Error in using nco ncremap to remap one netcdf file to grid of another

I have a data set with multiple netcdf files with the same variables and structure, though the grid shifts in the time series periodically. I am working on simply remapping one file to another. However, the following command when run with the linked data files, 2016090618.nc and 2016090712.nc:

ncremap  -d 2016090618.nc  -i 2016090712.nc  -o outputfile_2016090712.nc

results in the following error:

Input #00: /content/drive/MyDrive/2016090712.nc
Grid(src): /tmp/ncremap_tmp_grd_src.nc.pid198744
Grid(dst): /tmp/ncremap_tmp_grd_dst.nc.pid198744
Map/Wgt  : /tmp/ncremap_tmp_map_nco_nco_con.nc.pid198744
ncks: ERROR nco_rgr_wgt() reports frc_out == frac_b contains all zeros
ncremap: ERROR Failed to horizontally regrid. cmd_rgr[0] failed. Debug this:
 ncks -O -t 2 --no_tmp_fl --gaa remap_script=ncremap --gaa remap_command="'/usr/bin/ncremap -d 2016090618.nc -i 2016090712.nc -o outputfile_2016090712.nc'" --gaa remap_hostname=e3d132815114 --gaa remap_version=4.9.1 --hdr_pad=10000    --rgr lat_nm_out=lat#lon_nm_out=lon --map="/tmp/ncremap_tmp_map_nco_nco_con.nc.pid198744" "/content/drive/MyDrive/Projects/20220014_CMM3/RDRS_input_data/CaPA_coarse/2016090712.nc" "outputfile_2016090712.nc"

This is being run in Google Colab with nco installed (thus the /content/drive/MyDrive path, and I omitted the exclamation mark from the ncremap command above).

I have tried to unpack the data with the -U flag and looked at the -R argument to no avail.

Incidentally, the cdo command below works fine to remap the file, but results in changes of the variable organization and naming that doesn't work well for my purposes, so I am trying to solve this with nco.

cdo remapbil,2016090618.nc 2016090712.nc outputfile_2016090712.nc

The good news is that newer versions of NCO do not die like you show above, so you might try upgrading to NCO 5.1.4:

zender@spectral:~/Downloads$ ncremap --version
ncremap, the NCO regridder and grid, map, and weight-generator, version 5.1.5-alpha02 "Champignons"
...
zender@spectral:~/Downloads$ ncremap -d 2016090618.nc -i 2016090712.nc -o outputfile_2016090712.nc
Input #00: /Users/zender/Downloads/2016090712.nc
Grid(src): /var/folders/ct/rzzvxlqn4_3f9cr8wgn2pm480000gn/T/ncremap_tmp_grd_src.nc.pid33012
Grid(dst): /var/folders/ct/rzzvxlqn4_3f9cr8wgn2pm480000gn/T/ncremap_tmp_grd_dst.nc.pid33012
Map/Wgt  : /var/folders/ct/rzzvxlqn4_3f9cr8wgn2pm480000gn/T/ncremap_tmp_map_nco_nco_con.nc.pid33012
zender@spectral:~/Downloads$ 

The bad news is that the input files, and thus the output file, all contain NaN values. NCO does not like NaN for reasons described here. So I cannot tell whether it works as intended. BTW, if you want bilinear rather than conservative regridding, then use ncremap --alg_typ=bilinear ....