We Keep Coding

HDFS: namenode.FSEditLog (JournalSet.java:mapJournalsAndReportErrors(390)) - Error: flush failed for required journal

On one of our platforms, HDFS namenode is shutting down with following error message every 1 or 3 days
FATAL namenode.FSEditLog (JournalSet.java:mapJournalsAndReportErrors(390)) - Error: flush failed for required journal (JournalAndStream(mgr=QJM to [<ip1>:<port>,<ip2>:<port>, etc], stream=QuorumOutputStream starting at txid 29873171))
java.io.IOException: Timed out waiting 20000ms for a quorum of nodes to respond.
at org.apache.hadoop.hdfs.qjournal.client.AsyncLoggerSet.waitForWriteQuorum(AsyncLoggerSet.java:137)
at org.apache.hadoop.hdfs.qjournal.client.QuorumOutputStream.flushAndSync(QuorumOutputStream.java:109)
at org.apache.hadoop.hdfs.server.namenode.EditLogOutputStream.flush(EditLogOutputStream.java:113)
at org.apache.hadoop.hdfs.server.namenode.EditLogOutputStream.flush(EditLogOutputStream.java:107)
at org.apache.hadoop.hdfs.server.namenode.JournalSet$JournalSetOutputStream$8.apply(JournalSet.java:525)
at org.apache.hadoop.hdfs.server.namenode.JournalSet.mapJournalsAndReportErrors(JournalSet.java:385)
at org.apache.hadoop.hdfs.server.namenode.JournalSet.access$100(JournalSet.java:55)
at org.apache.hadoop.hdfs.server.namenode.JournalSet$JournalSetOutputStream.flush(JournalSet.java:521)
at org.apache.hadoop.hdfs.server.namenode.FSEditLog.logSync(FSEditLog.java:710)
at org.apache.hadoop.hdfs.server.namenode.FSEditLogAsync.run(FSEditLogAsync.java:188)
at java.lang.Thread.run(Thread.java:748)
Before this FATAL log we can see following kind of logs, on which we can detect a degradation of response time
WARN client.QuorumJournalManager (QuorumCall.java:waitFor(185)) - Waited 18014 ms (timeout=20000 ms) for a response for sendEdits. Succeeded so far: [<ip1>:<port>,<ip2>:<port>]
Have you already encountered this problem, and do you have any advices to fix it ?
We have already:
checked that our VMs are time synchronized
detected that when the problem occurs a burst of data on the network is in progress, without detecting the root cause yet
checked our network devices. Except a problem on a port which goes from UP state to DOWN state quickly that we are going to fix, the network seems correct
Thanks in advance

java.net.BindException: Address already in use: connect (I did read the others before posting)

I know there are a ton of these posts, but this is a little different. We are using vended code for part of our data processing system, and part of the system sends emails to clients if certain events take place on data insertion or deletion. Recently we have started getting address already in use exceptions. We checked the repository history, and nothing has changed in our code in the last 6 months for this system. We have already tried the typical solutions for this issue including increasing the number of connections allowed to the port with little success. We had a meeting with the vendor, and I asked if anything had changed in their code, and if they would assure that all connections in their code are explicitly closed. They indicated that they are explicitly closing all sockets. However they didn't show us the code so there is no way for us to know if this is true other than taking their word for it. So, the only thing I can think of to do is continue to increase the number of connections to the port until we stop getting bind exceptions. So, what is the industry standard for max number of connections to port 25; is there one? Also if anyone has any other suggestions I would greatly appreciate it? Thanks so much in advance, Robert
20210505112127.716 ERROR m.fiserv.ppx.business.notification.EmailNotifier : MessagingException from notify
javax.mail.MessagingException: Could not connect to SMTP host: SERVER.URL.COM, port: 25;
nested exception is:
java.net.BindException: Address already in use: connect
at com.sun.mail.smtp.SMTPTransport.openServer(SMTPTransport.java:1545)
at com.sun.mail.smtp.SMTPTransport.protocolConnect(SMTPTransport.java:453)
Caused by:
java.net.BindException: Address already in use: connect
at java.net.DualStackPlainSocketImpl.connect0(Native Method)
at java.net.DualStackPlainSocketImpl.socketConnect(DualStackPlainSocketImpl.java:90)
at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:380)
20210505131529.950 ERROR erv.ppx.web.controller.AuditReportViewController : Error while generating HTML
net.sf.jasperreports.engine.JRException: Error writing to OutputStream writer : CorpAdminAuditReport
at net.sf.jasperreports.engine.export.JRHtmlExporter.exportReport(JRHtmlExporter.java:496)
at com.fiserv.ppx.web.controller.AuditReportViewController.generateReport(AuditReportViewController.java:184)
Caused by:
com.ibm.wsspi.webcontainer.ClosedConnectionException: OutputStream encountered error during write
at com.ibm.ws.webcontainer.channel.WCCByteBufferOutputStream.write(WCCByteBufferOutputStream.java:188)
at com.ibm.ws.webcontainer.srt.SRTOutputStream.write(SRTOutputStream.java:97)
20210505140706.240 ERROR com.fiserv.ppx.business.db.DBConnectionUtil : Exception in getting for AppServer connection from DataSource.
com.ibm.websphere.ce.cm.ConnectionWaitTimeoutException: J2CA1010E: Connection not available; timed out waiting for 180,005 seconds.
at com.ibm.ws.rsadapter.AdapterUtil.toSQLException(AdapterUtil.java:1680)
at com.ibm.ws.rsadapter.jdbc.WSJdbcDataSource.getConnection(WSJdbcDataSource.java:661)
at com.ibm.ws.rsadapter.jdbc.WSJdbcDataSource.getConnection(WSJdbcDataSource.java:611)
Caused by:
com.ibm.websphere.ce.j2c.ConnectionWaitTimeoutException: J2CA1010E: Connection not available; timed out waiting for 180,005 seconds.
at com.ibm.ejs.j2c.FreePool.createOrWaitForConnection(FreePool.java:1781)
at com.ibm.ejs.j2c.PoolManager.reserve(PoolManager.java:3834)
at com.ibm.ejs.j2c.PoolManager.reserve(PoolManager.java:3082)
20210505140731.341 ERROR com.fiserv.ppx.business.db.DBConnectionUtil : Exception in getting for AppServer connection from DataSource.
com.ibm.websphere.ce.cm.ConnectionWaitTimeoutException: J2CA1010E: Connection not available; timed out waiting for 180,010 seconds.
at com.ibm.ws.rsadapter.AdapterUtil.toSQLException(AdapterUtil.java:1680)
at com.ibm.ws.rsadapter.jdbc.WSJdbcDataSource.getConnection(WSJdbcDataSource.java:661)
at com.ibm.ws.rsadapter.jdbc.WSJdbcDataSource.getConnection(WSJdbcDataSource.java:611)
Caused by:
com.ibm.websphere.ce.j2c.ConnectionWaitTimeoutException: J2CA1010E: Connection not available; timed out waiting for 180,010 seconds.
at com.ibm.ejs.j2c.FreePool.createOrWaitForConnection(FreePool.java:1781)
at com.ibm.ejs.j2c.PoolManager.reserve(PoolManager.java:3904)
at com.ibm.ejs.j2c.PoolManager.reserve(PoolManager.java:3082)
20210505140731.341 ERROR com.fiserv.ppx.sso.controller.SSOController : SSO Configuration error
java.lang.NullPointerException
at com.fiserv.ppx.business.db.PPXDbTransactionManager.<init>(PPXDbTransactionManager.java:60)
at com.fiserv.ppx.sso.impl.SSOLoginAuthenticator.authenticateSSOUser(SSOLoginAuthenticator.java:157)

How to solve "Socket read timed out" when using hikari connection pool

I am developing an application using play framework (version 2.8.0), java(version 1.8) with an oracle database(version 12C).
There is only zero or one hit to the database in a day, I am getting below error.
java.sql.SQLRecoverableException: IO Error: Socket read timed out
at oracle.jdbc.driver.T4CConnection.logoff(T4CConnection.java:919)
at oracle.jdbc.driver.PhysicalConnection.close(PhysicalConnection.java:2005)
at com.zaxxer.hikari.pool.PoolBase.quietlyCloseConnection(PoolBase.java:138)
at com.zaxxer.hikari.pool.HikariPool.lambda$closeConnection$1(HikariPool.java:447)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.net.SocketTimeoutException: Socket read timed out
at oracle.net.nt.TimeoutSocketChannel.read(TimeoutSocketChannel.java:174)
at oracle.net.ns.NIOHeader.readHeaderBuffer(NIOHeader.java:82)
at oracle.net.ns.NIOPacket.readFromSocketChannel(NIOPacket.java:139)
at oracle.net.ns.NIOPacket.readFromSocketChannel(NIOPacket.java:101)
at oracle.net.ns.NIONSDataChannel.readDataFromSocketChannel(NIONSDataChannel.java:80)
at oracle.jdbc.driver.T4CMAREngineNIO.prepareForReading(T4CMAREngineNIO.java:98)
at oracle.jdbc.driver.T4CMAREngineNIO.unmarshalUB1(T4CMAREngineNIO.java:534)
at oracle.jdbc.driver.T4CTTIfun.receive(T4CTTIfun.java:485)
at oracle.jdbc.driver.T4CTTIfun.doRPC(T4CTTIfun.java:252)
at oracle.jdbc.driver.T4C7Ocommoncall.doOLOGOFF(T4C7Ocommoncall.java:62)
at oracle.jdbc.driver.T4CConnection.logoff(T4CConnection.java:908)
... 6 common frames omitted
db {
default {
driver=oracle.jdbc.OracleDriver
url="jdbc:oracle:thin:#XXX.XXX.XXX.XX:XXXX/XXXXXXX"
username="XXXXXXXXX"
password="XXXXXXXXX"
hikaricp {
dataSource {
cachePrepStmts = true
prepStmtCacheSize = 250
prepStmtCacheSqlLimit = 2048
}
}
}
}
It seems it is causing due to inactive database connection, How can I solve this?
Please let me know if any other information is required?

You can enable TCP keepalive for JDBC - either be setting directive or by adding "ENABLE=BROKEN" into connection string.
Usually Cisco/Juniper cuts off TCP connection when it is inactive for more that on hour.
While Linux kernel starts sending keepalive probes after two hours(tcp_keepalive_time). So if you decide to turn tcp keepalive on, you will also need root, to change this kernel tunable to lower value(10-15 minutes)
Moreover HikariCP should not keep open any connection for longer than 30 minutes - by default.
So if your FW, Linux kernel and HikariCP all use default settings, then this error should not occur in your system.
See HikariCP official documentation
maxLifetime:
This property controls the maximum lifetime of a connection in the
pool. An in-use connection will never be retired, only when it is
closed will it then be removed. On a connection-by-connection basis,
minor negative attenuation is applied to avoid mass-extinction in the
pool. We strongly recommend setting this value, and it should be
several seconds shorter than any database or infrastructure imposed
connection time limit. A value of 0 indicates no maximum lifetime
(infinite lifetime), subject of course to the idleTimeout setting. The
minimum allowed value is 30000ms (30 seconds). Default: 1800000 (30
minutes)

I have added the below configuration for hickaricp in configuration file and it is
working fine.
## Database Connection Pool
play.db.pool = hikaricp
play.db.prototype.hikaricp.connectionTimeout=120000
play.db.prototype.hikaricp.idleTimeout=15000
play.db.prototype.hikaricp.leakDetectionThreshold=120000
play.db.prototype.hikaricp.validationTimeout=10000
play.db.prototype.hikaricp.maxLifetime=120000

Infinispan TimeoutException ISPN000476

I am experiencing Embedded InfiniSpan cache issue where nodes timeout on re-joining the cluster.
Caused by: org.infinispan.util.concurrent.TimeoutException: ISPN000476: Timed out waiting for responses for request 7 from vvshost
at org.infinispan.remoting.transport.impl.SingleTargetRequest.onTimeout(SingleTargetRequest.java:64)
at org.infinispan.remoting.transport.AbstractRequest.call(AbstractRequest.java:86)
at org.infinispan.remoting.transport.AbstractRequest.call(AbstractRequest.java:21)
The only way I can get the node to re-join is to switch off the cache and delete all local cache persistence files.
Here is the configuration which I am using:
Transport:
TransportConfigurationBuilder - defaultClusteredBuild
JMX Statistics - Enabled
Duplicate domains - Allowed
Cache Manager:
Manager Class - EmbeddedCacheManager
Memory - Memory Size: 0
Persistence: Single File Store
async: disabled
Clustering Cache Mode - CacheMode.DIST_SYNC

It seems right to me, but the value of remote-timeout is "15000" milliseconds by default. Increase the timeout until you stop getting the error.
Hope it helps

Websphere HTTP outbound connection pool usage

I have an application running on Websphere Application Server 6.1.0.43. And I'm having slowdown issues when thrying to invoke a remote service.
The slowdown is on the method findGroupAndGetConnection from the class outboundConnectionCache.
According to the IBM APAR PK94494:
The delay occurs after the client-side JAX-RPC handler (if present) is invoked and before the actual SOAP message is sent to the provider.
Because the delay occurs in the IBM web services engine, this problem
can be difficult to detect.
A com.ibm.ws.webservices.engine.transport.*=all trace will show entries similar to these which repeat:
[8/19/09 18:08:29:658 GMT] 00000047 OutboundConne 1 Enter:
WSWS3595I: Current pool size: 25. Connections-in-use size: 0.
Configured pool size: 25
In addition, that same trace spec will show long delays in executing
the .findGroupAndGetConnection() method:
[8/19/09 18:08:03:428 GMT] 00000047 OutboundConne >
OutboundConnectionCache.findGroupAndGetConnection()
WAITING_THREADS_THRESHOLD is 5 Entry
[8/19/09 18:08:38:358 GMT] 00000047 OutboundConne <
OutboundConnectionCache.findGroupAndGetConnection() Exit
And they recommend the following:
Reduce the 'com.ibm.websphere.webservices.http.connectionPoolCleanUpTime' from
the default of 180 to 120 seconds
Increase the max connections 'com.ibm.websphere.webservices.http.maxConnection' property from
default of 25 to 50. This will also require increasing the web
container thread pool size to 100.
Before changing the default properties I decided to monitor the Web Container thread usage and I noticed that maximum thread pool size (50) is never reached, but the minimum pool size (10) is reached very often, forcing connections to be destroyed and recreated.
Running over the minimum pool size will cause this slowdown? Should I increase the minimum pool size? Is my problem something other than http outbound connection pool?