dabaizzt opened a new issue, #26661:
URL: https://github.com/apache/beam/issues/26661
### What happened?
**My issue:**
When I read the mysql table using JDBCIO non-partitioned read mode, I get
the following error:
```
Caused by: java.lang.OutOfMemoryError: GC overhead limit exceeded
at
com.mysql.cj.protocol.a.NativePacketPayload.readBytes(NativePacketPayload.java:574)
at
com.mysql.cj.protocol.a.NativePacketPayload.readBytes(NativePacketPayload.java:524)
at
com.mysql.cj.protocol.a.TextRowFactory.createFromMessage(TextRowFactory.java:66)
at
com.mysql.cj.protocol.a.TextRowFactory.createFromMessage(TextRowFactory.java:42)
at
com.mysql.cj.protocol.a.ResultsetRowReader.read(ResultsetRowReader.java:87)
at
com.mysql.cj.protocol.a.ResultsetRowReader.read(ResultsetRowReader.java:42)
at com.mysql.cj.protocol.a.NativeProtocol.read(NativeProtocol.java:1651)
at
com.mysql.cj.protocol.a.TextResultsetReader.read(TextResultsetReader.java:87)
at
com.mysql.cj.protocol.a.TextResultsetReader.read(TextResultsetReader.java:48)
at com.mysql.cj.protocol.a.NativeProtocol.read(NativeProtocol.java:1664)
at
com.mysql.cj.protocol.a.NativeProtocol.readAllResults(NativeProtocol.java:1718)
at
com.mysql.cj.protocol.a.NativeProtocol.sendQueryPacket(NativeProtocol.java:1064)
at com.mysql.cj.NativeSession.execSQL(NativeSession.java:665)
at
com.mysql.cj.jdbc.ClientPreparedStatement.executeInternal(ClientPreparedStatement.java:893)
at
com.mysql.cj.jdbc.ClientPreparedStatement.executeQuery(ClientPreparedStatement.java:972)
at
org.apache.commons.dbcp2.DelegatingPreparedStatement.executeQuery(DelegatingPreparedStatement.java:122)
at
org.apache.commons.dbcp2.DelegatingPreparedStatement.executeQuery(DelegatingPreparedStatement.java:122)
at
org.apache.beam.sdk.io.jdbc.JdbcIO$ReadFn.processElement(JdbcIO.java:1399)
at
org.apache.beam.sdk.io.jdbc.JdbcIO$ReadFn$DoFnInvoker.invokeProcessElement(Unknown
Source)
at
org.apache.beam.runners.core.SimpleDoFnRunner.invokeProcessElement(SimpleDoFnRunner.java:211)
at
org.apache.beam.runners.core.SimpleDoFnRunner.processElement(SimpleDoFnRunner.java:188)
at
org.apache.beam.runners.spark.translation.DoFnRunnerWithMetrics.processElement(DoFnRunnerWithMetrics.java:65)
at
org.apache.beam.runners.spark.translation.SparkProcessContext$ProcCtxtIterator.computeNext(SparkProcessContext.java:140)
at
org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.AbstractIterator.tryToComputeNext(AbstractIterator.java:141)
at
org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.AbstractIterator.hasNext(AbstractIterator.java:136)
at
scala.collection.convert.Wrappers$JIteratorWrapper.hasNext(Wrappers.scala:43)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:511)
at scala.collection.Iterator$$anon$10.hasNext(Iterator.scala:458)
at
scala.collection.convert.Wrappers$IteratorWrapper.hasNext(Wrappers.scala:31)
at
org.apache.beam.runners.spark.translation.MultiDoFnFunction.call(MultiDoFnFunction.java:128)
at
org.apache.beam.runners.spark.translation.MultiDoFnFunction.call(MultiDoFnFunction.java:63)
at
org.apache.spark.api.java.JavaRDDLike.$anonfun$mapPartitionsToPair$1(JavaRDDLike.scala:186)
```
Below code is trying to read mysql table:
```
public static PCollection<Row> ReadFromJdbc(Pipeline pipeline,
JdbcConfig inputConfig, Schema inputSchema) {
LOG.info("read from jdbc, tablename is {}",
inputConfig.getTableName());
String fieldNames = Joiner.on(",").join(inputSchema.getFieldNames());
return pipeline.apply(JdbcIO.<Row>read().withDataSourceConfiguration(
JdbcIO.DataSourceConfiguration.create(inputConfig.getDriverClassName(),
inputConfig.getUrl())
.withUsername(inputConfig.getUsername()).withPassword(inputConfig.getPassword()))
.withQuery("select " + fieldNames + " from " +
inputConfig.getTableName())
.withRowMapper(new JdbcIO.RowMapper<Row>() {
@Override
public Row mapRow(ResultSet resultSet) throws Exception {
Row.Builder builder = Row.withSchema(inputSchema);
for (int i = 1; i <= inputSchema.getFieldCount();
i++) {
Schema.TypeName type = inputSchema.getField(i -
1).getType().getTypeName();
switch (type) {
case DATETIME:
builder.addValue(new
DateTime(resultSet.getTimestamp(i).getTime()));
continue;
default:
builder.addValue(resultSet.getObject(i));
}
}
return builder.build();
}
}).withCoder(SchemaCoder.of(inputSchema))
);
}
```
Test table:
10w records, 50 fields
### Issue Priority
Priority: 0 (outage / urgent vulnerability)
### Issue Components
- [ ] Component: Python SDK
- [ ] Component: Java SDK
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