Hi,
I couldn't find the option to set the limit for Query in S3
GC.(<https://jdbc.postgresql.org/documentation/head/connect.html#connection-parameters>).
________________________________
From: Tanvi Shah
Sent: 19 October 2020 12:07
To: oak-dev@jackrabbit.apache.org
Subject: Error in S3 Garbage Collection
Hi ,
We have started Se Garbage Collection and S3 size is more than 2 TB.
We are facing memory issues while executing GC even when we have given 11 GB of
memory to the application.
Code is:
final MarkSweepGarbageCollector gc =
documentNodeStore.createBlobGarbageCollector(seconds, repository.toString(),
wb, new DefaultStatisticsProvider(Executors.newScheduledThreadPool(1)));
gc.collectGarbage(markOnly);
final OperationsStatsMBean stats = gc.getOperationStats();
log.info(
"number deleted : " + stats.numDeleted() + " Size deleted : " +
stats.sizeDeleted());
The exceptions are :
java.lang.RuntimeException: org.postgresql.util.PSQLException: Ran out of
memory retrieving query results.
at
org.apache.jackrabbit.oak.plugins.document.rdb.RDBDocumentStore$3.iterator(RDBDocumentStore.java:1876)
at
org.apache.jackrabbit.oak.plugins.document.rdb.RDBBlobReferenceIterator.getIteratorOverDocsWithBinaries(RDBBlobReferenceIterator.java:48)
at
org.apache.jackrabbit.oak.plugins.document.BlobReferenceIterator.loadBatch(BlobReferenceIterator.java:64)
at
org.apache.jackrabbit.oak.plugins.document.BlobReferenceIterator.computeNext(BlobReferenceIterator.java:52)
at
org.apache.jackrabbit.oak.plugins.document.BlobReferenceIterator.computeNext(BlobReferenceIterator.java:36)
at
com.google.common.collect.AbstractIterator.tryToComputeNext(AbstractIterator.java:143)
at
com.google.common.collect.AbstractIterator.hasNext(AbstractIterator.java:138)
at
org.apache.jackrabbit.oak.plugins.document.DocumentBlobReferenceRetriever.collectReferences(DocumentBlobReferenceRetriever.java:49)
at
org.apache.jackrabbit.oak.plugins.blob.MarkSweepGarbageCollector.iterateNodeTree(MarkSweepGarbageCollector.java:600)
at
org.apache.jackrabbit.oak.plugins.blob.MarkSweepGarbageCollector.mark(MarkSweepGarbageCollector.java:397)
at
org.apache.jackrabbit.oak.plugins.blob.MarkSweepGarbageCollector.markAndSweep(MarkSweepGarbageCollector.java:347)
at
org.apache.jackrabbit.oak.plugins.blob.MarkSweepGarbageCollector.collectGarbage(MarkSweepGarbageCollector.java:235)
at
com.springernature.mango.cms.common.helper.RepositoryUtil.s3GarbageCollection(RepositoryUtil.java:324)
at
com.springernature.mango.cms.services.rest.service.ServicesController.lambda$runS3GC$1(ServicesController.java:460)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at
java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:180)
at
java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
org.postgresql.util.PSQLException: Ran out of memory retrieving query results.
at
org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2145)
at
org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:306)
at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:441)
at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:365)
at
org.postgresql.jdbc.PgPreparedStatement.executeWithFlags(PgPreparedStatement.java:155)
at
org.postgresql.jdbc.PgPreparedStatement.executeQuery(PgPreparedStatement.java:118)
at sun.reflect.GeneratedMethodAccessor49.invoke
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at
org.apache.tomcat.jdbc.pool.interceptor.StatementDecoratorInterceptor$StatementProxy.invoke(StatementDecoratorInterceptor.java:237)
at com.sun.proxy.$Proxy93.executeQuery
at sun.reflect.GeneratedMethodAccessor49.invoke
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at
org.apache.tomcat.jdbc.pool.interceptor.AbstractQueryReport$StatementProxy.invoke(AbstractQueryReport.java:210)
at com.sun.proxy.$Proxy93.executeQuery
at sun.reflect.GeneratedMethodAccessor49.invoke
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at
org.apache.tomcat.jdbc.pool.StatementFacade$StatementProxy.invoke(StatementFacade.java:114)
at com.sun.proxy.$Proxy93.executeQuery
at
org.apache.jackrabbit.oak.plugins.document.rdb.RDBDocumentStoreJDBC$ResultSetIterator.<init>(RDBDocumentStoreJDBC.java:591)
at
org.apache.jackrabbit.oak.plugins.document.rdb.RDBDocumentStoreJDBC.queryAsIterator(RDBDocumentStoreJDBC.java:558)
at
org.apache.jackrabbit.oak.plugins.document.rdb.RDBDocumentStore$3.iterator(RDBDocumentStore.java:1865)
at
org.apache.jackrabbit.oak.plugins.document.rdb.RDBBlobReferenceIterator.getIteratorOverDocsWithBinaries(RDBBlobReferenceIterator.java:48)
at
org.apache.jackrabbit.oak.plugins.document.BlobReferenceIterator.loadBatch(BlobReferenceIterator.java:64)
at
org.apache.jackrabbit.oak.plugins.document.BlobReferenceIterator.computeNext(BlobReferenceIterator.java:52)
at
org.apache.jackrabbit.oak.plugins.document.BlobReferenceIterator.computeNext(BlobReferenceIterator.java:36)
at
com.google.common.collect.AbstractIterator.tryToComputeNext(AbstractIterator.java:143)
at
com.google.common.collect.AbstractIterator.hasNext(AbstractIterator.java:138)
at
org.apache.jackrabbit.oak.plugins.document.DocumentBlobReferenceRetriever.collectReferences(DocumentBlobReferenceRetriever.java:49)
at
org.apache.jackrabbit.oak.plugins.blob.MarkSweepGarbageCollector.iterateNodeTree(MarkSweepGarbageCollector.java:600)
at
org.apache.jackrabbit.oak.plugins.blob.MarkSweepGarbageCollector.mark(MarkSweepGarbageCollector.java:397)
at
org.apache.jackrabbit.oak.plugins.blob.MarkSweepGarbageCollector.markAndSweep(MarkSweepGarbageCollector.java:347)
at
org.apache.jackrabbit.oak.plugins.blob.MarkSweepGarbageCollector.collectGarbage(MarkSweepGarbageCollector.java:235)
at
com.springernature.mango.cms.common.helper.RepositoryUtil.s3GarbageCollection(RepositoryUtil.java:324)
at
com.springernature.mango.cms.services.rest.service.ServicesController.lambda$runS3GC$1(ServicesController.java:460)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at
java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:180)
at
java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
java.lang.OutOfMemoryError: GC overhead limit exceeded
at org.postgresql.core.PGStream.receiveTupleV3(PGStream.java:401)
at
org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2141)
at
org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:306)
at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:441)
at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:365)
at
org.postgresql.jdbc.PgPreparedStatement.executeWithFlags(PgPreparedStatement.java:155)
at
org.postgresql.jdbc.PgPreparedStatement.executeQuery(PgPreparedStatement.java:118)
at sun.reflect.GeneratedMethodAccessor49.invoke
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at
org.apache.tomcat.jdbc.pool.interceptor.StatementDecoratorInterceptor$StatementProxy.invoke(StatementDecoratorInterceptor.java:237)
at com.sun.proxy.$Proxy93.executeQuery
at sun.reflect.GeneratedMethodAccessor49.invoke
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at
org.apache.tomcat.jdbc.pool.interceptor.AbstractQueryReport$StatementProxy.invoke(AbstractQueryReport.java:210)
at com.sun.proxy.$Proxy93.executeQuery
at sun.reflect.GeneratedMethodAccessor49.invoke
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at
org.apache.tomcat.jdbc.pool.StatementFacade$StatementProxy.invoke(StatementFacade.java:114)
at com.sun.proxy.$Proxy93.executeQuery
at
org.apache.jackrabbit.oak.plugins.document.rdb.RDBDocumentStoreJDBC$ResultSetIterator.<init>(RDBDocumentStoreJDBC.java:591)
at
org.apache.jackrabbit.oak.plugins.document.rdb.RDBDocumentStoreJDBC.queryAsIterator(RDBDocumentStoreJDBC.java:558)
at
org.apache.jackrabbit.oak.plugins.document.rdb.RDBDocumentStore$3.iterator(RDBDocumentStore.java:1865)
at
org.apache.jackrabbit.oak.plugins.document.rdb.RDBBlobReferenceIterator.getIteratorOverDocsWithBinaries(RDBBlobReferenceIterator.java:48)
at
org.apache.jackrabbit.oak.plugins.document.BlobReferenceIterator.loadBatch(BlobReferenceIterator.java:64)
at
org.apache.jackrabbit.oak.plugins.document.BlobReferenceIterator.computeNext(BlobReferenceIterator.java:52)
at
org.apache.jackrabbit.oak.plugins.document.BlobReferenceIterator.computeNext(BlobReferenceIterator.java:36)
at
com.google.common.collect.AbstractIterator.tryToComputeNext(AbstractIterator.java:143)
at
com.google.common.collect.AbstractIterator.hasNext(AbstractIterator.java:138)
at
org.apache.jackrabbit.oak.plugins.document.DocumentBlobReferenceRetriever.collectReferences(DocumentBlobReferenceRetriever.java:49)
So I wanted to ask is there any other way how can we restrict this and
successfully run S3 Garbage Collection.
Thanks.
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