hey matei, ok when i switch to java 7 with G1 the GC time for all the "quick" tasks goes from 150ms to 10ms, but the slow ones stay just as slow. all i did was add -XX:+UseG1GC so maybe thats wrong, i still have to read up on G1.
an example of GC in a slow task is below. best, koert [GC pause (young), 0.0100070 secs] [Parallel Time: 7.3 ms, GC Workers: 18] [GC Worker Start (ms): Min: 2889329.4, Avg: 2889329.8, Max: 2889330.0, Diff: 0.6] [Ext Root Scanning (ms): Min: 2.0, Avg: 2.5, Max: 3.2, Diff: 1.2, Sum: 44.2] [Update RS (ms): Min: 0.0, Avg: 0.3, Max: 3.5, Diff: 3.5, Sum: 5.8] [Processed Buffers: Min: 0, Avg: 3.3, Max: 14, Diff: 14, Sum: 59] [Scan RS (ms): Min: 0.0, Avg: 0.0, Max: 0.0, Diff: 0.0, Sum: 0.1] [Object Copy (ms): Min: 0.2, Avg: 0.7, Max: 1.0, Diff: 0.8, Sum: 12.0] [Termination (ms): Min: 0.0, Avg: 2.4, Max: 2.6, Diff: 2.6, Sum: 43.8] [GC Worker Other (ms): Min: 0.0, Avg: 0.0, Max: 0.1, Diff: 0.0, Sum: 0.5] [GC Worker Total (ms): Min: 5.7, Avg: 5.9, Max: 6.3, Diff: 0.6, Sum: 106.4] [GC Worker End (ms): Min: 2889335.7, Avg: 2889335.7, Max: 2889335.7, Diff: 0.0] [Code Root Fixup: 0.0 ms] [Clear CT: 1.1 ms] [Other: 1.6 ms] [Choose CSet: 0.0 ms] [Ref Proc: 1.0 ms] [Ref Enq: 0.0 ms] [Free CSet: 0.3 ms] [Eden: 20.0M(752.0M)->0.0B(304.0M) Survivors: 2048.0K->2048.0K Heap: 5917.7M(6144.0M)->5898.8M(6144.0M)] [Times: user=0.12 sys=0.00, real=0.01 secs] [Full GC 5898M->2057M(6144M), 5.7978580 secs] [Eden: 2048.0K(304.0M)->0.0B(1064.0M) Survivors: 2048.0K->0.0B Heap: 5898.9M(6144.0M)->2057.5M(6144.0M)] [Times: user=9.24 sys=0.00, real=5.80 secs] On Tue, Mar 11, 2014 at 4:35 PM, Matei Zaharia <matei.zaha...@gmail.com>wrote: > Yeah, System.gc() is a suggestion but in practice it does invoke full GCs > on the Sun JVM. > > Matei > > On Mar 11, 2014, at 12:35 PM, Koert Kuipers <ko...@tresata.com> wrote: > > hey matei, > ha i will definitely that one! looks like a total hack... i might just > schedule it after the precaching of rdds defensively. > > also trying java 7 with g1 > > > On Tue, Mar 11, 2014 at 3:17 PM, Matei Zaharia <matei.zaha...@gmail.com>wrote: > >> Right, that's it. I think what happened is the following: all the nodes >> generated some garbage that put them very close to the threshold for a full >> GC in the first few runs of the program (when you cached the RDDs), but on >> the subsequent queries, only a few nodes are hitting full GC per query, so >> every query sees a slowdown but the problem persists for a whille. You can >> try manually forcing a GC on the nodes like this after you do your loading: >> >> sc.parallelize(1 to numNodes, numNodes).foreach(x => System.gc()) >> >> Where numNodes is your number of nodes. (Actually it's also okay to just >> make this higher, System.gc() returns fast when there's no GC to run.) >> >> Matei >> >> On Mar 11, 2014, at 7:12 AM, Koert Kuipers <ko...@tresata.com> wrote: >> >> hey matei, >> most tasks have GC times of 200ms or less, and then a few tasks take many >> seconds. example GC activity for a slow one: >> >> [GC [PSYoungGen: 1051814K->262624K(1398144K)] >> 3789259K->3524429K(5592448K), 0.0986800 secs] [Times: user=1.53 sys=0.01, >> real=0.10 secs] >> [GC [PSYoungGen: 786935K->524512K(1398144K)] >> 4048741K->4048762K(5592448K), 0.1132490 secs] [Times: user=1.70 sys=0.01, >> real=0.11 secs] >> [Full GC [PSYoungGen: 524512K->0K(1398144K)] [PSOldGen: >> 3524250K->2207344K(4194304K)] 4048762K->2207344K(5592448K) [PSPermGen: >> 56545K->54639K(83968K)], 7.7059350 secs] [Times:\ >> user=7.71 sys=0.00, real=7.70 secs] >> >> >> so looks like i am hit by stop-the-world gc? >> >> >> On Mon, Mar 10, 2014 at 7:00 PM, Koert Kuipers <ko...@tresata.com> wrote: >> >>> hey matei, >>> it happens repeatedly. >>> >>> we are currently runnning on java 6 with spark 0.9. >>> >>> i will add -XX:+PrintGCDetails and collect details, and also look into >>> java 7 G1. thanks >>> >>> >>> >>> >>> >>> >>> On Mon, Mar 10, 2014 at 6:27 PM, Matei Zaharia >>> <matei.zaha...@gmail.com>wrote: >>> >>>> Does this happen repeatedly if you keep running the computation, or >>>> just the first time? It may take time to move these Java objects to the old >>>> generation the first time you run queries, which could lead to a GC pause >>>> that also slows down the small queries. >>>> >>>> If you can run with -XX:+PrintGCDetails in your Java options, it would >>>> also be good to see what percent of each GC generation is used. >>>> >>>> The concurrent mark-and-sweep GC -XX:+UseConcMarkSweepGC or the G1 GC >>>> in Java 7 (-XX:+UseG1GC) might also avoid these pauses by GCing >>>> concurrently with your application threads. >>>> >>>> Matei >>>> >>>> On Mar 10, 2014, at 3:18 PM, Koert Kuipers <ko...@tresata.com> wrote: >>>> >>>> hello all, >>>> i am observing a strange result. i have a computation that i run on a >>>> cached RDD in spark-standalone. it typically takes about 4 seconds. >>>> >>>> but when other RDDs that are not relevant to the computation at hand >>>> are cached in memory (in same spark context), the computation takes 40 >>>> seconds or more. >>>> >>>> the problem seems to be GC time, which goes from milliseconds to tens >>>> of seconds. >>>> >>>> note that my issue is not that memory is full. i have cached about 14G >>>> in RDDs with 66G available across workers for the application. also my >>>> computation did not push any cached RDD out of memory. >>>> >>>> any ideas? >>>> >>>> >>>> >>> >> >> > >