parallel NetCDF: One or more variable sizes violate format constraints

[Felicity Graham]

Hi Wei-keng and Jim,

Thanks very much for your replies.

I think the file may be corrupted, as I can¹t read even a small segment in
serial.

I was wondering about that note in the ³Netcdf classic format limitations²
documentation. But, ncdump -k on the file returns Œclassic¹, so it
obviously hadn¹t been enabled at creation.

Thanks again,
Felicity


On 10/11/2015 3:51 pm, "Wei-keng Liao" <wkliao at eecs.northwestern.edu>
wrote:

>Hi, Felicity and Hi, Jim
>
>From netCDF 3.6.3 C Interface Guide, NC_64BIT_OFFSET is supported. See URL
>http://www.unidata.ucar.edu/software/netcdf/old_docs/docs_3_6_3/netcdf-c/n
>c_005fcreate.html#nc_005fcreate
>This flag, when used at file creation, allows creating a single file of
>size larger than 4 GB,
>but the number of elements in each array variable is still limited by 2
>billions.
>
>You can verify whether or not your file is created with this feature
>enabled by running command
>'ncdump -k file.nc' and the output should be '64-bit offset'. If you got
>'classic', then
>this feature is not enabled and your file may be corrupt, as Jim guessed.
>
>In PnetCDF, command 'ncmpidump -k' can also be used in the similar way.
>
>
>Wei-keng
>
>On Nov 9, 2015, at 9:24 PM, Jim Edwards wrote:
>
>> The netcdf-3 classic file is incorrect and probably corrupt -  16GB
>>exceeds the variable size constraints of that format.  You can use CDF5
>>as output by pnetcdf to write the file and then read it again with
>>pnetcdf but netcdf doesn't support the CDF5 standard until version 4.4.
>>
>>
>>
>>
>> On Mon, Nov 9, 2015 at 7:47 PM, Felicity Graham
>><f.s.graham at utas.edu.au> wrote:
>> Hello,
>>
>> I¹d like to use parallel netcdf in C to read the only variable from a
>>16GB netcdf file and perform some operations.
>>
>> The file format is classic, and was created with netcdf 3.6.3. I¹m
>>using openmpi 1.6.3 and pnetcdf 1.4.1.
>>
>> I¹ve tested on a separate netcdf-4 formatted file, and the reading
>>works fine, but on the classic file, I get the error  NetCDF: One or
>>more variable sizes violate format constraints when I try to open the
>>file (ncmpi_open).
>>
>> A stripped down version of the C code is below.
>>
>> Your help is much appreciated.
>>
>> Cheers,
>> Felicity
>>
>>
>> #include <stdio.h>
>> #include <mpi.h>
>> #include <pnetcdf.h>
>>
>> #define FILE_NAME ³<path_to_file>/hf_topog.nc"
>> #define VAR_NAME "hf_topog"
>>
>> #define CHECK_ERR {\
>>     if (err!=NC_NOERR) {\
>>         printf("Error at line=%d: %s\n", __LINE__,
>>ncmpi_strerror(err));\
>>         goto fn_exit;\
>>     }}
>>
>> int main(int argc, char **argv)
>> {
>>   int err, varid, ncid;
>>   float * topog_in;
>>
>>   MPI_Init(&argc,&argv);
>>
>>   err = ncmpi_open(MPI_COMM_WORLD, FILE_NAME, NC_NOWRITE,
>>MPI_INFO_NULL, &ncid);
>>   CHECK_ERR;
>>
>>   err = ncmpi_close(ncid);
>>   CHECK_ERR;
>>
>> fn_exit:
>>   MPI_Finalize();
>>
>>   return 0;
>> }
>>
>>
>>
>>
>> University of Tasmania Electronic Communications Policy (December,
>>2014).
>> This email is confidential, and is for the intended recipient only.
>>Access, disclosure, copying, distribution, or reliance on any of it by
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>>
>>
>>
>>
>> --
>> Jim Edwards
>>
>> CESM Software Engineer
>> National Center for Atmospheric Research
>> Boulder, CO
>



University of Tasmania Electronic Communications Policy (December, 2014).
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