I want to use ncap2 to make a large number of variables a function of time in a netcdf file. I therefore wanted to build up the command argument in a loop and store in a bash variable command and then apply it as a variable, which I often do with cdo like this
cdo $command in.nc out.nc
I build up my command like this:
varlist="hfls hfss prlr prw rlds rlus rlut rsds rsdt rsus rsut clt evspsbl"
command=""
for var in $varlist ; do
command+=" -s '${var}[time,lat,lon]=${var}'"
done
echo $command
when I then attempt to do this :
ncap2 $command in.nc out.nc
I get a segmentation fault and core dump. But if I cut and paste the result of the echo command into the ncap2 statement,
ncap2 -s 'hfls[time,lat,lon]=hfls' -s 'hfss[time,lat,lon]=hfss' -s 'prlr[time,lat,lon]=prlr' -s 'prw[time,lat,lon]=prw' -s 'rlds[time,lat,lon]=rlds' -s 'rlus[time,lat,lon]=rlus' -s 'rlut[time,lat,lon]=rlut' -s 'rsds[time,lat,lon]=rsds' -s 'rsdt[time,lat,lon]=rsdt' -s 'rsus[time,lat,lon]=rsus' -s 'rsut[time,lat,lon]=rsut' -s 'clt[time,lat,lon]=clt' -s 'evspsbl[time,lat,lon]=evspsbl' $dir/$file /scratch/b/$USER/${file%???}_corrected.nc
It works fine... I'm sure it is something to do with the way I'm handling the strings, but my experiments trying to change around quotes etc, didn't seem to work.
Yes, it seems to be a shell-quoting issue. Rather than try to create a simpler analogue for testing, let me start by just asking, does it work if you use this instead?
eval ncap2 $command in.nc out.nc