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[netCDF #VUY-537245]: Segmentation fault in getvar for large files

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  • Subject: [netCDF #VUY-537245]: Segmentation fault in getvar for large files
  • Date: Thu, 05 Sep 2013 10:52:47 -0600
Hi Vladimir,

> I use netCDF library (parallel, fortran version) about 4 years and it
> works perfectly!
> 
> But, on the new supercomputer i start to get very strange error.
> I searched for it in my program and investigation resulted in small test
> program, which creates parallel communicator and sequentially read rather
> big file (16 bil integers field in 540 mb file).
> 
> It crushes with segmentation fault on NF90_GET_VAR randomly.  For example,
> first run is normal, and second and third results in seg fault.
> 
> Interestengly, that for small files (for example 1 bil integers in 200
> mb file) it works perfectly.
> 
> Admin cant give me any helpful answers.
> 
> Could you please to suggest where problem is?

We would need to be able to duplicate the problem here, and I think that
would require access to the file you are reading or to a program that
creates it.  Even the output from "netcdf -h" might be sufficient for us
to generate an example that would demonstrate the problem.

Since the Unidata developer who knew the most about parallel I/O took a 
different job a couple of years ago, we've been lacking in parallel I/O 
knowledge and experiencee, so sometimes we have to forward questions to 
NCAR's consultants instead.

There have been a few bug fixes since netCDF-4.1.3 that relate to parallel
I/O, including both the Fortran library (in netcdf-fortran-4.2) and in the
netCDF-C library it calls (netCDF-4.3.0 or netCDF-4.3.1-rc2 using 
HDF5-1.8.11).

> Write me which commands i should run to provide you information about
> supercomputer and installed netCDF.

It would be useful to know what version of HDF5 you are using, and whether
you tried netCDF-fortran-4.2 with the netCDF C library version 4.3.0 or
later.

It might be interesting to know what supercomputer and operating system
you are using (the output from "uname -a"), but we currently only have
easy access to Linux, Mac, Solaris, and Windows systems on which to test.

--Russ

Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: VUY-537245
Department: Support netCDF
Priority: Normal
Status: Closed