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Full Discussion: Process multiple large files with awk
Top Forums Shell Programming and Scripting Process multiple large files with awk Post 302961892 by camor on Saturday 5th of December 2015 10:16:14 PM
Old 12-05-2015
Process multiple large files with awk
Hi there, I'm camor and I'm trying to process huge files with bash scripting and awk.
I've got a dataset folder with 10 files (16 millions of row each one - 600MB), and I've got a sorted file with all keys inside.
For example:
Code:
a sample_1 200
a.b sample_2 10
a sample_3 10

Code:
a sample_1 10
a sample_3 67

Code:
a sample_1 1
a.b sample_2 10
a sample_4 20

I would like to obtain an output like this:
Code:
a sample_1 200 10 1 211
a.b sample_2 10 0 10 20
a sample_3 10 67 0 77
a sample_4 0 0 20 20

I create a bash script like this, It produces a sorted file with all of my keys, it's very huge, about 62 millions of record, I slice this file into pieces and I pass each piece to my awk script.
Code:
#! /bin/bash
clear
FILENAME=<result>
BASEPATH=<base_path>
mkdir processed/slice
cat $BASEPATH/dataset/* | cut -d' ' -f1,2 > $BASEPATH/processed/aggr
sort -u -k2 $BASEPATH/processed/aggr > $BASEPATH/processed/sorted
split -d -l 1000000 processed/sorted processed/slice/slice-
echo $(date "+START PROCESSING DATE: %d/%m/%y - TIME: %H:%M:%S")
for filename in processed/slice/*; do
  awk -v filename="$filename" -f algorithm.awk dataset/* >> processed/$FILENAME
done
echo $(date "+END PROCESSING DATE: %d/%m/%y - TIME: %H:%M:%S")
rm $BASEPATH/processed/aggr
rm $BASEPATH/processed/sorted
rm -rf $BASEPATH/processed/slice

Here is my AWK script:
Code:
BEGIN{
while(getline < filename){
 key=$1" "$2;
 sources[key];
 for(i=1;i<11;i++){
   keys[key"-"i] = "0";
 }
}
close(filename);
}
{
if(FNR==1){
 ARGIND++;
}
key=$1" "$2;
keys[key"-"ARGIND] = $3
}END{
for (s in sources) {
 sum = 0
 printf "%s", s
 for (j=1;j<11;j++) {
   printf "%s%s", OFS, keys[s"-"j]
   sum += keys[s"-"j]
 }
print " "sum
}
}

I've figured out that my bottleneck came from iterating on dataset folder by awk input (10 files with 16.000.000 lines each). Everything is working on a small set of data, but with real data, RAM (30GB) congested. I thin the problem is " dataset/*" as AWK input.
Does anyone have any suggestions or advices? Thank you.
 

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LEARN ABOUT CENTOS

locale::codes::script

Locale::Codes::Script(3)				User Contributed Perl Documentation				  Locale::Codes::Script(3)

NAME

       Locale::Codes::Script - standard codes for script identification

SYNOPSIS

	  use Locale::Codes::Script;

	  $script  = code2script('phnx');		      # 'Phoenician'
	  $code    = script2code('Phoenician'); 	      # 'Phnx'
	  $code    = script2code('Phoenician',
				 LOCALE_CODE_NUMERIC);	      # 115

	  @codes   = all_script_codes();
	  @scripts = all_script_names();

DESCRIPTION

       The "Locale::Codes::Script" module provides access to standards codes used for identifying scripts, such as those defined in ISO 15924.

       Most of the routines take an optional additional argument which specifies the code set to use. If not specified, the default ISO 15924
       four-letter codes will be used.

SUPPORTED CODE SETS

       There are several different code sets you can use for identifying scripts. A code set may be specified using either a name, or a constant
       that is automatically exported by this module.

       For example, the two are equivalent:

	  $script = code2script('phnx','alpha');
	  $script = code2script('phnx',LOCALE_SCRIPT_ALPHA);

       The codesets currently supported are:

       alpha, LOCALE_SCRIPT_ALPHA
	   This is a set of four-letter (capitalized) codes from ISO 15924 such as 'Phnx' for Phoenician.  It also includes additions to this set
	   included in the IANA language registry.

	   The Zxxx, Zyyy, and Zzzz codes are not used.

	   This is the default code set.

       num, LOCALE_SCRIPT_NUMERIC
	   This is a set of three-digit numeric codes from ISO 15924 such as 115 for Phoenician.

ROUTINES

       code2script ( CODE [,CODESET] )
       script2code ( NAME [,CODESET] )
       script_code2code ( CODE ,CODESET ,CODESET2 )
       all_script_codes ( [CODESET] )
       all_script_names ( [CODESET] )
       Locale::Codes::Script::rename_script  ( CODE ,NEW_NAME [,CODESET] )
       Locale::Codes::Script::add_script  ( CODE ,NAME [,CODESET] )
       Locale::Codes::Script::delete_script  ( CODE [,CODESET] )
       Locale::Codes::Script::add_script_alias	( NAME ,NEW_NAME )
       Locale::Codes::Script::delete_script_alias  ( NAME )
       Locale::Codes::Script::rename_script_code  ( CODE ,NEW_CODE [,CODESET] )
       Locale::Codes::Script::add_script_code_alias  ( CODE ,NEW_CODE [,CODESET] )
       Locale::Codes::Script::delete_script_code_alias	( CODE [,CODESET] )
	   These routines are all documented in the Locale::Codes::API man page.

SEE ALSO

       Locale::Codes
	   The Locale-Codes distribution.

       Locale::Codes::API
	   The list of functions supported by this module.

       http://www.unicode.org/iso15924/
	   Home page for ISO 15924.

       http://www.iana.org/assignments/language-subtag-registry
	   The IANA language subtag registry.

AUTHOR

       See Locale::Codes for full author history.

       Currently maintained by Sullivan Beck (sbeck@cpan.org).

COPYRIGHT

	  Copyright (c) 1997-2001 Canon Research Centre Europe (CRE).
	  Copyright (c) 2001-2010 Neil Bowers
	  Copyright (c) 2010-2013 Sullivan Beck

       This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

perl v5.16.3							    2013-02-27						  Locale::Codes::Script(3)
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