Re: StarCluster Digest, Vol 49, Issue 1

From: Jacob Barhak <no email>
Date: Mon, 2 Sep 2013 00:20:56 -0500

Thanks Lyn,

This does seem to resolve the issue and get the desirable effect! It worked well enough on a single test machine. Although I have not tested on the cloud.

For the sake of completeness for others reading the list let me explain your resolution.

Lyn noticed that weight_priority is set to zero by default on SGE. This means that the priority parameter in the -p option in qsub is ignored by the system by default. Therefore even if a job is released from dependencies it does not jump in priority like I wanted and just waits its turn in FIFO line - even if I asked for higher priority when launching the job.

Lyn proposed the following solution:
1. Retrieving the current configuration file
2. Modifying the weight_priority parameter in the configuration to allow the qsub -p priority to have influence
3. Loading the modified configuration file back to the system for the change to take effect

Lyn, you actually helped me fix something else related to this issue in my code - so double thanks.

      Jacob


Sent from my iPhone

On Sep 1, 2013, at 8:35 PM, Lyn Gerner <schedulerqueen_at_gmail.com> wrote:

> Jacob, Hugh's approach sounds good to me, but I believe you want to do something like this:
>
> qconf -ssconf > $file.
> vi $file # edit the file to change (to a non-zero value) the weight_priority value, then feed it back into the config with:
> qconf -Msconf $file.
>
> See man pages sched_conf(5) and sge_priority(5) for reference.
>
>
> On Sun, Sep 1, 2013 at 8:46 AM, Jacob Barhak <jacob.barhak_at_gmail.com> wrote:
>> Thanks Lyn,
>>
>> Yes. The -hold_jid option works well. Yet the issue is more complicated and has to do with priorities along with dependencies.
>>
>> Someone who knows the scheduler may have an answer here.
>>
>> I am using the -hold_jid to hold job 50001 until job 1 is complete. Yet I want job 50001 to start after job 1 completes because of higher priority than jobs 2-50000.
>> The ideal sequence I am trying to get is:
>> 1, 50001 , 2, 50002, ...
>>
>> I don't mind if this takes a few more jobs before 50001 kicks in after 1 is done. Yet currently the jobs are executed in FIFO order so by the time 50001 is reached there will be 50000 files in a directory. In a cluster this may slow up things significantly. However, if the files are processed close to the way I want, there will not be too many files.
>>
>> I rather not chance the order of submission if possible.
>>
>> I hope someone knows how to get the desired behavior from SGE.
>>
>> Jacob
>>
>> Sent from my iPhone
>>
>> On Sep 1, 2013, at 12:08 PM, Lyn Gerner <schedulerqueen_at_gmail.com> wrote:
>>
>>> Hey Jacob,
>>>
>>> Have you looked at the qsub man page -hold_jid option? You can give it multiple jids or jobnames (or regex patterns).
>>> http://gridscheduler.sourceforge.net/htmlman/manuals.html
>>> http://gridscheduler.sourceforge.net/htmlman/htmlman1/sge_types.html
>>>
>>> This preso has a couple of examples:
>>> http://www.bioteam.net/wp-content/uploads/2011/03/02-SGE-SimpleWorkflow.pdf
>>>
>>> Best of luck,
>>> Lyn
>>>
>>>
>>>
>>> On Sun, Sep 1, 2013 at 6:26 AM, <starcluster-request_at_mit.edu> wrote:
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>>>> Today's Topics:
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>>>> 1. SGE priorities and job dependency (Jacob Barhak)
>>>>
>>>>
>>>> ---------- Forwarded message ----------
>>>> From: Jacob Barhak <jacob.barhak_at_gmail.com>
>>>> To: "starcluster_at_mit.edu" <starcluster_at_mit.edu>
>>>> Cc:
>>>> Date: Sun, 1 Sep 2013 02:19:12 -0500
>>>> Subject: [StarCluster] SGE priorities and job dependency
>>>> Hello,
>>>>
>>>> Does someone have experience with the SGE scheduler that comes with StarCluster? Experienced enough to figure out how make a dependent job launch before other jobs once its dependencies are gone?
>>>>
>>>> I have been trying to give the dependent job a high priority, yet it seems the scheduler ignores this and launches the jobs in FIFO order.
>>>>
>>>> Here is a simplified description of my problem. Lets say I have 100k jobs. The first 50k are generating files in a shared directory and the last 50k are processing those files and deleting them.
>>>>
>>>> Jobs 1-50000 are independent while job 50001 is dependent on job 50000 and job 50000+n is dependent on job n.
>>>>
>>>> I tried lowering the priority of the first 50k jobs using qsub -p -100. I was hoping to get the effect of job 1 completing and since job 50001 dependency was satisfied and has the highest priority then it would be launched next. The idea is to perform cleanup of the file after each job - otherwise too many files can accumulate in a shared directory and may slow down the NFS I/O significantly - not to mention disk space.
>>>>
>>>> However, I cannot get this behavior from SGE on a single test machine outside StarCluster. So I assume this needs some special configuration.
>>>>
>>>> I am trying to avoid the I/O bottleneck I experienced on the cloud due to too many files in a shared directory.
>>>>
>>>> Can someone help with this without changing the order if the jobs when being launched?
>>>>
>>>> I hope there is a simple one line / qsub option for this.
>>>>
>>>> Jacob
>>>>
>>>>
>>>>
>>>> Sent from my iPhone
>>>>
>>>>
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Received on Mon Sep 02 2013 - 01:21:11 EDT