77=gfortran F90=gfortran
>>>>>
>>>>>
>>>>> Netcdf4 build:
>>>>> It was created by netCDF configure 4.0, which was
>>>>> generated by GNU Autoconf 2.62. Invocation command line was
>>>>>
>>>>> $ ./configure --prefix=/usr/local/netcdf-4.0_gcc
>>>>> --with-hdf5=/usr/local/hdf5-g
>>>>> cc --with-szlib=/usr/local/szip --enable-netcdf-4 CC=gcc CXX=g++
>>>>> FC=gfortran F90
>>>>> =gfortran F77=gfortran
>>>>>
>>>>> Make Output from ncl_ncarg-5.0.0:
>>>>> f77 Compiler gfortran
>>>>> f77 Flags -fPIC -fno-second-underscore -fno-range-check -O
>>>>> C Compiler gcc
>>>>> cc Flags -ansi -fPIC -O -I./include -I/usr/X11R6/include
>>>>> -I/usr/l
>>>>> ocal/hdf4/include -I/usr/local/netcdf-4.0_gcc/include
>>>>> -I/usr/local/hdf5-gcc/incl
>>>>> ude -DSYSV -D_POSIX_SOURCE -D_XOPEN_SOURCE -DByteSwapped
>>>>> -DNeedFuncProto
>>>>> _______________________________________________
>>>>> pyngl-talk mailing list
>>>>> List instructions, subscriber options, unsubscribe:
>>>>> http://mailman.ucar.edu/mailman/listinfo/pyngl-talk
>>>>
>>>
>>
>>
Received on Tue Apr 07 2009 - 14:38:20 MDT