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<mailto: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<mailto: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$>
is the wrong number of records in the
file header.
Wei-keng
On Feb 4, 2022, at 8:51 AM, Ramakrishnan N
<ram.n.krishnan@xxxxxxxxx<mailto:ram.n.krishnan@xxxxxxxxx>> wrote:
I have a netcdf file
(prod.nc<https://urldefense.com/v3/__http://prod.nc__;!!Dq0X2DkFhyF93HkjWTBQKhk!FK2mESqDdiPm0bi9x3pxACU8dfAUrVQrXaTHKWSRfp5xONugHQH7flIruBbX7k-Hkz6Y$>)
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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