Performance Tuning and Cost Optimization / Internals, Research, Consulting
Let’s review how EC2 vCPUs correspond to YARN vCores in Amazon EMR and Qubole Hadoop clusters. As an example, I will choose m4.4xlarge, r4.4xlarge and c4.4xlarge EC2 instance types.
EC2 vCPU is a thread of a CPU core (typically, there are two threads per core). Does it mean that YARN vCores should be equal to the number of EC2 vCPU? That’s not always the case.
Let’s review major REST API requests for uploading files to S3 (PutObject, CreateMultipartUpload, UploadPart and CompleteMultipartUpload) that you can observe in S3 access logs.
This can be helpful for monitoring S3 write performance. See also S3 Multipart Upload – S3 Access Log Messages.
On one of my clusters I got my favorite YARN error, although now it was in a Flink application:
Container is running beyond physical memory limits. Current usage: 99.5 GB of 99.5 GB physical memory used; 105.1 GB of 227.8 GB virtual memory used. Killing container.
Why did the container take so much physical memory and fail? Let’s investigate in detail.
Most applications writing data into S3 use the S3 multipart upload API to upload data in parts. First, you initiate the load, then upload parts and finally complete the multipart upload.
Let’s see how this operation is reflected in the S3 access log. My application uploaded the file data.gz into S3, and I can view it as follows:
One of our Flink streaming jobs had significant variance in the time spent on writing files to S3 by the same Task Manager process.
What settings do you need to check first?
On one of the clusters I noticed an increased rate of shuffle errors, and the restart of a job did not help, it still failed with the same error.
The error was as follows:
Error: Error while running task ( failure ) :
org.apache.tez.runtime.library.common.shuffle.orderedgrouped.Shuffle$ShuffleError:
error in shuffle in Fetcher
at org.apache.tez.runtime.library.common.shuffle.orderedgrouped.Shuffle$RunShuffleCallable.callInternal
(Shuffle.java:301)
Caused by: java.io.IOException:
Shuffle failed with too many fetch failures and insufficient progress!failureCounts=1,
pendingInputs=1, fetcherHealthy=false, reducerProgressedEnough=true, reducerStalled=true
In the previous article about YARN container memory (see, Tez Memory Tuning – Container is Running Beyond Physical Memory Limits) I wrote about the physical memory. Now I would like to pay attention to the virtual memory in YARN.
A typical YARN memory error may look like this:
Container is running beyond virtual memory limits. Current usage: 1.0 GB of 1.1 GB physical memory used; 2.9 GB of 2.4 GB virtual memory used. Killing container.
So what is the virtual memory, how to solve such errors and why is the virtual memory size often so large?
In the previous article Calculating Utilization of Cluster using Resource Manager Logs I showed how to estimate per-second utilization for a Hadoop cluster.
This information can be useful to calculate the idle time statistics for a cluster i.e. time when no any containers are running.
I have a Spark job that transforms incoming data from compressed text files into Parquet format and loads them into a daily partition of a Hive table. This is a typical job in a data lake, it is quite simple but in my case it was very slow.
Initially it took about 4 hours to convert ~2,100 input .gz files (~1.9 TB of data) into Parquet, while the actual Spark job took just 38 minutes to run and the remaining time was spent on loading data into a Hive partition.
Let’s see what is the reason of such behavior and how we can improve the performance.
I was asked to tune a Hive query that ran more than 10 hours. It was running on a 100 node cluster with 16 GB available for YARN containers on each node.
Although the query processed about 2 TB of input data, it did a fairly simple aggregation on user_id column and did not look too complex. It had 1 Map stage with 1,500 tasks and 1 Reduce stage with 7,000 tasks.
All map tasks completed within 30 minutes, and the query stuck on the Reduce phase. So what was wrong?