Hi Joe, Thanks for the multi-stage rechunking example. I've downloaded the example file you provided and will study it as I get time. --Russ > Hi Russ, > > Thank you for your answer! > > If it works like you say, that each input chunk is read just once and spread > out over the necessary output chunks, shouldn't there be an almost insatiable > need for chunk cache in the case where I'm rechunking from e.g. 1x360x720 to > 36890x1x1 (in other words changing from a map oriented layout to a time > series oriented one, each map is read in and spread out over every single > output chunk). > > Here's an example where rechunking in steps helps (I've made the example > original file available below): > > # First as one step: > address@hidden temp]$ time nccopy -c 'time/365,lon/1,lat/1' -m 1G -h 1G > Tair_daily_WFD_TYX_format_detrended_1901.nc Tair.nc > real 102m14.108s > > > # Then several: > address@hidden temp]$ time nccopy -c 'time/60,lon/60,lat/60' -m 1G -h 1G > Tair_daily_WFD_TYX_format_detrended_1901.nc Tair_60_60_60.nc > real 0m17.023s > > address@hidden temp]$ time nccopy -c 'time/183,lon/5,lat/5' -m 1G -h 1G > Tair_60_60_60.nc Tair_183_5_5.nc > real 0m44.065s > > address@hidden temp]$ time nccopy -c 'time/365,lon/1,lat/1' -m 1G -h 1G > Tair_183_5_5.nc Tair_365_1_1.nc > real 0m44.717s > > > The example file is available here if you wish to try it yourself (73 MB): > > http://stormbringer.nateko.lu.se/~joe/Tair_daily_WFD_TYX_format_detrended_1901.nc > > Note that it's compressed, I think a lot of the time in the first step above > is spent just compressing/decompressing (there's almost 100% CPU utilization). > > Thanks and best regards, > - Joe > > ________________________________________ > From: Unidata netCDF Support address@hidden > Sent: 08 April 2014 15:51 > To: Joe Siltberg > Cc: address@hidden > Subject: [netCDF #ACI-624328]: Experiences from rechunking with nccopy > > Hi Joe, > > > Thank you for that detailed answer! > > No problem. I'm at a conference all this week, so can't provide much detail > until next week. > However, I'm very interested in chunking issues, and would like to get back > to finding a > good solution for your use case. > > > So the chunk cache is only used to cache output chunks? Then it makes sense > > that it doesn't need much. > > Right, nccopy reads the input one chunk at (if it's chunked), and writes to > the output, > spreading the values among as many output chunks as needed. So if there's > insufficient > cache for holding all the output chunks that have values from one input > chunk, it will > have to write the same chunk multiple times, for each chunk that gets kicked > out of > the chunk cache to make room for other chunks. > > > So in the example file you looked at, rechunked from 1x360x720 to 60x60x60, > > nccopy will read in the first 60 time slices in order to create the first > > output chunk, and then restart and read them again (hopefully from OS disk > > cache next time) to create the next output chunk? > > No, I think it works as described above, only reading each input chunk once. > It might work > faster in some cases to read input values multiple times in order to write > output chunks > fewer times, but nccopy isn't smart enough to know how to do that yet. > > > My real data files are 100 times larger than the one I sent you (~7GB > > compressed, ~70GB decompressed). I can easily rechunk them to fairly square > > chunks, takes 20 minutes or so, but with very large chunk sizes on the time > > dimension (say 4000x1x1) it takes hours. Currently my strategy has been to > > do it in several steps, which seems to help. Is that a reasonable approach > > for large files or am I doing something wrong if it's that slow? > > I'm very interested in knowing about an example that works faster by > rechunking in several > nccopy steps. I've suspected that might sometimes be a better strategy, but > haven't figured > out a good example that demonstrates it. > > --Russ > > > I've been rechunking compressed files, and it seems to be CPU bound, if > > there's no input chunk cache (except the OS disk cache) that makes sense > > since it would need to decompress the same chunks over and over. > > > > Thanks and have a nice weekend! > > > > - Joe > > ________________________________________ > > From: Unidata netCDF Support address@hidden > > Sent: 03 April 2014 19:25 > > To: Joe Siltberg > > Cc: address@hidden > > Subject: [netCDF #ACI-624328]: Experiences from rechunking with nccopy > > > > Hi Joe, > > > > > I've been doing some rechunking of large files with nccopy, and have > > > encountered two potential issues. > > > > > > The first is that the -h switch seems to work only up to around 1.7 > > > GB. Specifying -h 2G or 5G doesn't seem to affect memory usage of > > > the process, or its performance. This was tested with 22.214.171.124 on 64 > > > bit CentOS, and also with your prebuilt 64 bit Windows binaries (also > > > 126.96.36.199). > > > > What you're seeing is that the performance isn't limited by the chunk > > cache size, it's limited by the actual I/O. Although you requested 5 > > GBytes of chunk cache, the library doesn't malloc that much, but only > > mallocs what it needs up to that amount. So it doesn't need more than > > 1.7 GBytes for the output file chunk cache in your case. > > > > Here's a demonstration you can see from the example file you sent, > > where you want to rechunk the variable Tair: > > > > dimensions: > > lon = 720 ; > > lat = 360 ; > > time = UNLIMITED ; // (365 currently) > > ... > > double Tair(time, lat, lon) ; > > > > from 365 x 360 x 720 to 60 x 60 x 60. I renamed your input file > > "htest.nc" and time each of the following commands after purging the > > OS disk buffers, so the data is actually read from the disk rather > > than from OS cache. If I run (and time) > > > > $ ./purge; time nccopy -c 'time/60,lat/60,lon/60' -m 5g -h 5g htest.nc > > tmp.nc > > real 0m28.33s > > > > But I get essentially the same time if I only reserve enough chunk > > cache for one output chunk, 60*60*60*8 bytes: > > > > $ ./purge; time nccopy -c 'time/60,lat/60,lon/60' -m 5g -h 1.728m htest.nc > > tmp.nc > > real 0m27.89s > > > > And I don't actually need to reserve any memory at all for the input > > buffer, because all it needs is enough for one chunk of the input, and > > it allocates that much by default: > > > > $ ./purge; time nccopy -c 'time/60,lat/60,lon/60' -h 1.728m htest.nc tmp.nc > > real 0m24.86s > > > > But if I don't have enough chunk cache to hold at least one chunk of > > the output file, it takes *much* longer: > > > > $ ./purge; time nccopy -c 'time/60,lat/60,lon/60' -h 1.727m htest.nc tmp.nc > > real 16m20.36s > > > > Your results will vary with more variables and more times. For > > example, with 2 variables of the size of Tair, you need to hold two > > chunks of output (about 3.5m), but in that case it turns out to be > > good to specify a larger input file buffer: > > > > $./purge; time nccopy -c 'time/60,lat/60,lon/60' -m 100m -h 3.5m htest2.nc > > tmp.nc > > real 2m49.04s > > > > Incidentally, I get better performance on the small example by using > > the "-w" option to use a diskless write and keep the output in memory > > until the output is closed, not using -h at all: > > > > $ ./purge; time nccopy -c 'time/60,lat/60,lon/60' -m 100m -w htest2.nc > > tmp.nc > > real 2m13.14s > > > > --Russ > > > > Russ Rew UCAR Unidata Program > > address@hidden http://www.unidata.ucar.edu > > > > > > > > Ticket Details > > =================== > > Ticket ID: ACI-624328 > > Department: Support netCDF > > Priority: Normal > > Status: Closed > > > > > > Russ Rew UCAR Unidata Program > address@hidden http://www.unidata.ucar.edu > > > > Ticket Details > =================== > Ticket ID: ACI-624328 > Department: Support netCDF > Priority: Normal > Status: Closed > > Russ Rew UCAR Unidata Program address@hidden http://www.unidata.ucar.edu Ticket Details =================== Ticket ID: ACI-624328 Department: Support netCDF Priority: High Status: Closed
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