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<p>Thank you, from a fellow SUNY Albany alumni! Using reshape is a creative idea. </p>
<p>Michael</p>
<p><br>
</p>
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<div id="divtagdefaultwrapper" style="font-size:12pt; color:#000000; background-color:#FFFFFF; font-family:Calibri,Arial,Helvetica,sans-serif">
Michael Notaro<br>
<div>Associate Director<br>
</div>
<div>Nelson Institute Center for Climatic Research<br>
</div>
<div>University of Wisconsin-Madison<br>
</div>
<div>Phone: (608) 261-1503<br>
</div>
<div>Email: mnotaro@wisc.edu<br>
</div>
</div>
</div>
<br>
<br>
<div style="color: rgb(0, 0, 0);">
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Alan Brammer <abrammer@albany.edu><br>
<b>Sent:</b> Tuesday, January 12, 2016 9:30 AM<br>
<b>To:</b> Michael Notaro<br>
<b>Cc:</b> ncl-talk@ucar.edu<br>
<b>Subject:</b> Re: [ncl-talk] Slow code</font>
<div> </div>
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<div><span class="" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; background-color:rgb(255,255,255)">Hi Michael, </span>
<div class=""><font face="Calibri, Arial, Helvetica, sans-serif" size="3" class=""><span class="" style="background-color:rgb(255,255,255)"><br class="">
</span></font></div>
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</span></font>
<div class=""><font face="Calibri, Arial, Helvetica, sans-serif" size="3" class=""><span class="" 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 class="">
<div class=""><br class="">
</div>
<div class=""><font face="Calibri, Arial, Helvetica, sans-serif" size="3" class=""><span class="" style="background-color:rgb(255,255,255)"> This is </span></font><span class="" style="background-color:rgb(255,255,255); font-family:Calibri,Arial,Helvetica,sans-serif; font-size:medium">obviously
untested so may need editing. </span></div>
<div class=""><font face="Calibri, Arial, Helvetica, sans-serif" size="3" class=""><span class="" style="background-color:rgb(255,255,255)">(requires 6.1.1 or newer. )</span></font></div>
<div class=""><font face="Calibri, Arial, Helvetica, sans-serif" size="3" class=""><span class="" style="background-color:rgb(255,255,255)"><br class="">
</span></font></div>
<div class=""><font face="Calibri, Arial, Helvetica, sans-serif" size="3" class=""><span class="" style="background-color:rgb(255,255,255)"><br class="">
</span></font></div>
<div class=""><font face="Calibri, Arial, Helvetica, sans-serif" size="3" class=""><span class="" style="background-color:rgb(255,255,255)">
<div class="">mns=(/"01","02","03","04","05","06","07","08","09","10","11","12"/)</div>
<div class="">ndays=(/31,28,31,30,31,30,31,31,30,31,30,31/)</div>
<div class=""><br class="">
</div>
<div class="">daily=new((/141,217,20,12,31/),float) ; hourly data</div>
<div class="">daily@_FillValue=1e+35</div>
<div class="">daily=1e+35</div>
<div class=""><br class="">
</div>
<div class="">cnt=0</div>
<div class="">do iyr=0,19</div>
<div class=""> do im=0,11</div>
<div class=""> prefix=(1980+iyr)+""+mns(im)</div>
<div class=""> b=addfile("/volumes/data1/yafang/Downscaling/ACCESS1-0/historical/output/ACCESS_SRF."+(1980+iyr)+""+mns(im)+"0100.nc","r") ; read hourly SRF data</div>
<div class=""> iy=b->iy</div>
<div class=""> jx=b->jx</div>
<div class=""> xlat=b->xlat <span class="Apple-tab-span" style="white-space:pre">
</span>; These aren’t doing anything?</div>
<div class=""> xlon=b->xlon <span class="Apple-tab-span" style="white-space:pre">
</span>; These aren’t doing anything?</div>
</span></font><font face="Calibri, Arial, Helvetica, sans-serif" size="3" class=""><span class="" style="background-color:rgb(255,255,255)">
<div class=""> snow =b->snv ; liquid equiv of snow on ground</div>
<div class=""> dims=dimsizes(snow)</div>
<div class=""> nt=dims(0)</div>
<div class=""><br class="">
</div>
<div class=""> snow4d := reshape( snow(iy|:,jx|:,time|:), (/dims(1), dims(2), ndays(im), 24/) ) ; I assume snow is originally (time|:,iy|:,ix|:)</div>
<div class=""> daily(:,:,iyr,im,:ndays(im)-1)=dim_avg_n(snow4d, 3)</div>
<div class=""><br class="">
</div>
<div class=""> delete(snow)</div>
<div class=""> delete(b)</div>
<div class=""> delete(dims)</div>
<div class=""> cnt=cnt+1</div>
<div class=""> end do</div>
<div class="">end do</div>
<div class=""><br class="">
</div>
<div class="">daily@_FillValue=1e+20</div>
<div class=""><br class="">
</div>
</span></font></div>
<div class=""><br class="">
</div>
<div class=""><font face="Calibri, Arial, Helvetica, sans-serif" size="3" class=""><span class="" style="background-color:rgb(255,255,255)">Good luck, </span></font></div>
<div class=""><font face="Calibri, Arial, Helvetica, sans-serif" size="3" class=""><span class="" style="background-color:rgb(255,255,255)"><br class="">
</span></font></div>
<div class=""><font face="Calibri, Arial, Helvetica, sans-serif" size="3" class=""><span class="" style="background-color:rgb(255,255,255)"><br class="">
</span></font></div>
<div class=""><font face="Calibri, Arial, Helvetica, sans-serif" size="3" class=""><span class="" style="background-color:rgb(255,255,255)">Alan Brammer.</span></font></div>
<div class=""><font face="Calibri, Arial, Helvetica, sans-serif" size="3" class=""><span class="" style="background-color:rgb(255,255,255)"><br class="">
</span></font></div>
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<blockquote type="cite" class="">
<div class="">On 12 Jan 2016, at 10:00, Michael Notaro <<a href="mailto:mnotaro@wisc.edu" class="">mnotaro@wisc.edu</a>> wrote:</div>
<br class="Apple-interchange-newline">
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<div class="" style="margin-top:0px; margin-bottom:0px">Thanks for your email.</div>
<div class="" style="margin-top:0px; margin-bottom:0px"><br class="">
</div>
<div class="" style="margin-top:0px; margin-bottom:0px">Actually, this is the main part slowing me down, not the top part of the code with the addfiles.</div>
<div class="" style="margin-top:0px; margin-bottom:0px"><br class="">
</div>
<p class="" style="margin-top:0px; margin-bottom:0px"></p>
<blockquote type="cite" class="" style="color:rgb(33,33,33); font-size:15px">
<div class="">
<div id="x_divtagdefaultwrapper" class="" style="widows:auto; font-size:12pt; font-family:Calibri,Arial,Helvetica,sans-serif">
<div class="" style="margin-top:0px; margin-bottom:0px">cnt=0</div>
<div class="" style="margin-top:0px; margin-bottom:0px">do id=0,30</div>
<div class="" style="margin-top:0px; margin-bottom:0px"> daily(:,:,:,:,id)=dim_avg(data(:,:,:,:,cnt:cnt+23)) ; convert hourly to daily data ***** THIS PART IS SLOW *****</div>
<div class="" style="margin-top:0px; margin-bottom:0px"> cnt=cnt+24</div>
<div class="" style="margin-top:0px; margin-bottom:0px">end do</div>
</div>
</div>
</blockquote>
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<div class="" style="margin-top:0px; margin-bottom:0px">Any way to perform this task quicker?</div>
<div class="" style="margin-top:0px; margin-bottom:0px"><br class="">
</div>
<div class="" style="margin-top:0px; margin-bottom:0px">Michael</div>
</div>
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<p class="" style="margin-top:0px; margin-bottom:0px"></p>
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<div id="Signature" class="">
<div id="divtagdefaultwrapper" class="" style="font-size:12pt; background-color:rgb(255,255,255); font-family:Calibri,Arial,Helvetica,sans-serif">
Michael Notaro<br class="">
<div class="">Associate Director<br class="">
</div>
<div class="">Nelson Institute Center for Climatic Research<br class="">
</div>
<div class="">University of Wisconsin-Madison<br class="">
</div>
<div class="">Phone: (608) 261-1503<br class="">
</div>
<div class="">Email:<span class="Apple-converted-space"> </span><a href="mailto:mnotaro@wisc.edu" class="">mnotaro@wisc.edu</a><br class="">
</div>
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<div id="divRplyFwdMsg" dir="ltr" class=""><font face="Calibri, sans-serif" class="" style="font-size:11pt"><b class="">From:</b><span class="Apple-converted-space"> </span>Guido Cioni <<a href="mailto:guidocioni@gmail.com" class="">guidocioni@gmail.com</a>><br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Tuesday, January 12, 2016 8:57 AM<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>Michael Notaro<br class="">
<b class="">Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:ncl-talk@ucar.edu" class="">ncl-talk@ucar.edu</a><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [ncl-talk] Slow code</font>
<div class=""> </div>
</div>
<div class="">Everyone here will tell you that using loops in NCL it’s not efficient :)
<div class="">But from my experience I think that the main thing slowing you down is that you are using addfile at every iteration. </div>
<div class="">Does creating a whole file and reading that in the beginning would change what you are trying to compute? <br class="">
<div class="">
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<br class="Apple-interchange-newline">
Guido Cioni</div>
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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 ...</div>
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<blockquote type="cite" class="">
<div class="">On 12 Jan 2016, at 15:35, Michael Notaro <<a href="mailto:mnotaro@wisc.edu" class="">mnotaro@wisc.edu</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div id="divtagdefaultwrapper" class="" style="font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px; font-size:12pt; background-color:rgb(255,255,255); font-family:Calibri,Arial,Helvetica,sans-serif">
<div class="" style="margin-top:0px; margin-bottom:0px">Does anyone have a recommendation to speed up my code?</div>
<div class="" style="margin-top:0px; margin-bottom:0px">It's been running for a day now. I put asterisks next to the real slow loop.</div>
<div class="" style="margin-top:0px; margin-bottom:0px">Basically, that part is converting a large array of hourly data into daily data.</div>
<div class="" style="margin-top:0px; margin-bottom:0px">Thanks, Michael</div>
<div class="" style="margin-top:0px; margin-bottom:0px"><br class="">
</div>
<div class="" style="margin-top:0px; margin-bottom:0px"><br class="">
</div>
<p class="" style="margin-top:0px; margin-bottom:0px"></p>
<div class="" style="margin-top:0px; margin-bottom:0px">mns=(/"01","02","03","04","05","06","07","08","09","10","11","12"/)</div>
<div class="" style="margin-top:0px; margin-bottom:0px">ndays=(/31,28,31,30,31,30,31,31,30,31,30,31/)</div>
<div class="" style="margin-top:0px; margin-bottom:0px"><br class="">
</div>
<div class="" style="margin-top:0px; margin-bottom:0px">data=new((/141,217,20,12,744/),float) ; hourly data</div>
<div class="" style="margin-top:0px; margin-bottom:0px">data@_FillValue=1e+35</div>
<div class="" style="margin-top:0px; margin-bottom:0px">data=1e+35</div>
<div class="" style="margin-top:0px; margin-bottom:0px"><br class="">
</div>
<div class="" style="margin-top:0px; margin-bottom:0px">cnt=0</div>
<div class="" style="margin-top:0px; margin-bottom:0px">do iyr=0,19</div>
<div class="" style="margin-top:0px; margin-bottom:0px"> do im=0,11</div>
<div class="" style="margin-top:0px; margin-bottom:0px"> prefix=(1980+iyr)+""+mns(im)</div>
<div class="" style="margin-top:0px; margin-bottom:0px"> b=addfile("/volumes/data1/yafang/Downscaling/ACCESS1-0/historical/output/ACCESS_SRF."+(1980+iyr)+""+mns(im)+"0100.nc","r") ; read hourly SRF data</div>
<div class="" style="margin-top:0px; margin-bottom:0px"> iy=b->iy</div>
<div class="" style="margin-top:0px; margin-bottom:0px"> jx=b->jx</div>
<div class="" style="margin-top:0px; margin-bottom:0px"> xlat=b->xlat</div>
<div class="" style="margin-top:0px; margin-bottom:0px"> xlon=b->xlon</div>
<div class="" style="margin-top:0px; margin-bottom:0px"> snow=b->snv ; liquid equiv of snow on ground</div>
<div class="" style="margin-top:0px; margin-bottom:0px"> dims=dimsizes(snow)</div>
<div class="" style="margin-top:0px; margin-bottom:0px"> nt=dims(0)</div>
<div class="" style="margin-top:0px; margin-bottom:0px"> data(:,:,iyr,im,0:nt-1)=snow(iy|:,jx|:,time|:)</div>
<div class="" style="margin-top:0px; margin-bottom:0px"> delete(snow)</div>
<div class="" style="margin-top:0px; margin-bottom:0px"> delete(b)</div>
<div class="" style="margin-top:0px; margin-bottom:0px"> delete(dims)</div>
<div class="" style="margin-top:0px; margin-bottom:0px"> cnt=cnt+1</div>
<div class="" style="margin-top:0px; margin-bottom:0px"> end do</div>
<div class="" style="margin-top:0px; margin-bottom:0px">end do</div>
<div class="" style="margin-top:0px; margin-bottom:0px">data@_FillValue=1e+20</div>
<div class="" style="margin-top:0px; margin-bottom:0px"><br class="">
</div>
<div class="" style="margin-top:0px; margin-bottom:0px">daily=new((/141,217,20,12,31/),float) ; daily data per month</div>
<div class="" style="margin-top:0px; margin-bottom:0px">daily@_FillValue=1e+35</div>
<div class="" style="margin-top:0px; margin-bottom:0px">daily=1e+35</div>
<div class="" style="margin-top:0px; margin-bottom:0px"><br class="">
</div>
<div class="" style="margin-top:0px; margin-bottom:0px">cnt=0</div>
<div class="" style="margin-top:0px; margin-bottom:0px">do id=0,30</div>
<div class="" style="margin-top:0px; margin-bottom:0px"> daily(:,:,:,:,id)=dim_avg(data(:,:,:,:,cnt:cnt+23)) ; convert hourly to daily data ***** THIS PART IS SLOW *****</div>
<div class="" style="margin-top:0px; margin-bottom:0px"> cnt=cnt+24</div>
<div class="" style="margin-top:0px; margin-bottom:0px">end do</div>
<div class="" style="margin-top:0px; margin-bottom:0px"><br class="">
</div>
<div class="" style="margin-top:0px; margin-bottom:0px">delete(data)</div>
<br class="">
<p class="" style="margin-top:0px; margin-bottom:0px"></p>
<div class="" style="margin-top:0px; margin-bottom:0px"><br class="">
</div>
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</div>
<div class="" style="margin-top:0px; margin-bottom:0px"><br class="">
</div>
<div id="Signature" class="">
<div id="divtagdefaultwrapper" class="" style="font-size:12pt; background-color:rgb(255,255,255); font-family:Calibri,Arial,Helvetica,sans-serif">
Michael Notaro<br class="">
<div class="">Associate Director<br class="">
</div>
<div class="">Nelson Institute Center for Climatic Research<br class="">
</div>
<div class="">University of Wisconsin-Madison<br class="">
</div>
<div class="">Phone: (608) 261-1503<br class="">
</div>
<div class="">Email:<span class="Apple-converted-space"> </span><a href="mailto:mnotaro@wisc.edu" class="">mnotaro@wisc.edu</a><br class="">
</div>
</div>
</div>
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<a href="http://mailman.ucar.edu/mailman/listinfo/ncl-talk" class="" style="font-family:Helvetica; font-size:13px; font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px">http://mailman.ucar.edu/mailman/listinfo/ncl-talk</a></div>
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<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px; float:none; display:inline!important">_______________________________________________</span><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px">
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<a href="mailto:ncl-talk@ucar.edu" class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px">ncl-talk@ucar.edu</a><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px">
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<a href="http://mailman.ucar.edu/mailman/listinfo/ncl-talk" class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px">http://mailman.ucar.edu/mailman/listinfo/ncl-talk</a><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px">
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