Some bash addendum scripts

[Hamilton Turner]

Here are some shell scripts that I'm using with success to help me manage running jug across a cluster. Luis, if you're interested in using something like this, I can put these on the git and they can be upgraded to be more release-ready, although perhaps they should be renamed if so. I like being able to hit Tab after typing jug and see both plain old jug and all of my commands for managing the slaves

[hamiltont@foo ~]$ jug

jug        jughalt    juglog     jugoutput  jugrun     jugstatus  

__________________________________________

# Using parallel ssh with IP addresses of all slave computers

alias pssh='pssh -i -h workers.iplist '

# Allows me to keep an eye on all workers

alias jugstatus='watch -n 10 -d jug status --cache benchmark_jug.py'

# Rapidly starts a ton of workers, and also starts a screen session that will write to the log file once the entire job is complete. The waitonjug.sh is posted below

alias jugrun='echo "`date`: Start" >> .juglog; screen -d -m -S jugwatcher sh ~/.waitonjug; pssh screen -d -S jug -m sh run_workers.sh'

# Allows me to see the output of all executors

alias jugoutput='pssh cat /mnt/localhd/.jug*'

# Kills all jug workers 

alias jughalt='echo "`date`: Halt ">> .juglog; screen -S jugwatcher -X quit;  pssh pkill jug;'

# Simply outputs my log file

alias juglog='cat ~/.juglog'

_______________

[hamiltont@foo ~]$ cat run_workers.sh 

#!/bin/sh

# Removing output from old runs

rm /mnt/localhd/.jug*

# Starting 10 executors on each slave machine, and forwarding output to some slave-machine specific files in a directory not shared via NFS

for i in {1..10}

do

jug execute benchmark_jug.py > /mnt/localhd/.jug$i.out 2> /mnt/localhd/.jug$i.err &

done

# Waiting for all sub-processes to complete before we terminate

wait

__________________________________

[hamiltont@foo ~]$ juglog 

Wed Nov 14 02:46:39 EST 2012: Start

Wed Nov 14 02:46:39 EST 2012: Completed

Wed Nov 14 02:47:39 EST 2012: Halt 

Wed Nov 14 02:49:10 EST 2012: Start

Wed Nov 14 03:00:00 EST 2012: Completed

[Luis Pedro Coelho]

Thanks.

This could be generally useful, I agree. Either as full-blown scripts to
be distributed with jug (they'd need generalizing & proper
documentation, &c) or, less work involved, as examples in the package
documentation.

Luis

[Hamilton Turner]

I think the examples might be best for now, as making these general purpose is beyond my shell abilities. Having them as a general setup example might be most useful to others in setting up their own version.

Thanks,
Hamy

[Luis Pedro Coelho]

On Sunday, November 25, 2012 02:18:00 PM Hamilton Turner wrote:
> I think the examples might be best for now, as making these general purpose
> is beyond my shell abilities. Having them as a general setup example might
> be most useful to others in setting up their own version.

K.

Do you want to write something up or should I just copy and paste the stuff
from your email?

Thanks,
--
Luis Pedro Coelho | Institute for Molecular Medicine | http://luispedro.org

[Hamilton Turner]

I can write something a bit cleaner, is there any specific markup style you prefer? 

[Luis Pedro Coelho]

On 11/26/2012 10:53 PM, Hamilton Turner wrote:
> I can write something a bit cleaner, is there any specific markup style
> you prefer?

Awesome!

The docs in jug are in restructured text:

https://github.com/luispedro/jug/tree/master/docs/source

Thanks,
Luis

[Hamilton Turner]

Luis, 

It took me forever, but check out the pull request on github. I (clearly) don't have enough time to dedicate here, so 

hopefully someone else can take the time to make them more general if they are useful. 

Best, 

Hamy

[Luis Pedro Coelho]

Thank you!

I have merged.

This is very complete, excellent documentation work!

--
Luis Pedro Coelho

LxMLS 2013: http://lxmls.it.pt/2013/

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[Hamilton Turner]

Glad you like them. Do be sure to check my rst syntax - I've never used it and I didn't compile the docs (*ducks head in shame*)

[Luis Pedro Coelho]

Just a tiny error, which I have just fixed.

Tx again,

--
Luis Pedro Coelho

LxMLS 2013: http://lxmls.it.pt/2013/