I am not getting anywhere with any of the suggestions so far. :( Trying some more outlets, I will share any solution I find.
- Isaac On Jan 23, 2016, at 1:48 AM, Renu Yadav <yren...@gmail.com<mailto:yren...@gmail.com>> wrote: If you turn on spark.speculation on then that might help. it worked for me On Sat, Jan 23, 2016 at 3:21 AM, Darren Govoni <dar...@ontrenet.com<mailto:dar...@ontrenet.com>> wrote: 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<mailto:bablo...@gmail.com>> Date: 01/22/2016 3:50 PM (GMT-05:00) To: Darren Govoni <dar...@ontrenet.com<mailto:dar...@ontrenet.com>>, "Sanders, Isaac B" <sande...@rose-hulman.edu<mailto:sande...@rose-hulman.edu>>, Ted Yu <yuzhih...@gmail.com<mailto:yuzhih...@gmail.com>> Cc: user@spark.apache.org<mailto: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<mailto: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<mailto:sande...@rose-hulman.edu>> Date: 01/21/2016 11:18 PM (GMT-05:00) To: Ted Yu <yuzhih...@gmail.com<mailto:yuzhih...@gmail.com>> Cc: user@spark.apache.org<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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
