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

> Hello John!
> 
> Apologies for the possible dupe, I had previously replied through
> webmail during my vacations but never knew if the mail went out
> correctly.
> 
> I'm very glad to hear the bug will be addressed in 4.2!
> I see the current downloadable dev version doesn't yet include that
> bugfix, I know you must have a lot on your hands.
> I was wondering if you could tell me what the release schedule for that
> version is, if there is one. I need to break the news to my boss and
> having an expected date for a fix may lift his mood a little. :)

ill make one later today and send you an email

> 
> As for using char type instead of binary, I chose to use that as I
> wanted to minimize type conversions over millions of variables over and
> over again while performing write and read operations, which could be a
> problem performance-wise. I may reconsider this, but have to make some
> benchmarks to justify redesigning how I handle the information
> internally.

yes, i would benchmark

> 
> Cheers!
> Fernando
> 
> On Fri, 2010-07-30 at 14:20 -0600, Unidata netCDF Java Support wrote:
> 
> > 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
> >
> 
> 
> 
> 


Ticket Details
===================
Ticket ID: KYX-566702
Department: Support netCDF Java
Priority: High
Status: Closed