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[netCDFJava #KYX-566702]: negative seek offset error while reading variable

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  • Subject: [netCDFJava #KYX-566702]: negative seek offset error while reading variable
  • Date: Fri, 30 Jul 2010 14:20:15 -0600
Hi Fernando:

Yes, it was a bug in my code when the variable sizes are very large. 
Unfortunately, I cant retrofit this, so it will only get fixed in the latest 
(4.2) code. I will send you a notice when i have that ready. 

BTW, why do you use a char type? it looks like byte would be better. Although 
it doesnt much matter in C, in Java we are forced to map to a java char, which 
is 16 bits instead of 8, so size is doubled.

John


> Hi John,
> 
> I have made a tar.gz compressed netCDF file available at
> 
> http://bhusers.upf.edu/~fmuniz/inb/gwaspi/downloads/GT_73010105803CEST.nc.tar.gz
> 
> I'm afraid it's quite large, 1,4GB, but that's the nature of the beast.
> The variable I'm concerned with is called "genotypes". It's the only one
> with 3 dimensions as you will see.
> 
> Cheers!
> Fernando
> 
> On Fri, 2010-07-30 at 08:35 -0600, Unidata netCDF Java Support wrote:
> 
> > Hi Fernando:
> >
> > Can you send us an example file, or a URL to it? thanks
> >
> > John
> >
> > > Full Name: Fernando Mu?iz
> > > Email Address: address@hidden
> > > Organization: Universitat Pompeu Fabra
> > > Package Version: netcdfAll-4.1
> > > Operating System: Linux (Ubuntu)
> > > Hardware: 7.5GB of JVM ram
> > > Description of problem: Hello!
> > >
> > > I am getting an "java.io.IOException: Negative seek offset" error when 
> > > READING a variable with netCDF4.1 java API.
> > > The variable is a D3 array of CHAR datatype, with shape 1053 (unlimited 
> > > record), 2618957, 2.
> > >
> > > I get the error when reading subsets of it that are larger than 409 in 
> > > the first dimension (e.g 0:410:1, 0:0:1, 0:1:1).
> > > I note that the product of 410*2618957*2 = 2147544740 while 409*2618957*2 
> > > = 2142306826, results that encase 2147483647,
> > > the maximum signed integer in java.
> > >
> > > I'd have to mention that I was encountering problems with this type of 
> > > big datasets while WRITING as well in the netCDF4.0,
> > > but this bug was corrected in the netCDF4.1 version.
> > >
> > > I was wondering if you were using a signed integer for indexing intenally 
> > > and why not a long or double?
> > > My question is: is this a bug or a unmovable limitation of netCDF4.1?
> > >
> > > I don't send any code example mainly because this error is reproducible 
> > > using the netCDF Tools visualizer.
> > > If you need the data file I'm using, please reply to me and I'll give you 
> > > access to a downloadable compressed file.
> > >
> > > Kindly,
> > > Fernando Mu?iz
> > >
> > >
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: KYX-566702
> > Department: Support netCDF Java
> > Priority: Normal
> > Status: Open
> >
> 
> 
> 
> 


Ticket Details
===================
Ticket ID: KYX-566702
Department: Support netCDF Java
Priority: Normal
Status: Open