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Top Forums UNIX for Advanced & Expert Users Help optimizing sort of large files Post 302924356 by kogorman3 on Saturday 8th of November 2014 08:31:23 AM
Old 11-08-2014
My own results

Being the impatient sort, I tried a few things.

It appears that, on my machine at least, the default --buffer-size is 4 GB, which yields 1.8GB temporary files. Don't ask me why the roughly half-sized results. I surmise that pass 1 uses qsort on a full buffer to produce the initial temporaries.

It appears that, on my machine at least, the default --batch-size is 16, which for some reason forms the next level of temporaries by merging 15 small ones into a bigger one. Again, don't ask my why the disparity of -1.

As I fooled with things, the execution times I got were in discrete steps, approximate multiples of each other.

I surmise that the execution time is determined largely by the number of passes over the data. I am able to get that down to two passes on most of my datasets, and 3 at most. I did this by upping the limit on open files to the hard limit of 4096, and setting the batch size to 1000, plus setting the buffer size to 10 GB. I'm still experimenting to find a sweet spot.

I think staging multiple sorts might be counter-productive, since if I'm right, 2 is the minimum number of passes -- one to create temporaries, one to write the final result.

The idea of encoding the data is interesting. I'll explore it when I'm sure everything else works. I really like having readable data when debugging, which I am still doing.

BTW, you already have more than 10 lines of input. You can sort them to see the output. I sort on the whole record for this testing phase. Nothing to see here, folks.

My bash code now looks something like this:
Code:
ulimit -Sn hard
export TMPDIR=/mnt/h2/tmp
export LC_ALL=C
export SORT="--buffer-size=1000 --buffer-size=10g"

sort $SORT <infile> --output <outfile>


Last edited by kogorman3; 11-08-2014 at 09:35 AM.. Reason: typo
 

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SORT(1) 							   User Commands							   SORT(1)

NAME
sort - sort lines of text files SYNOPSIS
sort [OPTION]... [FILE]... sort [OPTION]... --files0-from=F DESCRIPTION
Write sorted concatenation of all FILE(s) to standard output. Mandatory arguments to long options are mandatory for short options too. Ordering options: -b, --ignore-leading-blanks ignore leading blanks -d, --dictionary-order consider only blanks and alphanumeric characters -f, --ignore-case fold lower case to upper case characters -g, --general-numeric-sort compare according to general numerical value -i, --ignore-nonprinting consider only printable characters -M, --month-sort compare (unknown) < `JAN' < ... < `DEC' -n, --numeric-sort compare according to string numerical value -R, --random-sort sort by random hash of keys --random-source=FILE get random bytes from FILE (default /dev/urandom) -r, --reverse reverse the result of comparisons --sort=WORD sort according to WORD: general-numeric -g, month -M, numeric -n, random -R, version -V -V, --version-sort sort by numeric version Other options: --batch-size=NMERGE merge at most NMERGE inputs at once; for more use temp files -c, --check, --check=diagnose-first check for sorted input; do not sort -C, --check=quiet, --check=silent like -c, but do not report first bad line --compress-program=PROG compress temporaries with PROG; decompress them with PROG -d --files0-from=F read input from the files specified by NUL-terminated names in file F; If F is - then read names from standard input -k, --key=POS1[,POS2] start a key at POS1 (origin 1), end it at POS2 (default end of line) -m, --merge merge already sorted files; do not sort -o, --output=FILE write result to FILE instead of standard output -s, --stable stabilize sort by disabling last-resort comparison -S, --buffer-size=SIZE use SIZE for main memory buffer -t, --field-separator=SEP use SEP instead of non-blank to blank transition -T, --temporary-directory=DIR use DIR for temporaries, not $TMPDIR or /tmp; multiple options specify multiple directories -u, --unique with -c, check for strict ordering; without -c, output only the first of an equal run -z, --zero-terminated end lines with 0 byte, not newline --help display this help and exit --version output version information and exit POS is F[.C][OPTS], where F is the field number and C the character position in the field; both are origin 1. If neither -t nor -b is in effect, characters in a field are counted from the beginning of the preceding whitespace. OPTS is one or more single-letter ordering options, which override global ordering options for that key. If no key is given, use the entire line as the key. SIZE may be followed by the following multiplicative suffixes: % 1% of memory, b 1, K 1024 (default), and so on for M, G, T, P, E, Z, Y. With no FILE, or when FILE is -, read standard input. *** WARNING *** The locale specified by the environment affects sort order. Set LC_ALL=C to get the traditional sort order that uses native byte values. AUTHOR
Written by Mike Haertel and Paul Eggert. REPORTING BUGS
Report sort bugs to bug-coreutils@gnu.org GNU coreutils home page: <http://www.gnu.org/software/coreutils/> General help using GNU software: <http://www.gnu.org/gethelp/> COPYRIGHT
Copyright (C) 2009 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>. This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. SEE ALSO
The full documentation for sort is maintained as a Texinfo manual. If the info and sort programs are properly installed at your site, the command info coreutils 'sort invocation' should give you access to the complete manual. GNU coreutils 7.1 July 2010 SORT(1)
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