Re: Instances are not accepting jobs when the slots are available.

From: Rayson Ho <no email>
Date: Thu, 17 Jul 2014 18:58:59 -0400

What R program or module are you using?? As there are 32 virtual cores on
the C3.8xlarge, if your code by default creates 1 thread per virtual core,
then there will be 3200% CPU usage on the C3.8xlarge. And also, may be your
local machine has much fewer cores and that's why this is not happening??

Rayson

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On Thu, Jul 17, 2014 at 6:06 PM, Jin Yu <yujin2004_at_gmail.com> wrote:

> Here is a followup of my investigation of the unusual high CPU/core usage
> in EC2 instances.
>
> In the last post, I reported my observations of 1. unusual high CPU/core
> usage of the R process in EC2 instances, which is designed to use one core
> on the local machine; And 2. unusual high percentage of kernel time in CPU
> usage.
>
> I looked more into the R processes using htop and found a lot of threads
> were created in each of them. And there are tons of sched_yield() system
> calls in each thread.
>
> Do these phenomenons with starcluster at EC2 ring a bell for someone?
>
> Thanks!
> Jin
>
>
>
>
> On Thu, Jul 17, 2014 at 3:48 PM, Jin Yu <yujin2004_at_gmail.com> wrote:
>
>> Hi Chris,
>>
>> Thanks for your prompt reply and point me to look the unusual high load
>> of the instance! And I found something more mysterious in EC2 instances
>> (C3.8xlarge, to be more specific) :
>>
>> 1. I found some of my jobs are using CPU as much as 900%, although these
>> job are designed to use only one core and behave so in my local machine,
>> which lead to the unexpected high load of the system. Following is an
>> example snapshot of these process.
>>
>> 2. While all the 8 running jobs takes 3000% CPU which is close to the
>> full of 32 cores. The kernel time takes up to 70% of the CPU time.
>>
>> Are these problem related to the visualization nature of the EC2
>> instances? Can you give me a hint to investigate them?
>>
>> Thanks!
>> Jin
>>
>>
>>
>> [image: Inline image 1]
>>
>>
>>
>>
>>
>>
>> On Thu, Jul 17, 2014 at 1:48 PM, Chris Dagdigian <dag_at_bioteam.net> wrote:
>>
>>>
>>> Hi Jin,
>>>
>>> The cluster is not accepting jobs into those open slots because your
>>> compute nodes are reporting alarm state "a" - your first host has a
>>> reported load average of 148!
>>>
>>> Alarm state 'a' means "load threshold alarm level reached" it basically
>>> means that the server load is high enough that the nodes are refusing
>>> new work until the load average goes down.
>>>
>>> All of those load alarm thresholds are configurable values within SGE so
>>> you can revise them upwards if you want
>>>
>>> Regards,
>>> Chris
>>>
>>>
>>> Jin Yu wrote:
>>> > Hello,
>>> >
>>> > I just started a cluster of 20 c3.8xlarge instances, which have 32
>>> > virtual cores in each. In my understanding, each instance should have
>>> > 32 slots available to run the jobs by default. But after running it
>>> > for a while, I found a lot of nodes are not running at the full speed.
>>> >
>>> > Following as an example, you can see node016 has only 13 jobs running
>>> > and node017 has 9 jobs running, while node018 has 32 jobs running. I
>>> > have another ~10000 jobs waiting in the queue, so it is not a matter
>>> > of running out of jobs.
>>> >
>>> > Can anyone give me a hint what is going on here?
>>> >
>>> > Thanks!
>>> > Jin
>>> >
>>> >
>>> > all.q_at_node016 BIP 0/13/32 148.35 linux-x64
>>> > a
>>> > 784 0.55500 job.part.a sgeadmin r 07/17/2014 11:25:59
>>> > 1
>>> > 982 0.55500 job.part.a sgeadmin r 07/17/2014 14:43:59
>>> > 1
>>> > 1056 0.55500 job.part.a sgeadmin r 07/17/2014 16:34:44
>>> > 1
>>> > 1057 0.55500 job.part.a sgeadmin r 07/17/2014 16:34:44
>>> > 1
>>> > 1058 0.55500 job.part.a sgeadmin r 07/17/2014 16:34:59
>>> > 1
>>> > 1121 0.55500 job.part.a sgeadmin r 07/17/2014 17:22:44
>>> > 1
>>> > 1122 0.55500 job.part.a sgeadmin r 07/17/2014 17:22:44
>>> > 1
>>> > 1123 0.55500 job.part.a sgeadmin r 07/17/2014 17:22:44
>>> > 1
>>> > 1124 0.55500 job.part.a sgeadmin r 07/17/2014 17:22:44
>>> > 1
>>> > 1125 0.55500 job.part.a sgeadmin r 07/17/2014 17:22:44
>>> > 1
>>> > 1126 0.55500 job.part.a sgeadmin r 07/17/2014 17:22:44
>>> > 1
>>> > 1127 0.55500 job.part.a sgeadmin r 07/17/2014 17:22:44
>>> > 1
>>> > 1128 0.55500 job.part.a sgeadmin r 07/17/2014 17:22:44
>>> > 1
>>> >
>>> ---------------------------------------------------------------------------------
>>> > all.q_at_node017 BIP 0/9/32 83.86 linux-x64
>>> > a
>>> > 568 0.55500 job.part.a sgeadmin r 07/17/2014 04:01:14
>>> > 1
>>> > 1001 0.55500 job.part.a sgeadmin r 07/17/2014 15:07:29
>>> > 1
>>> > 1002 0.55500 job.part.a sgeadmin r 07/17/2014 15:07:29
>>> > 1
>>> > 1072 0.55500 job.part.a sgeadmin r 07/17/2014 16:53:29
>>> > 1
>>> > 1116 0.55500 job.part.a sgeadmin r 07/17/2014 17:19:29
>>> > 1
>>> > 1117 0.55500 job.part.a sgeadmin r 07/17/2014 17:19:29
>>> > 1
>>> > 1118 0.55500 job.part.a sgeadmin r 07/17/2014 17:19:44
>>> > 1
>>> > 1119 0.55500 job.part.a sgeadmin r 07/17/2014 17:19:59
>>> > 1
>>> > 1120 0.55500 job.part.a sgeadmin r 07/17/2014 17:19:59
>>> > 1
>>> >
>>> ---------------------------------------------------------------------------------
>>> > all.q_at_node018 BIP 0/32/32 346.00 linux-x64
>>> > a
>>> >
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>>>
>>
>>
>
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Received on Thu Jul 17 2014 - 18:59:02 EDT