Sqoop import postgres to S3 failing

Question

I'm currently importing postgres data to hdfs. I'm planning to move the storage from hdfs to S3. When i'm trying to provide S3 location, the sqoop job is failing. I'm running it on EMR(emr-5.27.0) cluster and I've read/write access to that s3 bucket from all nodes in the cluster.

sqoop import \
--connect "jdbc:postgresql://<machine_ip>:<port>/<database>?sslfactory=org.postgresql.ssl.NonValidatingFactory&ssl=true" \
--username <username> \
--password-file <password_file_path> \
--table addresses \
--target-dir s3://my-bucket/data/temp \
--num-mappers 100 \
--split-by id \
--as-parquetfile

Exception is,

Warning: /usr/lib/sqoop/../accumulo does not exist! Accumulo imports will fail.
Please set $ACCUMULO_HOME to the root of your Accumulo installation.
19/10/21 09:27:32 INFO sqoop.Sqoop: Running Sqoop version: 1.4.7
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/usr/lib/hadoop/lib/slf4j-log4j12-1.7.10.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/usr/lib/hive/lib/log4j-slf4j-impl-2.6.2.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory]
19/10/21 09:27:33 INFO manager.SqlManager: Using default fetchSize of 1000
19/10/21 09:27:33 INFO tool.CodeGenTool: Beginning code generation
19/10/21 09:27:33 INFO tool.CodeGenTool: Will generate java class as codegen_addresses
19/10/21 09:27:34 INFO manager.SqlManager: Executing SQL statement: SELECT t.* FROM "addresses" AS t LIMIT 1
19/10/21 09:27:34 INFO orm.CompilationManager: HADOOP_MAPRED_HOME is /usr/lib/hadoop-mapreduce
Note: /tmp/sqoop-hadoop/compile/412c4a70c10c6569443f4c38dbdc2c99/codegen_addresses.java uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
19/10/21 09:27:37 INFO orm.CompilationManager: Writing jar file: /tmp/sqoop-hadoop/compile/412c4a70c10c6569443f4c38dbdc2c99/codegen_addresses.jar
19/10/21 09:27:37 WARN manager.PostgresqlManager: It looks like you are importing from postgresql.
19/10/21 09:27:37 WARN manager.PostgresqlManager: This transfer can be faster! Use the --direct
19/10/21 09:27:37 WARN manager.PostgresqlManager: option to exercise a postgresql-specific fast path.
19/10/21 09:27:37 INFO mapreduce.ImportJobBase: Beginning import of addresses
19/10/21 09:27:37 INFO Configuration.deprecation: mapred.jar is deprecated. Instead, use mapreduce.job.jar
19/10/21 09:27:39 INFO manager.SqlManager: Executing SQL statement: SELECT t.* FROM "addresses" AS t LIMIT 1
19/10/21 09:27:39 INFO manager.SqlManager: Executing SQL statement: SELECT t.* FROM "addresses" AS t LIMIT 1
19/10/21 09:27:39 INFO conf.HiveConf: Found configuration file file:/etc/hive/conf.dist/hive-site.xml
19/10/21 09:27:39 ERROR sqoop.Sqoop: Got exception running Sqoop: org.kitesdk.data.DatasetNotFoundException: Unknown dataset URI pattern: dataset:s3://<bucket>/<data>/temp
Check that JARs for s3 datasets are on the classpath
org.kitesdk.data.DatasetNotFoundException: Unknown dataset URI pattern: dataset:s3://<bucket>/<data>/temp
Check that JARs for s3 datasets are on the classpath
    at org.kitesdk.data.spi.Registration.lookupDatasetUri(Registration.java:128)
    at org.kitesdk.data.Datasets.exists(Datasets.java:624)
    at org.kitesdk.data.Datasets.exists(Datasets.java:646)
    at org.apache.sqoop.mapreduce.ParquetJob.configureImportJob(ParquetJob.java:118)
    at org.apache.sqoop.mapreduce.DataDrivenImportJob.configureMapper(DataDrivenImportJob.java:132)
    at org.apache.sqoop.mapreduce.ImportJobBase.runImport(ImportJobBase.java:264)
    at org.apache.sqoop.manager.SqlManager.importTable(SqlManager.java:692)
    at org.apache.sqoop.manager.PostgresqlManager.importTable(PostgresqlManager.java:127)
    at org.apache.sqoop.tool.ImportTool.importTable(ImportTool.java:520)
    at org.apache.sqoop.tool.ImportTool.run(ImportTool.java:628)
    at org.apache.sqoop.Sqoop.run(Sqoop.java:147)
    at org.apache.hadoop.util.ToolRunner.run(ToolRunner.java:76)
    at org.apache.sqoop.Sqoop.runSqoop(Sqoop.java:183)
    at org.apache.sqoop.Sqoop.runTool(Sqoop.java:234)
    at org.apache.sqoop.Sqoop.runTool(Sqoop.java:243)
    at org.apache.sqoop.Sqoop.main(Sqoop.java:252)

Note : The same sqoop command with hdfs target dir is working. I'm also able to manually write to s3 bucket from the cluster node (using aws s3 command).

John John · Accepted Answer · 2020-05-25T14:42:31

The Kite SDK has been upgraded. All you have to do is to download the new SDK into EMR and run the sqoop command again.

Use wget to download the kite-data-s3-1.1.0.jar

wget https://repo1.maven.org/maven2/org/kitesdk/kite-data-s3/1.1.0/kite-data-s3-1.1.0.jar

Move the JAR to the Sqoop library directory (/usr/lib/sqoop/lib/)

sudo cp kite-data-s3-1.1.0.jar /usr/lib/sqoop/lib/

Grant permission on the JAR

sudo chmod 755 kite-data-s3-1.1.0.jar

Use the s3n connector to import the jar

sqoop import \ --connect "jdbc:postgresql://:/?sslfactory=org.postgresql.ssl.NonValidatingFactory&ssl=true" \ --username \ --password-file \ --table addresses \ --target-dir s3n://my-bucket/data/temp \ --num-mappers 100 \ --split-by id \ --as-parquetfile

Font: https://aws.amazon.com/premiumsupport/knowledge-center/unknown-dataset-uri-pattern-sqoop-emr/

Sqoop import postgres to S3 failing

5 Answers