Issue with ncvar_get

[arcel0n]

Hi, I'm using ncdf4 to read EVI data over a large area in the Western Ghats of India. My code is as below:

library(ncdf4)
library(raster) 

library(ggplot2)


nc_data <- nc_open("C:/Users/lab23-user/Desktop/aayush_m/hmsc/data/evi_data.nc")

lon <- ncvar_get(nc_data, "lon")
lat <- ncvar_get(nc_data, "lat", verbose = F)
t <- ncvar_get(nc_data, "time")

ndvi.array <- ncvar_get(nc_data, "_250m_16_days_EVI")

However, while doing so I run into the following errors:

Error in Rsx_nc4_get_vara_int: NetCDF: Memory allocation (malloc) failure
Var: _250m_16_days_EVI  Ndims: 3   Start: 0,0,0 Count: 461,8243,4305
Error in ncvar_get_inner(ncid2use, varid2use, nc$var[[li]]$missval, addOffset,  : 
  C function Rsx_nc4_get_var_int returned error

I've tried Googling to find solutions but cannot find any to this problem, any direction would be appreciated! As a solution I have tried to request a subset of the original data (the data is from https://appeears.earthdatacloud.nasa.gov/) - but I would like to solve the issue as is.

[pvanlaake]

You are asking about package ncdf4 but this repo is for package RNetCDF. That said, it appears that your computer RAM is too small for the data that you accessed. Try a package that does a lazy load of your data, such as ncdfCF, and subset your data before loading it.

[mjwoods]

My apologies for the late reply. As @pvanlaake says, RNetCDF is not the same package as ncdf4, although both support NetCDF read/write in different ways.

The ability to read and write array slices is a design feature of the NetCDF file formats. This allows you to process large arrays in chunks that can fit into memory.

For ncget_var in ncdf4, there are optional arguments start and count that you can use to read slices of data. RNetCDF has the equivalent function var.get.nc with start and count arguments.