Help optimizing sort of large files Post: 302925641

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Top Forums UNIX for Advanced & Expert Users Help optimizing sort of large files Post 302925641 by Corona688 on Tuesday 18th of November 2014 11:20:50 AM

11-18-2014

Registered User

Quote:

Originally Posted by kogorman3

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.

This is because we are talking about different problems. You are talking about how many files it must split into -- I am talking about how many files are being merged at once.

Merging fewer files at once will mean less disk thrashing but more passes. Since you do not have an SSD input, the performance penalties for sustained disk thrashing -- skipping from file1 to file2 to file3 to file4 back to file1 -- are very, very high, hundredsfold. This could also be throwing off your results if the disk only thrashes sometimes due to unfortunate coincidences of access and cache.

Using the SSD as temp space may still be useful too, even if it's smaller than your file. It's another independent "spindle" you could be using to merge partial files in, particularly with the 'external sort' idea. Create n 20-gig sorted files on your SSD, merge them into one big sorted file on your main spindle, rinse, repeat.

Last edited by Corona688; 11-18-2014 at 12:32 PM..

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LEARN ABOUT X11R4

merge

MERGE(1)						      General Commands Manual							  MERGE(1)

NAME

       merge - three-way file merge

SYNOPSIS

       merge [ options ] file1 file2 file3

DESCRIPTION

       merge  incorporates all changes that lead from file2 to file3 into file1.  The result ordinarily goes into file1.  merge is useful for com-
       bining separate changes to an original.	Suppose file2 is the original, and both file1 and file3 are modifications of  file2.   Then  merge
       combines both changes.

       A  conflict  occurs  if	both  file1 and file3 have changes in a common segment of lines.  If a conflict is found, merge normally outputs a
       warning and brackets the conflict with <<<<<<< and >>>>>>> lines.  A typical conflict will look like this:

	      <<<<<<< file A
	      lines in file A
	      =======
	      lines in file B
	      >>>>>>> file B

       If there are conflicts, the user should edit the result and delete one of the alternatives.

OPTIONS

       -A     Output conflicts using the -A style of diff3(1), if supported by diff3.  This merges all changes leading from file2  to  file3  into
	      file1, and generates the most verbose output.

       -E, -e These  options  specify conflict styles that generate less information than -A.  See diff3(1) for details.  The default is -E.  With
	      -e, merge does not warn about conflicts.

       -L label
	      This option may be given up to three times, and specifies labels to be used in place of the corresponding  file  names  in  conflict
	      reports.	 That  is, merge -L x -L y -L z a b c generates output that looks like it came from files x, y and z instead of from files
	      a, b and c.

       -p     Send results to standard output instead of overwriting file1.

       -q     Quiet; do not warn about conflicts.

       -V     Print RCS's version number.

DIAGNOSTICS

       Exit status is 0 for no conflicts, 1 for some conflicts, 2 for trouble.

IDENTIFICATION

       Author: Walter F. Tichy.
       Manual Page Revision: 5.8.1; Release Date: 2012-06-06.
       Copyright (C) 2010-2012 Thien-Thi Nguyen.
       Copyright (C) 1990, 1991, 1992, 1993, 1994, 1995 Paul Eggert.
       Copyright (C) 1982, 1988, 1989 Walter F. Tichy.

SEE ALSO

       diff3(1), diff(1), rcsmerge(1), co(1).

BUGS

       It normally does not make sense to merge binary files as if they were text, but merge tries to do it anyway.

GNU RCS 5.8.1							    2012-06-06								  MERGE(1)

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