Re: [netcdfgroup] segmentation fault when nc_close

• To: "Marston Sheldon Johnston" <marston@xxxxxxxxxxx>, <netcdfgroup@xxxxxxxxxxxxxxxx>
• Subject: Re: [netcdfgroup] segmentation fault when nc_close
• From: "Mark Rivers" <rivers@xxxxxxxxxxxxxxxxx>
• Date: Sun, 14 Mar 2010 08:00:43 -0500

I am having a somewhat similar problem.  When I write large (500MB to 4GB) 
netCDF files in IDL, every once in a while an error returned on the 
ncdf_varput() call.  When I close the file and compare it to one written 
without the error they are slightly different.  One or two rows in a very large 
3D array are garbage.  Doing the identical operation again it does not fail.
 
This only happens on 64-bit Linux, not on 32 or 64-bit Windows.  It happens 
both with 3.6.2 and 4.0.1.
 
ITT has been unable to reproduce it, so it may be something about my Linux 
version or hardware.
 
If you get a seqmentation fault then you should be able to enable core dumps 
("limit core 100000: for csh or "ulimit -c 100000" for bash).
 
Once you get a core dump you can run gdb on it to see the stack trace when the 
program crashed.
 
Mark
 

________________________________

From: netcdfgroup-bounces@xxxxxxxxxxxxxxxx on behalf of Marston Sheldon Johnston
Sent: Sun 3/14/2010 5:22 AM
To: netcdfgroup@xxxxxxxxxxxxxxxx
Subject: [netcdfgroup] segmentation fault when nc_close



Hi,

I'm using the netcdf C interface and CDI  to read and write very  large netcdf 
files.
My script is not very complicated, the netcdf interface gives me greater access 
to the data in the netcdf file than CDI but cdi gives me better access to the 
time steps in the file.
After accessing the data, I calculate the monthly averages and then write them 
to a new netcdf file for each month.
Over 1 year this is done 8 times each month. The program works for the most 
part well but when the final month's data is written and I close the newly 
created netcdf file, I get a segmentation fault.
The file seems to be closed and the data looks good but I cannot trace the 
problem. I placed a simple print statement after the nc_close command and error 
handling function but this statement is never reached.

I would like to know if there is anyone who have encountered something similar 
and can give some tips as to where to look and what may be the problem. I used 
the example given in the example map in the netcdf installation.
I can send the script if anyone is so kind as to assist me with this debugging 
:-)


Sincerely,
Marston

-
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
~ Marston S. Johnston                                   e-mail: 
marston@xxxxxxxxxxx  ~
~ Doctoral Student                                      Radio and Space Science 
        ~      
~ Chalmers Technical University                 http://www.chalmers.se 
<http://www.chalmers.se/>               ~
~ Gothenburg                                                    Tel. (46) 31 
772 2235                 ~    
~ Sweden                                                        Skype ID 
marston.johnston       ~      
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


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• References:
  • [netcdfgroup] segmentation fault when nc_close
    • From: Marston Sheldon Johnston