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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$> >> >_______________________________________________ >> NOTE: All exchanges posted to Unidata maintained email lists are >> recorded in the Unidata inquiry tracking system and made publicly >> available through the web. Users who post to any of the lists we >> maintain are reminded to remove any personal information that they >> do not want to be made public. >> >> >> netcdfgroup mailing list >> netcdfgroup@xxxxxxxxxxxxxxxx >> For list information or to unsubscribe, visit: >> https://urldefense.com/v3/__https://www.unidata.ucar.edu/mailing_lists/__;!!Dq0X2DkFhyF93HkjWTBQKhk!FK2mESqDdiPm0bi9x3pxACU8dfAUrVQrXaTHKWSRfp5xONugHQH7flIruBbX7peWmZi7$ >> >> >> >> >
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