CODEWITHSUNDEEP
hadoophbase
Sam Lee
Sam Lee

Reputation: 10463

Large MapReduce job keeps dying

I am trying to run a MapReduce job over a ~10TB HBase table with a subclass of TableMapper. It basically re-writes the entire table. The output is configured like this:

    FileOutputFormat.setOutputPath(job, tablePath);

    TableMapReduceUtil.initTableMapperJob(
            inputTableName,
            tblScanner,
            ResaltMapper.class,
            ImmutableBytesWritable.class, //outputKeyClass,
            KeyValue.class, // outputValueClass,
            job);

    HFileOutputFormat.configureIncrementalLoad(job, hTable);

I have tried running this job several times now, and each time it dies after a few hours. I see the following message in the application logs:

    {"timeStamp":"18/02/17 14:48:26,375","level":"WARN","category":"output.FileOutputCommitter","message":"Could not delete hdfs://trinity/data/trinity/hfiles/TABLE/_temporary/1/_temporary/attempt_1518830631967_0004_m_000063_0 "}
    {"timeStamp":"18/02/17 14:48:26,376","level":"WARN","category":"output.FileOutputCommitter","message":"Could not delete hdfs://trinity/data/trinity/hfiles/TABLE/_temporary/1/_temporary/attempt_1518830631967_0004_m_000101_0 "}
    {"timeStamp":"18/02/17 14:48:26,377","level":"WARN","category":"output.FileOutputCommitter","message":"Could not delete hdfs://trinity/data/trinity/hfiles/TABLE/_temporary/1/_temporary/attempt_1518830631967_0004_m_000099_0 "}
    {"timeStamp":"18/02/17 14:48:26,377","level":"WARN","category":"output.FileOutputCommitter","message":"Could not delete hdfs://trinity/data/trinity/hfiles/TABLE/_temporary/1/_temporary/attempt_1518830631967_0004_m_000112_0 "}
    {"timeStamp":"18/02/17 14:48:26,381","level":"WARN","category":"hdfs.DFSClient","message":"Slow ReadProcessor read fields took 152920ms (threshold=30000ms); ack: seqno: 1 reply: 0 reply: 0 reply: 0 downstreamAckTimeNanos: 20402922, targets: [DatanodeInfoWithStorage[10.40.177.236:50010,DS-4d0bd79b-eaf3-4ec0-93f1-203b74bdf87b,DISK], DatanodeInfoWithStorage[10.40.176.118:50010,DS-8506c9ff-206d-48c5-b476-04b8dc396a1c,DISK], DatanodeInfoWithStorage[10.40.186.216:50010,DS-36dece52-50c7-47b0-a202-2ee595fabbcc,DISK]] "}
    log4j:WARN No appenders could be found for logger (org.apache.hadoop.hdfs.DFSClient).
    log4j:WARN Please initialize the log4j system properly.
    log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.

I also see this message from the application report

NodeHealthReport    1/1 local-dirs are bad: /mnt/yarn/local; 1/1 log-dirs are bad: /mnt/yarn/logs

I'm not sure if these messages are related to the failure. There is plenty of space available on the cluster, which has 4 d2.8xlarge instances (96 2TB HDD across the 4 machines). However, specific hard drives are getting filled up. For example, on the current job, one only has ~9GB available, even though the other hardrives are almost half empty:

$ df -h
Filesystem                    Size  Used Avail Use% Mounted on
/dev/xvda1                     99G  5.0G   90G   6% /
none                          4.0K     0  4.0K   0% /sys/fs/cgroup
udev                          121G   12K  121G   1% /dev
tmpfs                          25G  672K   25G   1% /run
none                          5.0M     0  5.0M   0% /run/lock
none                          121G   32K  121G   1% /run/shm
none                          100M     0  100M   0% /run/user
/dev/mapper/ephemeral_luks0   1.8T  1.7T  9.0G 100% /mnt
/dev/mapper/ephemeral_luks1   1.8T  974G  767G  56% /mnt1
/dev/mapper/ephemeral_luks2   1.8T  982G  760G  57% /mnt2
/dev/mapper/ephemeral_luks3   1.8T  997G  745G  58% /mnt3
/dev/mapper/ephemeral_luks4   1.8T  982G  760G  57% /mnt4
...snip...

Does anyone have an idea of what is causing this? How can I solve the problem?

Upvotes: 1

Views: 637

Answers (1)

Sam Lee
Sam Lee

Reputation: 10463

I figured it out, it was because yarn.nodemanager.local-dirs was set to only a single HDD on each node in the cluster. Specifying every HDD for every node fixed the problem.

Upvotes: 1

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