Awesome Wei-Keng. This fixed the issue and the file now displays the data.
Thanks a lot for helping me out.
Best
Ram
On Fri, Feb 4, 2022 at 1:03 PM Wei-Keng Liao <wkliao@xxxxxxxxxxxxxxxx>
wrote:
> Attached is a C program that hacks into a NetCDF file and changes
> the number of records in the file header.
>
> Compile command:
> gcc hack_numrecs.c -o hack_numrecs
>
> Run command:
> ./hack_numrecs prod.nc 14
>
> Please backup your input file first.
>
> I tested it against file, prod.nc, by changing the number of
> records to 14 and verified the updated file with the utility
> program named 'ncvalidator'. It appears to me the only problem
> of the original prod.nc is the wrong number of records in the
> file header.
>
> Wei-keng
>
>
> On Feb 4, 2022, at 8:51 AM, Ramakrishnan N <ram.n.krishnan@xxxxxxxxx>
> wrote:
>
> I have a netcdf file (prod.nc
> <https://urldefense.com/v3/__http://prod.nc__;!!Dq0X2DkFhyF93HkjWTBQKhk!FK2mESqDdiPm0bi9x3pxACU8dfAUrVQrXaTHKWSRfp5xONugHQH7flIruBbX7k-Hkz6Y$>)
> that contains time series from a molecular dynamics simulation (Amber force
> field, OpenMM engine, parmed netCDFReporter). The netCDFReporter had some
> problems and as a result, the number of frames in the netcdf file is zero.
> Given below is the ncdump for the file:
>
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> *$ncdump -h prod.nc
> <https://urldefense.com/v3/__http://prod.nc__;!!Dq0X2DkFhyF93HkjWTBQKhk!FK2mESqDdiPm0bi9x3pxACU8dfAUrVQrXaTHKWSRfp5xONugHQH7flIruBbX7k-Hkz6Y$>
> netcdf prod { dimensions: frame = UNLIMITED ; // (0 currently)
> spatial = 3 ; atom = 20504 ; variables: char
> spatial(spatial) ; float time(frame) ; time:units =
> "picosecond" ; float coordinates(frame, atom, spatial) ;
> coordinates:units = "angstrom" ; // global attributes:
> :Conventions = "AMBER" ; :ConventionVersion = "1.0" ;
> :application = "AmberTools" ; :program =
> "ParmEd" ; :programVersion = "3.4.0+11.g1be8ca0f" ;
> :title = "ParmEd-created trajectory" ; }*
>
> However, the netcdf file has non-zero size (that increases linearly with
> the number of frames stored) which implies that it certainly has the data
> written into it. I tried a number of tools (nco tools, netCDF4, scipy
> netcdf reader, xarray) to access the missing data but have not succeeded.
>
>
>
>
>
> *I have two questions: 1. Does the file contain real data? 2. If the
> former, is there a way to retrieve the data and create a new netcdf file?*
>
> I am desperately looking to salvage near 3 microseconds of simulation data
> which would take more than 2 months to generate. I would greatly appreciate
> it if anyone can provide me with some insight into this problem.
>
> The attached netcdf file has 14 frames that can be used to examine the
> issue.
>
> Thanks in advance
>
> Best
> Ram
>
>
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