Thanks for the tip. I will try it. But this is the kind of thing spark is
supposed to figure out and handle. Or at least not get stuck forever.
Sent from my Verizon Wireless 4G LTE smartphone
-------- Original message --------
From: Muthu Jayakumar <bablo...@gmail.com>
Date: 01/22/2016 3:50 PM (GMT-05:00)
To: Darren Govoni <dar...@ontrenet.com>, "Sanders, Isaac B"
<sande...@rose-hulman.edu>, Ted Yu <yuzhih...@gmail.com>
Cc: user@spark.apache.org
Subject: Re: 10hrs of Scheduler Delay
Does increasing the number of partition helps? You could try out something 3
times what you currently have. Another trick i used was to partition the
problem into multiple dataframes and run them sequentially and persistent the
result and then run a union on the results.
Hope this helps.
On Fri, Jan 22, 2016, 3:48 AM Darren Govoni <dar...@ontrenet.com> wrote:
Me too. I had to shrink my dataset to get it to work. For us at least Spark
seems to have scaling issues.
Sent from my Verizon Wireless 4G LTE smartphone
-------- Original message --------
From: "Sanders, Isaac B" <sande...@rose-hulman.edu>
Date: 01/21/2016 11:18 PM (GMT-05:00)
To: Ted Yu <yuzhih...@gmail.com>
Cc: user@spark.apache.org
Subject: Re: 10hrs of Scheduler Delay
I have run the driver on a smaller dataset (k=2, n=5000) and it worked quickly
and didn’t hang like this. This dataset is closer to k=10, n=4.4m, but I am
using more resources on this one.
- Isaac
On Jan 21, 2016, at 11:06 PM, Ted Yu <yuzhih...@gmail.com> wrote:
You may have seen the following on github page:
Latest commit 50fdf0e on Feb 22, 2015
That was 11 months ago.
Can you search for similar algorithm which runs on Spark and is newer ?
If nothing found, consider running the tests coming from the project to
determine whether the delay is intrinsic.
Cheers
On Thu, Jan 21, 2016 at 7:46 PM, Sanders, Isaac B
<sande...@rose-hulman.edu> wrote:
That thread seems to be moving, it oscillates between a few different traces…
Maybe it is working. It seems odd that it would take that long.
This is 3rd party code, and after looking at some of it, I think it might not
be as Spark-y as it could be.
I linked it below. I don’t know a lot about spark, so it might be fine, but I
have my suspicions.
https://github.com/alitouka/spark_dbscan/blob/master/src/src/main/scala/org/alitouka/spark/dbscan/exploratoryAnalysis/DistanceToNearestNeighborDriver.scala
- Isaac
On Jan 21, 2016, at 10:08 PM, Ted Yu <yuzhih...@gmail.com> wrote:
You may have noticed the following - did this indicate prolonged computation in
your code ?
org.apache.commons.math3.util.MathArrays.distance(MathArrays.java:205)
org.apache.commons.math3.ml.distance.EuclideanDistance.compute(EuclideanDistance.java:34)
org.alitouka.spark.dbscan.spatial.DistanceCalculation$class.calculateDistance(DistanceCalculation.scala:15)
org.alitouka.spark.dbscan.exploratoryAnalysis.DistanceToNearestNeighborDriver$.calculateDistance(DistanceToNearestNeighborDriver.scala:16)
On Thu, Jan 21, 2016 at 5:13 PM, Sanders, Isaac B
<sande...@rose-hulman.edu> wrote:
Hadoop is: HDP 2.3.2.0-2950
Here is a gist (pastebin) of my versions en masse and a stacktrace:
https://gist.github.com/isaacsanders/2e59131758469097651b
Thanks
On Jan 21, 2016, at 7:44 PM, Ted Yu <yuzhih...@gmail.com> wrote:
Looks like you were running on YARN.
What hadoop version are you using ?
Can you capture a few stack traces of the AppMaster during the delay and
pastebin them ?
Thanks
On Thu, Jan 21, 2016 at 8:08 AM, Sanders, Isaac B
<sande...@rose-hulman.edu> wrote:
The Spark Version is 1.4.1
The logs are full of standard fair, nothing like an exception or even
interesting [INFO] lines.
Here is the script I am using:
https://gist.github.com/isaacsanders/660f480810fbc07d4df2
Thanks
Isaac
On Jan 21, 2016, at 11:03 AM, Ted Yu <yuzhih...@gmail.com> wrote:
Can you provide a bit more information ?
command line for submitting Spark job
version of Spark
anything interesting from driver / executor logs ?
Thanks
On Thu, Jan 21, 2016 at 7:35 AM, Sanders, Isaac B
<sande...@rose-hulman.edu> wrote:
Hey all,
I am a CS student in the United States working on my senior thesis.
My thesis uses Spark, and I am encountering some trouble.
I am using
https://github.com/alitouka/spark_dbscan, and to determine parameters, I am
using the utility class they supply,
org.alitouka.spark.dbscan.exploratoryAnalysis.DistanceToNearestNeighborDriver.
I am on a 10 node cluster with one machine with 8 cores and 32G of memory and
nine machines with 6 cores and 16G of memory.
I have 442M of data, which seems like it would be a joke, but the job stalls at
the last stage.
It was stuck in Scheduler Delay for 10 hours overnight, and I have tried a
number of things for the last couple days, but nothing seems to be helping.
I have tried:
- Increasing heap sizes and numbers of cores
- More/less executors with different amounts of resources.
- Kyro Serialization
- FAIR Scheduling
It doesn’t seem like it should require this much. Any ideas?
- Isaac
