<div dir="ltr"><div class="gmail_default"><font color="#000000">Hi folks,</font></div><div class="gmail_default"><font color="#000000"><br></font></div><div class="gmail_default"><font color="#000000">These are all good suggestions.</font></div><div class="gmail_default"><font color="#000000"><br></font></div><div class="gmail_default"><font color="#000000">Another thing that is expensive in NCL is reordering arrays with syntax like:</font></div><div class="gmail_default"><font color="#000000"><br></font></div><div class="gmail_default"><font color="#000000"><span style="font-family:Calibri,Arial,Helvetica,sans-serif">snow(iy|:,jx|:,time|:),</span><br></font></div><div class="gmail_default"><span style="font-family:Calibri,Arial,Helvetica,sans-serif"><font color="#000000"><br></font></span></div><div class="gmail_default"><span style="font-family:Calibri,Arial,Helvetica,sans-serif"><font color="#000000">NCL makes a copy of the array when you do this, and it has to swap all the dimensions every time in the loop.</font></span></div><div class="gmail_default"><span style="font-family:Calibri,Arial,Helvetica,sans-serif"><font color="#000000"><br></font></span></div><div class="gmail_default"><span style="font-family:Calibri,Arial,Helvetica,sans-serif"><font color="#000000">Isf reordering the array is absolutely necessary? I see that you are reordering and then calling "dim_avg_n". Since you are already using dim_avg_n, why not leave the array as is and just change the dimension you do the average on?</font></span></div><div class="gmail_default"><span style="font-family:Calibri,Arial,Helvetica,sans-serif"><font color="#000000"><br></font></span></div><div class="gmail_default"><span style="font-family:Calibri,Arial,Helvetica,sans-serif"><font color="#000000">--Mary</font></span></div><div class="gmail_default"><span style="font-family:Calibri,Arial,Helvetica,sans-serif"><font color="#000000"><br></font></span></div><div class="gmail_extra"><font color="#000000"><br></font><div class="gmail_quote"><font color="#000000">On Tue, Jan 12, 2016 at 8:30 AM, Alan Brammer <span dir="ltr"><<a href="mailto:abrammer@albany.edu" target="_blank">abrammer@albany.edu</a>></span> wrote:<br></font><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word"><span style="font-family:Calibri,Arial,Helvetica,sans-serif;background-color:rgb(255,255,255)"><font color="#000000">Hi Michael, </font></span><div><font face="Calibri, Arial, Helvetica, sans-serif" color="#000000"><span style="background-color:rgb(255,255,255)"><br></span></font></div><div><font face="Calibri, Arial, Helvetica, sans-serif" color="#000000"><span style="background-color:rgb(255,255,255)"><br></span></font><div><font color="#000000"><font face="Calibri, Arial, Helvetica, sans-serif"><span style="background-color:rgb(255,255,255)">I was going to suggest reshape that data array but it’s 20GB and is going to be unnecessarily slow whatever. Do you actually need to store all the hourly data? the below edits suggest that you don’t. The below uses less than a 1GB of memory rather than 20+GB. </span></font><br></font><div><font color="#000000"><br></font></div><div><font color="#000000"><font face="Calibri, Arial, Helvetica, sans-serif"><span style="background-color:rgb(255,255,255)"> This is </span></font><span style="font-family:Calibri,Arial,Helvetica,sans-serif;background-color:rgb(255,255,255)">obviously untested so may need editing. </span></font></div><div><font face="Calibri, Arial, Helvetica, sans-serif" color="#000000"><span style="background-color:rgb(255,255,255)">(requires 6.1.1 or newer. )</span></font></div><div><font face="Calibri, Arial, Helvetica, sans-serif" color="#000000"><span style="background-color:rgb(255,255,255)"><br></span></font></div><div><font face="Calibri, Arial, Helvetica, sans-serif" color="#000000"><span style="background-color:rgb(255,255,255)"><br></span></font></div><div><font color="#000000"><font face="Calibri, Arial, Helvetica, sans-serif"><span style="background-color:rgb(255,255,255)"><span class=""><div>mns=(/"01","02","03","04","05","06","07","08","09","10","11","12"/)</div><div>ndays=(/31,28,31,30,31,30,31,31,30,31,30,31/)</div><div><br></div></span><div>daily=new((/141,217,20,12,31/),float) ; hourly data</div><div>daily@_FillValue=1e+35</div><div>daily=1e+35</div><span class=""><div><br></div><div>cnt=0</div><div>do iyr=0,19</div><div> do im=0,11</div><div> prefix=(1980+iyr)+""+mns(im)</div><div> b=addfile("/volumes/data1/yafang/Downscaling/ACCESS1-0/historical/output/ACCESS_SRF."+(1980+iyr)+""+mns(im)+"<a href="http://0100.nc" target="_blank">0100.nc</a>","r") ; read hourly SRF data</div><div> iy=b->iy</div><div> jx=b->jx</div></span><div> xlat=b->xlat <span style="white-space:pre-wrap"> </span>; These aren’t doing anything?</div><div> xlon=b->xlon <span style="white-space:pre-wrap"> </span>; These aren’t doing anything?</div></span></font><font face="Calibri, Arial, Helvetica, sans-serif"><span style="background-color:rgb(255,255,255)"><div> snow =b->snv ; liquid equiv of snow on ground</div><div> dims=dimsizes(snow)</div><div> nt=dims(0)</div><div><br></div><div> snow4d := reshape( snow(iy|:,jx|:,time|:), (/dims(1), dims(2), ndays(im), 24/) ) ; I assume snow is originally (time|:,iy|:,ix|:)</div><div> daily(:,:,iyr,im,:ndays(im)-1)=dim_avg_n(snow4d, 3)</div><span class=""><div><br></div><div> delete(snow)</div><div> delete(b)</div><div> delete(dims)</div><div> cnt=cnt+1</div><div> end do</div><div>end do</div><div><br></div></span><div>daily@_FillValue=1e+20</div><div><br></div></span></font></font></div><div><font color="#000000"><br></font></div><div><font face="Calibri, Arial, Helvetica, sans-serif" color="#000000"><span style="background-color:rgb(255,255,255)">Good luck, </span></font></div><span class="HOEnZb"><font color="#000000"><div><font face="Calibri, Arial, Helvetica, sans-serif"><span style="background-color:rgb(255,255,255)"><br></span></font></div><div><font face="Calibri, Arial, Helvetica, sans-serif"><span style="background-color:rgb(255,255,255)"><br></span></font></div><div><font face="Calibri, Arial, Helvetica, sans-serif"><span style="background-color:rgb(255,255,255)">Alan Brammer.</span></font></div></font></span><div><div class="h5"><div><font face="Calibri, Arial, Helvetica, sans-serif" color="#000000"><span style="background-color:rgb(255,255,255)"><br></span></font></div><div><font color="#000000"><br></font></div><div><font face="Calibri, Arial, Helvetica, sans-serif" color="#000000"><span style="background-color:rgb(255,255,255)"><br></span></font></div><div><font face="Calibri, Arial, Helvetica, sans-serif" color="#000000"><span style="background-color:rgb(255,255,255)"><br></span></font><div><blockquote type="cite"><div><font color="#000000">On 12 Jan 2016, at 10:00, Michael Notaro <<a href="mailto:mnotaro@wisc.edu" target="_blank">mnotaro@wisc.edu</a>> wrote:</font></div><font color="#000000"><br></font><div><div style="font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;font-family:Calibri,Arial,Helvetica,sans-serif;background-color:rgb(255,255,255)"><div style="margin-top:0px;margin-bottom:0px"><font color="#000000">Thanks for your email.</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"><br></font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000">Actually, this is the main part slowing me down, not the top part of the code with the addfiles.</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"><br></font></div><p style="margin-top:0px;margin-bottom:0px"></p><blockquote type="cite"><div><div style="font-family:Calibri,Arial,Helvetica,sans-serif"><div style="margin-top:0px;margin-bottom:0px"><font color="#000000">cnt=0</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000">do id=0,30</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"> daily(:,:,:,:,id)=dim_avg(data(:,:,:,:,cnt:cnt+23)) ; convert hourly to daily data ***** THIS PART IS SLOW *****</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"> cnt=cnt+24</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000">end do</font></div></div></div></blockquote><div><div><div style="font-family:Calibri,Arial,Helvetica,sans-serif"><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"><br></font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000">Any way to perform this task quicker?</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"><br></font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000">Michael</font></div></div></div></div><font color="#000000"><br></font><p style="margin-top:0px;margin-bottom:0px"></p><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"><br></font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"><br></font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"><br></font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"><br></font></div><div><div style="font-family:Calibri,Arial,Helvetica,sans-serif;background-color:rgb(255,255,255)"><font color="#000000">Michael Notaro<br></font><div><font color="#000000">Associate Director<br></font></div><div><font color="#000000">Nelson Institute Center for Climatic Research<br></font></div><div><font color="#000000">University of Wisconsin-Madison<br></font></div><div><font color="#000000">Phone: <a href="tel:%28608%29%20261-1503" value="+16082611503" target="_blank">(608) 261-1503</a><br></font></div><div><font color="#000000">Email:<span> </span><a href="mailto:mnotaro@wisc.edu" target="_blank">mnotaro@wisc.edu</a><br></font></div></div></div><font color="#000000"><br><br></font><div><font color="#000000"><hr style="display:inline-block;width:1120.125px"></font><div dir="ltr"><font face="Calibri, sans-serif" color="#000000"><b>From:</b><span> </span>Guido Cioni <<a href="mailto:guidocioni@gmail.com" target="_blank">guidocioni@gmail.com</a>><br><b>Sent:</b><span> </span>Tuesday, January 12, 2016 8:57 AM<br><b>To:</b><span> </span>Michael Notaro<br><b>Cc:</b><span> </span><a href="mailto:ncl-talk@ucar.edu" target="_blank">ncl-talk@ucar.edu</a><br><b>Subject:</b><span> </span>Re: [ncl-talk] Slow code</font><div><font color="#000000"> </font></div></div><div><font color="#000000">Everyone here will tell you that using loops in NCL it’s not efficient :)</font><div><font color="#000000">But from my experience I think that the main thing slowing you down is that you are using addfile at every iteration. </font></div><div><font color="#000000">Does creating a whole file and reading that in the beginning would change what you are trying to compute? <br></font><div><div style="font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><font color="#000000"><br>Guido Cioni</font></div><div style="font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><font color="#000000"><a href="http://guidocioni.altervista.org/" target="_blank">http://guidocioni.altervista.org</a> </font></div><div style="margin-bottom:20px;overflow:auto;width:1143px"><table cellspacing="0" style="width:1028px;overflow:auto;padding-top:20px;padding-bottom:20px;margin-top:20px;border-top-width:1px;border-top-style:dotted;border-top-color:rgb(200,200,200);border-bottom-width:1px;border-bottom-style:dotted;border-bottom-color:rgb(200,200,200);background-color:rgb(255,255,255)"><tbody><tr valign="top" style="border-spacing:0px"><td colspan="1" style="width:250px;display:table-cell;padding-right:20px"><div style="min-height:145px;margin:auto;display:table;width:250px;background-color:rgb(255,255,255)"><a href="http://guidocioni.altervista.org/" style="display:table-cell;text-align:center" target="_blank"><font color="#000000"><img width="250" height="145" src="http://guidocioni.altervista.org/nuovosito/wp-content/uploads/2015/10/Screenshot.png" style="display:inline-block;margin-left:auto;margin-right:auto;max-width:250px;max-height:250px;min-height:145px;width:250px;border-width:0px;vertical-align:bottom"></font></a></div></td><td colspan="2" style="vertical-align:top;padding:0px;display:table-cell"><div></div><div style="font-weight:normal;font-family:wf_segoe-ui_light,'Segoe UI Light','Segoe WP Light','Segoe UI','Segoe WP',Tahoma,Arial,sans-serif;line-height:21px"><a href="http://guidocioni.altervista.org/" style="text-decoration:none" target="_blank"><font color="#000000">Guido Cioni</font></a></div><div style="margin:10px 0px 16px;font-weight:normal;font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif;line-height:14px"><a href="http://guidocioni.altervista.org/" target="_blank"><font color="#000000">guidocioni.altervista.org</font></a></div><div style="display:block;font-weight:normal;font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif;line-height:20px;max-height:100px;overflow:hidden"><font color="#000000">Le stazioni sono state riparate ed i dati vengono nuovamente aggiornati in tempo reale. Purtroppo a causa di numerosi malfunzionamenti i dati pluviometrici di Pisa e ...</font></div></td></tr></tbody></table></div><font color="#000000"><br></font></div><font color="#000000"><br></font><div><blockquote type="cite"><div><font color="#000000">On 12 Jan 2016, at 15:35, Michael Notaro <<a href="mailto:mnotaro@wisc.edu" target="_blank">mnotaro@wisc.edu</a>> wrote:</font></div><font color="#000000"><br></font><div><div style="font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;font-family:Calibri,Arial,Helvetica,sans-serif;background-color:rgb(255,255,255)"><div style="margin-top:0px;margin-bottom:0px"><font color="#000000">Does anyone have a recommendation to speed up my code?</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000">It's been running for a day now. I put asterisks next to the real slow loop.</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000">Basically, that part is converting a large array of hourly data into daily data.</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000">Thanks, Michael</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"><br></font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"><br></font></div><p style="margin-top:0px;margin-bottom:0px"></p><div style="margin-top:0px;margin-bottom:0px"><font color="#000000">mns=(/"01","02","03","04","05","06","07","08","09","10","11","12"/)</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000">ndays=(/31,28,31,30,31,30,31,31,30,31,30,31/)</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"><br></font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000">data=new((/141,217,20,12,744/),float) ; hourly data</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000">data@_FillValue=1e+35</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000">data=1e+35</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"><br></font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000">cnt=0</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000">do iyr=0,19</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"> do im=0,11</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"> prefix=(1980+iyr)+""+mns(im)</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"> b=addfile("/volumes/data1/yafang/Downscaling/ACCESS1-0/historical/output/ACCESS_SRF."+(1980+iyr)+""+mns(im)+"<a href="http://0100.nc" target="_blank">0100.nc</a>","r") ; read hourly SRF data</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"> iy=b->iy</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"> jx=b->jx</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"> xlat=b->xlat</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"> xlon=b->xlon</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"> snow=b->snv ; liquid equiv of snow on ground</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"> dims=dimsizes(snow)</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"> nt=dims(0)</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"> data(:,:,iyr,im,0:nt-1)=snow(iy|:,jx|:,time|:)</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"> delete(snow)</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"> delete(b)</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"> delete(dims)</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"> cnt=cnt+1</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"> end do</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000">end do</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000">data@_FillValue=1e+20</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"><br></font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000">daily=new((/141,217,20,12,31/),float) ; daily data per month</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000">daily@_FillValue=1e+35</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000">daily=1e+35</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"><br></font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000">cnt=0</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000">do id=0,30</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"> daily(:,:,:,:,id)=dim_avg(data(:,:,:,:,cnt:cnt+23)) ; convert hourly to daily data ***** THIS PART IS SLOW *****</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"> cnt=cnt+24</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000">end do</font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"><br></font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000">delete(data)</font></div><font color="#000000"><br></font><p style="margin-top:0px;margin-bottom:0px"></p><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"><br></font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"><br></font></div><div style="margin-top:0px;margin-bottom:0px"><font color="#000000"><br></font></div><div><div style="font-family:Calibri,Arial,Helvetica,sans-serif;background-color:rgb(255,255,255)"><font color="#000000">Michael Notaro<br></font><div><font color="#000000">Associate Director<br></font></div><div><font color="#000000">Nelson Institute Center for Climatic Research<br></font></div><div><font color="#000000">University of Wisconsin-Madison<br></font></div><div><font color="#000000">Phone: <a href="tel:%28608%29%20261-1503" value="+16082611503" target="_blank">(608) 261-1503</a><br></font></div><div><font color="#000000">Email:<span> </span><a href="mailto:mnotaro@wisc.edu" target="_blank">mnotaro@wisc.edu</a><br></font></div></div></div></div><font color="#000000"><span 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