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Top Forums UNIX for Advanced & Expert Users Help optimizing sort of large files Post 302925640 by kogorman3 on Tuesday 18th of November 2014 11:13:36 AM
Old 11-18-2014
Quote:
Originally Posted by Corona688
It doesn't work that way. It doesn't run 16384 individual merges simultaneously, then 4096 merges simultaneously, then 1024, etc etc. It always does the number you tell it to, as many times as it takes to process the list of things to do.
That makes no sense to me. If I tell it to make 1GB temporaries, my 13GB test file will make 13 of them and probably merge just once. If I tell it to make 1MB temporaries, it will make 13,000 of them, and likely have to merge the outputs of the first set of merges at least one extra time, handling the same data more times with more disk I/O.

My real TB-sized inputs will see this even more.

BTW, on skimming the sort source code, I found that by default it tries to make the buffer-size parameter 1/8 of physical memory: 4GB. That was so slow that I started this investigation. Smaller turned out to be better, possibly because none of the TLB or caches could deal with it effectively during the initial in-RAM merges because of the huge working set.

Quote:
I don't think small sorts hurt you, especially since they're small enough to be cached. What hurts you are merges on too many files at once for the disk to seek between, reducing it's I/O throughput.

Remember you are trying to find a "sweet spot" where CPU use and disk throughput are both at peak -- where the system can sustain full disk and cpu use.
Not sure what you mean about small sorts; I can't have them. I have large files, requiring large sorts. The files are large enough that I do not expect anything from previous merges to be available if the data has to be merged again, and I expect the data from different inputs to be far enough apart on disk to require seeks no matter what I do. Accordingly, I'd like to minimize the number of merge passes.

Even with these large sizes, sweet spots are exactly what I'm looking for.

Quote:
Check if you're eating into swap sometimes. Hitting swap could have severe performance penalties that throw off your tests.
I'm looking. But with the modest parameters I'm giving it, I hardly expect my 32-GB RAM to need to swap. The largest buffer-size I've ever tried is 4g, and that was already a bad idea and I don't do that any more. I'm distinctly sub-G now.
 

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SORT(1) 						      General Commands Manual							   SORT(1)

NAME
sort - sort a file of ASCII lines SYNOPSIS
sort [-bcdfimnru] [-tc] [-o name] [+pos1] [-pos2] file ... OPTIONS
-b Skip leading blanks when making comparisons -c Check to see if a file is sorted -d Dictionary order: ignore punctuation -f Fold upper case onto lower case -i Ignore nonASCII characters -m Merge presorted files -n Numeric sort order -o Next argument is output file -r Reverse the sort order -t Following character is field separator -u Unique mode (delete duplicate lines) EXAMPLES
sort -nr file # Sort keys numerically, reversed sort +2 -4 file # Sort using fields 2 and 3 as key sort +2 -t: -o out # Field separator is : sort +.3 -.6 # Characters 3 through 5 form the key DESCRIPTION
Sort sorts one or more files. If no files are specified, stdin is sorted. Output is written on standard output, unless -o is specified. The options +pos1 -pos2 use only fields pos1 up to but not including pos2 as the sort key, where a field is a string of characters delim- ited by spaces and tabs, unless a different field delimiter is specified with -t. Both pos1 and pos2 have the form m.n where m tells the number of fields and n tells the number of characters. Either m or n may be omitted. SEE ALSO
comm(1), grep(1), uniq(1). SORT(1)
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