This has indeed been caused by the network backend that dropped several
outgoing packets. I'm not sure why this wasn't "caught" by TCP.
We ended up with setting send_queue_size=256 recv_queue_size=512 for
ib_ipoib and krcvqs=4 fpr hfi1. We also updated our OmniPath switch
firmware to the current version. We still have _some_ dropped packets,
but so far jobs haven't died because of it.
As far as I can tell, it was also only Spark manifesting the problem.
The usual Hadoop mapred jobs were running fine.
Best,
-jhz
On Fri, 18 Aug 2017 19:59:26 +0200
Jan-Hendrik Zab <z...@l3s.de> wrote:
> Hello!
>
> I've some weird problems with Spark running on top of Yarn. (Spark 2.2
> on Cloudera CDH 5.12)
>
> There are a lot of "java.net.SocketException: Network is unreachable"
> in the executors, part of a log file:
> http://support.l3s.de/~zab/spark-errors.txt and the jobs also fail at
> rather random times with only several MBs up the GBs worth of the
> above errors.
>
> In the driver output I get the following:
> http://support.l3s.de/~zab/spark-errors.txt
>
> These errors usually go hand in hand with some dropped packets, but I
> would assume that TCP can actually handle that?
>
> The network backend is based on Intel OmniPath hardware running in
> connected mode with a MTU of 1500 (just as a save default at the
> moment).
>
> The nodes can also ping each other without a problem, their DNS
> configuration is also the same. Same hosts file deployed to all hosts
> via Ansible and same data configured in unbound DNS forwarder.
>
> I've several code snippets that manifest with that problem, current
> example:
>
> val data = session.read
> .schema(schema)
> .option("sep", "\t")
> .option("header", false)
> .csv(config.input)
> .as[LinkRecord]
>
> val filtered = data
> .filter(_.elem === "A@/href")
>
> val transformed = filtered.map(e => e.copy(date =
> e.date.slice(0, 10) +
> "T00:00:00.000-00:00")) .dropDuplicates(Array("src", "date", "dst"))
> transformed.write .option("sep", "\t")
> .option("header", "false")
> .option("compression", "gzip")
> .mode(SaveMode.Append)
> .csv(config.output)
>
> The input data is roughly 2.1TB (~ 500 billion lines I think) and on
> HDFS.
>
> I'm honestly running out of ideas on how to debug this problem. I'm
> half thinking that the above errors are just masking the real problem.
>
> I would greatly appreciate any help!
>
> ps.
> Please CC me, since I'm not subscribed to the mailing list.
>
> Kinds regards,
>
> Jan
>
>
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