Thanks Wei-Keng. It is certainly a bug in parmEd and I have already filed
an issue report with them.
Best
Ram
On Sat, Feb 5, 2022 at 2:48 PM Wei-Keng Liao <wkliao@xxxxxxxxxxxxxxxx>
wrote:
> Great!
>
> As Gus pointed out that the corrupted file may be caused by a bug in
> the Amber IO routines, I encourage you to submit a github issue in
> ParmED repo if the problem persists and is reproducible.
>
> Wei-keng
>
> On Feb 4, 2022, at 12:12 PM, Ramakrishnan N <ram.n.krishnan@xxxxxxxxx>
> wrote:
>
> 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
>> <https://urldefense.com/v3/__http://prod.nc__;!!Dq0X2DkFhyF93HkjWTBQKhk!G72gvh3CO95w1D0Xt6zAA4C6D80DaZD8lCq5dp9UUGLyhFDrXU-31otuJESKItgINMRo$>
>> 14
>>
>> Please backup your input file first.
>>
>> I tested it against file, prod.nc
>> <https://urldefense.com/v3/__http://prod.nc__;!!Dq0X2DkFhyF93HkjWTBQKhk!G72gvh3CO95w1D0Xt6zAA4C6D80DaZD8lCq5dp9UUGLyhFDrXU-31otuJESKItgINMRo$>,
>> 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
>> <https://urldefense.com/v3/__http://prod.nc__;!!Dq0X2DkFhyF93HkjWTBQKhk!G72gvh3CO95w1D0Xt6zAA4C6D80DaZD8lCq5dp9UUGLyhFDrXU-31otuJESKItgINMRo$>
>> is the wrong number of records in the
>> file header.
>>
>> Wei-keng
>>
>>
>> On Feb 4, 2022, at 8:51 AM, Ramakrishnan N <ram.n.krishnan@xxxxxxxxx>
>> wrote:
>>
>> I have a netcdf file (prod.nc
>> <https://urldefense.com/v3/__http://prod.nc__;!!Dq0X2DkFhyF93HkjWTBQKhk!FK2mESqDdiPm0bi9x3pxACU8dfAUrVQrXaTHKWSRfp5xONugHQH7flIruBbX7k-Hkz6Y$>)
>> 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:
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> *$ncdump -h prod.nc
>> <https://urldefense.com/v3/__http://prod.nc__;!!Dq0X2DkFhyF93HkjWTBQKhk!FK2mESqDdiPm0bi9x3pxACU8dfAUrVQrXaTHKWSRfp5xONugHQH7flIruBbX7k-Hkz6Y$>
>> 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
>>
>>
>> <prod.nc
>> <https://urldefense.com/v3/__http://prod.nc__;!!Dq0X2DkFhyF93HkjWTBQKhk!G72gvh3CO95w1D0Xt6zAA4C6D80DaZD8lCq5dp9UUGLyhFDrXU-31otuJESKItgINMRo$>
>> >_______________________________________________
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>>
>>
>>
>>
>
