[netCDFPerl #GUU-870609]: undefined symbol: PL_stack_max

Drew,

> Last Friday we had a hard disk failure on a server containing all relevant
netcdf files.  We then copied the backup of the failed disks to a new server
and have had issues attempting to use netcdf reliant scripts since then.
>
> I am seeing issues similar to ours on the troubleshooting segment but would
like to confirm the issue with support.
>
> Here is the error:
> Can't load
'/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi/auto/NetCDF/NetCDF.so'
for module NetCDF:
/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi/auto/NetCDF/NetCDF.so:
undefined symbol: PL_stack_max at
/usr/lib/perl5/5.8.0/i386-linux-thread-multi/DynaLoader.pm line 229.
> at /usr/lib/perl5/5.8.0/AGRID.pm line 5
> Compilation failed in require at /usr/lib/perl5/5.8.0/AGRID.pm line 5.
>
> It meets the format I've seen where there is an error due to an "undefined
symbol" somewhere in DynaLoader.pm.
>
> The general consensus seems to be that these errors are due to incompatible
compilers, and a perl -V is request.  Here is the ouput:
> Summary of my perl5 (revision 5.0 version 8 subversion 0) configuration:
> Platform:
> osname=linux, osvers=2.4.18-11smp, archname=i386-linux-thread-multi
> uname='linux daffy.perf.redhat.com 2.4.18-11smp #1 smp thu aug 15 06:41:59
edt 2002 i686 i686 i386 gnulinux '
> config_args='-des -Doptimize=-O2 -march=i386 -mcpu=i686
-Dmyhostname=localhost -Dperladmin=root@localhost -Dcc=gcc -Dcf_by=Red Hat,
Inc. -Dinstallprefix=/usr -Dprefix=/usr -Darchname=i386-linux
-Dvendorprefix=/usr -Dsiteprefix=/usr -Duseshrplib -Dusethreads -Duseithreads
-Duselargefiles -Dd_dosuid -Dd_semctl_semun -Di_db -Ui_ndbm -Di_gdbm -Di_shadow
-Di_syslog -Dman3ext=3pm -Duseperlio -Dinstallusrbinperl -Ubincompat5005
-Uversiononly -Dpager=/usr/bin/less -isr'
> hint=recommended, useposix=true, d_sigaction=define
> usethreads=define use5005threads=undef useithreads=define
usemultiplicity=define
> useperlio=define d_sfio=undef uselargefiles=define usesocks=undef
> use64bitint=undef use64bitall=undef uselongdouble=undef
> usemymalloc=n, bincompat5005=undef
> Compiler:
> cc='gcc', ccflags ='-D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm',
> optimize='-O2 -march=i386 -mcpu=i686',
> cppflags='-D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing
-I/usr/include/gdbm'
> ccversion='', gccversion='3.2 20020822 (Red Hat Linux Rawhide 3.2-5)',
gccosandvers=''
> intsize=4, longsize=4, ptrsize=4, doublesize=8, byteorder=1234
> d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=12
> ivtype='long', ivsize=4, nvtype='double', nvsize=8, Off_t='off_t',
lseeksize=8
> alignbytes=4, prototype=define
> Linker and Libraries:
> ld='gcc', ldflags =' -L/usr/local/lib'
> libpth=/usr/local/lib /lib /usr/lib
> libs=-lnsl -lgdbm -ldb -ldl -lm -lpthread -lc -lcrypt -lutil
> perllibs=-lnsl -ldl -lm -lpthread -lc -lcrypt -lutil
> libc=/lib/libc-2.2.92.so, so=so, useshrplib=true, libperl=libperl.so
> gnulibc_version='2.2.92'
> Dynamic Linking:
> dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-rdynamic
-Wl,-rpath,/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE'
> cccdlflags='-fpic', lddlflags='-shared -L/usr/local/lib'
>
>
> Characteristics of this binary (from libperl):
> Compile-time options: MULTIPLICITY USE_ITHREADS USE_LARGE_FILES
PERL_IMPLICIT_CONTEXT
> Built under linux
> Compiled at Sep  1 2002 23:56:49
> %ENV:
> PERL5LIB="/apps/utils/agrid/AGRID-1.07"
> @INC:
> /apps/utils/agrid/AGRID-1.07
> /usr/lib/perl5/5.8.0/i386-linux-thread-multi
> /usr/lib/perl5/5.8.0
> /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
> /usr/lib/perl5/site_perl/5.8.0
> /usr/lib/perl5/site_perl
> /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
> /usr/lib/perl5/vendor_perl/5.8.0
> /usr/lib/perl5/vendor_perl

It's not clear to me what the problem is, but I suspect an incompatiblity
between your perl5 installation, your netCDF-Perl installation, and
(possibly) the netCDF installation.  I suggest that you rebuild the
netCDF-Perl package from scratch and execute it's "make test" command to
see if that might fix the problem.  The following steps should do it.

1.  Go to the top-level source-directory of the netCDF-Perl package.

2.  Execute the command "make distclean".

3.  Set the environment variable CC to "gcc" and the environment variable
CPPFLAGS to "-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64".

4.  Execute the configure script.  Redirect the standard output and
standard error streams to the file "configure.log".  Send me that
file if an error occurs.

5.  Execute the command "make".  Redirect the standard output and
standard error streams to the file "make.log".  Send me that
file if an error occurs.

6.  Execute the command "make test".  Redirect the standard output and
standard error streams to the file "test.log".  Send me that
file if an error occurs.

7.  As the superuser (root) execute the command "make install".

Please let me know if this helps.

Regards,
Steve Emmerson

Ticket Details
===================
Ticket ID: GUU-870609
Department: Support netCDF Perl
Priority: Normal
Status: On Hold