AWS Big Data Blog
Enhancing data durability in Amazon EMR HBase on Amazon S3 with the Amazon EMR WAL feature
Apache HBase, an open source NoSQL database, enables quick access to massive datasets. Amazon EMR, from version 5.2.0, lets you use HBase on Amazon Simple Storage Service (Amazon S3). This combines HBase’s speed with the durability advantages of Amazon S3. Also, it helps achieve the data lake architecture benefits such as the ability to scale storage and compute requirements separately. We see our customers choosing Amazon S3 over Hadoop Distributed File Systems (HDFS) when they want to achieve greater durability, availability, and simplified storage management. Amazon EMR continually improves HBase on Amazon S3, focusing on performance, availability, and reliability.
Despite these durability benefits of HBase on Amazon S3 architecture, a critical concern remains regarding data recovery when the Write-Ahead Log (WAL) is lost. Within the EMR framework, HBase data attains durability when it’s flushed, or written, to Amazon S3. This flushing process is triggered by reaching specific size and time thresholds or through manual initiation. Until data is successfully flushed to S3, it persists within the WAL, which is stored in HDFS. In this post, we dive deep into the new Amazon EMR WAL feature to help you understand how it works, how it enhances durability, and why it’s needed. We explore several scenarios that are well-suited for this feature.
HBase WAL overview
Each RegionServer in HBase is responsible for managing data from multiple tables. These tables are horizontally partitioned into regions, where each region represents a contiguous range of row keys. A RegionServer can host multiple such regions, potentially from different tables. At the RegionServer level, there is a single, shared WAL that records all write operations across all regions and tables in a sequential, append-only manner. This shared WAL makes sure durability is maintained by persisting each mutation before applying it to in-memory structures, enabling recovery in case of unexpected failures. Within each region, the memory structure of the MemStore is further divided by column families, which are the fundamental units of physical storage and I/O in HBase. Each column family maintains:
- Its own MemStore, which holds recently written data in memory for fast access and buffering before it flushes to disk.
- A set of HFiles, which are immutable data files stored on HDFS (or Amazon S3 in HBase on S3 mode) that hold the persistent, flushed data.
Although all column families within a region are served by the same RegionServer process, they operate independently in terms of memory buffering, flushing, and compaction. However, they still share the same WAL and RegionServer-level resources, which introduces a degree of coordination, hence they operate semi-independently within the broader region context. This architecture is shown in the following diagram.
Understanding the HBase write process: WAL, MemStore, and HFiles
The HBase write path initiates when a client issues a write request, typically through an RPC call directed to the appropriate RegionServer that hosts the target region. Upon receiving the request, the RegionServer identifies the correct HBase region based on the row key and forwards the KeyValue pair accordingly. The write operation follows a two-step process. First, the data is appended to the WAL, which promotes durability by recording every change before it’s committed to memory. The WAL resides on HDFS by default and exists independently on each RegionServer. Its primary purpose is to provide a recovery mechanism in the event of a failure, particularly for edits that have not yet been flushed to disk. When the WAL append is successful, the data is written to the MemStore, an in-memory store for each column family within the region. The MemStore accumulates updates until it reaches a predefined size threshold, controlled by the hbase.hregion.memstore.flush.size parameter (default is 128 MB). When this threshold is exceeded, a flush is triggered.Flushing is handled asynchronously by a background thread in the RegionServer. The thread writes the contents of the MemStore to a new HFile, which is then persisted to long-term storage. In Amazon EMR, the location of this HFile depends on the deployment mode: for HBase on Amazon S3, HFiles are stored in Amazon S3, but for HBase on HDFS, they’re stored in HDFS.This workflow is shown in the following diagram.
A region server serves multiple regions, and they all share a common WAL. The WAL records all data changes, storing them in local HDFS. Puts and deletes are initially logged to the WAL by the region server before being recorded in the MemStore for the affected store. Scan and get operations in HBase don’t require the use of the WAL. In the event of a region server crash or unavailability before MemStore flushing, the WAL is crucial for replaying data changes, which promotes data integrity. Because this log by default resides on a replicated filesystem, it enables an alternate server to access and replay the log, requiring nothing from the physically failed server for a complete recovery. When a RegionServer fails abruptly, HBase initiates an automated recovery process orchestrated by the HMaster. First, the ZooKeeper session timeout detects the RegionServer failure, notifying the HMaster. The HMaster then identifies all regions previously hosted on the failed RegionServer and marks them as unassigned. The WAL files from the failed RegionServer are split by region, and these split WAL files are distributed to the new RegionServers that will host the reassigned regions. Each new RegionServer replays its assigned WAL segments to recover the MemStore state that existed before the failure, preventing data loss. When WAL replay is complete, the regions become operational on their new RegionServers, and the recovery process concludes.
The effectiveness of the HDFS WAL model relies on the successful completion of the write request in the WAL and the subsequent data replication in HDFS. In cases where some nodes are terminated, HDFS can still recover from the WAL files, allowing HBase to autonomously heal by replaying data from the WALs and rebalancing the regions. However, if all CORE nodes are simultaneously terminated, achieving complete cluster recovery is a challenge because the data to replay from the WAL is lost. The issue arises when WALs are lost due to CORE node shutdown (for example, all three replicas of a file block). In this scenario, HBase enters a loop attempting to replay data from the WALs. Unfortunately, the absence of available blocks in this case causes the HBase server crash procedure to fail and retry indefinitely.
Amazon EMR WAL
To address the mentioned challenge of HDFS WAL and to provide data durability in HBase, Amazon EMR introduces a new EMR WAL feature starting from versions emr-7.0 and emr-6.15. This feature facilitates the recovery of data that hasn’t been flushed to Amazon S3 (HFile). Using this feature provides thorough backup for your HBase clusters. Behind the scenes, the RegionServer writes WAL data to EMR WAL, which is a service outside the EMR cluster. With this feature enabled, concerns about loss of WAL data in HDFS are alleviated. Also, in the event of cluster or Availability Zone failure issues, you can create a new cluster, directing it to the same Amazon S3 root directory and EMR WAL workspace. This enables the automatic recovery of data in the WAL in the order of minutes. Recovery of unflushed data is supported for a duration of 30 days, after which remaining unflushed data is deleted. This workflow is shown in the following diagram.
Key benefits
Upon enabling EMR WAL, the WALs are located external to the EMR cluster. The key benefits are:
- High availability – You can remain confident about data integrity even in the face of Availability Zone failures. Their HFiles are stored in Amazon S3, and the WALs are externally stored in EMR WAL. This setup enables cluster recovery and WAL replay in the same or a different Availability Zone within the region. However, for true high availability with zero downtime, relying solely on EMR WAL is not sufficient because recovery still involves brief interruptions. To provide seamless failover and uninterrupted service, HBase replication across multiple Availability Zones is essential along with EMR WAL, providing robust zero-downtime high availability.
- Data durability improvement – Customers no longer need to concern themselves with potential data loss in scenarios involving WAL data corruption in HDFS or the removal of all replicas in HDFS due to instance terminations.
The following flow diagram compares the sequence of events with and without EMR WAL enabled.
Key EMR WAL features
In this section, we explore the key enhancements introduced in the EMR WAL service across recent Amazon EMR versions. From grouping multiple HBase regions into a single EMR WAL to advanced configuration options, these new capabilities address specific usage scenarios.
Grouping multiple HBase regions into a single Amazon EMR WAL
In Amazon EMR versions up to 7.2, a separate EMR WAL is created for each region, which can become expensive due to the EMR-WAL-WALHours pricing model, especially when the HBase cluster contains many regions. To address this, starting from Amazon EMR 7.3, we introduced the EMR WAL grouping feature, which enables consolidating multiple HBase regions per EMR WAL, offering significant cost savings (over 99% cost savings in our sample evaluation) and improved operational efficiency. By default, each HBase RegionServer has two Amazon EMR WALs. If you have many regions per RegionServer and want to increase throughput, you can customize the number of WALs per RegionServer by configuring the hbase.wal.regiongrouping.numgroups property. For instance, to set 10 EMR WALs per HBase RegionServer, you can use the following configuration:
The two HBase system tables hbase:meta and hbase:master (masterstore) don’t participate in the WAL grouping mechanisms.
In a performance test using m5.8xlarge instances with 1,000 regions per RegionServer, we observed a significant increase in throughput as the number of WALs grew from 1 to 20 per RegionServer (from 1,570 to 3,384 operations per sec). This led to a 54% improvement in average latency (from 40.5 ms to 18.8 ms) and a 72% reduction in 95th percentile latency (from 231 ms to 64 ms). However, beyond 20 WALs, we noted diminishing returns, with only slight performance improvements between 20 and 50 WALs, and average latency stabilized around 18.7ms. Based on these results, we recommend maintaining a lower region density (around 10 regions per WAL) for optimal performance. Nonetheless, it’s crucial to fine-tune this configuration according to your specific workload characteristics and performance requirements and conduct tests in your lower environment to validate the best setup.
Configurable maximum record size in EMR WAL
Until Amazon EMR version 7.4, the EMR WAL had a record size limit of 4 MB, which was insufficient for some customers. Starting from EMR 7.5, the maximum record size in EMR WAL is configurable through the emr.wal.max.payload.size property. The default value is set to 1 GB. The following is an example of how to set the maximum record size to 2 GB:
AWS PrivateLink support
EMR WAL supports AWS PrivateLink, if you want to keep your connection within the AWS network. To set it up, create a virtual private cloud (VPC) endpoint using the AWS Management Console or AWS Command Line Interface (AWS CLI) and select the service labeled com.amazonaws.region.emrwal.prod. Make sure your VPC endpoint uses the same security groups as the EMR cluster. You have two DNS configuration options: enabling private DNS, which uses the standard endpoint format and automatically routes traffic privately, or using the provided VPC endpoint-specific DNS name for more explicit control. Regardless of the DNS option chosen, both methods mean that traffic remains within the AWS network, enhancing security. To implement this in the EMR cluster, update your cluster configuration to use the PrivateLink endpoint, as shown in the following code sample (for private DNS):
For more details, refer to Access Amazon EMR WAL through AWS PrivateLink in the Amazon EMR documentation.
Encryption options for WAL in Amazon EMR
Amazon EMR automatically encrypts data in transit in the EMR WAL service. You can enable server-side encryption (SSE) for WAL (data at rest) with two key management options:
- SSE-EMR-WAL: Amazon EMR manages the encryption keys
- SSE-KMS-WAL: You use an AWS Key Management Service (AWS KMS) key for encryption policies
EMR WAL cross-cluster replication
From EMR 7.5, EMR WAL supports cross-cluster replay, allowing clusters in an active-passive HBase replication setup to use EMR WAL.
For more details on the setup, refer to EMR WAL cross-cluster replication in the Amazon EMR documentation.
EMR WAL enhancement: Minimizing CPU load from HBase sync threads
Starting from EMR 7.9, we’ve implemented code optimizations in EMR WAL to address the high CPU utilization caused by sync threads used by HBase processes to write WAL edits, leading to improved CPU efficiency.
Sample use cases benefitting from this feature
Based on our customer interactions and feedback, this feature can help in the following scenarios.
Continuity during service disruptions
If your business demands disaster recovery with no data loss for an HBase on an S3 cluster due to unexpected service disruptions, such as an Availability Zone failure, the newly introduced feature means you don’t have to rely on a persistent event store solution using Amazon Managed Streaming for Apache Kafka (Amazon MSK) or Amazon Kinesis. Without EMR WAL, you had to set up a complex event-streaming pipeline to retain the most recently ingested data and enable replay from the point of failure. This new feature eliminates that dependency by storing Hbase WALs in the EMR WAL service.
Note: During an Availability Zone (AZ) failure or service-level issue, make sure to fully terminate the original Hbase cluster before launching a new one that points to the same S3 root directory. Running two active Hbase clusters that access the same S3 root can lead to data corruption.
Upgrading to the latest EMR releases or cluster rotations
Without EMR WAL, moving to the latest EMR version or managing cluster rotations with HBase on Amazon S3 necessitated manual interruptions for data flushing to S3. With the new feature, the requirement for data flushing is eliminated. However, during cluster termination and the subsequent launch of a new HBase cluster, there is an inevitable service downtime, during which data producers or ingestion pipelines must handle write disruptions or buffer incoming data until the system is fully restored. Also, the downstream services should account for temporary unavailability, which can be mitigated using a read replica cluster.
Overcoming HDFS challenges during HBase auto scaling
Without EMR WAL feature, having HDFS for your WAL files was a requirement. When implementing custom auto scaling for your HBase clusters, it sometimes resulted in WAL data corruption due to issues linked to HDFS. This is because, to prevent data loss, data blocks had to be moved to different HDFS nodes when one HDFS node was being decommissioned. When nodes continued to be terminated swiftly during scale-down process without allowing sufficient time for graceful decommissioning, it could result in WAL data corruption issues, primarily attributed to missing blocks.
Addressing HDFS disk space issues due to old WALs
When a WAL file is no longer required for recovery, indicating that HBase has made sure all data within the WAL file has been flushed, it’s transferred to the oldWALs folder for archival purposes. The log remains in this location until all other references to the WAL file are completed. In HBase use cases with high write activity, some customers have expressed concerns about the oldWALs directory (/usr/hbase/oldWALs) expanding and occupying excessive disk space and eventually causing disk space issues. With the complete relocation of these WALs to an external EMR WAL service, you will no longer encounter this issue.
Assessing HBase in Amazon EMR clusters with and without EMR WAL for fault tolerance
We conducted a data durability test employing two scripts. The first was for installing YCSB, creating a pre-split table, and loading 8 million records on the master node. The second was for terminating a core node every 90 seconds after a 3-minute wait, totaling five terminations. Two EMR clusters with eight core nodes each were created, one configured with EMR WAL enabled and the other as a standard EMR HBase cluster with the WAL stored in HDFS. After completion of EMR steps, a count was run on the HBase table. In the EMR cluster with EMR WAL enabled, all records were successfully inserted without corruption. In the cluster not using EMR WALs, regions in HBase remained “OPENING” if the node hosting the meta was terminated. For other core node terminations, inserts failed, resulting in a lower record count during validation.
Understanding when EMR WAL read charges apply in HBase
In HBase, standard table read operations such as Get and Scan don’t access WALs. Therefore, EMR WAL read (GiB) charges are only incurred during operations that involve reading from WALs, such as:
- Restoring data from EMR WALs in a newly launched cluster
- Replaying WALs to recover data on a crashed RegionServer
- Performing HBase replication, which involves reading WALs to replicate data across clusters
In a normal scenario, you’re billed only for the following two components related to EMR WAL usage:
- EMR-WAL-WALHours – Represents the hourly cost of WAL storage, calculated based on the number of WALs maintained. You can use the EMRWALCount metric in Amazon CloudWatch to monitor the number of WALs and track associated usage over time.
- EMR-WAL-WriteRequestGiB – This reflects the volume of data written to the WAL service, charged by the amount of data written in GiB.
For further details on pricing, refer to Amazon EMR pricing and Amazon EMR Release Guide.
To monitor and analyze EMR WAL related costs in the AWS Cost and Usage Reports (CUR), look under product_servicecode = ‘ElasticMapReduce’, where you’ll find the following product_usagetype entries associated with WAL usage:
- USE1-EMR-WAL-ReadRequestGiB
- USE1-EMR-WAL-WALHours
- USE1-EMR-WAL-WriteRequestGiB
The prefix USE1 indicates the Region (in this case, us-east-1) and will vary depending on where your EMR cluster is deployed.
Summary
This new EMR WAL feature allows you to improve durability of your Amazon EMR HBase on S3 clusters, addressing critical workload scenarios by eliminating the need for streaming solutions for Availability Zone level service disruptions, streamlining processes for upgrading or rotating clusters, preventing data corruption during HBase auto scaling or node termination events, and resolving disk space issues associated with old WALs. Because many of the EMR WAL features are added on the latest releases of Amazon EMR, we recommend that customers use Amazon EMR version 7.9 or later to fully benefit from these improvements.
About the authors
Suthan Phillips is a Senior Analytics Architect at AWS, where he helps customers design and optimize scalable, high-performance data solutions that drive business insights. He combines architectural guidance on system design and scalability with best practices to ensure efficient, secure implementation across data processing and experience layers. Outside of work, Suthan enjoys swimming, hiking and exploring the Pacific Northwest.