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20030425: GMT on RH9: pscoast core dump on nc_open()

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  • Subject: 20030425: GMT on RH9: pscoast core dump on nc_open()
  • Date: Fri, 25 Apr 2003 16:19:30 -0600
Chris,

> To: address@hidden,
> To: address@hidden
> From: Chris Webster <address@hidden>
> Subject: GMT on RH9: pscoast core dump on nc_open()
> Organization: NCAR Research Aviation Facility

The above message contained the following:

> I'm rebuilding the latest GMT for Redhat 9 with netCDF 3.5.1 beta.
> 
> Upon running my classic pscoast(1) command I receive a core dump in 
> nc_open().  The file nc_open() is going after does exist and is 
> readable.  I couldn't figure out how to compile netcdf with debugging 
> (at least no CFLAGS in the Makefiles).  Any advice?

I would be very surprised if the problem lay with the nc_open()
function.

Do this to build a netCDF library with support for debugging:

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

    2.  Perform steps 3 through 5 described near the end of the file
        INSTALL.html.

    3.  Ensure that the environment variable CFLAGS contains the string 
        "-g". e.g.,

            export CFLAGS -g

        or

            setenv CFLAGS -g

        depending on your user shell.

    4.  Perform steps 6 through 9 described near the end of the file
        INSTALL.html.

If you don't want to install the netCDF package with debugging enabled,
then don't do the "make install" in step 4 above.  You should then
change the build of your program to reference the netCDF library in the
"src/" directory rather than the installed library.

> 
> --Chris
> 
> 
> 237% pscoast -R-97/-94/-6/21 -M -Na -W -Ia -Df
> Segmentation fault (core dumped)
> 238% gdb pscoast core.13077
> 
> [SNIP]
> 
> (gdb) where
> #0  0x42074245 in _int_malloc () from /lib/tls/libc.so.6
> #1  0x4207335b in malloc () from /lib/tls/libc.so.6
> #2  0x08051f11 in nc_redef ()
> #3  0x0805252c in nc_redef ()
> #4  0x0805103b in nc_create ()
> #5  0x08050fea in nc_create ()
> #6  0x080510ca in nc_open ()
> #7  0x4007e7e6 in GMT_init_shore (res=102 'f', c=0x42131300, w=263, 
> e=266, s=-6, n=21)
>      at gmt_shore.c:107
> #8  0x0804b8db in strcpy ()
> #9  0x42015574 in __libc_start_main () from /lib/tls/libc.so.6
> (gdb) up
> #1  0x4207335b in malloc () from /lib/tls/libc.so.6
> (gdb) up
> #2  0x08051f11 in nc_redef ()
> (gdb) up
> #3  0x0805252c in nc_redef ()
> (gdb) up
> #4  0x0805103b in nc_create ()
> (gdb) up
> #5  0x08050fea in nc_create ()
> (gdb) up
> #6  0x080510ca in nc_open ()
> (gdb) up
> #7  0x4007e7e6 in GMT_init_shore (res=102 'f', c=0x42131300, w=263, 
> e=266, s=-6, n=21)
>      at gmt_shore.c:107
> 107             check_nc_status (nc_open (path, NC_NOWRITE,&c->cdfid));
> (gdb) p path
> $1 = "/jnet/linux/GMT/share/binned_GSHHS_f.cdf\000

Regards,
Steve Emmerson