<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Tomoko,<div class="">9 GB is anything but "large", although the concept of "large" is highly subjective :P </div><div class=""><br class=""></div><div class="">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.</div><div class=""><br class=""></div><div class="">You are setting a lot of options which I think are not needed. Did you just try to read the file with this line? </div><div class=""><br class=""></div><div class=""><blockquote type="cite" class="">fn=addfile(fdir+fili,"r")<br class=""></blockquote><br class=""></div><div class="">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...</div><div class=""><br class=""></div><div class="">Let us know.</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 18. Dec 2017, at 07:17, Tomoko Koyama <<a href="mailto:Tomoko.Koyama@Colorado.EDU" class="">Tomoko.Koyama@Colorado.EDU</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">I’d like to extract some data from a large netcdf file, which size is about 9GB.<br class=""><br class="">The following shows the partial script, but a submitted job was killed before “Data is stored” message appeared.<br class="">(I attempted several times with 3-hr max walltime )<br class=""><br class=""> setfileoption("nc", "FileStructure", "Advanced")<br class=""> fdir=“/root/dir4ncl/“<br class=""> fili="tas_day_IPSL-CM5A-LR_rcp85_r1i1p1_20060101-22051231.rgrd.nc"<br class=""> fn=addfile(fdir+fili,"r")<br class=""> setfileoption("nc","Format","NetCDF4Classic")<br class=""> buff=fn->tas<br class=""> print(“Data is stored”)<br class=""><br class="">Does it simply take a long time to read?<br class="">Is there anyway to speed up to read a large netcdf file?<br class=""><br class=""><br class="">Thank you,<br class="">Tomoko<br class="">_______________________________________________<br class="">ncl-talk mailing list<br class=""><a href="mailto:ncl-talk@ucar.edu" class="">ncl-talk@ucar.edu</a><br class="">List instructions, subscriber options, unsubscribe:<br class="">http://mailman.ucar.edu/mailman/listinfo/ncl-talk<br class=""></div></div></blockquote></div><br class=""><div class="">
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