Hm. Interesting. Yeah, I really haven't seen the error after setting mapred.child.java.opts=-Xmx1024m. Probably I won't have to fix the Pig script:)
-----Original Message----- From: Jonathan Coveney [mailto:[email protected]] Sent: 23 ноября 2011 г. 11:46 To: [email protected] Subject: Re: java.lang.OutOfMemoryError when using TOP udf I have seen issues with spilling if it had less than 1GB of heap. Once I allocated enough ram, no issues. It seems unlikely to me that the bag implementation fails on this because it's such a common use and nobody has reported an error, and running with less than 1GB of heap is definitely not recommended. Very curious if the error crops up again. 2011/11/22 pablomar <[email protected]> > just a guess .. could it be possible that the Bag is kept in memory > instead of being spilled to disk ? > browsing the code of InternalCachedBag, I saw: > > private void init(int bagCount, float percent) { > factory = TupleFactory.getInstance(); > mContents = new ArrayList<Tuple> < > http://javasourcecode.org/html/open-source/jdk/jdk-6u23/java/util/Arra > yList.java.html > >(); > > long max = Runtime.getRuntime().maxMemory(); > maxMemUsage = (long)(((float)max * percent) / (float)bagCount); > cacheLimit = Integer.MAX_VALUE; > > // set limit to 0, if memusage is 0 or really really small. > // then all tuples are put into disk if (maxMemUsage < 1) { > cacheLimit = 0; > } > > addDone = false; > } > > my guess is the cacheLimit was set to Integer.MAX_VALUE and it's > trying to keep all in memory when it is not big enough but not so > small to have cacheLimit reset to 0 > > > > > On Tue, Nov 22, 2011 at 10:08 AM, Ruslan Al-fakikh < > [email protected]> wrote: > > > Jonathan, > > > > I am running it on Prod cluster in MR mode, not locally. I started > > to see the issue when input size grew. A few days ago I found a > > workaround of putting this property: > > mapred.child.java.opts=-Xmx1024m > > But I think this is a temporary solution and the job will fail when > > the input size will grow again. > > > > Dmitriy, > > > > Thanks a lot for the investigation. I'll try it. > > > > -----Original Message----- > > From: Dmitriy Ryaboy [mailto:[email protected]] > > Sent: 22 ноября 2011 г. 2:21 > > To: [email protected] > > Subject: Re: java.lang.OutOfMemoryError when using TOP udf > > > > Ok so this: > > > > thirdLevelsTopVisitorsWithBots = FOREACH thirdLevelsByCategory { > > count = COUNT(thirdLevelsSummed); > > result = TOP( (int)(count * (double) > > ($THIRD_LEVELS_PERCENTAGE + > > $BOTS_PERCENTAGE) ), 3, thirdLevelsSummed); > > GENERATE FLATTEN(result); } > > > > requires "count" to be calculated before TOP can be applied. Since > > count can't be calculated until the reduce side, naturally, TOP > > can't start working on the map side (as it doesn't know its arguments yet). > > > > Try generating the counts * ($TLP + $BP) separately, joining them in > > (I > am > > guessing you have no more than a few K categories -- in that case, > > you > can > > do a replicated join), and then do group and TOP on. > > > > On Mon, Nov 21, 2011 at 1:53 PM, Jonathan Coveney > > <[email protected]> > > wrote: > > > You're right pablomar...hmm > > > > > > Ruslan: are you running this in mr mode on a cluster, or locally? > > > > > > I'm noticing this: > > > [2011-11-16 12:34:55] INFO (SpillableMemoryManager.java:154) - > > > first memory handler call- Usage threshold init = > > > 175308800(171200K) used = > > > 373454552(364701K) committed = 524288000(512000K) max = > > > 524288000(512000K) > > > > > > It looks like your max memory is 512MB. I've had issues with bag > > > spilling with less than 1GB allocated (-Xmx1024mb). > > > > > > 2011/11/21 pablomar <[email protected]> > > > > > >> i might be wrong, but it seems the error comes from > > >> while(itr.hasNext()) > > >> not from the add to the queue > > >> so i don't think it is related to the number of elements in the > > >> queue ... maybe the field lenght? > > >> > > >> On 11/21/11, Jonathan Coveney <[email protected]> wrote: > > >> > Internally, TOP is using a priority queue. It tries to be smart > > >> > about pulling off excess elements, but if you ask it for enough > > >> > elements, it > > >> can > > >> > blow up, because the priority queue is going to have n > > >> > elements, where n > > >> is > > >> > the ranking you want. This is consistent with the stack trace, > > >> > which died on updateTop which is when elements are added to the > > priority queue. > > >> > > > >> > Ruslan, how large are the limits you're setting? ie (int)(count > > >> > * > > >> (double) > > >> > ($THIRD_LEVELS_PERCENTAGE + $BOTS_PERCENTAGE) ) > > >> > > > >> > As far as TOP's implementation, I imagine you could get around > > >> > the issue > > >> by > > >> > using a sorted data bag, but that might be much slower. hmm. > > >> > > > >> > 2011/11/21 Ruslan Al-fakikh <[email protected]> > > >> > > > >> >> Ok. Here it is: > > >> >> https://gist.github.com/1383266 > > >> >> > > >> >> -----Original Message----- > > >> >> From: Dmitriy Ryaboy [mailto:[email protected]] > > >> >> Sent: 21 ноября 2011 г. 20:32 > > >> >> To: [email protected] > > >> >> Subject: Re: java.lang.OutOfMemoryError when using TOP udf > > >> >> > > >> >> Ruslan, I think the mailing list is set to reject attachments > > >> >> -- can you post it as a github gist or something similar, and > > >> >> send a > > link? > > >> >> > > >> >> D > > >> >> > > >> >> On Mon, Nov 21, 2011 at 6:11 AM, Ruslan Al-Fakikh > > >> >> <[email protected]> wrote: > > >> >> > Hey Dmitriy, > > >> >> > > > >> >> > I attached the script. It is not a plain-pig script, because > > >> >> > I make some preprocessing before submitting it to cluster, > > >> >> > but the general idea of what I submit is clear. > > >> >> > > > >> >> > Thanks in advance! > > >> >> > > > >> >> > On Fri, Nov 18, 2011 at 12:07 AM, Dmitriy Ryaboy > > >> >> > <[email protected]> > > >> >> wrote: > > >> >> >> Ok, so it's something in the rest of the script that's > > >> >> >> causing this to happen. Ruslan, if you send your script, I > > >> >> >> can probably figure out why (usually, it's using another, > > >> >> >> non-agebraic udf in your foreach, or for pig 0.8, > > >> >> >> generating a constant in the > > foreach). > > >> >> >> > > >> >> >> D > > >> >> >> > > >> >> >> On Thu, Nov 17, 2011 at 9:59 AM, pablomar > > >> >> >> <[email protected]> wrote: > > >> >> >>> according to the stack trace, the algebraic is not being > > >> >> >>> used it says > > >> >> >>> updateTop(Top.java:139) > > >> >> >>> exec(Top.java:116) > > >> >> >>> > > >> >> >>> On 11/17/11, Dmitriy Ryaboy <[email protected]> wrote: > > >> >> >>>> The top udf does not try to process all data in memory if > > >> >> >>>> the algebraic optimization can be applied. It does need > > >> >> >>>> to keep the topn numbers in memory of course. Can you > > >> >> >>>> confirm algebraic mode is > > >> >> used? > > >> >> >>>> > > >> >> >>>> On Nov 17, 2011, at 6:13 AM, "Ruslan Al-fakikh" > > >> >> >>>> <[email protected]> > > >> >> >>>> wrote: > > >> >> >>>> > > >> >> >>>>> Hey guys, > > >> >> >>>>> > > >> >> >>>>> > > >> >> >>>>> > > >> >> >>>>> I encounter java.lang.OutOfMemoryError when using TOP udf. > > >> >> >>>>> It seems that the udf tries to process all data in memory. > > >> >> >>>>> > > >> >> >>>>> Is there a workaround for TOP? Or maybe there is some > > >> >> >>>>> other way of getting top results? I cannot use LIMIT > > >> >> >>>>> since I need to 5% of data, not a constant number of rows. > > >> >> >>>>> > > >> >> >>>>> > > >> >> >>>>> > > >> >> >>>>> I am using: > > >> >> >>>>> > > >> >> >>>>> Apache Pig version 0.8.1-cdh3u2 (rexported) > > >> >> >>>>> > > >> >> >>>>> > > >> >> >>>>> > > >> >> >>>>> The stack trace is: > > >> >> >>>>> > > >> >> >>>>> [2011-11-16 12:34:55] INFO (CodecPool.java:128) - Got > > >> >> >>>>> brand-new decompressor > > >> >> >>>>> > > >> >> >>>>> [2011-11-16 12:34:55] INFO (Merger.java:473) - Down to > > >> >> >>>>> the last merge-pass, with 21 segments left of total size: > > >> >> >>>>> 2057257173 bytes > > >> >> >>>>> > > >> >> >>>>> [2011-11-16 12:34:55] INFO > > >> >> >>>>> (SpillableMemoryManager.java:154) - first memory handler > > >> >> >>>>> call- Usage threshold init = > > >> >> >>>>> 175308800(171200K) used = > > >> >> >>>>> 373454552(364701K) committed = 524288000(512000K) max = > > >> >> >>>>> 524288000(512000K) > > >> >> >>>>> > > >> >> >>>>> [2011-11-16 12:36:22] INFO > > >> >> >>>>> (SpillableMemoryManager.java:167) - first memory handler > > >> >> >>>>> call - Collection threshold init = > > >> >> >>>>> 175308800(171200K) used = > > >> >> >>>>> 496500704(484863K) committed = 524288000(512000K) max = > > >> >> >>>>> 524288000(512000K) > > >> >> >>>>> > > >> >> >>>>> [2011-11-16 12:37:28] INFO (TaskLogsTruncater.java:69) > > >> >> >>>>> - Initializing logs' > > >> >> >>>>> truncater with mapRetainSize=-1 and reduceRetainSize=-1 > > >> >> >>>>> > > >> >> >>>>> [2011-11-16 12:37:28] FATAL (Child.java:318) - Error > > >> >> >>>>> running > > >> child : > > >> >> >>>>> java.lang.OutOfMemoryError: Java heap space > > >> >> >>>>> > > >> >> >>>>> at > > >> >> >>>>> java.util.Arrays.copyOfRange(Arrays.java:3209) > > >> >> >>>>> > > >> >> >>>>> at > > >> >> >>>>> java.lang.String.<init>(String.java:215) > > >> >> >>>>> > > >> >> >>>>> at > > >> >> >>>>> java.io.DataInputStream.readUTF(DataInputStream.java:644 > > >> >> >>>>> ) > > >> >> >>>>> > > >> >> >>>>> at > > >> >> >>>>> java.io.DataInputStream.readUTF(DataInputStream.java:547 > > >> >> >>>>> ) > > >> >> >>>>> > > >> >> >>>>> at > > >> >> >>>>> org.apache.pig.data.BinInterSedes.readCharArray(BinInter > > >> >> >>>>> Sede > > >> >> >>>>> s.java > > >> >> >>>>> :210) > > >> >> >>>>> > > >> >> >>>>> at > > >> >> >>>>> org.apache.pig.data.BinInterSedes.readDatum(BinInterSede > > >> >> >>>>> s.ja > > >> >> >>>>> va:333 > > >> >> >>>>> ) > > >> >> >>>>> > > >> >> >>>>> at > > >> >> >>>>> org.apache.pig.data.BinInterSedes.readDatum(BinInterSede > > >> >> >>>>> s.ja > > >> >> >>>>> va:251 > > >> >> >>>>> ) > > >> >> >>>>> > > >> >> >>>>> at > > >> >> >>>>> org.apache.pig.data.BinInterSedes.addColsToTuple(BinInte > > >> >> >>>>> rSed > > >> >> >>>>> es.jav > > >> >> >>>>> a:555) > > >> >> >>>>> > > >> >> >>>>> at > > >> >> >>>>> org.apache.pig.data.BinSedesTuple.readFields(BinSedesTup > > >> >> >>>>> le.j > > >> >> >>>>> ava:64 > > >> >> >>>>> ) > > >> >> >>>>> > > >> >> >>>>> at > > >> >> >>>>> org.apache.pig.data.InternalCachedBag$CachedBagIterator. > > >> >> >>>>> hasN > > >> >> >>>>> ext(In > > >> >> >>>>> ternalCach > > >> >> >>>>> edBag.java:237) > > >> >> >>>>> > > >> >> >>>>> at > > >> >> >>>>> org.apache.pig.builtin.TOP.updateTop(TOP.java:139) > > >> >> >>>>> > > >> >> >>>>> at > > >> >> >>>>> org.apache.pig.builtin.TOP.exec(TOP.java:116) > > >> >> >>>>> > > >> >> >>>>> at > > >> >> >>>>> org.apache.pig.builtin.TOP.exec(TOP.java:65) > > >> >> >>>>> > > >> >> >>>>> at > > >> >> >>>>> org.apache.pig.backend.hadoop.executionengine.physicalLayer. > > >> >> >>>>> expres > > >> >> >>>>> sionOperat > > >> >> >>>>> ors.POUserFunc.getNext(POUserFunc.java:245) > > >> >> >>>>> > > >> >> >>>>> at > > >> >> >>>>> org.apache.pig.backend.hadoop.executionengine.physicalLayer. > > >> >> >>>>> expres > > >> >> >>>>> sionOperat > > >> >> >>>>> ors.POUserFunc.getNext(POUserFunc.java:287) > > >> >> >>>>> > > >> >> >>>>> at > > >> >> >>>>> org.apache.pig.backend.hadoop.executionengine.physicalLayer. > > >> >> >>>>> relati > > >> >> >>>>> onalOperat > > >> >> >>>>> ors.POForEach.processPlan(POForEach.java:338) > > >> >> >>>>> > > >> >> >>>>> at > > >> >> >>>>> org.apache.pig.backend.hadoop.executionengine.physicalLayer. > > >> >> >>>>> relati > > >> >> >>>>> onalOperat > > >> >> >>>>> ors.POForEach.getNext(POForEach.java:290) > > >> >> >>>>> > > >> >> >>>>> at > > >> >> >>>>> org.apache.pig.backend.hadoop.executionengine.physicalLayer. > > >> >> >>>>> Physic > > >> >> >>>>> alOperator > > >> >> >>>>> .processInput(PhysicalOperator.java:276) > > >> >> >>>>> > > >> >> >>>>> at > > >> >> >>>>> org.apache.pig.backend.hadoop.executionengine.physicalLayer. > > >> >> >>>>> relati > > >> >> >>>>> onalOperat > > >> >> >>>>> ors.POForEach.getNext(POForEach.java:240) > > >> >> >>>>> > > >> >> >>>>> at > > >> >> >>>>> org.apache.pig.backend.hadoop.executionengine.mapReduceL > > >> >> >>>>> ayer > > >> >> >>>>> .PigMa > > >> >> >>>>> pReduce$Re > > >> >> >>>>> duce.runPipeline(PigMapReduce.java:434) > > >> >> >>>>> > > >> >> >>>>> at > > >> >> >>>>> org.apache.pig.backend.hadoop.executionengine.mapReduceL > > >> >> >>>>> ayer > > >> >> >>>>> .PigMa > > >> >> >>>>> pReduce$Re > > >> >> >>>>> duce.processOnePackageOutput(PigMapReduce.java:402) > > >> >> >>>>> > > >> >> >>>>> at > > >> >> >>>>> org.apache.pig.backend.hadoop.executionengine.mapReduceL > > >> >> >>>>> ayer > > >> >> >>>>> .PigMa > > >> >> >>>>> pReduce$Re > > >> >> >>>>> duce.reduce(PigMapReduce.java:382) > > >> >> >>>>> > > >> >> >>>>> at > > >> >> >>>>> org.apache.pig.backend.hadoop.executionengine.mapReduceL > > >> >> >>>>> ayer > > >> >> >>>>> .PigMa > > >> >> >>>>> pReduce$Re > > >> >> >>>>> duce.reduce(PigMapReduce.java:251) > > >> >> >>>>> > > >> >> >>>>> at > > >> >> >>>>> org.apache.hadoop.mapreduce.Reducer.run(Reducer.java:176 > > >> >> >>>>> ) > > >> >> >>>>> > > >> >> >>>>> at > > >> >> >>>>> > > org.apache.hadoop.mapred.ReduceTask.runNewReducer(ReduceTask.java: > > >> >> >>>>> 572) > > >> >> >>>>> > > >> >> >>>>> at > > >> >> >>>>> org.apache.hadoop.mapred.ReduceTask.run(ReduceTask.java: > > >> >> >>>>> 414) > > >> >> >>>>> > > >> >> >>>>> at > > >> >> >>>>> org.apache.hadoop.mapred.Child$4.run(Child.java:270) > > >> >> >>>>> > > >> >> >>>>> at > > >> >> >>>>> java.security.AccessController.doPrivileged(Native > > >> >> >>>>> Method) > > >> >> >>>>> > > >> >> >>>>> at > > >> >> >>>>> javax.security.auth.Subject.doAs(Subject.java:396) > > >> >> >>>>> > > >> >> >>>>> at > > >> >> >>>>> org.apache.hadoop.security.UserGroupInformation.doAs(Use > > >> >> >>>>> rGro > > >> >> >>>>> upInfo > > >> >> >>>>> rmation.ja > > >> >> >>>>> va:1127) > > >> >> >>>>> > > >> >> >>>>> at > > >> >> >>>>> org.apache.hadoop.mapred.Child.main(Child.java:264) > > >> >> >>>>> > > >> >> >>>>> > > >> >> >>>>> > > >> >> >>>>> > > >> >> >>>>> > > >> >> >>>>> > > >> >> >>>>> > > >> >> >>>>> stderr logs > > >> >> >>>>> > > >> >> >>>>> Exception in thread "Low Memory Detector" > > >> >> >>>>> java.lang.OutOfMemoryError: Java heap space > > >> >> >>>>> > > >> >> >>>>> at > > >> >> >>>>> sun.management.MemoryNotifInfoCompositeData.getComposite > > >> >> >>>>> Data > > >> >> >>>>> (Memor > > >> >> >>>>> yNotifInfo > > >> >> >>>>> CompositeData.java:42) > > >> >> >>>>> > > >> >> >>>>> at > > >> >> >>>>> sun.management.MemoryNotifInfoCompositeData.toCompositeD > > >> >> >>>>> ata( > > >> >> >>>>> Memory > > >> >> >>>>> NotifInfoC > > >> >> >>>>> ompositeData.java:36) > > >> >> >>>>> > > >> >> >>>>> at > > >> >> >>>>> sun.management.MemoryImpl.createNotification(MemoryImpl. > > >> >> >>>>> java > > >> >> >>>>> :168) > > >> >> >>>>> > > >> >> >>>>> at > > >> >> >>>>> > > >> >> > > >> >> > > >> > > > sun.management.MemoryPoolImpl$CollectionSensor.triggerAction(MemoryPoolImpl. > > >> >> >>>>> java:300) > > >> >> >>>>> > > >> >> >>>>> at > > >> >> >>>>> sun.management.Sensor.trigger(Sensor.java:120) > > >> >> >>>>> > > >> >> >>>>> > > >> >> >>>>> > > >> >> >>>>> > > >> >> >>>>> > > >> >> >>>>> Thanks in advance! > > >> >> >>>>> > > >> >> >>>> > > >> >> >>> > > >> >> >> > > >> >> > > > >> >> > > > >> >> > > > >> >> > -- > > >> >> > Best Regards, > > >> >> > Ruslan Al-Fakikh > > >> >> > > > >> >> > > >> >> > > >> > > > >> > > > > > > > >
