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hibernate running error, restart normally

The program runs for a period of time and always reports an error, restarting and returning to normal, the error is as follows：
javax.persistence.PersistenceException: org.hibernate.exception.GenericJDBCException: could not prepare statementat org.hibernate.internal.ExceptionConverterImpl.convert(ExceptionConverterImpl.java:154)at org.hibernate.query.internal.AbstractProducedQuery.list(AbstractProducedQuery.java:1626)at org.hibernate.query.Query.getResultList(Query.java:165)at net.skycloud.platform.user.repository.KeycloakGroupDao.findAll(KeycloakGroupDao.java:111)at net.skycloud.platform.user.service.UserGroupService.getAllUserGroups(UserGroupService.java:247)at net.skycloud.platform.user.api.rest.UserController.searchUserAndGroup(UserController.java:362)at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)at java.base/java.lang.reflect.Method.invoke(Method.java:566)at org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:205)at org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:150)at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:117)at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:895)at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:808)at org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:87)at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:1067)at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:963)at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:1006)at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:898)at javax.servlet.http.HttpServlet.service(HttpServlet.java:645)at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:883)at javax.servlet.http.HttpServlet.service(HttpServlet.java:750)at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:227)at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162)at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:53)at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189)at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162)at org.springframework.boot.actuate.metrics.web.servlet.WebMvcMetricsFilter.doFilterInternal(WebMvcMetricsFilter.java:96)at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:117)at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189)at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162)at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:201)at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:117)at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189)at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162)at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:197)at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:97)at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:540)at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:135)at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:92)at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:78)at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:687)at org.apache.catalina.valves.RemoteIpValve.invoke(RemoteIpValve.java:769)at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:357)at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:382)at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:65)at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:895)at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1732)at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)at org.apache.tomcat.util.threads.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1191)at org.apache.tomcat.util.threads.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:659)at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)at java.base/java.lang.Thread.run(Thread.java:829)Caused by: org.hibernate.exception.GenericJDBCException: could not prepare statementat org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:42)at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:113)at org.hibernate.engine.jdbc.internal.StatementPreparerImpl$StatementPreparationTemplate.prepareStatement(StatementPreparerImpl.java:186)at org.hibernate.engine.jdbc.internal.StatementPreparerImpl.prepareQueryStatement(StatementPreparerImpl.java:151)at org.hibernate.loader.Loader.prepareQueryStatement(Loader.java:2122)at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:2059)at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:2037)at org.hibernate.loader.Loader.doQuery(Loader.java:956)at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:357)at org.hibernate.loader.Loader.doList(Loader.java:2868)at org.hibernate.loader.Loader.doList(Loader.java:2850)at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2682)at org.hibernate.loader.Loader.list(Loader.java:2677)at org.hibernate.loader.custom.CustomLoader.list(CustomLoader.java:338)at org.hibernate.internal.SessionImpl.listCustomQuery(SessionImpl.java:2181)at org.hibernate.internal.AbstractSharedSessionContract.list(AbstractSharedSessionContract.java:1204)at org.hibernate.query.internal.NativeQueryImpl.doList(NativeQueryImpl.java:177)at org.hibernate.query.internal.AbstractProducedQuery.list(AbstractProducedQuery.java:1617)... 52 common frames omittedCaused by: java.sql.SQLException: Connection is closedat com.zaxxer.hikari.pool.ProxyConnection$ClosedConnection.lambda$getClosedConnection$0(ProxyConnection.java:515)at com.sun.proxy.$Proxy156.prepareStatement(Unknown Source)at com.zaxxer.hikari.pool.ProxyConnection.prepareStatement(ProxyConnection.java:337)at com.zaxxer.hikari.pool.HikariProxyConnection.prepareStatement(HikariProxyConnection.java)at org.hibernate.engine.jdbc.internal.StatementPreparerImpl$5.doPrepare(StatementPreparerImpl.java:149)at org.hibernate.engine.jdbc.internal.StatementPreparerImpl$StatementPreparationTemplate.prepareStatement(StatementPreparerImpl.java:176)... 67 common frames omitted
I hope to fix this bug

Its a database operations level exception using EntityManager or any other session manager (which is not your case) as exception suggest, how ever it can have many reasons such database has closed the connection or network terminated the connection socket, and to solve it you can configure to keep the connection alive but remember you can not hold the hibernate session alive for long time by default .
Also you may have look on OSIV anti pattern.

How do deal with h2 databases inability to deal with interrupts

How do deal with h2 database inability to deal with interrupts, I was occasionally seeing that my embedded h2 database appeared to get corrupted, in particular I had amended an ExecutorService so that if a task took too long it would cancel the task. The task would be cancelled okay but then subsequent database access failed with exceptions such as
23/07/2019 14.23.31:BST:DeleteDuplicatesController:start:SEVERE: commit failed
org.hibernate.TransactionException: commit failed
at org.hibernate.engine.transaction.spi.AbstractTransactionImpl.commit(AbstractTransactionImpl.java:187)
at com.jthink.songkong.db.ReportCache.save(ReportCache.java:46)
at com.jthink.songkong.reports.AbstractReport.setReportDatabaseObject(AbstractReport.java:365)
at com.jthink.songkong.reports.DeleteDuplicatesReport.setReportDatabaseObject(DeleteDuplicatesReport.java:333)
at com.jthink.songkong.reports.DeleteDuplicatesReport.closeReport(DeleteDuplicatesReport.java:377)
at com.jthink.songkong.analyse.toplevelanalyzer.DeleteDuplicatesController.deleteAnyDups(DeleteDuplicatesController.java:606)
at com.jthink.songkong.analyse.toplevelanalyzer.DeleteDuplicatesController.start(DeleteDuplicatesController.java:665)
at com.jthink.songkong.ui.swingworker.DeleteDuplicates.doInBackground(DeleteDuplicates.java:43)
at com.jthink.songkong.ui.swingworker.DeleteDuplicates.doInBackground(DeleteDuplicates.java:20)
at javax.swing.SwingWorker$1.call(SwingWorker.java:295)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at javax.swing.SwingWorker.run(SwingWorker.java:334)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: org.hibernate.TransactionException: unable to commit against JDBC connection
at org.hibernate.engine.transaction.internal.jdbc.JdbcTransaction.doCommit(JdbcTransaction.java:116)
at org.hibernate.engine.transaction.spi.AbstractTransactionImpl.commit(AbstractTransactionImpl.java:180)
... 14 more
Caused by: org.h2.jdbc.JdbcSQLNonTransientException: General error: "java.lang.IllegalStateException: Reading from nio:C:/Users/Paul/AppData/Roaming/SongKong/Database/Database.mv.db failed; file length -1 read length 4096 at 1541494 [1.4.199/1]"; SQL statement:
COMMIT [50000-199]
at org.h2.message.DbException.getJdbcSQLException(DbException.java:502)
at org.h2.message.DbException.getJdbcSQLException(DbException.java:427)
at org.h2.message.DbException.get(DbException.java:194)
at org.h2.message.DbException.convert(DbException.java:347)
at org.h2.command.Command.executeUpdate(Command.java:280)
at org.h2.jdbc.JdbcConnection.commit(JdbcConnection.java:542)
at com.mchange.v2.c3p0.impl.NewProxyConnection.commit(NewProxyConnection.java:1284)
at org.hibernate.engine.transaction.internal.jdbc.JdbcTransaction.doCommit(JdbcTransaction.java:112)
... 15 more
Caused by: java.lang.IllegalStateException: Reading from nio:C:/Users/Paul/AppData/Roaming/SongKong/Database/Database.mv.db failed; file length -1 read length 4096 at 1541494 [1.4.199/1]
at org.h2.mvstore.DataUtils.newIllegalStateException(DataUtils.java:883)
at org.h2.mvstore.DataUtils.readFully(DataUtils.java:420)
at org.h2.mvstore.FileStore.readFully(FileStore.java:98)
at org.h2.mvstore.MVStore.readBufferForPage(MVStore.java:1048)
at org.h2.mvstore.MVStore.readPage(MVStore.java:2186)
at org.h2.mvstore.MVMap.readPage(MVMap.java:554)
at org.h2.mvstore.Page$NonLeaf.getChildPage(Page.java:1086)
at org.h2.mvstore.Page.get(Page.java:221)
at org.h2.mvstore.MVMap.get(MVMap.java:402)
at org.h2.mvstore.MVMap.get(MVMap.java:389)
at org.h2.mvstore.MVStore.getMapName(MVStore.java:2737)
at org.h2.mvstore.MVStore.renameMap(MVStore.java:2650)
at org.h2.mvstore.tx.TransactionStore.commit(TransactionStore.java:453)
at org.h2.mvstore.tx.Transaction.commit(Transaction.java:389)
at org.h2.engine.Session.commit(Session.java:691)
at org.h2.command.dml.TransactionCommand.update(TransactionCommand.java:46)
at org.h2.command.CommandContainer.update(CommandContainer.java:133)
at org.h2.command.Command.executeUpdate(Command.java:267)
... 18 more
Caused by: java.nio.channels.ClosedChannelException
at sun.nio.ch.FileChannelImpl.ensureOpen(FileChannelImpl.java:110)
at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:721)
at org.h2.store.fs.FileNio.read(FilePathNio.java:74)
at org.h2.mvstore.DataUtils.readFully(DataUtils.java:406)
... 34 more
23/07/2019 14.23.31:BST:Errors:addError:SEVERE: Adding Error:commit failed
I have since found this issue
Basically if using H2 in embedded mode, and it receives an interrupt then all subsequent access fails until the thread pool is close and reopened. In the example I give of a process having to be cancelled because it appears to be stuck there is no solution except for interrupting
I also have another case whereby usually the controller thread that doesn't directly do a database work itself so I was struggling to see why when an interrupt occurred why this would cause database errors since this is handled by controller thread. I have now worked out the issue is that Im using an ExecutorService with a fixed size BlockingQueue (so that we dont have a big queue build up in memory), but if the queue gets full then new task is actually executed by the controller thread (because of CallerRunsPolicy), so the controller thread can be making calls to database after all.
Im using H2 with hibernate and in both cases calling the following immediately after the interrupt
HibernateUtil.closeFactory();
seems to solve the issue, however I guess this means that any other threads with hibernate sessions will be broken, but at least newly opened sessins will be okay. So im not particularly happy with this workaround, any other ideas ?
Using H2 as a server is not a solution since the whole point of H2 was an embedded db self contained within application.

Although not properly documented using the async protocol allows a connection to be interrupted without breaking all other connections.

java.net.SocketException: Socket closed: handle connection interruption

I have a weak connection with database server and time consuming query which is sometimes fails with exception:
Caused by: java.sql.SQLException: I/O Error: Socket closed
at net.sourceforge.jtds.jdbc.TdsCore.nextToken(TdsCore.java:2481)
at net.sourceforge.jtds.jdbc.TdsCore.getNextRow(TdsCore.java:805)
at net.sourceforge.jtds.jdbc.JtdsResultSet.next(JtdsResultSet.java:611)
Caused by: java.net.SocketException: Socket closed
at java.net.SocketInputStream.socketRead0(Native Method)
at java.net.SocketInputStream.read(SocketInputStream.java:152)
at java.net.SocketInputStream.read(SocketInputStream.java:122)
at java.io.DataInputStream.readFully(DataInputStream.java:195)
at net.sourceforge.jtds.jdbc.SharedSocket.readPacket(SharedSocket.java:885)
at net.sourceforge.jtds.jdbc.SharedSocket.getNetPacket(SharedSocket.java:731)
at net.sourceforge.jtds.jdbc.ResponseStream.getPacket(ResponseStream.java:477)
at net.sourceforge.jtds.jdbc.ResponseStream.read(ResponseStream.java:146)
at net.sourceforge.jtds.jdbc.TdsData.readData(TdsData.java:901)
at net.sourceforge.jtds.jdbc.TdsCore.tdsRowToken(TdsCore.java:3175)
at net.sourceforge.jtds.jdbc.TdsCore.nextToken(TdsCore.java:2433)
How can connection interruption be handled? currently I have to manually re-run the operation until it executes successfully, maybe it could be done at jdbc driver level
ps socketTimeout property doesn't seem to affect this

Are you sure this is because of query/procedure taking long time ? As Socket closed error normally means something went wrong with the network connection itself, basically something that your driver could not control...
In general, I would suggest to move to a Pool based mechanism, which allows greater control on your persistence layer interaction.

Why doesn't Future.get(...) kill the thread?

I have an application that is using future for asynchronous execution.
I set the parameter on get method, that the thread should get killed after 10 seconds, when it does not get the response:
Future<RecordMetadata> meta = producer.send(record, new ProducerCallBack());
RecordMetadata data = meta.get(10, TimeUnit.SECONDS);
But the thread get killed after 60 second:
java.util.concurrent.ExecutionException: org.apache.kafka.common.errors.TimeoutException: Failed to update metadata after 60000 ms.
at org.apache.kafka.clients.producer.KafkaProducer$FutureFailure.<init>(KafkaProducer.java:1124)
at org.apache.kafka.clients.producer.KafkaProducer.doSend(KafkaProducer.java:823)
at org.apache.kafka.clients.producer.KafkaProducer.send(KafkaProducer.java:760)
at io.khinkali.KafkaProducerClient.main(KafkaProducerClient.java:49)
Caused by: org.apache.kafka.common.errors.TimeoutException: Failed to update metadata after 60000 ms.
What am I doing wrong?

From the docs:
The threshold for time to block is determined by max.block.ms after
which it throws a TimeoutException.
Check Kafka Appender config in logback.xml, look for:
<producerConfig>max.block.ms=60000</producerConfig>

I set the parameter on get method, that the thread should get killed after 10 seconds, when it does not get the response:
If we are talking about Future.get(...) there is nothing about it that "kills" the thread at all. To quote from the javadocs, the Future.get(...) method:
Waits if necessary for at most the given time for the computation to complete, and then retrieves its result, if available.
If the get(...) method times out then it will throw TimeoutException but your thread is free to continue to run. If you want to stop the thread running then you'll need to catch TimeoutException and then call meta.cancel(true) but even that doesn't guarantee that the thread will be "killed". That causes the thread to be interrupted which means that certain methods will throw InterruptedException or the thread needs to be checking for Thread.currentThread().isInterrupted().
java.util.concurrent.ExecutionException: org.apache.kafka.common.errors.TimeoutException: Failed to update metadata after 60000 ms.
Yeah this timeout has nothing to do with the Future.get(...) timeout.

Read Timed Out Error in reading URL using java

I have return a code to read a web page using jsoup-1.7.3.jar, Its working for some websites but giviing Read timed out error for some of the URls....
.
Exception in thread "main" java.net.SocketTimeoutException: Read timed
out at java.net.SocketInputStream.socketRead0(Native Method) at
java.net.SocketInputStream.read(SocketInputStream.java:152) at
java.net.SocketInputStream.read(SocketInputStream.java:122) at
java.io.BufferedInputStream.fill(BufferedInputStream.java:235) at
java.io.BufferedInputStream.read1(BufferedInputStream.java:275) at
java.io.BufferedInputStream.read(BufferedInputStream.java:334) at
sun.net.www.http.HttpClient.parseHTTPHeader(HttpClient.java:687) at
sun.net.www.http.HttpClient.parseHTTP(HttpClient.java:633) at
sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1323)
at
java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:468)
at
org.jsoup.helper.HttpConnection$Response.execute(HttpConnection.java:443)
at
org.jsoup.helper.HttpConnection$Response.execute(HttpConnection.java:424)
at org.jsoup.helper.HttpConnection.execute(HttpConnection.java:178)
at org.jsoup.helper.HttpConnection.get(HttpConnection.java:167) at
Main.main(Main.java:10)

As ooxi mentioned, you can set a timeout
Jsoup.connect("").timeout(5*1000).get() //which sets timeout for 5 seconds
Edit: You can specify the timeout though the Connection
Connection connection = Jsoup.connect("");
connection.timeout(5*1000); // which sets timeout for 5 seconds

Before calling .get you can set a timeout for example
Jsoup.connect(url).timeout(0).get();
Have a look at the JavaDocs of Jsoup and Connection