Most file sorting programs will follow the design noted in External sorting - Wikipedia, the free encyclopedia -- i.e. they will create smaller temporary sorted files, then do as many merges as necessary to accomplish a final sort. If you think about it, this is very reasonable: you sort a memory-load of data (as an array, using one of any number of algorithms), write it out to a temporary file until all input files are read, then you read chunks from each sorted temporary to produce a final file. If there too many temporary files, you might need to do an intermediate merge, etc.
I just glanced though a few thousand lines of GNU sort ( part of coreutils, coreutils-8.5/src/sort.c ) and it seems to do the sorting into temporary files.
I think the most you could do to help a system sort is to provide one or more directories for the temporary files on devices different from the input file:
You could experiment with your own splitting by splitting a sample of your data, using utility split, and then sorting those files. I'd guess that would be slower than sort's internal splitting, but it might be worth a try, at least it would be educational.
You could also use a trace facility to look at the sort while it is going on. That would probably show scratch files being opened and child processes being created to help with the overall process: strace - trace system calls and signals, for example.
Hi,
May I know, if a pipe separated File is large, what is the best method to calculate the unique row count of 3rd column and get a list of unique value of the 3rdcolum?
Thanks in advance! (20 Replies)
This may sound like a trivial problem, but I still need some help:
I have a file with ids and I want to split it 'n' ways (could be any number) into files:
1
1
1
2
2
3
3
4
5
5
Let's assume 'n' is 3, and we cannot have the same id in two different partitions. So the partitions may... (8 Replies)
Input file
---------
12:name1:|host1|host1|host2|host1
13:name2:|host1|host1|host2|host3
14:name3:
......
Required output
---------------
12:name1:host1(2)|host1(1)
13:name2:host1(2)|host2(1)|host3(1)
14:name3:
where (x) - Count how many times field appears in last column
... (3 Replies)
Hi. I am not sure the title gives an optimal description of what I want to do.
I have several text files that contain data in many columns. All the files are organized the same way, but the data in the columns might differ. I want to count the number of times data occur in specific columns,... (0 Replies)
I would like to print unique lines without sort or unique. Unfortunately the server I am working on does not have sort or unique. I have not been able to contact the administrator of the server to ask him to add it for several weeks. (7 Replies)
Hi,
I have an input file that I have sorted in a previous stage by $1 and $4. I now need something that will take the first record from each group of data based on the key being $1
Input file
1000AAA|"ZZZ"|"Date"|"1"|"Y"|"ABC"|""|AA
1000AAA|"ZZZ"|"Date"|"2"|"Y"|"ABC"|""|AA... (2 Replies)
Dear community, I am facing a problem and I kindly ask your help:
I have 4 different data sets consisted from 3 different types of array.
On each file, column 1 is chromosome position, column 2 is SNP id etc... Lets say I have the following (bim) datasets:
x2014:
1 rs3094315... (4 Replies)
Discussion started by: fondan
4 Replies
LEARN ABOUT CENTOS
sort
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'
-h, --human-numeric-sort
compare human readable numbers (e.g., 2K 1G)
-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
-r, --reverse
reverse the result of comparisons
--sort=WORD
sort according to WORD: general-numeric -g, human-numeric -h, month -M, numeric -n, random -R, version -V
-V, --version-sort
natural sort of (version) numbers within text
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
--debug
annotate the part of the line used to sort, and warn about questionable usage to stderr
--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=KEYDEF
sort via a key; KEYDEF gives location and type
-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
--parallel=N
change the number of sorts run concurrently to N
-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
KEYDEF is F[.C][OPTS][,F[.C][OPTS]] for start and stop position, where F is a field number and C a character position in the field; both
are origin 1, and the stop position defaults to the line's end. 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 [bdfgiMhnRrV], which override global order-
ing 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.
GNU coreutils online help: <http://www.gnu.org/software/coreutils/> Report sort translation bugs to <http://translationproject.org/team/>
AUTHOR
Written by Mike Haertel and Paul Eggert.
COPYRIGHT
Copyright (C) 2013 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 uniq(1)
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 8.22 June 2014 SORT(1)