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From Eric Kimbrel <Eric.Kimb...@soteradefense.com>
Subject Re: Broadcast of large aggregated value is slow.
Date Tue, 21 May 2013 17:43:53 GMT
I use only one aggregator.  The code for it is extremely simple as it is not actually used
as an aggregator at all.  The only use is for the master compute class to set a large object
value, and then for each vertex to read that value.  The Size of the Bytes writable is ~ 100M



Heres the code for the aggregator:



public class BroadcastAggregator extends BasicAggregator<RowListWritable>{


// no user code ever calls aggregate.

// Master compute class calls setAggregatedValue once per superstep.



// This method is not used, but is provided for flexibility.

//If a non empty value is added it will be added to the current value and then set

@Override

public void aggregate(RowListWritable rw) {

if (rw.index.length == 0) return;

if (this.getAggregatedValue().index.length > 0){

rw.add(this.getAggregatedValue());

}

this.setAggregatedValue(rw);

}


@Override

public RowListWritable createInitialValue() {

return new RowListWritable();

}


}



Eric Kimbrel
Software Engineer I Data Fusion & Analytics
Sotera Defense Solutions, Inc.
o: 360-516-6621
c: 360-990-1873
e: Eric.Kimbrel@soteradefense.com<mailto:First.Last@soteradefense.com>
w: www.potomacfusion.com<http://www.potomacfusion.com/> | www.soteradefense.com<http://www.soteradefense.com/>
Agility. Ingenuity. Integrity.


From: Maja Kabiljo <majakabiljo@fb.com<mailto:majakabiljo@fb.com>>
Reply-To: "user@giraph.apache.org<mailto:user@giraph.apache.org>" <user@giraph.apache.org<mailto:user@giraph.apache.org>>
Date: Thursday, May 16, 2013 8:18 PM
To: "user@giraph.apache.org<mailto:user@giraph.apache.org>" <user@giraph.apache.org<mailto:user@giraph.apache.org>>
Subject: Re: Broadcast of large aggregated value is slow.
Resent-From: <eric.kimbrel@soteradefense.com<mailto:eric.kimbrel@soteradefense.com>>

Thanks, Eric. I'm not sure what's going on, it's strange that there are a couple of machines
which wait for aggregators for a very long time, but then in exactly same moment they receive
them. Can you send us the code for Aggregator which you are using? Do you know approximately
how big aggregators are and how many of them do you have?

Maja

From: Eric Kimbrel <Eric.Kimbrel@soteradefense.com<mailto:Eric.Kimbrel@soteradefense.com>>
Reply-To: "user@giraph.apache.org<mailto:user@giraph.apache.org>" <user@giraph.apache.org<mailto:user@giraph.apache.org>>
Date: Thursday, May 16, 2013 2:36 PM
To: "user@giraph.apache.org<mailto:user@giraph.apache.org>" <user@giraph.apache.org<mailto:user@giraph.apache.org>>
Subject: Re: Broadcast of large aggregated value is slow.

My apologies. You are correct, I attached the wrong long.   Correct one attached here.


Eric Kimbrel
Software Engineer I Data Fusion & Analytics
Sotera Defense Solutions, Inc.
o: 360-516-6621
c: 360-990-1873
e: Eric.Kimbrel@soteradefense.com<mailto:First.Last@soteradefense.com>
w: www.potomacfusion.com<https://urldefense.proofpoint.com/v1/url?u=http://www.potomacfusion.com/&k=ZVNjlDMF0FElm4dQtryO4A%3D%3D%0A&r=RGg8bUFUf%2FM2K95hnYD1RGWK1CQ%2BbcclArMcjzJodKY%3D%0A&m=JneyqIVoubY0J4ko9BK2DwfsA%2BN6Qy8nBTZj%2BVg78Uw%3D%0A&s=9cf5380dcf55ff5999b2f5b12c9a93b206777c47e775a949e9da6f6a8ce4f173>
| www.soteradefense.com<https://urldefense.proofpoint.com/v1/url?u=http://www.soteradefense.com/&k=ZVNjlDMF0FElm4dQtryO4A%3D%3D%0A&r=RGg8bUFUf%2FM2K95hnYD1RGWK1CQ%2BbcclArMcjzJodKY%3D%0A&m=JneyqIVoubY0J4ko9BK2DwfsA%2BN6Qy8nBTZj%2BVg78Uw%3D%0A&s=70d18c70634f46634d557cf4f36276e3e5936b40e403d69a1ac10e3e4e5ff52b>
Agility. Ingenuity. Integrity.


From: Maja Kabiljo <majakabiljo@fb.com<mailto:majakabiljo@fb.com>>
Reply-To: "user@giraph.apache.org<mailto:user@giraph.apache.org>" <user@giraph.apache.org<mailto:user@giraph.apache.org>>
Date: Thursday, May 16, 2013 2:25 PM
To: "user@giraph.apache.org<mailto:user@giraph.apache.org>" <user@giraph.apache.org<mailto:user@giraph.apache.org>>
Subject: Re: Broadcast of large aggregated value is slow.
Resent-From: <eric.kimbrel@soteradefense.com<mailto:eric.kimbrel@soteradefense.com>>

Eric,

Can you please check it again, in both logs you attached we are waiting on the worker 13 to
send data, so none of those can't be worker 13's log.

Maja

From: Eric Kimbrel <Eric.Kimbrel@soteradefense.com<mailto:Eric.Kimbrel@soteradefense.com>>
Reply-To: "user@giraph.apache.org<mailto:user@giraph.apache.org>" <user@giraph.apache.org<mailto:user@giraph.apache.org>>
Date: Thursday, May 16, 2013 2:15 PM
To: "user@giraph.apache.org<mailto:user@giraph.apache.org>" <user@giraph.apache.org<mailto:user@giraph.apache.org>>
Subject: Re: Broadcast of large aggregated value is slow.

One of the attached logs is worker 13,  During this time period it is waiting for an aggregator
request so that it can start the super step.


Eric Kimbrel
Software Engineer I Data Fusion & Analytics
Sotera Defense Solutions, Inc.
o: 360-516-6621
c: 360-990-1873
e: Eric.Kimbrel@soteradefense.com<mailto:First.Last@soteradefense.com>
w: www.potomacfusion.com<https://urldefense.proofpoint.com/v1/url?u=http://www.potomacfusion.com/&k=ZVNjlDMF0FElm4dQtryO4A%3D%3D%0A&r=RGg8bUFUf%2FM2K95hnYD1RGWK1CQ%2BbcclArMcjzJodKY%3D%0A&m=IVLhuSbQeHVpz2XEdAMnlmA5DbtqWgrwg930PpuMQoQ%3D%0A&s=b933c5068d68b34f5bfbac0db0f8eb919a01dacd3555330fe3147bbf53399d72>
| www.soteradefense.com<https://urldefense.proofpoint.com/v1/url?u=http://www.soteradefense.com/&k=ZVNjlDMF0FElm4dQtryO4A%3D%3D%0A&r=RGg8bUFUf%2FM2K95hnYD1RGWK1CQ%2BbcclArMcjzJodKY%3D%0A&m=IVLhuSbQeHVpz2XEdAMnlmA5DbtqWgrwg930PpuMQoQ%3D%0A&s=f5fe0f489b7bfc207fb44206c50b2f74d0763169d0db18557586da3ce1d83443>
Agility. Ingenuity. Integrity.


From: Maja Kabiljo <majakabiljo@fb.com<mailto:majakabiljo@fb.com>>
Reply-To: "user@giraph.apache.org<mailto:user@giraph.apache.org>" <user@giraph.apache.org<mailto:user@giraph.apache.org>>
Date: Thursday, May 16, 2013 2:11 PM
To: "user@giraph.apache.org<mailto:user@giraph.apache.org>" <user@giraph.apache.org<mailto:user@giraph.apache.org>>
Subject: Re: Broadcast of large aggregated value is slow.
Resent-From: <eric.kimbrel@soteradefense.com<mailto:eric.kimbrel@soteradefense.com>>

Eric,

Can you please take a look at the logs of one of the workers listed (13, 34, 38, 50, 48, 52,
58, 56), what are they doing? The fact that a worker is waiting on aggregator can have different
causes, it doesn’t necessarily mean that sending aggregators is slow. It can for example
mean that some workers finished computing before others and are now waiting for others to
finish and send their data.
How big are aggregators which you are using?

Thanks,
Maja

From: Eric Kimbrel <Eric.Kimbrel@soteradefense.com<mailto:Eric.Kimbrel@soteradefense.com>>
Reply-To: "user@giraph.apache.org<mailto:user@giraph.apache.org>" <user@giraph.apache.org<mailto:user@giraph.apache.org>>
Date: Thursday, May 16, 2013 2:00 PM
To: "user@giraph.apache.org<mailto:user@giraph.apache.org>" <user@giraph.apache.org<mailto:user@giraph.apache.org>>
Subject: Re: Broadcast of large aggregated value is slow.

>From the attached logs in original post, you can see that both workers use about 4 seconds
of compute time on super step 4, but they complete super step 4 about 10 minutes apart.


Eric Kimbrel
Software Engineer I Data Fusion & Analytics
Sotera Defense Solutions, Inc.
o: 360-516-6621
c: 360-990-1873
e: Eric.Kimbrel@soteradefense.com<mailto:First.Last@soteradefense.com>
w: www.potomacfusion.com<https://urldefense.proofpoint.com/v1/url?u=http://www.potomacfusion.com/&k=ZVNjlDMF0FElm4dQtryO4A%3D%3D%0A&r=RGg8bUFUf%2FM2K95hnYD1RGWK1CQ%2BbcclArMcjzJodKY%3D%0A&m=rMjEN5TrXaS2BX1KqSuqFERFV5ssM40qL4bcaGFCtvE%3D%0A&s=206a9bd1407d0a4e7cdc6007d5c113baf96438de1c17043e501877ff185a6a3c>
| www.soteradefense.com<https://urldefense.proofpoint.com/v1/url?u=http://www.soteradefense.com/&k=ZVNjlDMF0FElm4dQtryO4A%3D%3D%0A&r=RGg8bUFUf%2FM2K95hnYD1RGWK1CQ%2BbcclArMcjzJodKY%3D%0A&m=rMjEN5TrXaS2BX1KqSuqFERFV5ssM40qL4bcaGFCtvE%3D%0A&s=e2806a46969606798541933625edcd907e560f71b173ad03f7eda8fb18ff175a>
Agility. Ingenuity. Integrity.


From: Eric Kimbrel <Eric.Kimbrel@soteradefense.com<mailto:Eric.Kimbrel@soteradefense.com>>
Reply-To: "user@giraph.apache.org<mailto:user@giraph.apache.org>" <user@giraph.apache.org<mailto:user@giraph.apache.org>>
Date: Thursday, May 16, 2013 1:50 PM
To: "user@giraph.apache.org<mailto:user@giraph.apache.org>" <user@giraph.apache.org<mailto:user@giraph.apache.org>>
Subject: Broadcast of large aggregated value is slow.


I have an giraph job in which the Master will read a chunk of a file from HDFS, and then use
an aggregator to broadcast the data to all vertices.  No other messages are sent, and no vertices
aggregate values, only the master.

In the attached logs you can see that the time spent to broadcast the data to all vertices
is slow, and seems to be hanging up somehwere.  It appears that the majority of workers receive
the data in 10-15 seconds, but then nothing happens for around 10 minutes.  Log snippet shown
below

Is there a known reason why transmitting this data during the synchronization is taking so
long, or anything that can be done to speed it up?


2013-05-16 11:09:03,041 INFO org.apache.giraph.utils.TaskIdsPermitsBarrier: waitForRequiredPermits:
Waiting for 30 more tasks to send their aggregator data
2013-05-16 11:09:14,444 INFO org.apache.giraph.utils.TaskIdsPermitsBarrier: waitForRequiredPermits:
Waiting for 10 more tasks to send their aggregator data, task ids: [13, 20, 22, 34, 38, 50,
48, 52, 58, 56]
2013-05-16 11:09:25,190 INFO org.apache.giraph.utils.TaskIdsPermitsBarrier: waitForRequiredPermits:
Waiting for 8 more tasks to send their aggregator data, task ids: [13, 34, 38, 50, 48, 52,
58, 56]
2013-05-16 11:09:45,191 INFO org.apache.giraph.utils.TaskIdsPermitsBarrier: waitForRequiredPermits:
Waiting for 8 more tasks to send their aggregator data, task ids: [13, 34, 38, 50, 48, 52,
58, 56]
2013-05-16 11:10:05,191 INFO org.apache.giraph.utils.TaskIdsPermitsBarrier: waitForRequiredPermits:
Waiting for 8 more tasks to send their aggregator data, task ids: [13, 34, 38, 50, 48, 52,
58, 56]
2013-05-16 11:10:15,192 INFO org.apache.giraph.utils.TaskIdsPermitsBarrier: waitForRequiredPermits:
Waiting for 8 more tasks to send their aggregator data, task ids: [13, 34, 38, 50, 48, 52,
58, 56]
2013-05-16 11:10:35,193 INFO org.apache.giraph.utils.TaskIdsPermitsBarrier: waitForRequiredPermits:
Waiting for 8 more tasks to send their aggregator data, task ids: [13, 34, 38, 50, 48, 52,
58, 56]
2013-05-16 11:10:55,193 INFO org.apache.giraph.utils.TaskIdsPermitsBarrier: waitForRequiredPermits:
Waiting for 8 more tasks to send their aggregator data, task ids: [13, 34, 38, 50, 48, 52,
58, 56]
2013-05-16 11:11:05,194 INFO org.apache.giraph.utils.TaskIdsPermitsBarrier: waitForRequiredPermits:
Waiting for 8 more tasks to send their aggregator data, task ids: [13, 34, 38, 50, 48, 52,
58, 56]
2013-05-16 11:11:25,195 INFO org.apache.giraph.utils.TaskIdsPermitsBarrier: waitForRequiredPermits:
Waiting for 8 more tasks to send their aggregator data, task ids: [13, 34, 38, 50, 48, 52,
58, 56]
2013-05-16 11:11:45,196 INFO org.apache.giraph.utils.TaskIdsPermitsBarrier: waitForRequiredPermits:
Waiting for 8 more tasks to send their aggregator data, task ids: [13, 34, 38, 50, 48, 52,
58, 56]
2013-05-16 11:12:05,196 INFO org.apache.giraph.utils.TaskIdsPermitsBarrier: waitForRequiredPermits:
Waiting for 8 more tasks to send their aggregator data, task ids: [13, 34, 38, 50, 48, 52,
58, 56]
2013-05-16 11:12:15,197 INFO org.apache.giraph.utils.TaskIdsPermitsBarrier: waitForRequiredPermits:
Waiting for 8 more tasks to send their aggregator data, task ids: [13, 34, 38, 50, 48, 52,
58, 56]
2013-05-16 11:12:35,198 INFO org.apache.giraph.utils.TaskIdsPermitsBarrier: waitForRequiredPermits:
Waiting for 8 more tasks to send their aggregator data, task ids: [13, 34, 38, 50, 48, 52,
58, 56]
2013-05-16 11:12:55,198 INFO org.apache.giraph.utils.TaskIdsPermitsBarrier: waitForRequiredPermits:
Waiting for 8 more tasks to send their aggregator data, task ids: [13, 34, 38, 50, 48, 52,
58, 56]
2013-05-16 11:13:05,199 INFO org.apache.giraph.utils.TaskIdsPermitsBarrier: waitForRequiredPermits:
Waiting for 8 more tasks to send their aggregator data, task ids: [13, 34, 38, 50, 48, 52,
58, 56]
2013-05-16 11:13:25,200 INFO org.apache.giraph.utils.TaskIdsPermitsBarrier: waitForRequiredPermits:
Waiting for 8 more tasks to send their aggregator data, task ids: [13, 34, 38, 50, 48, 52,
58, 56]
2013-05-16 11:13:45,201 INFO org.apache.giraph.utils.TaskIdsPermitsBarrier: waitForRequiredPermits:
Waiting for 8 more tasks to send their aggregator data, task ids: [13, 34, 38, 50, 48, 52,
58, 56]
2013-05-16 11:14:05,201 INFO org.apache.giraph.utils.TaskIdsPermitsBarrier: waitForRequiredPermits:
Waiting for 8 more tasks to send their aggregator data, task ids: [13, 34, 38, 50, 48, 52,
58, 56]
2013-05-16 11:14:15,202 INFO org.apache.giraph.utils.TaskIdsPermitsBarrier: waitForRequiredPermits:
Waiting for 8 more tasks to send their aggregator data, task ids: [13, 34, 38, 50, 48, 52,
58, 56]
2013-05-16 11:14:35,203 INFO org.apache.giraph.utils.TaskIdsPermitsBarrier: waitForRequiredPermits:
Waiting for 8 more tasks to send their aggregator data, task ids: [13, 34, 38, 50, 48, 52,
58, 56]
2013-05-16 11:14:55,204 INFO org.apache.giraph.utils.TaskIdsPermitsBarrier: waitForRequiredPermits:
Waiting for 8 more tasks to send their aggregator data, task ids: [13, 34, 38, 50, 48, 52,
58, 56]
2013-05-16 11:15:15,205 INFO org.apache.giraph.utils.TaskIdsPermitsBarrier: waitForRequiredPermits:
Waiting for 8 more tasks to send their aggregator data, task ids: [13, 34, 38, 50, 48, 52,
58, 56]
2013-05-16 11:15:35,205 INFO org.apache.giraph.utils.TaskIdsPermitsBarrier: waitForRequiredPermits:
Waiting for 8 more tasks to send their aggregator data, task ids: [13, 34, 38, 50, 48, 52,
58, 56]
2013-05-16 11:15:45,206 INFO org.apache.giraph.utils.TaskIdsPermitsBarrier: waitForRequiredPermits:
Waiting for 8 more tasks to send their aggregator data, task ids: [13, 34, 38, 50, 48, 52,
58, 56]
2013-05-16 11:16:05,207 INFO org.apache.giraph.utils.TaskIdsPermitsBarrier: waitForRequiredPermits:
Waiting for 8 more tasks to send their aggregator data, task ids: [13, 34, 38, 50, 48, 52,
58, 56]
2013-05-16 11:16:25,208 INFO org.apache.giraph.utils.TaskIdsPermitsBarrier: waitForRequiredPermits:
Waiting for 8 more tasks to send their aggregator data, task ids: [13, 34, 38, 50, 48, 52,
58, 56]
2013-05-16 11:16:45,208 INFO org.apache.giraph.utils.TaskIdsPermitsBarrier: waitForRequiredPermits:
Waiting for 8 more tasks to send their aggregator data, task ids: [13, 34, 38, 50, 48, 52,
58, 56]
2013-05-16 11:16:55,209 INFO org.apache.giraph.utils.TaskIdsPermitsBarrier: waitForRequiredPermits:
Waiting for 8 more tasks to send their aggregator data, task ids: [13, 34, 38, 50, 48, 52,
58, 56]
2013-05-16 11:17:15,210 INFO org.apache.giraph.utils.TaskIdsPermitsBarrier: waitForRequiredPermits:
Waiting for 8 more tasks to send their aggregator data, task ids: [13, 34, 38, 50, 48, 52,
58, 56]
2013-05-16 11:17:35,210 INFO org.apache.giraph.utils.TaskIdsPermitsBarrier: waitForRequiredPermits:
Waiting for 8 more tasks to send their aggregator data, task ids: [13, 34, 38, 50, 48, 52,
58, 56]
2013-05-16 11:17:45,211 INFO org.apache.giraph.utils.TaskIdsPermitsBarrier: waitForRequiredPermits:
Waiting for 8 more tasks to send their aggregator data, task ids: [13, 34, 38, 50, 48, 52,
58, 56]
2013-05-16 11:18:05,212 INFO org.apache.giraph.utils.TaskIdsPermitsBarrier: waitForRequiredPermits:
Waiting for 8 more tasks to send their aggregator data, task ids: [13, 34, 38, 50, 48, 52,
58, 56]
2013-05-16 11:18:19,841 INFO org.apache.giraph.comm.netty.handler.RequestDecoder: decode:
Server window metrics MBytes/sec sent = 0, MBytes/sec received = 0.027, MBytesSent = 0.0006,
MBytesReceived = 15.4028, ave sent req MBytes = 0, ave received req MBytes = 0.0034, secs
waited = 571.136






Eric Kimbrel
Software Engineer I Data Fusion & Analytics
Sotera Defense Solutions, Inc.
o: 360-516-6621
c: 360-990-1873
e: Eric.Kimbrel@soteradefense.com<mailto:First.Last@soteradefense.com>
w: www.potomacfusion.com<https://urldefense.proofpoint.com/v1/url?u=http://www.potomacfusion.com/&k=ZVNjlDMF0FElm4dQtryO4A%3D%3D%0A&r=RGg8bUFUf%2FM2K95hnYD1RGWK1CQ%2BbcclArMcjzJodKY%3D%0A&m=rMjEN5TrXaS2BX1KqSuqFERFV5ssM40qL4bcaGFCtvE%3D%0A&s=206a9bd1407d0a4e7cdc6007d5c113baf96438de1c17043e501877ff185a6a3c>
| www.soteradefense.com<https://urldefense.proofpoint.com/v1/url?u=http://www.soteradefense.com/&k=ZVNjlDMF0FElm4dQtryO4A%3D%3D%0A&r=RGg8bUFUf%2FM2K95hnYD1RGWK1CQ%2BbcclArMcjzJodKY%3D%0A&m=rMjEN5TrXaS2BX1KqSuqFERFV5ssM40qL4bcaGFCtvE%3D%0A&s=e2806a46969606798541933625edcd907e560f71b173ad03f7eda8fb18ff175a>
Agility. Ingenuity. Integrity.


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