terra package on geo cluster

[mitchellmanware]

When importing NCEP NARR data with terra::rast() on the ddn/, the extent and resolution are not recognized.

ddn/

> getwd()
[1] "/ddn/gs1/home/manwareme/function_copies/process"
> w <- terra::rast("data/weasd/weasd.2018.nc")
Warning message:
[rast] GDAL did not find an extent. installing the ncdf4 package may help 
> w
class       : SpatRaster 
dimensions  : 277, 349, 365  (nrow, ncol, nlyr)
resolution  : 1, 1  (x, y)
extent      : 0, 349, 0, 277  (xmin, xmax, ymin, ymax)
coord. ref. : +proj=lcc +lat_0=50 +lon_0=-107 +lat_1=50 +lat_2=50 +x_0=5632642.22547 +y_0=4612545.65137 +datum=WGS84 +units=m +no_defs 
source      : weasd.2018.nc:weasd 
varname     : weasd (Daily Accumulated Snow at Surface) 
names       : weasd_1, weasd_2, weasd_3, weasd_4, weasd_5, weasd_6, ... 
unit        :  kg/m^2,  kg/m^2,  kg/m^2,  kg/m^2,  kg/m^2,  kg/m^2, ... 
time        : 2018-01-01 to 2018-12-31 UTC 
> 

This problem does not occur, however, when the same data set (using the /Volumes/... path) is read on my machines local version of R.
local

> getwd()
[1] "/Volumes/manwareme/function_copies/process"
> w <- terra::rast("data/weasd/weasd.2018.nc")
> w
class       : SpatRaster 
dimensions  : 277, 349, 365  (nrow, ncol, nlyr)
resolution  : 32462.99, 32463  (x, y)
extent      : -16231.49, 11313351, -16231.5, 8976020  (xmin, xmax, ymin, ymax)
coord. ref. : +proj=lcc +lat_0=50 +lon_0=-107 +lat_1=50 +lat_2=50 +x_0=5632642.22547 +y_0=4612545.65137 +datum=WGS84 +units=m +no_defs 
source      : weasd.2018.nc:weasd 
varname     : weasd (Daily Accumulated Snow at Surface) 
names       : weasd_1, weasd_2, weasd_3, weasd_4, weasd_5, weasd_6, ... 
unit        :  kg/m^2,  kg/m^2,  kg/m^2,  kg/m^2,  kg/m^2,  kg/m^2, ... 
time        : 2018-01-01 to 2018-12-31 UTC 
> 

The recommended next step is to install the ncdf4 package, which I believe needs to be done by OSC. Two questions related to this are:

1. Has any experienced a similar problem when using the terra package on the new geo cluster?
2. Might this be related to the other gdal-bin related issue @sigmafelix noted with the conversion of NLCD *.img to *.tif files?

[mitchellmanware]

Note:
Importing data with terra::rast() on ddn/ version of R does recognize extent and resolution for an .nc4 file from GEOS-CF. Will continue to look into this.

> getwd()
[1] "/ddn/gs1/home/manwareme/function_copies/process/data/aqc_tavg_1hr_g1440x721_v1"
> library(terra)
terra 1.7.46
> aqc <- terra::rast("GEOS-CF.v01.rpl.aqc_tavg_1hr_g1440x721_v1.20230901_0030z.nc4")
> aqc
class       : SpatRaster 
dimensions  : 721, 1440, 5  (nrow, ncol, nlyr)
resolution  : 0.25, 0.25  (x, y)
extent      : -180.125, 179.875, -90.125, 90.125  (xmin, xmax, ymin, ymax)
coord. ref. :  
sources     : GEOS-CF.v01.rpl.aqc_tavg_1hr_g1440x721_v1.20230901_0030z.nc4:CO  
              GEOS-CF.v01.rpl.aqc_tavg_1hr_g1440x721_v1.20230901_0030z.nc4:NO2  
              GEOS-CF.v01.rpl.aqc_tavg_1hr_g1440x721_v1.20230901_0030z.nc4:O3  
              ... and 2 more source(s)
varnames    : CO (Carbon monoxide (CO, MW = 28.00 g mol-1) volume mixing ratio dry air) 
              NO2 (Nitrogen dioxide (NO2, MW = 46.00 g mol-1) volume mixing ratio dry air) 
              O3 (Ozone (O3, MW = 48.00 g mol-1) volume mixing ratio dry air) 
              ...
names       : CO_lev=72, NO2_lev=72, O3_lev=72, PM25_R~lev=72, SO2_lev=72 
unit        : mol mol-1,  mol mol-1, mol mol-1,        ug m-3,  mol mol-1 
time (raw)  : 0 
> 

[sigmafelix]

@mitchellmanware

I found the same issue both in geo cluster (via SLURM job submission) and triton (ssh). I think Frank at OSC can help you to install NetCDF system library both on geo and triton (as far as I experienced, he installs a requested package on all HPC clusters managed by OSC). Please refer to the link to ask the exact package to be installed (NetCDF on Rocky Linux 8)

[mitchellmanware]

Thank you, Insang. I will consult with Frank.

[mitchellmanware]

Frank installed the ncdf4 package on geo/triton which fixed issues.