Re: relocation against dynamic symbol

Steve,

As you mentioned below, the problem seems to be when you mix PIC code
with non-PIC code. That is, if you compile some code with -fPIC and
some without.

Usually -fPIC is the default, so I'm surprised that you are running
into this issue. I think we have to assume this is still the issue
and just make sure that all your code gets built with -fPIC.

My recommendation is to compile everything with -fPIC (if you haven't
already), and then make sure that NCL and PyNIO get built with -fPIC
as well.

Before building NetCDF, HDF4, HDF5, etc, I set the following
environment variables:

   export CC=gcc
   export CXX=g++
   export FC=gfortran
   export F77=gfortran
   export CFLAGS=-fPIC
   export FFLAGS=-fPIC
   export F90FLAGS=-fPIC
   export CXXFLAGS=-fPIC

When building NCL, you can get the -fPIC option by editing
$NCARG/config/LINUX and making sure you have "-fPIC" on the CcOptions
and FcOptions lines. You will need to rerun "make Everything" to make
sure this takes effect.

I believe PyNIO should get the -fPIC option by virture of FFLAGS being
set.

Keep me posted.

--Mary

On Tue, 7 Apr 2009, Steve Fletcher wrote:

> 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
>>>>>
>>>>
>>>
>>>
>
>
_______________________________________________
pyngl-talk mailing list
List instructions, subscriber options, unsubscribe:
http://mailman.ucar.edu/mailman/listinfo/pyngl-talk
Received on Tue Apr 07 2009 - 16:10:38 MDT