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Re: 20051101: netCDF Perl Interface - problem using netcdf-perl: __buitin__alloca

John,

I believe the problem you're having stems from different compilers being
used to compile the perl(1), netCDF(3), and NetCDF-Perl(3) packages.  You
used pgcc(1) to compile the NetCDF-Perl package.  You can discover the
compiler used for the perl(1) utility via the command

    perl -V

You'll have to look in the source-directory of the netCDF package to
discover which compiler was used (I suspect it was gcc(1)).

You're more likely to obtain a successful build if you can use the same
compiler for all these packages.

Regards,
Steve Emmerson

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------- Original Message

>To: address@hidden
>From: "John Nordlie" <address@hidden>
>Subject: netCDF Perl Interface - problem using netcdf-perl: __buitin__alloca
>Organization: University of North Dakota
>Keywords: 200511020006.jA206YNS028796 netCDF Perl

Institution: University of North Dakota
Package Version: 1.2.3
Operating System: Redhat Linux Enterprise Worstation 3
Hardware Information: Dual Opteron, 1GB RAM, RAID
Inquiry: System has PGI compilers (C and FORTRAN).  Built and installed
NetCDF 3.5.1, using following environment variables:

setenv CPP_NETCDF -I/usr/local/include
setenv LD_NETCDF "-L/usr/local/lib -lnetcdf"
setenv PERL /usr/bin/perl
setenv PERL_MANDIR /usr/local/man
setenv CC pgcc
setenv CFLAGS "-O -Msignextend -V -fPIC"
setenv FC pgf90
setenv F90 pgf90
setenv FFLAGS "-g -w -V"
setenv CXX pgCC
setenv CPPFLAGS "-DNDEBUG -DpgiFortran"

as per PGI webpage:
http://www.pgroup.com/resources/netcdf/netcdf351_pgi5x_64.htm

Package built and installed with no errors in /usr/local.

Built netcdf-perl-1.2.8 using same enviro variables and installed in default lo
cation (didn't specify prefix in ./configure) with no errors, however when tryi
ng to use, we get this:

mdssfp@lisa:../scripts/perl> perl mos2nc /home/mdssfp/etc/mav_mos.cdl 
test < 
/home/mdssfp/mdss_data/raw_data/mos/mav_mos/20051101/mav_mos.20051101.1200.asc
23:47:47 Starting.
perl: relocation error: 
/usr/lib64/perl5/site_perl/5.8.0/auto/NetCDF/NetCDF.so: undefined 
symbol: __builtin_alloca

Verified as per PGI page that CXX was set to pgCC in macros.make (it was).

'make test' in build directory also dies:

[nordlie@lisa src]$ make test
make[1]: Entering directory `/home/nordlie/download/netcdf-perl-1.2.3/src'

making `test' in directory /home/nordlie/download/netcdf-perl-1.2.3/src/perl

make[2]: Entering directory `/home/nordlie/download/netcdf-perl-1.2.3/src/perl'
PERL_DL_NONLAZY=1 /usr/bin/perl "-Iblib/lib" "-Iblib/arch" test.pl
Can't load 'blib/arch/auto/NetCDF/NetCDF.so' for module NetCDF: blib/arch/auto/
NetCDF/NetCDF.so: undefined symbol: __builtin_alloca at /usr/lib64/perl5/5.8.0/
x86_64-linux-thread-multi/DynaLoader.pm line 229.
 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 255
make[2]: Leaving directory `/home/nordlie/download/netcdf-perl-1.2.3/src/perl'
make[1]: *** [perl/test] Error 1
make[1]: Leaving directory `/home/nordlie/download/netcdf-perl-1.2.3/src'
make: *** [test] Error 2

------- End of Original Message