Multi thread awk command for faster performance Post: 302632149

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Top Forums Shell Programming and Scripting Multi thread awk command for faster performance Post 302632149 by drl on Sunday 29th of April 2012 09:50:03 AM

04-29-2012

Registered User

Hi.

Quote:

A thread is a lightweight process. The implementation of threads and processes differs from one operating system to another, but in most cases, a thread is contained inside a process. Multiple threads can exist within the same process and share resources such as memory, while different processes do not share these resources. -- excerpt from http://en.wikipedia.org/wiki/Thread_(computing)

Here is a sample use of GNU parallel that counts file contents with wc:

Code:

#!/usr/bin/env bash

# @(#) s1	Demonstrate multiple processes simultaneously, with "GNU parallel".

pe() { for _i;do printf "%s" "$_i";done; printf "\n"; }
pl() { pe;pe "-----" ;pe "$*"; }
db() { ( printf " db, ";for _i;do printf "%s" "$_i";done;printf "\n" ) >&2 ; }
db() { : ; }
C=$HOME/bin/context && [ -f $C ] && $C parallel

pl " Structure of directories:"
tree d1 d2

pl " Results of parallel processes:"
ls d1/* d2/* |
grep txt |
parallel --ungroup 'echo -n job {#}, process $$", wc = "; wc {}' |
align

exit 0

producing:

Code:

% ./s1

Environment: LC_ALL = C, LANG = C
(Versions displayed with local utility "version")
OS, ker|rel, machine: Linux, 2.6.26-2-amd64, x86_64
Distribution        : Debian GNU/Linux 5.0.8 (lenny) 
bash GNU bash 3.2.39
parallel GNU parallel 20111122

-----
 Structure of directories:
d1
|-- a.txt
|-- b.txt
|-- binary-1.exe
`-- c.txt
d2
|-- frog-town.jpg
|-- x.txt
`-- y.txt

0 directories, 7 files

-----
 Results of parallel processes:
job 1, process 27495, wc =  4  16   70 d1/a.txt
job 2, process 27515, wc = 16  16  123 d1/b.txt
job 3, process 27535, wc = 26 265 1464 d1/c.txt
job 4, process 27555, wc =  4  16   70 d2/x.txt
job 5, process 27575, wc = 16  16  123 d2/y.txt

Each one of the tasks was run as a separate process. The calling sequence for parallel is complex, so some experimentation might be useful. I have not tried it, but I think parallel claims to be able to utilize different computers for tasks.

The code for the (perl) parallel script is at GNU Parallel - GNU Project - Free Software Foundation

Best wishes ... cheers, drl

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srun_cr

SRUN_CR(1)							 slurm components							SRUN_CR(1)

NAME

       srun_cr - run parallel jobs with checkpoint/restart support

SYNOPSIS

       srun_cr [OPTIONS...]

DESCRIPTION

       The  design of srun_cr is inspired by mpiexec_cr from MVAPICH2 and cr_restart form BLCR.  It is a wrapper around the srun command to enable
       batch job checkpoint/restart support when used with SLURM's checkpoint/blcr plugin.

OPTIONS

       The srun_cr execute line options are identical to those of the srun command.  See "man srun" for details.

DETAILS

       After initialization, srun_cr registers a thread context callback function.  Then it forks a process and executes "cr_run --omit srun" with
       its  arguments.	 cr_run  is  employed to exclude the srun process from being dumped upon checkpoint.  All catchable signals except SIGCHLD
       sent to srun_cr will be forwarded to the child srun process.  SIGCHLD will be captured to mimic the exit status	of  srun  when	it  exits.
       Then srun_cr loops waiting for termination of tasks being launched from srun.

       The  step  launch  logic  of  SLURM  is	augmented  to  check  if  srun	is  running  under  srun_cr.   If  true,  the environment variable
       SURN_SRUN_CR_SOCKET should be present, the value of which is the address of a Unix domain socket created and listened to be srun_cr.  After
       launching the tasks, srun tires to connect to the socket and sends the job ID, step ID and the nodes allocated to the step to srun_cr.

       Upon  checkpoint, srun_cr checks to see if the tasks have been launched.  If not srun_cr first forwards the checkpoint request to the tasks
       by calling the SLURM API slurm_checkpoint_tasks() before dumping its process context.

       Upon restart, srun_cr checks to see if the tasks have been previously  launched	and  checkpointed.   If  true,	the  environment  variable
       SLURM_RESTART_DIR  is  set to the directory of the checkpoint image files of the tasks.	Then srun is forked and executed again.  The envi-
       ronment variable will be used by the srun command to restart execution of the tasks from the previous checkpoint.

COPYING

       Copyright (C) 2009 National University of Defense Technology, China.  Produced at National University of  Defense  Technology,  China  (cf,
       DISCLAIMER).  CODE-OCEC-09-009. All rights reserved.

       This file is part of SLURM, a resource management program.  For details, see <http://www.schedmd.com/slurmdocs/>.

       SLURM is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free
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       SLURM is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY	or
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SEE ALSO

       srun(1)

srun_cr 2.0							    March 2009								SRUN_CR(1)