renaming dimension in netcdf file - netcdf

Question

I am a beginner with nco and I would appreciate some advice on my workflow and some help with a problem I an struggling with.
I have these data which contain 3D salinity values at two different time steps:
dimensions:
t = 780 ;
z = 54 ;
y = 450 ;
x = 3600 ;
variables:
double time(t) ;
time:units = "days since 1-1-1 00:00:0.0" ;
float level(z) ;
level:units = "[m]" ;
float lat(y) ;
float lon(x) ;
float salt(x, y, z) ;
salt:units = "psu * 1000 + 35" ;
salt:missingvalue = "-1.0E34" ;
salt:longname = "salinity" ;
I want to concatenate the two netcdf files.
To do so I first use ncecat *.nc -O merged.nc:
dimensions:
record = UNLIMITED ; // (2 currently)
t = 780 ;
z = 54 ;
y = 450 ;
x = 3600 ;
variables:
double time(record, t) ;
time:units = "days since 1-1-1 00:00:0.0" ;
float level(record, z) ;
level:units = "[m]" ;
float lat(record, y) ;
float lon(record, x) ;
float salt(record, x, y, z) ;
salt:units = "psu * 1000 + 35" ;
salt:missingvalue = "-1.0E34" ;
salt:longname = "salinity" ;
where now the variable time and dimension t are spurious. So, I delete them with ncks -O -x -v time merged.nc merged.nc:
record = UNLIMITED ; // (2 currently)
y = 450 ;
z = 54 ;
x = 3600 ;
variables:
float lat(record, y) ;
float level(record, z) ;
level:units = "[m]" ;
float lon(record, x) ;
float salt(record, x, y, z) ;
salt:units = "psu * 1000 + 35" ;
salt:missingvalue = "-1.0E34" ;
salt:longname = "salinity" ;
Now, I want to rename the dimension record with: ncrename -d record,time merged.nc. The command runs with no errors or warnings. But when I do ncdump -h merged.nc I get this error:
ncdump: merged.nc: NetCDF: HDF error
What does this mean? Where do I do wrong?
EDIT
Following the answer posted by Charlie Zender
ncecat -O -u time *.nc merged.nc
ncks -O -x -v time merged.nc merged.nc
result in:
dimensions:
time = UNLIMITED ; // (2 currently)
y = 450 ;
z = 54 ;
x = 3600 ;
t = 780 ;
variables:
float lat(time, y) ;
float level(time, z) ;
level:units = "[m]" ;
float lon(time, x) ;
float salt(time, x, y, z) ;
salt:units = "psu * 1000 + 35" ;
salt:missingvalue = "-1.0E34" ;
salt:longname = "salinity" ;
double time(time, t) ;
time:units = "days since 1-1-1 00:00:0.0" ;
// global attributes:
:history = "Tue Jun 5 09:08:25 2018: ncks -O -x -v time merged.nc merged.nc\nTue Jun 5 09:08:19 2018: ncecat -O -u time OFES_salt_mmean_607.nc OFES_salt_mmean_608.nc merged.nc" ;
:NCO = "netCDF Operators version 4.7.4 (http://nco.sf.net)" ;
:nco_openmp_thread_number = 1 ;

Answer 1

Firstly, the command I recommend is
ncecat -O -u time *.nc merged.nc
That prevents the need to rename record to time. Then
ncks -O -x -v time merged.nc merged.nc
Does that work?
Answer to EDITed question:
Regarding the error received with ncrename, you may have encountered a netCDF4 library bug described here. The recommended solution is to convert to netCDF3, rename, then convert back to netCDF4 if desired:
ncks -3 in.nc out.nc
ncrename -d record,time out.nc
ncks -4 out.nc out.nc