Using Yandex Object Storage in Yandex Data Processing

Written by

Updated at October 14, 2024

DistCp
Optimizing file reads from Object Storage
Optimizing file writes to Object Storage
Using s3fs
Using Object Storage from Spark

This section describes various ways that processes running in Yandex Data Processing clusters can access objects from Object Storage buckets.

Note

Configure a cluster network before setting up access to Yandex Cloud services and internet resources.

Component settings impact bucket file read and write performance:

The settings specified when creating a cluster affect all the jobs running in the cluster.
The settings specified when creating jobs override cluster-level settings and can be job-specific.

DistCp

To copy files from Object Storage to HDFS, use the DistCp utility. It is designed to copy data both within a cluster and between clusters and external storage.

To authenticate in Object Storage, you can use one of the following approaches:

Use the IAM token of the cluster service account.
Use CredentialProvider.
Provide the access key and secret key parameters of static access keys when creating jobs.

Accessing S3 with authentication via the IAM token of a cluster service account

When creating a cluster, specify a service account. If the cluster is already created, add a service account using the Edit button in the management console.

Make sure to assign the following roles to the service account:
- dataproc.agent: To enable the service account to get info on cluster host states, jobs, and log groups.
- dataproc.provisioner: To enable the service account to work with an autoscaling instance group. This will enable subcluster autoscaling.
The service account must have access to the appropriate bucket. To do this, grant the service account permissions in the bucket ACL, or the storage.viewer or storage.editor role.

For more information about these roles, see the Object Storage documentation.

For example, get a list of files located in the yc-mdb-examples public bucket at dataproc/example01/set01. To do this, connect to the cluster and run the command:

hadoop fs -ls s3a://yc-mdb-examples/dataproc/example01/set01

Result:

Found 12 items
-rw-rw-rw-   1 root root   19327838 2019-09-13 17:17 s3a://yc-mdb-examples/dataproc/example01/set01/On_Time_Reporting_Carrier_On_Time_Performance_(1987_present)_2018_1.parquet
-rw-rw-rw-   1 root root   21120204 2019-09-13 17:17 s3a://yc-mdb-examples/dataproc/example01/set01/On_Time_Reporting_Carrier_On_Time_Performance_(1987_present)_2018_10.parquet
-rw-rw-rw-   1 root root   20227757 2019-09-13 17:17 s3a://yc-mdb-examples/dataproc/example01/set01/
...

Copying via CredentialProvider

To use a secret storage provider, place the secrets within the components that need access to Object Storage. To do this, you can use JCEKS (Java Cryptography Extension KeyStore).
In this example, you first create a file with secrets and then place it in HDFS:

Specify the static and secret keys, e.g.:

hadoop credential create fs.s3a.access.key \
       -value <static_key> \
       -provider localjceks://file/home/jack/yc.jceks && \
hadoop credential create fs.s3a.secret.key \
       -value <secret_key> \
       -provider localjceks://file/home/jack/yc.jceks

Copy the secrets file to your local HDFS:

hdfs dfs -put /home/jack/yc.jceks /user/root/

Copy the file from Object Storage directly to HDFS:

hadoop distcp \
       -D fs.s3a.bucket.dataproc-examples.endpoint=storage.yandexcloud.net \
       -D hadoop.security.credential.provider.path=jceks://hdfs/user/root/yc.jceks \
       -update \
       -skipcrccheck \
       -numListstatusThreads 10 \
       s3a://yc-mdb-examples/dataproc/example01/set01 \
       hdfs://<HDFS_host>/<path>/

<HDFS_host> is the target HDFS server you are using. You can get the default server using the command:

hdfs getconf -confKey fs.defaultFS

Example of the command to copy files from the bucket:

hadoop distcp \
       -D fs.s3a.bucket.dataproc-examples.endpoint=storage.yandexcloud.net \
       -D hadoop.security.credential.provider.path=jceks://hdfs/user/root/yc.jceks \
       -update \
       -skipcrccheck \
       -numListstatusThreads 10 \
       s3a://yc-mdb-examples/dataproc/example01/set01 \
       hdfs://rc1b-dataproc-m-d31bs470ivkyrz60.mdb.yandexcloud.net/user/root/datasets/set01/

Copying files by passing keys in arguments

Instead of creating a secrets file, you can pass keys in the command arguments:

hadoop distcp \
       -D fs.s3a.bucket.dataproc-examples.endpoint=storage.yandexcloud.net \
       -D fs.s3a.bucket.dataproc-examples.access.key=<static_key> \
       -D fs.s3a.bucket.dataproc-examples.secret.key=<secret_key> \
       -update \
       -skipcrccheck \
       -numListstatusThreads 10 \
       s3a://yc-mdb-examples/dataproc/example01/set01 \
       hdfs://rc1b-dataproc-m-d31bs470ivkyrz60.mdb.yandexcloud.net/user/root/datasets/set01/

Optimizing file reads from Object Storage

The method for reading data from a bucket is decided by the fs.s3a.experimental.input.fadvise setting. Its value depends on the image version used:

Image versions 1.0 through 1.4 use sequential as the default value. It is a good choice for sequential file reads, but slow for random access. If you use random file access more frequently, add random to the cluster component properties or job settings.
For version 2.0 images, the default is normal: files are accessed sequentially; however, if an application is performing random access operations, random mode activates automatically.

For more information on the component versions used, see Runtime environment.

Optimizing file writes to Object Storage

To speed up file writes to Object Storage, you can:

Using S3A committers

S3A committers are Apache Hadoop software modules used for writing data to object storage over the S3 protocol to ensure efficient and near-atomic commits of the changes made. For more information, see the Apache Hadoop and Apache Spark documentation.

Note

S3A committers are not used or required for operations with tables that are managed using the tools of the DeltaLake library that implements its own logic of working with data in object stores.

S3A committers run in three basic modes:

Mode	Environment	HDFS required	Writing data to partitioned tables	Write speed
`directory`	MapReduce, Spark	Yes^*	Complete overwrite	Standard
`magic`	MapReduce, Spark	No (data is written directly to S3)	Not supported	Maximum
`partitioned`	Spark	Yes^*	Replacing partitions and appending them	Standard

^* In directory and partitioned modes, no checks are made for actual presence of HDFS for storing intermediate data. Some jobs may be successfully completed without HDFS. However, this may cause issues with complex jobs, such as "file not found" errors or incomplete uploads of job results to Object Storage.

To enable S3A committers, configure the following settings:

core:fs.s3a.committer.magic.enabled : true if jobs will use the magic mode.
core:fs.s3a.committer.name with directory, magic, or partitioned as the default mode.
core:fs.s3a.committer.staging.abort.pending.uploads : false for Hadoop 3.2.2 as part of Yandex Data Processing image 2.0 or core:fs.s3a.committer.abort.pending.uploads : false for Hadoop 3.3.2 as part of image 2.1 if multiple concurrent jobs are writing data to the same table.
core:mapreduce.outputcommitter.factory.scheme.s3a : org.apache.hadoop.fs.s3a.commit.S3ACommitterFactory.
spark:spark.hadoop.fs.s3a.committer.name with directory, magic, or partitioned as the default mode.
spark:spark.sql.parquet.output.committer.class : org.apache.spark.internal.io.cloud.BindingParquetOutputCommitter.
spark:spark.sql.sources.commitProtocolClass : org.apache.spark.internal.io.cloud.PathOutputCommitProtocol.
(Optional) core:fs.s3a.committer.staging.conflict-mode: Action if existing data partitions are found in the target table (for partitioned mode):
- append: Append new data to an existing partition.
- fail: When attempting to overwrite an existing partition, the job terminates with an error.
- replace: Existing partition data is replaced with new partition data.

The current S3A committer mode may be overridden for a specific job by setting fs.s3a.committer.name and spark.hadoop.fs.s3a.committer.name to directory, magic, or partitioned as required.

Do not change the default value for spark.hadoop.mapreduce.fileoutputcommitter.algorithm.version because Yandex Object Storage does not support atomic folder renames.

Apache Hadoop settings

The method of writing data to an Object Storage bucket is decided by the core:fs.s3a.fast.upload setting. Its value depends on the image version used:

Image versions 1.0 through 1.4 use false as the default value to save RAM. Set it to true in the cluster component properties or job settings. This will improve bucket write performance for large files and prevent node storage from filling up.
In image 2.0, fs.s3a.fast.upload is enabled by default.

If required, configure other settings responsible for write mode in Object Storage:

fs.s3a.committer.threads: Number of threads committing changes in Object Storage towards the end of the job.
fs.s3a.connection.maximum: Number of allowed Object Storage connections.
fs.s3a.connection.timeout: Maximum Object Storage connection timeout in milliseconds.
fs.s3a.fast.upload.active.blocks: Maximum number of blocks in a single output thread.
fs.s3a.fast.upload.buffer: Type of buffer used for temporary storage of the upload data:
- disk: Save data to the folder specified in fs.s3a.buffer.dir.
- array: Use arrays in the JVM heap.
- bytebuffer: Use RAM from outside the JVM heap.
fs.s3a.max.total.tasks: Size of queued Object Storage bucket operations that cannot run due to reaching the thread limit.
fs.s3a.multipart.size: Size of chunks in bytes the data will be broken down into when copying or uploading to a bucket.
fs.s3a.threads.max: Number of threads in the AWS Transfer Manager.

Note

Large values of these parameters might cause an increase in the usage of computing resources on Yandex Data Processing cluster hosts.

For more information, see the Apache Hadoop documentation and the Component properties section.

Apache Spark settings

When accessing data in Object Storage from Spark jobs, we recommend setting spark.sql.hive.metastorePartitionPruning to true.

When working with data in Parquet format, the following Spark job settings are recommended:

spark.hadoop.parquet.enable.summary-metadata : false
spark.sql.parquet.mergeSchema : false
spark.sql.parquet.filterPushdown : true

When working with data in Orc format, the following Spark job settings are recommended:

spark.sql.orc.cache.stripe.details.size : 10000
spark.sql.orc.filterPushdown : true
spark.sql.orc.splits.include.file.footer : true

It may take a long time for the jobs creating or updating massive numbers (hundreds and thousands) of table partitions to update partition records in the Hive Metastore cluster. To speed up this process, increase the following values:

hive:datanucleus.connectionPool.maxPoolSize: Maximum size of the Metastore DB connection pool.
hive:hive.metastore.fshandler.threads: Number of threads running background operations with the file system within Metastore.
spark:spark.sql.addPartitionInBatch.size: Number of partitions updated per Metastore call. The optimal value is 10 × <hive:hive.metastore.fshandler.threads_setting_value> or higher.

Note

If these values are excessively high, you may run out of Metastore system resources. A large Metastore database connection pool may require updating the settings and ramping up the cluster's computing resources.

For more information, see the Apache Spark documentation and the Component properties section.

Using s3fs

s3fs allows mounting Object Storage buckets using Fuse. Read more about using the utility at s3fs.

Using Object Storage from Spark

Spark Shell

PySpark Shell

Implement the desired access option:

Using JCEKS:

sc.hadoopConfiguration.set("fs.s3a.endpoint", "storage.yandexcloud.net");
sc.hadoopConfiguration.set("fs.s3a.signing-algorithm", "");
sc.hadoopConfiguration.set("fs.s3a.aws.credentials.provider", "org.apache.hadoop.fs.s3a.SimpleAWSCredentialsProvider");
sc.hadoopConfiguration.set("hadoop.security.credential.provider.path", "jceks://hdfs/<path_to_JCEKS_file>");

Using your access key and secret:

sc.hadoopConfiguration.set("fs.s3a.endpoint", "storage.yandexcloud.net");
sc.hadoopConfiguration.set("fs.s3a.signing-algorithm", "");
sc.hadoopConfiguration.set("fs.s3a.aws.credentials.provider", "org.apache.hadoop.fs.s3a.SimpleAWSCredentialsProvider");
sc.hadoopConfiguration.set("fs.s3a.access.key","<access_key>");
sc.hadoopConfiguration.set("fs.s3a.secret.key","<bucket_secret>");

You can then read the file from Object Storage:

val sqlContext = new org.apache.spark.sql.SQLContext(sc)
val df = sqlContext.read.parquet("s3a://<bucket_name>/<object_path>")

Select the access method:

Accessing the Object Storage objects using JCEKS:

sc._jsc.hadoopConfiguration().set("fs.s3a.endpoint", "storage.yandexcloud.net")
sc._jsc.hadoopConfiguration().set("fs.s3a.signing-algorithm", "")
sc._jsc.hadoopConfiguration().set("fs.s3a.aws.credentials.provider", "org.apache.hadoop.fs.s3a.SimpleAWSCredentialsProvider")
sc._jsc.hadoopConfiguration().set("hadoop.security.credential.provider.path", "jceks://hdfs/<path_to_JCEKS_file>")

Reading a file using an access key and bucket secret:

sc._jsc.hadoopConfiguration().set("fs.s3a.endpoint", "storage.yandexcloud.net")
sc._jsc.hadoopConfiguration().set("fs.s3a.signing-algorithm", "")
sc._jsc.hadoopConfiguration().set("fs.s3a.aws.credentials.provider", "org.apache.hadoop.fs.s3a.SimpleAWSCredentialsProvider")
sc._jsc.hadoopConfiguration().set("fs.s3a.access.key","<access_key>")
sc._jsc.hadoopConfiguration().set("fs.s3a.secret.key","<bucket_secret>")

Once you have access, you can read the file directly from Object Storage:

from pyspark.sql import SQLContext

sql = SQLContext(sc)
df = sql.read.parquet("s3a://<bucket_name>/<object_path>")

For more information, see Spark settings for integration with Yandex Object Storage.

Using Yandex Object Storage in Yandex Data Processing

DistCpDistCp

Accessing S3 with authentication via the IAM token of a cluster service accountAccessing S3 with authentication via the IAM token of a cluster service account

Copying via CredentialProviderCopying via CredentialProvider

Copying files by passing keys in argumentsCopying files by passing keys in arguments

Optimizing file reads from Object StorageOptimizing file reads from Object Storage

Optimizing file writes to Object StorageOptimizing file writes to Object Storage

Using S3A committersUsing S3A committers

Apache Hadoop settingsApache Hadoop settings

Apache Spark settingsApache Spark settings

Using s3fsUsing s3fs

Using Object Storage from SparkUsing Object Storage from Spark

Was the article helpful?

DistCp

Accessing S3 with authentication via the IAM token of a cluster service account

Copying via CredentialProvider

Copying files by passing keys in arguments

Optimizing file reads from Object Storage

Optimizing file writes to Object Storage

Using S3A committers

Apache Hadoop settings

Apache Spark settings

Using s3fs

Using Object Storage from Spark