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
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