<div dir="ltr"><div>1] Like Alessandra wrote .... "a memory issue".<br><br> fatal:NclMalloc Failed <=== memory allocation error<br><br>[2] Like Wei wrote, the following will likely solve your problem<br><br> try change line:<br> cru = f->pre(iYYYY,:,:)<br> to:<br> cru = f->pre(iYYYY,{lat|latS:latN},{lon|lonE:lonE})<br><br> *** BUT THERE IS MORE TO IT THAN THIS ****<br><br>[3] Examine what you are doing:<br><br> yrStrt = 1958<br> yrLast = 2008<br> :<br> iYYYY = ind(YYYY.ge.yrStrt .and. YYYY.le.yrLast)<br> :<br> cru = f->pre(iYYYY,:,:)<br> printVarSummary(cru) ; variable overview<br><br><br>Look at the output from 'printVarSummary'<br><br>Based on the 'print(f)', there are 51(years)*12(months)= 612 time steps (iYYYY)<br><br>double pre ( time, lat, lon ) ; (612,360,720)<br><br>Since type 'double (8 bytes) ====> 8*612*360*720= 1,269,043,200 is approximately 1.3 GB<br><br><br>===========<br><br>According to your code, you only want the region<br><br> latS = -13.<br> latN = 16.<br> lonE = 21. <=== this is wrong .. should be lonW = 21.<br> lonE = 53. <br><br>so **why** are you reading in the **whole** array???<br><br>Also, why are you doing the following .... It is **not** needed. It uses another 1.3GB<br>because a copy of the array is made.<br><br> cru = lonFlip( cru )<br> printVarSummary(cru) ; note the longitude coord<br><br>The data span -180 to 180 ... lonW=21 to lonE=53 are readily available.<br><br><br>***<br>The point of this is that<br><br> USERS SHOULD NOT DIRECTLY USE THE PROVIDED EXAMPLES.<br><br>They are provided as templates and are not 'plug and use'.<br>***<br><br>======== My *guess* is that you want something like the following<br> ... PLEASE look at all of the output<br><br><br> cru = f->pre(iYYYY,{latS;latN},{lonW:lonE})<br> printVarSummary(cru) ; variable overview<br><br>; ==============================================================<br>; compute desired global seasonal mean: month_to_season (contributed.ncl)<br>; ==============================================================<br> SLP = month_to_season (cru, season)<br> nyrs = dimsizes(SLP&time)<br> printVarSummary(SLP)<br><br>; =================================================================<br>; create weights: sqrt(cos(lat)) [or sqrt(gw) ]<br>; =================================================================<br> rad = 4.*atan(1.)/180.<br> clat = SLP&lat ; use 'lat' associated with data<br> clat = sqrt( cos(rad*clat) ) ; gw for gaussian grid<br><br>; =================================================================<br>; weight all observations<br>; =================================================================<br> wSLP = SLP ; copy meta data<br> wSLP = SLP*conform(SLP, clat, 1)<br> wSLP@long_name = "Wgt: "+wSLP@long_name<br><br>; =================================================================<br>; Reorder (lat,lon,time) the *weighted* input data<br>; Access the area of interest via coordinate subscripting<br>; =================================================================<br> x = wSLP(lat|:,lon|:,time|:)<br><br> :<br><br><br>[4] Please read the NCL documentation<br><br><a href="http://www.ncl.ucar.edu/Document/Manuals/language_man.pdf">http://www.ncl.ucar.edu/Document/Manuals/language_man.pdf</a><br><br></div>or, a very nice tutorial created by DKRZ <br><div><br><a href="https://dl.dropboxusercontent.com/u/8357888/homepage/tutoriais/ncl/NCL_Tutorial_V1.1.pdf">https://dl.dropboxusercontent.com/u/8357888/homepage/tutoriais/ncl/NCL_Tutorial_V1.1.pdf</a><br><a href="https://dl.dropboxusercontent.com/u/8357888/homepage/tutoriais/ncl/NCL_Exercises_and_Tasks_all.pdf">https://dl.dropboxusercontent.com/u/8357888/homepage/tutoriais/ncl/NCL_Exercises_and_Tasks_all.pdf</a><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Sun, Apr 26, 2015 at 9:16 PM, Wei Huang <span dir="ltr"><<a href="mailto:huangwei@ucar.edu" target="_blank">huangwei@ucar.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_default"><span style="font-size:12.8000001907349px">Nana,</span></div><div class="gmail_default"><span style="font-size:12.8000001907349px"><br></span></div><div class="gmail_default"><span style="font-size:12.8000001907349px">Try change line:</span></div><div class="gmail_default"><span style="font-size:12.8000001907349px"> cru = f->pre(iYYYY,:,:)</span><br></div><div class="gmail_default"><span style="font-size:12.8000001907349px">to:</span></div><div class="gmail_default"><span style="font-size:12.8000001907349px"> cru = f->pre(iYYYY,</span>{lat|latS:latN},{lon|lonE:lonE})</div><div class="gmail_default"><br></div><div class="gmail_default">Which may solve your memory problem.</div><div class="gmail_default"><br></div><div class="gmail_default">Good luck.</div><div class="gmail_default"><br></div><div class="gmail_default">Wei</div></div><div class="gmail_extra"><br clear="all"><div><div><div dir="ltr"><font face="tahoma, sans-serif">================================================</font><div><font face="tahoma, sans-serif">1850 Table Mesa Dr.</font></div><div><font face="tahoma, sans-serif">Boulder, CO 80307</font></div><div><font face="tahoma, sans-serif">Phone: <a href="tel:303-497-8924" value="+13034978924" target="_blank">303-497-8924</a></font></div></div></div></div><div><div class="h5">
<br><div class="gmail_quote">On Sat, Apr 25, 2015 at 2:55 PM, Alessandra Giannini <span dir="ltr"><<a href="mailto:alesall@iri.columbia.edu" target="_blank">alesall@iri.columbia.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
Hello Nana,<br>
<br>
it looks like this could be generically a memory issue - your computer has a hard time managing all the data it is ingesting.<br>
<br>
As boring as this will sound, my suggestion is that you execute your script line by line, to see where it fails.<br>
By this I mean starting NCL and copying and pasting into the NCL environment line by line…<br>
<br>
warm regards, ale<br>
<br>
<br>
<br>
<br>
<br>
<br>
--<br>
Alessandra Giannini<br>
IRI for Climate and Society - The Earth Institute at Columbia University<br>
P.O. Box 1000, Palisades NY 10964-8000<br>
phone/fax: <a href="tel:%2B1%20845%20680-4473" value="+18456804473" target="_blank">+1 845 680-4473</a>/4864 - email: <a href="mailto:alesall@iri.columbia.edu" target="_blank">alesall@iri.columbia.edu</a><br>
<div><div><br>
On Apr 25, 2015, at 1:41 PM, Nana kofi Appiah-badu <<a href="mailto:justappia@gmail.com" target="_blank">justappia@gmail.com</a>> wrote:<br>
<br>
> Hello everyone,<br>
><br>
> I downloaded the eof script and using it to perform an eof analysis to obtain the first three eofs and their corresponding time series from the cru data from 1958 to 2008 during the MAM (MARCH, APRIL, MAY ) season. but this error message pops up after i start to run the script:<br>
><br>
> fatal:NclMalloc Failed:[errno=12]<br>
> Segmentation fault (core dumped)<br>
><br>
> below is the full output when i run the script.<br>
><br>
> Variable: f<br>
> Type: file<br>
> filename: cru<br>
> path: <a href="http://cru.nc" target="_blank">cru.nc</a><br>
> file global attributes:<br>
> Conventions : CF-1.4<br>
> title : CRU TS3.21 Precipitation<br>
> institution : Data held at British Atmospheric Data Centre, RAL, UK.<br>
> source : Run ID = 1307101324<br>
> Data generated by BADC from:<br>
> pre.1307101049.dtb<br>
> history : Wed 10 Jul 2013 18:28:10 BST : User ianharris : Program makegridsauto.for called by update.for<br>
> references : Information on the data is available at <a href="http://badc.nerc.ac.uk/data/cru/" target="_blank">http://badc.nerc.ac.uk/data/cru/</a><br>
> comment : Data restrictions: for academic research use only.Contact BADC for details<br>
> contact : BADC <<a href="mailto:badc@rl.ac.uk" target="_blank">badc@rl.ac.uk</a>><br>
> dimensions:<br>
> lon = 720<br>
> lat = 360<br>
> time = 1344 // unlimited<br>
> variables:<br>
> double lon ( lon )<br>
> long_name : longitude<br>
> units : degrees_east<br>
><br>
> double lat ( lat )<br>
> long_name : latitude<br>
> units : degrees_north<br>
><br>
> double time ( time )<br>
> long_name : time<br>
> units : days since 1900-1-1<br>
> calendar : gregorian<br>
><br>
> double pre ( time, lat, lon )<br>
> long_name : precipitation<br>
> units : mm<br>
> correlation_decay_distance : 450<br>
> _FillValue : 9.969209968386869e+36<br>
> missing_value : 9.969209968386869e+36<br>
><br>
><br>
> Variable: cru<br>
> Type: double<br>
> Total Size: 1269043200 bytes<br>
> 158630400 values<br>
> Number of Dimensions: 3<br>
> Dimensions and sizes: [time | 612] x [lat | 360] x [lon | 720]<br>
> Coordinates:<br>
> time: [21199..39796]<br>
> lat: [-89.75..89.75]<br>
> lon: [-179.75..179.75]<br>
> Number Of Attributes: 5<br>
> long_name : precipitation<br>
> units : mm<br>
> correlation_decay_distance : 450<br>
> _FillValue : 9.969209968386869e+36<br>
> missing_value : 9.969209968386869e+36<br>
> fatal:NclMalloc Failed:[errno=12]<br>
> Segmentation fault (core dumped<br>
><br>
> i have attached the script and the error after starting to run.<br>
><br>
> Thank you for your time and assistance.<br>
><br>
> Regards,<br>
><br>
> Nana.<br>
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