Re: Seg Fault when Subsetting Large Files

Hi Carl,

What platform and ncl-version are you running on? Can you run ncl under gdb with this script and when it SEGV's, do a "bt" command?

Curiously, the script below works fine on my 8GB Mac. (It failed gracefully on my 4GB linux machine with a "can't allocate 3.7GB" error message).

Rick

On Feb 28, 2014, at 12:28 PM, Carl Schreck <cjschrec@ncsu.edu> wrote:

> I'm getting a seg fault when I try to subset a large file (5 GB). Consider this small example:
>
> path = "/snfs0/scratch/carl/u850.anom.nc"
> inFile = addfile( path, "r" )
>
> x0 = 5
> xn = 200
>
> data1 = inFile->u850(:,:,x0:xn)
> printVarSummary(data1)
> delete(data1)
>
> xInd = ispan(x0,xn,1)
> data2 = inFile->u850(:,:,xInd)
> printVarSummary(data2)
>
> It works fine on the first attempt when I read it using a range x0:xn. However, it seg faults on the second attempt where I try to subset it by an array (xInd). The machine I'm on has 120 GB of RAM, so it shouldn't be a memory issue.
>
> You can download the file at:
> ftp://filsrv.cicsnc.org/carl/largeFile/
> I also made the file in NCL, so I'll be curious if it's something that's improperly formatted there.
>
> Thanks for your help!
>
> Carl
>
> --
>
>
>
> Carl J. Schreck III, PhD
> Research Associate
> Cooperative Institute for Climate and Satellites NC
> North Carolina State University
> NOAA's National Climatic Data Center
> 151 Patton Ave, Asheville, NC 28801
> e: cjschrec@ncsu.edu
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Received on Fri Feb 28 14:37:44 2014