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From mark <manwoodv...@googlemail.com>
Subject Re: Partitions with zero records & variable task times
Date Wed, 09 Sep 2015 01:14:11 GMT
As I understand things (maybe naively), my input data are stored in equal
sized blocks in HDFS, and each block  represents a partition within Spark
when read from HDFS, therefore each block should hold roughly the same
number of records.

So something is missing in my understanding - what can cause some
partitions to have zero records and others to have roughly equal sized
chunks (~50k in this case)?

Before writing a custom partitioner, I would like to understand why has the
default partitioner failed in my case?
On 8 Sep 2015 3:00 pm, "Akhil Das" <akhil@sigmoidanalytics.com> wrote:

> Try using a custom partitioner for the keys so that they will get evenly
> distributed across tasks
>
> Thanks
> Best Regards
>
> On Fri, Sep 4, 2015 at 7:19 PM, mark <manwoodvice@googlemail.com> wrote:
>
>> I am trying to tune a Spark job and have noticed some strange behavior -
>> tasks in a stage vary in execution time, ranging from 2 seconds to 20
>> seconds. I assume tasks should all run in roughly the same amount of time
>> in a well tuned job.
>>
>> So I did some investigation - the fast tasks appear to have no records,
>> whilst the slow tasks do. I need help understanding why this is happening.
>>
>> The code in the stage is pretty simple. All it does is:
>>
>> - filters records
>> - maps records to a (key, record) tuple
>> - reduces by key
>>
>> The data are Avro objects stored in Parquet files in 16MB blocks in HDFS.
>>
>> To establish how many records in each partition I added this snippet:
>>
>> val counts = rdd.mapPartitions(iter => {
>>       val ctx = TaskContext.get
>>       val stageId = ctx.stageId
>>       val partId = ctx.partitionId
>>       val attemptid = ctx.taskAttemptId()
>>         Array(Array(stageId, partId, attemptid, iter.size)).iterator }
>>       , true).collect()
>>
>> Which produces the following:
>>
>> 1              1              0              0
>> 1              2              1              50489
>> 1              3              2              0
>> 1              4              3              0
>> 1              5              4              0
>> 1              6              5              53200
>> 1              7              6              0
>> 1              8              7              0
>> 1              9              8              0
>> 1              10           9              56946
>> 1              11           10           0
>> 1              12           11           0
>> 1              13           12           0
>> 1              14           13           59209
>> 1              15           14           0
>> 1              16           15           0
>> 1              17           16           0
>> 1              18           17           50202
>> 1              19           18           0
>> 1              20           19           0
>> 1              21           20           0
>> 1              22           21           54613
>> 1              23           22           0
>> 1              24           23           0
>> 1              25           24           54157
>> 1              26           25           0
>> 1              27           26           0
>> 1              28           27           0
>> 1              29           28           53595
>> 1              30           29           0
>> 1              31           30           0
>> 1              32           31           10750
>>
>>
>> Looking at the logs, you can see the tasks that contain records have the
>> longest run time:
>>
>> 15/09/03 16:26:36 INFO TaskSetManager: Finished task 25.0 in stage 1.0
>> (TID 26) in 2782 ms on DG1322 (6/32)
>> 15/09/03 16:26:36 INFO TaskSetManager: Finished task 7.0 in stage 1.0
>> (TID 8) in 2815 ms on DG1322 (7/32)
>> 15/09/03 16:26:36 INFO TaskSetManager: Finished task 19.0 in stage 1.0
>> (TID 20) in 2815 ms on DG1322 (8/32)
>> 15/09/03 16:26:36 INFO TaskSetManager: Finished task 23.0 in stage 1.0
>> (TID 24) in 2840 ms on DG1321 (9/32)
>> 15/09/03 16:26:36 INFO TaskSetManager: Finished task 29.0 in stage 1.0
>> (TID 30) in 2839 ms on DG1321 (10/32)
>> 15/09/03 16:26:36 INFO TaskSetManager: Finished task 11.0 in stage 1.0
>> (TID 12) in 2878 ms on DG1321 (11/32)
>> 15/09/03 16:26:36 INFO TaskSetManager: Finished task 30.0 in stage 1.0
>> (TID 31) in 2870 ms on DG1321 (12/32)
>> 15/09/03 16:26:36 INFO TaskSetManager: Finished task 18.0 in stage 1.0
>> (TID 19) in 2892 ms on DG1321 (13/32)
>> 15/09/03 16:26:36 INFO TaskSetManager: Finished task 0.0 in stage 1.0
>> (TID 1) in 2930 ms on DG1321 (14/32)
>> 15/09/03 16:26:36 INFO TaskSetManager: Finished task 6.0 in stage 1.0
>> (TID 7) in 2934 ms on DG1321 (15/32)
>> 15/09/03 16:26:36 INFO TaskSetManager: Finished task 12.0 in stage 1.0
>> (TID 13) in 2931 ms on DG1321 (16/32)
>> 15/09/03 16:26:36 INFO TaskSetManager: Finished task 3.0 in stage 1.0
>> (TID 4) in 3246 ms on DG1323 (17/32)
>> 15/09/03 16:26:36 INFO TaskSetManager: Finished task 27.0 in stage 1.0
>> (TID 28) in 3226 ms on DG1323 (18/32)
>> 15/09/03 16:26:36 INFO TaskSetManager: Finished task 15.0 in stage 1.0
>> (TID 16) in 3249 ms on DG1323 (19/32)
>> 15/09/03 16:26:36 INFO TaskSetManager: Finished task 10.0 in stage 1.0
>> (TID 11) in 3669 ms on DG1323 (20/32)
>> 15/09/03 16:26:36 INFO TaskSetManager: Finished task 16.0 in stage 1.0
>> (TID 17) in 3666 ms on DG1323 (21/32)
>> 15/09/03 16:26:36 INFO TaskSetManager: Finished task 22.0 in stage 1.0
>> (TID 23) in 3664 ms on DG1323 (22/32)
>> 15/09/03 16:26:36 INFO TaskSetManager: Finished task 4.0 in stage 1.0
>> (TID 5) in 3692 ms on DG1323 (23/32)
>> *15/09/03 16:26:39 INFO TaskSetManager: Finished task 31.0 in stage 1.0
>> (TID 32) in 6668 ms on DG1322 (24/32)*
>> *15/09/03 16:26:48 INFO TaskSetManager: Finished task 17.0 in stage 1.0
>> (TID 18) in 15690 ms on DG1321 (25/32)*
>> *15/09/03 16:26:49 INFO TaskSetManager: Finished task 1.0 in stage 1.0
>> (TID 2) in 16194 ms on DG1322 (26/32)*
>> *15/09/03 16:26:49 INFO TaskSetManager: Finished task 5.0 in stage 1.0
>> (TID 6) in 16384 ms on DG1321 (27/32)*
>> *15/09/03 16:26:50 INFO TaskSetManager: Finished task 28.0 in stage 1.0
>> (TID 29) in 17194 ms on DG1323 (28/32)*
>> *15/09/03 16:26:50 INFO TaskSetManager: Finished task 21.0 in stage 1.0
>> (TID 22) in 17408 ms on DG1323 (29/32)*
>> *15/09/03 16:26:50 INFO TaskSetManager: Finished task 13.0 in stage 1.0
>> (TID 14) in 17711 ms on DG1322 (30/32)*
>> *15/09/03 16:26:51 INFO TaskSetManager: Finished task 24.0 in stage 1.0
>> (TID 25) in 17995 ms on DG1321 (31/32)*
>> *15/09/03 16:26:51 INFO TaskSetManager: Finished task 9.0 in stage 1.0
>> (TID 10) in 18183 ms on DG1323 (32/32)*
>>
>>
>> The Spark UI for the stage shows this:
>>
>> Summary Metrics for 32 Completed Tasks
>>
>> Metric Min 25th percentile Median 75th percentile Max
>>
>> Duration
>> 0.9s 2s 2s 16s 18 s
>>
>> GC Time
>> 0ms 0ms 0ms 0.5s 1s
>>
>> Input Size / Records
>> 0.0 B/0     0.0 B/0     0.0 B / 0     0.0 B / 53437      122.0 MB / 59209
>>
>> Shuffle Write Size / Records
>> 0.0 B / 0      0.0 B / 0      0.0 B / 0      3.7 KB / 1     127.8 KB / 35
>>
>> Aggregated Metrics by Executor
>> Executor ID      Address      Task Time      Total Tasks      Failed
>> Tasks      Succeeded Tasks      Input Size / Records      Shuffle Write
>> Size / Records
>>
>> 0      DG1322:41308      35 s      5      0      5      243.9 MB /
>> 106948      224.3 KB / 63
>> 1      DG1321:33576      48 s      5      0      5      0.0 B / 111750
>>           7.4 KB / 2
>> 2      DG1323:49348      30 s      5      0      5      0.0 B / 53595
>>           3.7 KB / 1
>> 3      DG1321:43093      12 s      5      0      5      0.0 B / 0
>>              0.0 B / 0
>> 4      DG1323:51009      34 s      6      0      6      0.0 B / 54767
>>           98.7 KB / 28
>> 5      DG1322:36787      50 s      6      0      6      0.0 B / 123977
>>          138.9 KB / 38
>>
>>
>> *** Edited for brevity - included an example of a short and long task ***
>> Tasks
>> Index   ID   Attempt   Status   Locality Level   Executor ID / Host
>> Duration   GC Time   Accumulators            Input Size / Records
>> Shuffle Write Size / Records
>> 0          1          0    SUCCESS NODE_LOCAL 4 / DG1323            2 s
>>                                                         0.0 B (hadoop) / 0
>>         0.0 B / 0
>> 1          2          0    SUCCESS NODE_LOCAL 5 / DG1322            16 s
>>         0.5 s         RecordCount: 54018   0.0 B (hadoop) / 54018 127.8 KB
>> / 35
>>
>>
>> Why are the tasks in the stage not processing an equal number of records?
>> What are the empty tasks doing? How can I even the tasks in this stage out?
>>
>> Any insights much appreciated...
>>
>>
>

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