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Due to the current gap in continued funding from the U.S. National Science Foundation (NSF), the NSF Unidata Program Center has temporarily paused most operations. See NSF Unidata Pause in Most Operations for details.
I emailed a couple weeks ago about an error we were seeing when moving from netcdf 4.4.2.1 to 4.3.1.1 when trying to create an unlimited
time dimension in our output in the GEOS 5 model.We just tried the new release candidate 4.3.2-rc1 and we were still seeing the crashing on line 274 of nc4var.c Unfortunately I still can't reproduce this outside of our model in a stand alone tester.
I did notice on thing that struck me as peculiar. In my stand alone tester, when I run with 4.4.2.1 and create a netcdf 4 file with an unlimited dimension called time and make 1-D variable time using this dimension an ncdump shows this for the time variable:
int time(time) ;
time:_Storage = "chunked" ;
time:_ChunkSizes = 1 ;
time:_Endianness = "little" ;
with the same code and 4.3.2-rc1 I get this
int time(time) ;
time:_Storage = "chunked" ;
time:_ChunkSizes = 1048576 ;
time:_Endianness = "little" ;
in both cases it says this about the time dimension
time = UNLIMITED ; // (0 currently)
In any case, I am sending the ncdump -sh output for a typical file we
had no problem creating with 4.4.2.1
On 03/05/2014 02:46 PM, Russ Rew wrote:
Hi Ben,A couple of questions. Your suggestion of setting the the chunking explicit doesn't seem like it would help as one first has to define the variable before you can set the chunk size and we are crashing when defining it unless I am missing something. We did notice that there are several code changes between 4.2.1 and 4.3.1.1 in the nc4_find_default_chunksizes2 in nc4var.c which is where we are crashing. In 4.2.1 if the dimension is unlimited the the chunksize is set to 1 and it looks like one would skip the code where we are crashing: suggested_size = (pow((double)DEFAULT_CHUNK_SIZE/(num_values * type_size), 1/(double)(var->ndims - num_set)) * var->dim[d]->len - .5); In 4.3.1.1 the setting of the unlimited dimension chunksize to 1 was removed. I'm guessing the code previous to 4.3.1.1 that set the chunksize to 1 for unlimited dimensions was saving us. We did notice that the latest version of nc4var.c on github has extra code after the line in question for set chunksizes of 1-D record variables as well as a few other changes so I'm wondering if this is a bug fix?I committed a change to make sure the statement above wouldn't divide by zero if num_values is zero, but I'm not sure that was the cause of the crash you encountered.Unfortunately we have not been able to reproduce this in a small example program but has there been some change underneath the hood that that might have occurred that we should be taking a look at?Could you please capture the output of "ncdump -sh yourfile.nc", for the file you were able to create using netCDF version 4.2.1, and send it to support-netcdf@xxxxxxxxxxxxxxxx? With that, we might be able to reproduce the problem using the ncgen utility. Thanks. --Russ
-- Ben Auer, PhD SSAI, Scientific Programmer/Analyst NASA GSFC, Global Modeling and Assimilation Office Code 610.1, 8800 Greenbelt Rd, Greenbelt, MD 20771 Phone: 301-286-9176 Fax: 301-614-6246
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