Re: [netcdfgroup] PDL-NetCDF

[Doug Hunt <dhunt@xxxxxxxx>]

Hi Tyler:  It looks to me as if the -fPIC flag needs to be specified when 
compiling the netcdf library.  This has to be done before installing 
PDL-NetCDF.

We have CentOS5x x86_64 machines here.  Our recipe for compiling netcdf 
and PDL-NetCDF is in the attached file.

Regards,

  Doug

dhunt@xxxxxxxx
Software Engineer IV
UCAR - COSMIC, Tel. (303) 497-2611

On Mon, 23 Mar 2009, Tyler Cruickshank wrote:

> Hi Doug.
>
> I've run into a problem installing PDL-NetCDF on my CentOS5x x86_64 machine.  I can create a 
> makefile ok, but make is producing the error pasted below.  Following the advice in 
> PROBLEMS, I edited my Makefile.PL to reflect 'CCFLAGS'      => "-Dbool=int 
> -g3".  I see that the error messages wants me to recompile using -fPIC, but I am not 
> quite sure what to do with that.  Can you direct me?
>
> Thanks.
>
> -tyler
>
> ------------------------------------------------------------------------------
> [root@avalanche PDL-NetCDF-0.94]# make
>
> /usr/bin/perl -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi 
> "-MPDL::PP qw/PDL::NetCDF PDL::NetCDF NetCDF/" netcdf.pd
> cp NetCDF.pm blib/lib/PDL/NetCDF.pm
> /usr/bin/perl /usr/lib/perl5/5.8.8/ExtUtils/xsubpp  -typemap 
> /usr/lib/perl5/5.8.8/ExtUtils/typemap -typemap 
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/PDL/Core/typemap.pdl -typemap 
> typemap  NetCDF.xs > NetCDF.xsc && mv NetCDF.xsc NetCDF.c
> gcc -c  -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/PDL/Core -I/usr/local/include -Dbool=int 
> -g3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 
> -mtune=generic   -DVERSION=\"0.94\" -DXS_VERSION=\"0.94\" -fPIC 
> "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE"   NetCDF.c
> In file included from 
> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE/perl.h:2120,
>                 from NetCDF.xs:6:
> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE/handy.h:85:1: warning: 
> "bool" redefined
> <command line>:1:1: warning: this is the location of the previous definition
> NetCDF.xs: In function 'XS_PDL__NetCDF_nc_put_att_schar':
> NetCDF.xs:634: warning: pointer targets in passing argument 6 of 
> 'nc_put_att_schar' differ in signedness
> NetCDF.xs: In function 'XS_PDL__NetCDF_nc_get_att_schar':
> NetCDF.xs:652: warning: pointer targets in passing argument 4 of 
> 'nc_get_att_schar' differ in signedness
> NetCDF.xs: In function 'XS_PDL__NetCDF_nc_put_vara_schar':
> NetCDF.xs:1144: warning: pointer targets in passing argument 5 of 
> 'nc_put_vara_schar' differ in signedness
> NetCDF.xs: In function 'XS_PDL__NetCDF_nc_get_vara_schar':
> NetCDF.xs:1166: warning: pointer targets in passing argument 5 of 
> 'nc_get_vara_schar' differ in signedness
> NetCDF.xs: In function 'XS_PDL__NetCDF_nc_put_var_schar':
> NetCDF.xs:1476: warning: pointer targets in passing argument 3 of 
> 'nc_put_var_schar' differ in signedness
> NetCDF.xs: In function 'XS_PDL__NetCDF_nc_get_var_schar':
> NetCDF.xs:1493: warning: pointer targets in passing argument 3 of 
> 'nc_get_var_schar' differ in signedness
> Running Mkbootstrap for PDL::NetCDF ()
> chmod 644 NetCDF.bs
> rm -f blib/arch/auto/PDL/NetCDF/NetCDF.so
> gcc  -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions 
> -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic NetCDF.o   -o 
> blib/arch/auto/PDL/NetCDF/NetCDF.so     \
>           -L/usr/local/lib -lnetcdf    \
>
> /usr/bin/ld: /usr/local/lib/libnetcdf.a(attr.o): relocation R_X86_64_32 against 
> `a local symbol' can not be used when making a shared object; recompile with 
> -fPIC
> /usr/local/lib/libnetcdf.a: could not read symbols: Bad value
> collect2: ld returned 1 exit status
> make: *** [blib/arch/auto/PDL/NetCDF/NetCDF.so] Error 1
For netcdf-3.6.3 and PDL-NetCDF-0.93, installing netcdf into 
/ops/tools/[lib|include] using
the Portland group F90 compiler.

If you want to install to the normal netcdf location, do not specify:

-I/ops/tools/include
--prefix=/ops/tools

and export NETCDF_LIBDIR and NETCDF_INCDIR appropriately (should not be 
necessary
for a default netcdf install).

If you do not need FORTRAN, then you should not worry about FC, F90 or the 
-DpgiFortran flag.


tar -xzf netcdf-3.6.3.tar.gz
cd netcdf-3.6.3
export FC=pgf90 # we use portland group FORTRAN 90
export F90=pgf90
export CC=gcc
export CFLAGS='-fPIC'
export CPPFLAGS='-DNDEBUG -DpgiFortran -fPIC'
export CXX='g++'
export FFLAGS='-I/usr/include -I/ops/tools/include'
./configure --prefix=/ops/tools
make
make install
cp f90/netcdf.mod    /ops/tools/include
cp f90/typesizes.mod /ops/tools/include

tar -xzf PDL-NetCDF-0.93.tar.gz
cd PDL-NetCDF-0.93
export NETCDF_LIBDIR='/ops/tools/lib'
export NETCDF_INCDIR='/ops/tools/include'
perl Makefile.PL
make
make test
make install