Sponsored Content
Top Forums Shell Programming and Scripting waiting on jobs in bash, allowing limited parallel jobs at one time, and then for all to finish Post 302536976 by srao on Wednesday 6th of July 2011 06:31:32 PM
Old 07-06-2011
waiting on jobs in bash, allowing limited parallel jobs at one time, and then for all to finish

Hello,

I am running GNU bash, version 3.2.39(1)-release (x86_64-pc-linux-gnu). I have a specific question pertaining to waiting on jobs run in sub-shells, based on the max number of parallel processes I want to allow, and then wait for the remaining sub-shell jobs to finish before the next step is executed in the pipeline (if I am making proper sense here)..
Essentially,my pseudo code looks like this:
Code:
MAX_PROCS=3
    for (( k = 0 ; $k < $kmerlen ; k += 1 ))
    do
    (
     ### Running a perl script here for each k (this script is a memory hog)...
    )&
    while [ $(ps -e | grep 'perlScriptAbove' | grep -v grep | wc -l) -gt ${MAX_PROCS} ] ; 
    do
             wait
    done

    done

###wait <- works fine without this wait, but I need all kmerlen jobs to finish first to proceed to the next part of the pipeline
## Run the rest of the pipeline...

The first wait statement in the while loop works fine spawning 3 jobs, but when I use the next wait statement, that property is lost, and the number of sub-shells spawned are equal to my kmerlen.

Thanks for any pointers that you can provide.

Last edited by Franklin52; 07-07-2011 at 03:26 AM.. Reason: Please use code tags for code and data samples, thank you
 

9 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Diff: Server n parallel jobs

Hi, Could any one please explain the difference between DataStage server edition jobs and DS parallel extender jobs...? In which scenarios or application areas do we use either of these jobs.? Regards Suresh (0 Replies)
Discussion started by: sureshg_sampat
0 Replies

2. Shell Programming and Scripting

background jobs exit status and limit the number of jobs to run

i need to execute 5 jobs at a time in background and need to get the exit status of all the jobs i wrote small script below , i'm not sure this is right way to do it.any ideas please help. $cat run_job.ksh #!/usr/bin/ksh #################################### typeset -u SCHEMA_NAME=$1 ... (1 Reply)
Discussion started by: GrepMe
1 Replies

3. Shell Programming and Scripting

Help with script that submits jobs at a certain time.

Here's the line I type everyday. echo "submit daily 00559 00010 00011" | at 21:00 I dunno. I'm totally new to this. Basically I want this to be fool-proof for everyone else we've had people do things like: subit daily 00559 00010 00011 submit daly 00559 00010 00011 Submit daily (no... (4 Replies)
Discussion started by: Modki
4 Replies

4. Shell Programming and Scripting

Conditional execution and parallel jobs

how can i process jobs parallel with conditions below. Script1.ksh Script2.ksh Script3.ksh Script4.ksh Script5.ksh Script6.ksh Script7.ksh Script8.ksh Script9.ksh Script10.ksh After successful completion of Script1.ksh I need to run Script7.ksh. After successful... (4 Replies)
Discussion started by: ford2020
4 Replies

5. Shell Programming and Scripting

Waiting for an arbitrary background process (limiting number of jobs running)

Hi, I'm trying to write a script to decompress a directory full of files. The decompression commands can run in the background, so that many can run at once. But I want to limit the number running at any one time, so that I don't overload the machine. Something like this: n=0 for i in *.gz... (15 Replies)
Discussion started by: p.f.moore
15 Replies

6. Shell Programming and Scripting

jobs run parallel - server consumption?

I have a requirement where jobs/scripts need to be run in the background.The concern here is there are around 20 scripts which need to be run in the bg.Does running all the 20 scripts/job at the same time in bg consumes much sever-utilization. If so wot would be the efficient way to run the jobs... (5 Replies)
Discussion started by: michaelrozar17
5 Replies

7. Shell Programming and Scripting

Running jobs in parallel

I need to process 50 sqlplus scripts which are listed in a text file. I need to develop a shell script that'll read this file and run these sqlplus scripts. At any point of time, the number of sqlplus scripts running shouldn't exceed 6. If any of the sqlplus scripts completes successfully then... (17 Replies)
Discussion started by: gctex
17 Replies

8. Shell Programming and Scripting

How to WAIT for jobs in each group to finish?

I have the shell script to call a Perl routine and pass the Informatica WorkFlow name to it. Jobs in each group executes in background do not seem to wait at all. How do I make it to WAIT for the prior group to complete before execute the next group of jobs? Sample of the jobs flow: { ... (6 Replies)
Discussion started by: lv99
6 Replies

9. Shell Programming and Scripting

Shell script to run multiple jobs and it's dependent jobs

I have multiple jobs and each job dependent on other job. Each Job generates a log and If job completed successfully log file end's with JOB ENDED SUCCESSFULLY message and if it failed then it will end with JOB ENDED with FAILURE. I need an help how to start. Attaching the JOB dependency... (3 Replies)
Discussion started by: santoshkumarkal
3 Replies
SEM(1)								     parallel								    SEM(1)

NAME
sem - semaphore for executing shell command lines in parallel SYNOPSIS
sem [--fg] [--id <id>] [--timeout <secs>] [-j <num>] [--wait] command DESCRIPTION
GNU sem is an alias for GNU parallel --semaphore. It works as a tool for executing shell commands in parallel. GNU sem acts as a counting semaphore. When GNU sem is called with command it will start the command in the background. When num number of commands are running in the background, GNU sem will wait for one of these to complete before starting another command. Before looking at the options you may want to check out the examples after the list of options. That will give you an idea of what GNU sem is capable of. OPTIONS
command Command to execute. The command may be followed by arguments for the command. --bg Run command in background thus GNU parallel will not wait for completion of the command before exiting. This is the default. See also: --fg -j N Run up to N commands in parallel. Default is 1 thus acting like a mutex. --jobs N -j N --max-procs N -P N Run up to N commands in parallel. Default is 1 thus acting like a mutex. --jobs +N -j +N --max-procs +N -P +N Add N to the number of CPU cores. Run up to this many jobs in parallel. For compute intensive jobs -j +0 is useful as it will run number-of-cpu-cores jobs simultaneously. --jobs -N -j -N --max-procs -N -P -N Subtract N from the number of CPU cores. Run up to this many jobs in parallel. If the evaluated number is less than 1 then 1 will be used. See also --use-cpus-instead-of-cores. --jobs N% -j N% --max-procs N% -P N% Multiply N% with the number of CPU cores. Run up to this many jobs in parallel. If the evaluated number is less than 1 then 1 will be used. See also --use-cpus-instead-of-cores. --jobs procfile -j procfile --max-procs procfile -P procfile Read parameter from file. Use the content of procfile as parameter for -j. E.g. procfile could contain the string 100% or +2 or 10. --semaphorename name --id name Use name as the name of the semaphore. Default is the name of the controlling tty (output from tty). The default normally works as expected when used interactively, but when used in a script name should be set. $$ or my_task_name are often a good value. The semaphore is stored in ~/.parallel/semaphores/ --fg Do not put command in background. --timeout secs (not implemented) -t secs (not implemented) If the semaphore is not released within secs seconds, take it anyway. --wait -w Wait for all commands to complete. EXAMPLE
: Gzipping *.log Run one gzip process per CPU core. Block until a CPU core becomes available. for i in `ls *.log` ; do echo $i sem -j+0 gzip $i ";" echo done done sem --wait EXAMPLE
: Protecting pod2html from itself pod2html creates two files: pod2htmd.tmp and pod2htmi.tmp which it does not clean up. It uses these two files for a short time. But if you run multiple pod2html in parallel (e.g. in a Makefile with make -j) you need to protect pod2html from running twice at the same time. sem running as a mutex will do just that: sem --fg --id pod2html pod2html foo.pod > foo.html sem --fg --id pod2html rm -f pod2htmd.tmp pod2htmi.tmp BUGS
None known. REPORTING BUGS
Report bugs to <bug-parallel@gnu.org>. AUTHOR
Copyright (C) 2010,2011 Ole Tange, http://ole.tange.dk and Free Software Foundation, Inc. LICENSE
Copyright (C) 2010,2011 Free Software Foundation, Inc. This program 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 Software Foundation; either version 3 of the License, or at your option any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>. Documentation license I Permission is granted to copy, distribute and/or modify this documentation under the terms of the GNU Free Documentation License, Version 1.3 or any later version published by the Free Software Foundation; with no Invariant Sections, with no Front-Cover Texts, and with no Back-Cover Texts. A copy of the license is included in the file fdl.txt. Documentation license II You are free: to Share to copy, distribute and transmit the work to Remix to adapt the work Under the following conditions: Attribution You must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work). Share Alike If you alter, transform, or build upon this work, you may distribute the resulting work only under the same, similar or a compatible license. With the understanding that: Waiver Any of the above conditions can be waived if you get permission from the copyright holder. Public Domain Where the work or any of its elements is in the public domain under applicable law, that status is in no way affected by the license. Other Rights In no way are any of the following rights affected by the license: o Your fair dealing or fair use rights, or other applicable copyright exceptions and limitations; o The author's moral rights; o Rights other persons may have either in the work itself or in how the work is used, such as publicity or privacy rights. Notice For any reuse or distribution, you must make clear to others the license terms of this work. A copy of the full license is included in the file as cc-by-sa.txt. DEPENDENCIES
GNU sem uses Perl, and the Perl modules Getopt::Long, Symbol, Fcntl. SEE ALSO
parallel(1) 20120422 2011-06-25 SEM(1)
All times are GMT -4. The time now is 07:42 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy