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20030613: Problems installing netcdf-perl on Red Hat Linux 8.0



Brian,

> To: "'address@hidden'" <address@hidden>
> From: "HOETH, BRIAN R. (JSC-ZS) (LM)" <address@hidden>
> Subject: Problems installing netcdf-perl on Red Hat Linux 8.0
> Organization: NASA/JSC
> Keywords: netCDF-Perl

The above message contained the following:

> I've run into a problem installing netcdf-perl on Red Hat Linux 8.0.  I am
> almost certain that the problem is because I tried running the install as
> user "ldm" instead of as "root" (I do not have root privileges
> unfortunately).

Unlike the LDM package, it is irrelevant who installs the netCDF-perl
package -- it is only necessary that the user have access permission to
the installation directories (in particular, the perl installation
directory).

> Before I ask my system administrator to try the install
> though, I had a few questions:
> 
> (1)  Here is a listing of my netcdf-perl/src/perl directory:
> total 1220
> drwxr-xr-x    4 ldm      users        4096 Jun 11 08:37 blib
> -rw-------    1 ldm      users     1400832 Jun 11 09:06 core.15816
> -rw-r--r--    1 ldm      users         568 Jun 11 09:06 foo.nc
> -rw-r--r--    1 ldm      users       22321 Jun 10 08:56 Makefile
> -rw-r--r--    1 ldm      users         743 Jun 10 08:55 Makefile.PL
> -rw-r--r--    1 ldm      users         631 Jan  7 11:37 Makefile.PL.in
> -rw-r--r--    1 ldm      users          55 Jun 30  1995 MANIFEST
> -rw-r--r--    1 ldm      users           0 Jun 10 08:56 NetCDF.bs
> -rw-r--r--    1 ldm      users       60414 Jun 10 08:56 NetCDF.c
> -rw-r--r--    1 ldm      users      102012 Jun 10 08:56 NetCDF.o
> -rw-r--r--    1 ldm      users        1668 May 20  1997 NetCDF.pm
> -rw-r--r--    1 ldm      users       46337 Jan  9 10:09 NetCDF.xs
> -rw-r--r--    1 ldm      users           0 Jun 11 08:37 pm_to_blib
> -rw-r--r--    1 ldm      users        1003 Jun 11 08:46 src_perl_listing
> -rwxr-xr-x    1 ldm      users       12586 Nov  5  2002 test.pl
> 
> Is it bad that the NetCDF.bs and pm_to_blib files are zero length?  The
> "make" seemed successful (see attached make.log file)?

I don't know how relevant the size of those files is.  You "make.log"
file:

> make[1]: Entering directory `/home/ldm/netcdf-perl-1.2.2/src'=0A=
> make[2]: Entering directory `/home/ldm/netcdf-perl-1.2.2/src'=0A=
> cd perl && /usr/bin/perl Makefile.PL POLLUTE=3D0=0A=
> WARNING: CC is not a known parameter.=0A=
> Writing Makefile for NetCDF=0A=
> =0A=
> making `dynamic' in directory /home/ldm/netcdf-perl/src/perl=0A=
> =0A=
> make[3]: Entering directory `/home/ldm/netcdf-perl-1.2.2/src/perl'=0A=
> /usr/bin/perl /usr/lib/perl5/5.8.0/ExtUtils/xsubpp  -typemap =
> /usr/lib/perl5/5.8.0/ExtUtils/typemap  NetCDF.xs > NetCDF.xsc && mv =
> NetCDF.xsc NetCDF.c=0A=
> Please specify prototyping behavior for NetCDF.xs (see perlxs =
> manual)=0A=
> /usr/bin/gcc -c  -I/home/ldm/netcdf/include -D_REENTRANT -D_GNU_SOURCE =
> -fno-strict-aliasing -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=3D64 =
> -I/usr/include/gdbm -O2 -march=3Di386 -mcpu=3Di686   =
> -DVERSION=3D\"1.2.2\" -DXS_VERSION=3D\"1.2.2\" -fpic =
> "-I/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE"   NetCDF.c=0A=
> Running Mkbootstrap for NetCDF ()=0A=
> chmod 644 NetCDF.bs=0A=
> rm -f blib/arch/auto/NetCDF/NetCDF.so=0A=
> LD_RUN_PATH=3D"/home/ldm/netcdf/lib" gcc  -shared -L/usr/local/lib =
> NetCDF.o  -o blib/arch/auto/NetCDF/NetCDF.so   -L/home/ldm/netcdf/lib =
> -lnetcdf  =0A=
> chmod 755 blib/arch/auto/NetCDF/NetCDF.so=0A=
> cp NetCDF.bs blib/arch/auto/NetCDF/NetCDF.bs=0A=
> chmod 644 blib/arch/auto/NetCDF/NetCDF.bs=0A=
> make[3]: Leaving directory `/home/ldm/netcdf-perl-1.2.2/src/perl'=0A=
> =0A=
> returning to directory /home/ldm/netcdf-perl/src=0A=
> =0A=
> make[2]: Leaving directory `/home/ldm/netcdf-perl-1.2.2/src'=0A=
> make[1]: Leaving directory `/home/ldm/netcdf-perl-1.2.2/src'=0A=
> test ! -f perl/so_locations || chmod a+w perl/so_locations=0A=

looks OK.

Your "test.log" file, however:

> make[1]: Entering directory `/home/ldm/netcdf-perl-1.2.2/src'=0A=
> =0A=
> making `test' in directory /home/ldm/netcdf-perl/src/perl=0A=
> =0A=
> make[2]: Entering directory `/home/ldm/netcdf-perl-1.2.2/src/perl'=0A=
> PERL_DL_NONLAZY=3D1 /usr/bin/perl "-Iblib/lib" "-Iblib/arch" test.pl=0A=
> Creating netCDF file...........................ok=0A=
> Setting fill mode..............................ok=0A=
> Defining fixed dimensions......................ok=0A=
> Defining fixed variables.......................ok=0A=
> Writing global attribute.......................ok=0A=
> Writing variable attributes....................ok=0A=
> Defining record dimension......................ok=0A=
> Defining record variables......................ok=0A=
> Ending definition..............................ok=0A=
> Writing fixed variable values..................ok=0A=
> Synchronizing netCDF I/O.......................ok=0A=
> Writing record values..........................ok=0A=
> Closing netCDF file............................ok=0A=
> Opening netCDF file for reading................ok=0A=
> Inquiring about netCDF file....................ok=0A=
> Checking global attribute name.................ok=0A=
> Checking global attribute value................ok=0A=
> Getting second dimension ID....................ok=0A=
> Checking second dimension information..........ok=0A=
> Checking fixed variable ID.....................ok=0A=
> Checking fixed variable information............ok=0A=
> Checking last value of first record variable...make[2]: *** =
> [test_dynamic] Segmentation fault (core dumped)=0A=
> make[2]: Leaving directory `/home/ldm/netcdf-perl-1.2.2/src/perl'=0A=
> make[1]: *** [perl/test] Error 1=0A=
> make[1]: Leaving directory `/home/ldm/netcdf-perl-1.2.2/src'=0A=
> make: *** [test] Error 2=0A=

indicates a problem that has been seen before but only in in certain
environments.  More information on this problem can be found at

    http://www.unidata.ucar.edu/cgi-bin/msgout?/glimpse/netcdf-perl/133

> (2) The core file in the above listing was a result of the "make test"
> failing.  I checked the online archives of netcdf-perl support and noticed
> that somebody had the same failure when running "make test" on Red Hat Linux
> 8.0 that I did (see attached test.log file).  Failing the "make test"
> shouldn't affect the installation should it??

Failure of the "make test" step should not affect the "make install" step.

> (3) Is the install portion of the make necessary for the Unidata decoders
> package (decoders.tar.Z) to work or will the decoders package work with just
> the compilation portion (i.e. "make") being successful, which it seems to
> have been successful?

The netCDF-perl packge must be installed in order for the decoders
package to work.  The decoders package has a perl script that uses the
NetCDFPerl module that is installed by the "make install" step of the
netCDF-perl package.

> Just to make sure I covered all the bases, I have attached all my log files.
> 
> 
> Also, the output of uname -a is:
> Linux etamodel 2.4.18-14smp #1 SMP Wed Sep 4 12:34:47 EDT 2002 i686 i686
> i386 GNU/Linux

It is likely that you have the environment on which the segmentation
fault occurs during the "make test".  You might try another version of
the perl package as mentioned in the above URL.

> And the output of "which gcc" is:
> /usr/bin/gcc
> 
> Thanks in advance for your help!
> 
> ---------------
> Brian Hoeth
> Spaceflight Meteorology Group
> Johnson Space Center   
> Ph: 281-483-3246
> Ops:  281-483-1051

Regards,
Steve Emmerson