[Support #SZN-475812]: help with building netcdf-perl

Jonathan,

> I removed the older netcdf installation (done by someone else) and
> downloaded 3.6.3 and built it with the -fPIC options there.
> 
> # grep PIC make.log
> gcc -c  -I/usr/local/netcdf-3.6.3/include -D_REENTRANT -D_GNU_SOURCE
> -fno-strict-aliasing -pipe -Wdeclaration-after-statement
> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
> -I/usr/include/gdbm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64
> -mtune=generic   -DVERSION=\"1.2.4\" -DXS_VERSION=\"1.2.4\" -fPIC
> "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE"   NetCDF.c
> 
> 
> now when trying to build netcdf-perl I get past the "make" (no errors)
> but the "make-test" errors out:
> 
> 
> # export PERL_MANDIR=/usr/share/man; export
> CPP_NETCDF=-I/usr/local/netcdf-3.6.3/include; export
> LD_NETCDF="-L/usr/local/netcdf-3.6.3/lib -lnetcdf"
> 
> # ./configure > configure.log
> expanding `include's in file `Makefile'
> expanding `include's in file `perl/Makefile.PL'
> expanding `include's in file `port/master.mk'
> expanding `include's in file `port/Makefile'
> 
> # make perl/Makefile > makefile.log
> Note (probably harmless): No library found for -lnetcdf

The "No library found..." message is an ill omen.  It means that perl(1) was 
unable to locate the netCDF library when it generated the makefile in the perl/ 
subdirectory.

> # cat makefile.log
> cd perl && perl Makefile.PL POLLUTE=0
> Checking if your kit is complete...
> Looks good
> Writing Makefile for NetCDF
> 
> # make > make.log
> Please specify prototyping behavior for NetCDF.xs (see perlxs manual)
> 
> # cat make.log
> make[1]: Entering directory `/root/netcdf-perl-1.2.4/src'
> make[2]: Entering directory `/root/netcdf-perl-1.2.4/src'
> 
> making `dynamic' in directory /root/netcdf-perl-1.2.4/src/perl
> 
> make[3]: Entering directory `/root/netcdf-perl-1.2.4/src/perl'
> /usr/bin/perl /usr/lib/perl5/5.8.8/ExtUtils/xsubpp  -typemap
> /usr/lib/perl5/5.8.8/ExtUtils/typemap  NetCDF.xs > NetCDF.xsc && mv
> NetCDF.xsc NetCDF.c
> gcc -c  -I/usr/local/netcdf-3.6.3/include -D_REENTRANT -D_GNU_SOURCE
> -fno-strict-aliasing -pipe -Wdeclaration-after-statement
> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
> -I/usr/include/gdbm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64
> -mtune=generic   -DVERSION=\"1.2.4\" -DXS_VERSION=\"1.2.4\" -fPIC
> "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE"   NetCDF.c
> Running Mkbootstrap for NetCDF ()
> chmod 644 NetCDF.bs
> rm -f blib/arch/auto/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/NetCDF/NetCDF.so       \
> \
> 
> chmod 755 blib/arch/auto/NetCDF/NetCDF.so
> cp NetCDF.bs blib/arch/auto/NetCDF/NetCDF.bs
> chmod 644 blib/arch/auto/NetCDF/NetCDF.bs
> make[3]: Leaving directory `/root/netcdf-perl-1.2.4/src/perl'
> 
> returning to directory /root/netcdf-perl-1.2.4/src
> 
> make[2]: Leaving directory `/root/netcdf-perl-1.2.4/src'
> make[1]: Leaving directory `/root/netcdf-perl-1.2.4/src'
> test ! -f perl/so_locations || chmod a+w perl/so_locations
> 
> 
> 
> # make test > test.log
> Can't load 'blib/arch/auto/NetCDF/NetCDF.so' for module NetCDF:
> blib/arch/auto/NetCDF/NetCDF.so: undefined symbol: ncopts at
> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/DynaLoader.pm line 230.
> at test.pl line 5
> Compilation failed in require at test.pl line 5.
> BEGIN failed--compilation aborted at test.pl line 5.
> make[2]: *** [test_dynamic] Error 2
> make[1]: *** [perl/test] Error 1
> make: *** [test] Error 2

"ncopts" being an undefined symbol is consistent with the build procedure not 
finding the netCDF library.  What does the /usr/local/netcdf-3.6.3/lib 
directory contain?

> # cat test.log
> make[1]: Entering directory `/root/netcdf-perl-1.2.4/src'
> 
> making `test' in directory /root/netcdf-perl-1.2.4/src/perl
> 
> make[2]: Entering directory `/root/netcdf-perl-1.2.4/src/perl'
> cp NetCDF.pm blib/lib/NetCDF.pm
> AutoSplitting blib/lib/NetCDF.pm (blib/lib/auto/NetCDF)
> PERL_DL_NONLAZY=1 /usr/bin/perl "-Iblib/lib" "-Iblib/arch" test.pl
> make[2]: Leaving directory `/root/netcdf-perl-1.2.4/src/perl'
> make[1]: Leaving directory `/root/netcdf-perl-1.2.4/src'
> 
> 
> 
> Jonathan

Regards,
Steve Emmerson

Ticket Details
===================
Ticket ID: SZN-475812
Department: Support netCDF Perl
Priority: Normal
Status: Closed