[ncl-talk] Reading a large netcdf file

[Guido Cioni]

Tomoko,
9 GB is anything but "large", although the concept of "large" is highly subjective :P 

I've successfully read SINGLE netcdf files in NCL whose size was ~500GB so that shouldn't be the problem. For some reason a netcdf file of some size, say 400 GB, which has many timesteps is read more slowly than a file with the same size but with less timesteps; that was my impression.

You are setting a lot of options which I think are not needed. Did you just try to read the file with this line? 

> fn=addfile(fdir+fili,"r")

If it still takes a lot of time it could be system-dependent. When creating the variable NCL stores it into the RAM. If the system does not have enough RAM, some virtual memory will be created on your hard drive, which can slow down everything. But honestly I don't think you're even close to saturate your system's RAM. The problem may lie somewhere else...

Let us know.


> On 18. Dec 2017, at 07:17, Tomoko Koyama <Tomoko.Koyama at Colorado.EDU> wrote:
> 
> I’d like to extract some data from a large netcdf file, which size is about 9GB.
> 
> The following shows the partial script, but a submitted job was killed before “Data is stored” message appeared.
> (I attempted several times with 3-hr max walltime )
> 
> setfileoption("nc", "FileStructure", "Advanced")
> fdir=“/root/dir4ncl/“
> fili="tas_day_IPSL-CM5A-LR_rcp85_r1i1p1_20060101-22051231.rgrd.nc"
> fn=addfile(fdir+fili,"r")
> setfileoption("nc","Format","NetCDF4Classic")
> buff=fn->tas
> print(“Data is stored”)
> 
> Does it simply take a long time to read?
> Is there anyway to speed up to read a large netcdf file?
> 
> 
> Thank you,
> Tomoko
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Guido Cioni
http://guidocioni.altervista <http://guidocioni.altervista/>.org

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