<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hello,<div class=""><br class=""></div><div class="">I noticed something else in your dox.ncl script that could potentially cause problems:</div><div class=""><font face="Menlo" class=""><br class=""></font></div><div class=""><font face="Menlo" class=""> a = addfile("dox_med_1.4-101.nc","r")<br class=""> ...</font></div><div class=""><font face="Menlo" class=""> diro = "./" ; Output directory<br class=""> filo = "dox_med_1.4-101.nc"<br class=""> system("/bin/rm -f " + diro + filo) ; remove if exists<br class=""> foutput = addfile (diro + filo, "c") ; open output file</font></div><div class=""><font face="Menlo" class=""> ...</font></div><div class=""><font face="Menlo" class=""> foutput->dox = (/dox_masked/)<br class=""></font><br class="">The possible issue I see with this is that the script reads from the file “dox_med_1.4-101.nc”, deletes the file, recreates the file, and then writes several variables back onto the file. If any errors occur before all of the desired variables are written to foutput, then you could end up with an incomplete input data file when you run this script in the future. If it’s absolutely necessary to use the same filename, you may want to instead use a temporary filename for “filo” and then rename the temporary file at the end of your script:</div><div class=""><span style="font-family: Menlo;" class=""><br class=""></span></div><div class=""><span style="font-family: Menlo;" class=""> </span><span style="font-family: Menlo;" class="">filo = "</span><font face="Menlo" class="">tmp_dox_med_1.4-101.nc"</font><br style="font-family: Menlo;" class=""><div class=""><font face="Menlo" class=""> foutput = addfile (diro + filo, "c") ; open output file</font></div></div><div class=""><font face="Menlo" class=""> ...</font></div><div class=""><font face="Menlo" class=""> </font><span style="font-family: Menlo;" class="">foutput->dox = </span><span style="font-family: Menlo;" class="">(/</span><span style="font-family: Menlo;" class="">dox_masked</span><span style="font-family: Menlo;" class="">/)</span></div><div class=""><span style="font-family: Menlo;" class=""> </span><span style="font-family: Menlo;" class="">system</span><span style="font-family: Menlo;" class="">(</span><span style="font-family: Menlo;" class="">"/bin/mv "</span><font face="Menlo" class=""> + diro + filo + " " + diro + "</font><span style="font-family: Menlo;" class="">dox_med_1.4-101.nc"</span><span style="font-family: Menlo;" class="">)</span></div><div class=""><br class=""></div><div class=""><br class="">I don’t think this is the cause of the memory allocation error, but I thought it might be worth mentioning anyway.</div><div class=""><br class=""></div><div class="">I hope this helps,</div><div class="">Kevin<br class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Dec 3, 2018, at 2:28 PM, Rick Brownrigg <<a href="mailto:brownrig@ucar.edu" class="">brownrig@ucar.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">Hi,</div><div class=""><br class=""></div><div class="">Errno=12 is "Cannot allocate memory".<br class=""></div><div class=""><br class=""></div><div class="">That dox variable looks to be about 2.6GB, and I can't quite tell, but it looks like you may be creating another 2 variables of comparable size(?) How much memory does you machine have? Can you tell how far the script gets executed (i.e., perhaps put some print statements at strategic places in the script to see how far it gets).</div><div class=""><br class=""></div><div class="">Rick<br class=""></div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="">On Mon, Dec 3, 2018 at 2:18 PM Amal Inge <<a href="mailto:amalingenieur89@gmail.com" class="">amalingenieur89@gmail.com</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class="">Dear NCL experts,</div><div class="">i tried to run the script attached but i had this error: fatal:NclMalloc Failed:[errno=12] Segmentation fault</div><div class="">what should be the solution please knowing that i have enough space in the memory ?</div><div class="">many thanks<br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">netcdf dox_med_1.4-101 {<br class="">dimensions:<br class=""> longitude = 670 ;<br class=""> latitude = 253 ;<br class=""> depth = 18 ;<br class=""> time = UNLIMITED ; // (215 currently)<br class="">variables:<br class=""> float longitude(longitude) ;<br class=""> longitude:standard_name = "longitude" ;<br class=""> longitude:long_name = "longitude" ;<br class=""> longitude:units = "degrees_east" ;<br class=""> longitude:axis = "X" ;<br class=""> float latitude(latitude) ;<br class=""> latitude:standard_name = "latitude" ;<br class=""> latitude:long_name = "latitude" ;<br class=""> latitude:units = "degrees_north" ;<br class=""> latitude:axis = "Y" ;<br class=""> float depth(depth) ;<br class=""> depth:standard_name = "depth" ;<br class=""> depth:long_name = "depth" ;<br class=""> depth:units = "m" ;<br class=""> depth:positive = "down" ;<br class=""> depth:axis = "Z" ;<br class=""> depth:_CoordinateAxisType = "Height" ;<br class=""> depth:_CoordinateZisPositive = "down" ;<br class=""> double time(time) ;<br class=""> time:standard_name = "time" ;<br class=""> time:long_name = "time" ;<br class=""> time:units = "seconds since 1970-01-01 00:00:00" ;<br class=""> time:calendar = "standard" ;<br class=""> time:axis = "T" ;<br class=""> float dox(time, depth, latitude, longitude) ;<br class=""> dox:standard_name = "mole_concentration_of_dissolved_molecular_oxygen_in_sea_water" ;<br class=""> dox:long_name = "Mole concentration of Dissolved Molecular Oxygen in sea water" ;<br class=""> dox:units = "millimol m-3" ;<br class=""> dox:_FillValue = 1.e+20f ;<br class=""> dox:missing_value = 1.e+20f ;<br class=""> dox:_ChunkSizes = 1, 22, 84, 161 ;<br class=""><br class="">// global attributes:<br class=""> :CDI = "Climate Data Interface version 1.8.1 (<a href="http://mpimet.mpg.de/cdi" target="_blank" class="">http://mpimet.mpg.de/cdi</a>)" ;<br class=""> :Conventions = "CF-1.0" ;<br class=""> :source = "3DVAR-OGSTM-BFM" ;<br class=""> :institution = "OGS (Istituto Nazionale di Oceanografia e di Geofisica Sperimentale) , Sgonico (Trieste) - Italy" ;<br class=""> :references = "Please check in CMEMS catalogue the INFO section for product MEDSEA_ANALYSIS_FORECAST_BIO_006_008 - <a href="http://marine.copernicus.eu/" target="_blank" class="">http://marine.copernicus.eu/</a>" ;<br class=""> :comment = "Please check in CMEMS catalogue the INFO section for product MEDSEA_ANALYSIS_FORECAST_BIO_006_008 - <a href="http://marine.copernicus.eu/" target="_blank" class="">http://marine.copernicus.eu/</a>" ;<br class=""> :contact = "<a href="mailto:servicedesk.cmems@mercator-ocean.eu" target="_blank" class="">servicedesk.cmems@mercator-ocean.eu</a>" ;<br class=""> :bulletin_date = "2017-12-01" ;<br class=""> :bulletin_type = "analysis" ;<br class=""> :field_type = "monthly_mean_beginning_at_time_field" ;<br class=""> :title = "Net Primary Production and Dissolved Oxygen (3D) - Monthly Mean" ;<br class=""> :History = "Translated to CF-1.0 Conventions by Netcdf-Java CDM (CFGridWriter2)\n",<br class=""> "Original Dataset = sv03-med-ogs-bio-rean-m; Translation Date = 2018-12-03T14:34:09.553Z" ;<br class=""> :geospatial_lat_min = 30.1875 ;<br class=""> :geospatial_lat_max = 45.9375 ;<br class=""> :geospatial_lon_min = -5.5625 ;<br class=""> :geospatial_lon_max = 36.25 ;<br class=""> :CDO = "Climate Data Operators version 1.8.1 (<a href="http://mpimet.mpg.de/cdo" target="_blank" class="">http://mpimet.mpg.de/cdo</a>)" ;<br class=""><br class=""></div></div></div></div>
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