Running SparkR on YARN outputs an "Rscript execution" error - r

I have Spark 1.4.1 installed on an Hadoop 2.7 cluster.
I've started the SparkR shell without error:
bin/sparkR --master yarn-client
I've run the R command without error (introductory example from spark.apache.org) :
df <- createDataFrame(sqlContext, faithful)
When I run the command :
head(select(df, df$eruptions))
I get the following error at 15/09/02 10:08:29 on the executor node :
"Rscript execution error: No such file or directory".
Any hint would be greatly appreciated.
Spark tasks other than SparkR run OK on my YARN cluster.
R 3.2.1 is installed and runs OK on the driver node.
15/09/02 10:04:06 INFO executor.CoarseGrainedExecutorBackend: Registered signal handlers for [TERM, HUP, INT]
15/09/02 10:04:09 WARN util.NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
15/09/02 10:04:10 INFO spark.SecurityManager: Changing view acls to: yarn,root
15/09/02 10:04:10 INFO spark.SecurityManager: Changing modify acls to: yarn,root
15/09/02 10:04:10 INFO spark.SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users with view permissions: Set(yarn, root); users with modify permissions: Set(yarn, root)
15/09/02 10:04:11 INFO slf4j.Slf4jLogger: Slf4jLogger started
15/09/02 10:04:12 INFO Remoting: Starting remoting
15/09/02 10:04:12 INFO Remoting: Remoting started; listening on addresses :[akka.tcp://driverPropsFetcher#datanode1.hp.com:46167]
15/09/02 10:04:12 INFO util.Utils: Successfully started service 'driverPropsFetcher' on port 46167.
15/09/02 10:04:12 INFO spark.SecurityManager: Changing view acls to: yarn,root
15/09/02 10:04:12 INFO spark.SecurityManager: Changing modify acls to: yarn,root
15/09/02 10:04:12 INFO spark.SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users with view permissions: Set(yarn, root); users with modify permissions: Set(yarn, root)
15/09/02 10:04:12 INFO remote.RemoteActorRefProvider$RemotingTerminator: Shutting down remote daemon.
15/09/02 10:04:12 INFO remote.RemoteActorRefProvider$RemotingTerminator: Remote daemon shut down; proceeding with flushing remote transports.
15/09/02 10:04:12 INFO remote.RemoteActorRefProvider$RemotingTerminator: Remoting shut down.
15/09/02 10:04:12 INFO slf4j.Slf4jLogger: Slf4jLogger started
15/09/02 10:04:12 INFO Remoting: Starting remoting
15/09/02 10:04:13 INFO util.Utils: Successfully started service 'sparkExecutor' on port 47919.
15/09/02 10:04:13 INFO Remoting: Remoting started; listening on addresses :[akka.tcp://sparkExecutor#datanode1.hp.com:47919]
15/09/02 10:04:13 INFO storage.DiskBlockManager: Created local directory at /data2/hadoop/yarn/local/usercache/root/appcache/application_1441180800595_0001/blockmgr-5e435e40-bd36-4746-9acd-8cf1619033ae
15/09/02 10:04:13 INFO storage.DiskBlockManager: Created local directory at /data3/hadoop/yarn/local/usercache/root/appcache/application_1441180800595_0001/blockmgr-28dfabe6-8e0d-4e49-bc95-27b3428c10a0
15/09/02 10:04:13 INFO storage.MemoryStore: MemoryStore started with capacity 534.5 MB
15/09/02 10:04:13 INFO executor.CoarseGrainedExecutorBackend: Connecting to driver: akka.tcp://sparkDriver#192.1.1.1:45596/user/CoarseGrainedScheduler
15/09/02 10:04:13 INFO executor.CoarseGrainedExecutorBackend: Successfully registered with driver
15/09/02 10:04:13 INFO executor.Executor: Starting executor ID 2 on host datanode1.hp.com
15/09/02 10:04:14 INFO util.Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 34166.
15/09/02 10:04:14 INFO netty.NettyBlockTransferService: Server created on 34166
15/09/02 10:04:14 INFO storage.BlockManagerMaster: Trying to register BlockManager
15/09/02 10:04:14 INFO storage.BlockManagerMaster: Registered BlockManager
15/09/02 10:06:35 INFO executor.CoarseGrainedExecutorBackend: Got assigned task 0
15/09/02 10:06:35 INFO executor.Executor: Running task 0.0 in stage 0.0 (TID 0)
15/09/02 10:06:35 INFO broadcast.TorrentBroadcast: Started reading broadcast variable 0
15/09/02 10:06:35 INFO storage.MemoryStore: ensureFreeSpace(854) called with curMem=0, maxMem=560497950
15/09/02 10:06:35 INFO storage.MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 854.0 B, free 534.5 MB)
15/09/02 10:06:35 INFO broadcast.TorrentBroadcast: Reading broadcast variable 0 took 159 ms
15/09/02 10:06:35 INFO storage.MemoryStore: ensureFreeSpace(1280) called with curMem=854, maxMem=560497950
15/09/02 10:06:35 INFO storage.MemoryStore: Block broadcast_0 stored as values in memory (estimated size 1280.0 B, free 534.5 MB)
15/09/02 10:06:35 INFO executor.Executor: Finished task 0.0 in stage 0.0 (TID 0). 11589 bytes result sent to driver
15/09/02 10:08:28 INFO executor.CoarseGrainedExecutorBackend: Got assigned task 1
15/09/02 10:08:28 INFO executor.Executor: Running task 0.0 in stage 1.0 (TID 1)
15/09/02 10:08:28 INFO broadcast.TorrentBroadcast: Started reading broadcast variable 1
15/09/02 10:08:28 INFO storage.MemoryStore: ensureFreeSpace(4022) called with curMem=0, maxMem=560497950
15/09/02 10:08:28 INFO storage.MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 3.9 KB, free 534.5 MB)
15/09/02 10:08:28 INFO broadcast.TorrentBroadcast: Reading broadcast variable 1 took 13 ms
15/09/02 10:08:28 INFO storage.MemoryStore: ensureFreeSpace(9536) called with curMem=4022, maxMem=560497950
15/09/02 10:08:28 INFO storage.MemoryStore: Block broadcast_1 stored as values in memory (estimated size 9.3 KB, free 534.5 MB)
15/09/02 10:08:29 INFO r.BufferedStreamThread: Rscript execution error: No such file or directory
15/09/02 10:08:39 ERROR executor.Executor: Exception in task 0.0 in stage 1.0 (TID 1)
java.net.SocketTimeoutException: Accept timed out
at java.net.PlainSocketImpl.socketAccept(Native Method)
at java.net.AbstractPlainSocketImpl.accept(AbstractPlainSocketImpl.java:398)
at java.net.ServerSocket.implAccept(ServerSocket.java:530)
at java.net.ServerSocket.accept(ServerSocket.java:498)
at org.apache.spark.api.r.RRDD$.createRWorker(RRDD.scala:425)
at org.apache.spark.api.r.BaseRRDD.compute(RRDD.scala:63)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:277)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:244)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:35)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:277)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:244)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:35)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:277)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:244)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:35)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:277)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:244)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:35)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:277)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:244)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:63)
at org.apache.spark.scheduler.Task.run(Task.scala:70)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:213)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)

Related

Access impossible to newly setup EJBCA PKI

I have just finished installing ejbca community edition on top of wildfly.
The EJBCA server is a VM in the azure cloud.
everything went fine during build : Build successful for every 3 steps of deployment.
- ant deployear
- ant runinstall
- ant deploy-keystore)
Versions :
Wildfly 18.0
EJBCA 7.4.3.2
Ant 1.10.10
Mysql Ver 15.1 Distrib 10.3.27-MariaDB
JDBC connector : mariadb 2.7.3
Debian 10 buster
However i am unable to reach the destination
https://<public ip address>:8443/ejbca/
Error message :
The connection has timed out
The server at <my public ip #> is taking too long to respond.
So, started checking the different ports open :
**remote** nmap scan from my local vm to the remote EJBCA VM :
nmap -Pn8080,22,8442,8443,9990,3306 52.188.59.103
Host is up (0.037s latency).
Not shown: 995 filtered ports
PORT STATE SERVICE
21/tcp open ftp
80/tcp open http
443/tcp open https
554/tcp open rtsp
1723/tcp open pptp
Nmap done: 1 IP address (1 host up) scanned in 5.62 seconds
On the EJBCA VM a local port scan shows that port 8443 and 8080 are open :
rDNS record for 127.0.0.1: localhost
Not shown: 996 closed ports
PORT STATE SERVICE
22/tcp open ssh
3306/tcp open mysql
8080/tcp open http-proxy
8443/tcp open https-alt
Azure connectivity tests from my ip to EJBCA host is OK for every ports tested.
however, online Port check says ports 8443 and 8442 are closed
https://portchecker.co/
So i don't know which test to trust ?
I tried disabling both my local firewall and my proxy but it didn't make any difference.
I did a tcpdump on the EJBCA server whilst trying to access ejbca url : but nothing was displayed.
What am i missing here ?
What other tests can i perform?
EDIT :
serverlog: (errors and warnings )
web admin error:
2021-06-14 13:00:07,332 ERROR [org.jboss.as.jsf] (MSC service thread 1-2) WFLYJSF0002: Could not load JSF managed bean class: org.ejbca.ui.web.admin.peerconnector.PeerConnectorsMBean
2021-06-14 13:00:07,433 ERROR [org.jboss.as.jsf] (MSC service thread 1-2) WFLYJSF0002: Could not load JSF managed bean class: org.ejbca.ui.web.admin.peerconnector.PeerConnectorMBean
Deprecated lib:
2021-06-14 13:00:14,598 WARN [org.jboss.weld.Bootstrap] (MSC service thread 1-4) WELD-000146: BeforeBeanDiscovery.addAnnotatedType(AnnotatedType<?>) used for class com.sun.faces.flow.FlowDiscoveryCDIHelper is deprecated from CDI 1.1!
Severe errors :
2021-06-14 13:00:15,967 SEVERE [javax.enterprise.resource.webcontainer.jsf.flow] (MSC service thread 1-4) Unable to obtain CDI 1.1 utilities for Mojarra
2021-06-14 13:00:15,971 SEVERE [javax.enterprise.resource.webcontainer.jsf.application.view] (MSC service thread 1-4) Unable to obtain CDI 1.1 utilities for Mojarra
Warnings:
2021-06-14 13:00:16,770 INFO [org.ejbca.core.ejb.StartupSingletonBean] (ServerService Thread Pool -- 94) Init, EJBCA 7.4.3.2 Community (67479006a69140e81d66e39871bed8255362effc) startup.
2021-06-14 13:00:16,780 WARN [io.undertow.servlet] (ServerService Thread Pool -- 66) UT015020: Path /* is secured for some HTTP methods, however it is not secured for [HEAD, POST, GET]
2021-06-14 13:00:16,780 WARN [io.undertow.servlet] (ServerService Thread Pool -- 73) UT015020: Path /* is secured for some HTTP methods [...]

During startup WildFly should log something like the following, so you can verify that WildFly is configured to listen on ports for all IPs.
16:58:12,890 INFO [org.wildfly.extension.undertow] (MSC service thread 1-7) WFLYUT0006: Undertow HTTPS listener httpspriv listening on 0.0.0.0:8443
16:58:12,920 INFO [org.wildfly.extension.undertow] (MSC service thread 1-8) WFLYUT0006: Undertow HTTPS listener httpspub listening on 0.0.0.0:8442
You can also try connecting to port 8442, to check that the problem is not that you don't have the client certificate in your browser.

Connect sparklyr 0.8.4 to remote spark 2.2.1 connection

I'm trying to connect from R to a remote spark cluster.
The spark cluster is build on debian jessie and the R version i can install on it is at most 3.3 but I need 3.4 to be able to run FactoMineR. So I installed R on another machine and try to connect the cluster using sparklyr 0.8.4
> sc <- spark_connect(master = "spark://spark-cluster-m:7077", spark_home="/usr/lib/spark/", version="2.2.1")
Error in start_shell(master = master, spark_home = spark_home, spark_version = version, :
SPARK_HOME directory '/usr/lib/spark/' not found
spark isn't installed on the local machine but on the spark-cluster-m, it is :
jc#spark-cluster-m:/usr/lib/spark$ ls
bin conf data examples external jars LICENSE licenses NOTICE python R README.md RELEASE sbin work yarn
Have I missed something ?
The spark cluster is on google cloud (test account) and so is the VM with R. How do I verify the port spark can be connected to ?
Thanks for your clues
#user16... You're right, this particular problem seems to be solved but my way is not ended.
I installed the same spark version (2.2.1 with hadoop > 2.7)
Here is my new error message :
Error in force(code) :
Failed during initialize_connection: java.lang.IllegalArgumentException: requirement failed: Can only call getServletHandlers on a running MetricsSystem
at scala.Predef$.require(Predef.scala:224)
at org.apache.spark.metrics.MetricsSystem.getServletHandlers(MetricsSystem.scala:91)
at org.apache.spark.SparkContext.<init>(SparkContext.scala:524)
at org.apache.spark.SparkContext$.getOrCreate(SparkContext.scala:2516)
at org.apache.spark.SparkContext.getOrCreate(SparkContext.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at sparklyr.Invoke.invoke(invoke.scala:137)
at sparklyr.StreamHandler.handleMethodCall(stream.scala:123)
at sparklyr.StreamHandler.read(stream.scala:66)
at sparklyr.BackendHandler.channelRead0(handler.scala:51)
at sparklyr.BackendHandler.channelRead0(handler.scala:4)
at io.netty.channel.SimpleChannelInboundHandler.channelRead(SimpleChannelInboundHandler.java:105)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343)
at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:336)
at io.netty.handler.codec.MessageToMessageDecoder.channelRead(MessageToMessageDecoder.java:102)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343)
at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:336)
at io.netty.handler.codec.ByteToMessageDecoder.fireChannelRead(ByteToMessageDecoder.java:293)
at io.netty.handler.codec.ByteToMessageDecoder.channelRead(ByteToMessageDecoder.java:267)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343)
at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:336)
at io.netty.channel.DefaultChannelPipeline$HeadContext.channelRead(DefaultChannelPipeline.java:1294)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343)
at io.netty.channel.DefaultChannelPipeline.fireChannelRead(DefaultChannelPipeline.java:911)
at io.netty.channel.nio.AbstractNioByteChannel$NioByteUnsafe.read(AbstractNioByteChannel.java:131)
at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:643)
at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:566)
at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:480)
at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:442)
at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:131)
at io.netty.util.concurrent.DefaultThreadFactory$DefaultRunnableDecorator.run(DefaultThreadFactory.java:144)
at java.lang.Thread.run(Thread.java:748)
Log: /tmp/RtmpTUh0z6/file5d231368db0_spark.log
---- Output Log ----
at io.netty.channel.nio.NioEventLoop.processS
at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:480)
at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:442)
at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:131)
at io.netty.util.concurrent.DefaultThreadFactory$DefaultRunnableDecorator.run(DefaultThreadFactory.java:144)
... 1 more
18/07/21 18:24:59 INFO StandaloneAppClient$ClientEndpoint: Connecting to master spark://spark-cluster-m:7077...
18/07/21 18:24:59 WARN StandaloneAppClient$ClientEndpoint: Failed to connect to master spark-cluster-m:7077
org.apache.spark.SparkException: Exception thrown in awaitResult:
at org.apache.spark.util.ThreadUtils$.awaitResult(ThreadUtils.scala:205)
at org.apache.spark.rpc.RpcTimeout.awaitResult(RpcTimeout.scala:75)
at org.apache.spark.rpc.RpcEnv.setupEndpointRefByURI(RpcEnv.scala:100)
at org.apache.spark.rpc.RpcEnv.setupEndpointRef(RpcEnv.scala:108)
at org.apache.spark.deploy.client.StandaloneAppClient$ClientEndpoint$$anonfun$tryRegisterAllMasters$1$$anon$1.run(StandaloneAppClient.scala:106)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
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.io.IOException: Failed to connect to spark-cluster-m/10.142.0.3:7077
at org.apache.spark.network.client.TransportClientFactory.createClient(TransportClientFactory.java:232)
at org.apache.spark.network.client.TransportClientFactory.createClient(TransportClientFactory.java:182)
at org.apache.spark.rpc.netty.NettyRpcEnv.createClient(NettyRpcEnv.scala:197)
at org.apache.spark.rpc.netty.Outbox$$anon$1.call(Outbox.scala:194)
at org.apache.spark.rpc.netty.Outbox$$anon$1.call(Outbox.scala:190)
... 4 more
Caused by: io.netty.channel.AbstractChannel$AnnotatedConnectException: Connection refused: spark-cluster-m/10.142.0.3:7077
at sun.nio.ch.SocketChannelImpl.checkConnect(Native Method)
at sun.nio.ch.SocketChannelImpl.finishConnect(SocketChannelImpl.java:717)
at io.netty.channel.socket.nio.NioSocketChannel.doFinishConnect(NioSocketChannel.java:257)
at io.netty.channel.nio.AbstractNioChannel$AbstractNioUnsafe.finishConnect(AbstractNioChannel.java:291)
at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:631)
at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:566)
at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:480)
at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:442)
at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:131)
at io.netty.util.concurrent.DefaultThreadFactory$DefaultRunnableDecorator.run(DefaultThreadFactory.java:144)
... 1 more
18/07/21 18:25:19 ERROR StandaloneSchedulerBackend: Application has been killed. Reason: All masters are unresponsive! Giving up.
18/07/21 18:25:19 WARN StandaloneSchedulerBackend: Application ID is not initialized yet.
18/07/21 18:25:19 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 46811.
18/07/21 18:25:19 INFO NettyBlockTransferService: Server created on 10.142.0.5:46811
18/07/21 18:25:19 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
18/07/21 18:25:19 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 10.142.0.5, 46811, None)
18/07/21 18:25:19 INFO BlockManagerMasterEndpoint: Registering block manager 10.142.0.5:46811 with 366.3 MB RAM, BlockManagerId(driver, 10.142.0.5, 46811, None)
18/07/21 18:25:19 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 10.142.0.5, 46811, None)
18/07/21 18:25:19 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 10.142.0.5, 46811, None)
18/07/21 18:25:19 INFO SparkUI: Stopped Spark web UI at http://10.142.0.5:4040
18/07/21 18:25:19 INFO StandaloneSchedulerBackend: Shutting down all executors
18/07/21 18:25:19 INFO CoarseGrainedSchedulerBackend$DriverEndpoint: Asking each executor to shut down
18/07/21 18:25:19 WARN StandaloneAppClient$ClientEndpoint: Drop Unregist
I can see it can resolve the name (=> 10.142.0.3)
Also, it seems to be the good port as if I use port 7000, i have the error :
18/07/21 18:32:54 ERROR TransportResponseHandler: Still have 1 requests outstanding when connection from spark-cluster-m/10.142.0.3:7000 is closed
18/07/21 18:32:54 WARN StandaloneAppClient$ClientEndpoint: Could not connect to spark-cluster-m:7000: java.io.IOException: Connection reset by peer
18/07/21 18:32:54 WARN StandaloneAppClient$ClientEndpoint: Failed to connect to master spark-cluster-m:7000
But I can't figure out what this means.
You say my configuration is "particular". If there is a better (and simple) approach, i would be glad to use it.
Here is how I proceeded in my tests :
I created a google dataproc cluster with spark (2.2.1)
I added Cassandra on each node
At this stage, everything works ok.
Then, i need to install FactoMineR as I'd like to try HMFA. It is said to run with R > 3.0.0 so it seems to be ok but it depends on nlme which can't be installed on R < 3.4.0 (and the one in the debian jessie backports is 3.3.)
So, what can I do ?
I must admit that i'm not very enthusiastic in restarting a full spark / cassandra cluster install from scratch...

Getting error while redeploying nodes

I am still using Corda 1.0 version. when i try to redeploy nodes with existing data, getting below error while start-up but able to access the nodes . If i clear the data and redeploy the nodes, i didn't face these error message.
Logs can be found in :
C:xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx\kotlin-
source\build\nodes\xxxxxxxx\logs
Database connection url is : jdbc:h2:tcp://xxxxxxxxx/node
E 18:38:46+0530 [main] core.client.createConnection - AMQ214016: Failed to
create netty connection
javax.net.ssl.SSLException: handshake timed out
at io.netty.handler.ssl.SslHandler.handshake(...)(Unknown Source) ~[netty
all-4.1.9.Final.jar:4.1.9.Final]
Incoming connection address : xxxxxxxxxxxx
Listening on port : 10014
RPC service listening on port : 10015
Loaded CorDapps : corda-finance-1.0.0, kotlin-
source-0.1, corda-core-1.0.0
Node for "xxxxxxxxxxx" started up and registered in 213.08 sec
Welcome to the Corda interactive shell.
Useful commands include 'help' to see what is available, and 'bye' to shut
down the node.
Wed May 23 18:39:20 IST 2018>>> E 18:39:24+0530 [Thread-6 (ActiveMQ-server-
org.apache.activemq.artemis.core.server.impl.ActiveMQServerImp
l$3#4a532271)] core.client.createConnection - AMQ214016: Failed to create
netty connection
javax.net.ssl.SSLException: handshake timed out
at io.netty.handler.ssl.SslHandler.handshake(...)(Unknown Source) ~[netty-
all-4.1.9.Final.jar:4.1.9.Final]

This looks like the Artemis failed to connect to the node which means the node fails to start.
You should look at the log and if there are any other previous Corda node started which occupy the node.
If there are any legacy Corda nodes that have not been killed, try ps -ef |grep java to see if there is any other java still alive. Especially look for the port number and check if they are overlapped

Errors while starting WSO2 API Manager 2.1.0

I am getting errors and warnings while trying to bring up WSO2 API Manager 2.1.0 for the first time. [CentOS Linux release 7.3.1611 (Core)]. Excerpts are given below. I have already tried the suggestions at: Failed to start wso2 API Manager v2.0.0 on centos 7.0
$ ./wso2server.sh
JAVA_HOME environment variable is set to /usr/java/jdk1.8.0_60
CARBON_HOME environment variable is set to /home/devwso2/wso2am-2.1.0
Using Java memory options: -Xms256m -Xmx1024m
[2017-02-22 06:03:46,688] INFO - QpidBundleActivator Setting BundleContext in PluginManager
[2017-02-22 06:03:48,217] INFO - CarbonCoreActivator Starting WSO2 Carbon...
[2017-02-22 06:03:48,217] INFO - CarbonCoreActivator Operating System : Linux 3.10.0-514.6.1.el7.x86_64, amd64
[2017-02-22 06:03:48,218] INFO - CarbonCoreActivator Java Home : /usr/java/jdk1.8.0_60/jre
[2017-02-22 06:03:48,218] INFO - CarbonCoreActivator Java Version : 1.8.0_60
[2017-02-22 06:03:48,218] INFO - CarbonCoreActivator Java VM : Java HotSpot(TM) 64-Bit Server VM 25.60-b23,Oracle Corporation
[2017-02-22 06:03:48,218] INFO - CarbonCoreActivator Carbon Home : /home/devwso2/wso2am-2.1.0
[2017-02-22 06:03:48,218] INFO - CarbonCoreActivator Java Temp Dir : /home/devwso2/wso2am-2.1.0/tmp
[2017-02-22 06:03:48,218] INFO - CarbonCoreActivator User : devwso2, en-US, UTC
[2017-02-22 06:03:48,387] WARN - ValidationResultPrinter Swap Memory size (MB): 0 of the system is below the recommended minimum size :2047
[2017-02-22 06:03:48,389] WARN - ValidationResultPrinter Carbon is configured to use the default keystore (wso2carbon.jks). To maximize security when deploying to a production environment, configure a new keystore with a unique password in the production server profile.
.....................
[2017-02-22 06:04:46,407] ERROR - Main Exception during startup. Triggering shutdown
org.wso2.andes.kernel.AndesException: Unable to initialise application registry
at org.wso2.andes.server.Broker.startupImpl(Broker.java:308)
at org.wso2.andes.server.Broker.startup(Broker.java:110)
at org.wso2.andes.server.Main.startBroker(Main.java:217)
at org.wso2.andes.server.Main.execute(Main.java:206)
at org.wso2.andes.server.Main.<init>(Main.java:54)
at org.wso2.andes.server.Main.main(Main.java:47)
at org.wso2.carbon.andes.internal.QpidServiceComponent.startAndesBroker(QpidServiceComponent.java:420)
at org.wso2.carbon.andes.internal.QpidServiceComponent.activate(QpidServiceComponent.java:165)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at org.eclipse.equinox.internal.ds.model.ServiceComponent.activate(ServiceComponent.java:260)
at org.eclipse.equinox.internal.ds.model.ServiceComponentProp.activate(ServiceComponentProp.java:146)
at org.eclipse.equinox.internal.ds.model.ServiceComponentProp.build(ServiceComponentProp.java:345)
at org.eclipse.equinox.internal.ds.InstanceProcess.buildComponent(InstanceProcess.java:620)
at org.eclipse.equinox.internal.ds.InstanceProcess.buildComponents(InstanceProcess.java:197)
at org.eclipse.equinox.internal.ds.Resolver.getEligible(Resolver.java:343)
at org.eclipse.equinox.internal.ds.SCRManager.serviceChanged(SCRManager.java:222)
at org.eclipse.osgi.internal.serviceregistry.FilteredServiceListener.serviceChanged(FilteredServiceListener.java:107)
at org.eclipse.osgi.framework.internal.core.BundleContextImpl.dispatchEvent(BundleContextImpl.java:861)
at org.eclipse.osgi.framework.eventmgr.EventManager.dispatchEvent(EventManager.java:230)
at org.eclipse.osgi.framework.eventmgr.ListenerQueue.dispatchEventSynchronous(ListenerQueue.java:148)
at org.eclipse.osgi.internal.serviceregistry.ServiceRegistry.publishServiceEventPrivileged(ServiceRegistry.java:819)
at org.eclipse.osgi.internal.serviceregistry.ServiceRegistry.publishServiceEvent(ServiceRegistry.java:771)
at org.eclipse.osgi.internal.serviceregistry.ServiceRegistrationImpl.register(ServiceRegistrationImpl.java:130)
at org.eclipse.osgi.internal.serviceregistry.ServiceRegistry.registerService(ServiceRegistry.java:214)
at org.eclipse.osgi.framework.internal.core.BundleContextImpl.registerService(BundleContextImpl.java:433)
at org.eclipse.osgi.framework.internal.core.BundleContextImpl.registerService(BundleContextImpl.java:451)
at org.wso2.carbon.server.admin.internal.ServerAdminServiceComponent.activate(ServerAdminServiceComponent.java:106)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at org.eclipse.equinox.internal.ds.model.ServiceComponent.activate(ServiceComponent.java:260)
at org.eclipse.equinox.internal.ds.model.ServiceComponentProp.activate(ServiceComponentProp.java:146)
at org.eclipse.equinox.internal.ds.model.ServiceComponentProp.build(ServiceComponentProp.java:345)
at org.eclipse.equinox.internal.ds.InstanceProcess.buildComponent(InstanceProcess.java:620)
at org.eclipse.equinox.internal.ds.InstanceProcess.buildComponents(InstanceProcess.java:197)
at org.eclipse.equinox.internal.ds.Resolver.getEligible(Resolver.java:343)
at org.eclipse.equinox.internal.ds.SCRManager.serviceChanged(SCRManager.java:222)
at org.eclipse.osgi.internal.serviceregistry.FilteredServiceListener.serviceChanged(FilteredServiceListener.java:107)
at org.eclipse.osgi.framework.internal.core.BundleContextImpl.dispatchEvent(BundleContextImpl.java:861)
at org.eclipse.osgi.framework.eventmgr.EventManager.dispatchEvent(EventManager.java:230)
at org.eclipse.osgi.framework.eventmgr.ListenerQueue.dispatchEventSynchronous(ListenerQueue.java:148)
at org.eclipse.osgi.internal.serviceregistry.ServiceRegistry.publishServiceEventPrivileged(ServiceRegistry.java:819)
at org.eclipse.osgi.internal.serviceregistry.ServiceRegistry.publishServiceEvent(ServiceRegistry.java:771)
at org.eclipse.osgi.internal.serviceregistry.ServiceRegistrationImpl.register(ServiceRegistrationImpl.java:130)
at org.eclipse.osgi.internal.serviceregistry.ServiceRegistry.registerService(ServiceRegistry.java:214)
at org.eclipse.osgi.framework.internal.core.BundleContextImpl.registerService(BundleContextImpl.java:433)
at org.eclipse.osgi.framework.internal.core.BundleContextImpl.registerService(BundleContextImpl.java:451)
at org.wso2.carbon.core.init.CarbonServerManager.initializeCarbon(CarbonServerManager.java:514)
at org.wso2.carbon.core.init.CarbonServerManager.start(CarbonServerManager.java:219)
at org.wso2.carbon.core.internal.CarbonCoreServiceComponent.activate(CarbonCoreServiceComponent.java:94)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at org.eclipse.equinox.internal.ds.model.ServiceComponent.activate(ServiceComponent.java:260)
at org.eclipse.equinox.internal.ds.model.ServiceComponentProp.activate(ServiceComponentProp.java:146)
at org.eclipse.equinox.internal.ds.model.ServiceComponentProp.build(ServiceComponentProp.java:345)
at org.eclipse.equinox.internal.ds.InstanceProcess.buildComponent(InstanceProcess.java:620)
at org.eclipse.equinox.internal.ds.InstanceProcess.buildComponents(InstanceProcess.java:197)
at org.eclipse.equinox.internal.ds.Resolver.getEligible(Resolver.java:343)
at org.eclipse.equinox.internal.ds.SCRManager.serviceChanged(SCRManager.java:222)
at org.eclipse.osgi.internal.serviceregistry.FilteredServiceListener.serviceChanged(FilteredServiceListener.java:107)
at org.eclipse.osgi.framework.internal.core.BundleContextImpl.dispatchEvent(BundleContextImpl.java:861)
at org.eclipse.osgi.framework.eventmgr.EventManager.dispatchEvent(EventManager.java:230)
at org.eclipse.osgi.framework.eventmgr.ListenerQueue.dispatchEventSynchronous(ListenerQueue.java:148)
at org.eclipse.osgi.internal.serviceregistry.ServiceRegistry.publishServiceEventPrivileged(ServiceRegistry.java:819)
at org.eclipse.osgi.internal.serviceregistry.ServiceRegistry.publishServiceEvent(ServiceRegistry.java:771)
at org.eclipse.osgi.internal.serviceregistry.ServiceRegistrationImpl.register(ServiceRegistrationImpl.java:130)
at org.eclipse.osgi.internal.serviceregistry.ServiceRegistry.registerService(ServiceRegistry.java:214)
at org.eclipse.osgi.framework.internal.core.BundleContextImpl.registerService(BundleContextImpl.java:433)
at org.eclipse.equinox.http.servlet.internal.Activator.registerHttpService(Activator.java:81)
at org.eclipse.equinox.http.servlet.internal.Activator.addProxyServlet(Activator.java:60)
at org.eclipse.equinox.http.servlet.internal.ProxyServlet.init(ProxyServlet.java:40)
at org.wso2.carbon.tomcat.ext.servlet.DelegationServlet.init(DelegationServlet.java:38)
at org.apache.catalina.core.StandardWrapper.initServlet(StandardWrapper.java:1269)
at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1182)
at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:1072)
at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:5368)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5660)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1571)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1561)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.wso2.andes.transport.TransportException: Could not bind to /0.0.0.0:5672
at org.wso2.andes.transport.network.mina.MinaNetworkTransport.accept(MinaNetworkTransport.java:147)
at org.wso2.andes.server.Broker.startAMQPListener(Broker.java:201)
at org.wso2.andes.server.Broker.startupImpl(Broker.java:295)
... 89 more
Caused by: java.net.BindException: Address already in use
at sun.nio.ch.Net.bind0(Native Method)
at sun.nio.ch.Net.bind(Net.java:433)
at sun.nio.ch.Net.bind(Net.java:425)
at sun.nio.ch.ServerSocketChannelImpl.bind(ServerSocketChannelImpl.java:223)
at sun.nio.ch.ServerSocketAdaptor.bind(ServerSocketAdaptor.java:74)
at org.apache.mina.transport.socket.nio.SocketAcceptor.registerNew(SocketAcceptor.java:363)
at org.apache.mina.transport.socket.nio.SocketAcceptor.access$800(SocketAcceptor.java:55)
at org.apache.mina.transport.socket.nio.SocketAcceptor$Worker.run(SocketAcceptor.java:222)
at org.apache.mina.util.NamePreservingRunnable.run(NamePreservingRunnable.java:51)
... 1 more
[2017-02-22 06:04:46,415] INFO - ApplicationRegistry Shutting down ApplicationRegistry(org.wso2.andes.server.registry.ConfigurationFileApplicationRegistry#1524f58a)
[2017-02-22 06:04:46,415] INFO - ApplicationRegistry Shutting down ApplicationRegistry:org.wso2.andes.server.registry.ConfigurationFileApplicationRegistry#1524f58a
[2017-02-22 06:04:46,418] INFO - PrincipalDatabaseAuthenticationManager Unregistering UserManagementMBean
[2017-02-22 06:04:46,421] INFO - CarbonServerManager Shutdown hook triggered....
[2017-02-22 06:04:46,426] INFO - CarbonServerManager Gracefully shutting down WSO2 API Manager...
[2017-02-22 06:04:46,428] INFO - ServerManagement Starting to switch to maintenance mode...
[2017-02-22 06:04:46,429] INFO - ServerManagement Stopped all transport listeners
[2017-02-22 06:04:46,429] INFO - ServerManagement Waiting for request service completion...
[2017-02-22 06:04:46,435] INFO - ServerManagement All requests have been served.
[2017-02-22 06:04:46,435] INFO - ServerManagement Waiting for deployment completion...
[2017-02-22 06:04:46,491] INFO - WebApplication Unloaded webapp: StandardEngine[Catalina].StandardHost[localhost].StandardContext[/api/am/admin/v0.11]
[2017-02-22 06:04:46,536] INFO - WebApplication Unloaded webapp: StandardEngine[Catalina].StandardHost[localhost].StandardContext[/throttle/data/v1]
[2017-02-22 06:04:46,566] INFO - WebApplication Unloaded webapp: StandardEngine[Catalina].StandardHost[localhost].StandardContext[/am/sample/calculator/v1]
[2017-02-22 06:04:46,627] INFO - WebApplication Unloaded webapp: StandardEngine[Catalina].StandardHost[localhost].StandardContext[/shindig]
[2017-02-22 06:04:46,653] INFO - WebApplication Unloaded webapp: StandardEngine[Catalina].StandardHost[localhost].StandardContext[/api/am/publisher/v0.11]
[2017-02-22 06:04:46,682] INFO - WebApplication Unloaded webapp: StandardEngine[Catalina].StandardHost[localhost].StandardContext[/api/am/store/v0.11]
[2017-02-22 06:04:46,699] INFO - WebApplication Unloaded webapp: StandardEngine[Catalina].StandardHost[localhost].StandardContext[/authenticationendpoint]
[2017-02-22 06:04:46,719] INFO - WebApplication Unloaded webapp: StandardEngine[Catalina].StandardHost[localhost].StandardContext[/oauth2]
[2017-02-22 06:04:46,735] INFO - WebApplication Unloaded webapp: StandardEngine[Catalina].StandardHost[localhost].StandardContext[/am/sample/pizzashack/v1]
[2017-02-22 06:04:46,756] INFO - WebApplication Unloaded webapp: StandardEngine[Catalina].StandardHost[localhost].StandardContext[/client-registration/v0.11]
[2017-02-22 06:04:46,764] INFO - WebApplication Unloaded webapp: StandardEngine[Catalina].StandardHost[localhost].StandardContext[/admin]
[2017-02-22 06:04:46,775] INFO - WebApplication Unloaded webapp: StandardEngine[Catalina].StandardHost[localhost].StandardContext[/portal]
[2017-02-22 06:04:46,783] INFO - WebApplication Unloaded webapp: StandardEngine[Catalina].StandardHost[localhost].StandardContext[/store]
[2017-02-22 06:04:46,791] INFO - WebApplication Unloaded webapp: StandardEngine[Catalina].StandardHost[localhost].StandardContext[/publisher]
[2017-02-22 06:04:46,791] INFO - ServerManagement All deployment tasks have been completed.
[2017-02-22 06:04:46,791] INFO - ServerManagement Waiting for server task completion...
[2017-02-22 06:04:46,805] INFO - ServerManagement All server tasks have been completed.
[2017-02-22 06:04:46,805] INFO - CarbonServerManager Shutting down WSO2 API Manager...
[2017-02-22 06:04:46,811] INFO - CarbonServerManager Shutting down OSGi framework...
[2017-02-22 06:04:54,812] INFO - CarbonEventManagementService Starting polling event receivers
[2017-02-22 06:05:15,404] WARN - BlockingConditionRetriever Failed retrieving Blocking Conditions from remote endpoint: Connection refused. Retrying after 15 seconds...
[2017-02-22 06:05:15,412] WARN - KeyTemplateRetriever Failed retrieving throttling data from remote endpoint: Connection refused. Retrying after 15 seconds...
[2017-02-22 06:05:17,532] WARN - AppDeployerServiceComponent Waiting for required OSGi services: org.wso2.carbon.application.deployer.synapse.service.SynapseAppDeployerService,
[2017-02-22 06:05:17,545] WARN - StartupFinalizerServiceComponent Waiting for required OSGi services: org.wso2.carbon.application.deployer.service.CappDeploymentService,org.wso2.carbon.server.admin.common.IServerAdmin,org.wso2.carbon.throttling.agent.ThrottlingAgent,
[2017-02-22 06:05:30,413] WARN - BlockingConditionRetriever Failed retrieving Blocking Conditions from remote endpoint: Connection refused. Retrying after 15 seconds...
[2017-02-22 06:05:30,418] WARN - KeyTemplateRetriever Failed retrieving throttling data from remote endpoint: Connection refused. Retrying after 15 seconds...
[2017-02-22 06:05:44,927] WARN - SynapseAppDeployerDSComponent Waiting for required OSGi services: org.wso2.carbon.message.processor.service.MessageProcessorDeployerService,org.wso2.carbon.message.store.service.MessageStoreDeployerService,org.wso2.carbon.proxyadmin.service.ProxyDeployerService,
[2017-02-22 06:05:45,415] WARN - BlockingConditionRetriever Failed retrieving Blocking Conditions from remote endpoint: Connection refused. Retrying after 15 seconds...
[2017-02-22 06:05:45,420] WARN - KeyTemplateRetriever Failed retrieving throttling data from remote endpoint: Connection refused. Retrying after 15 seconds...
[2017-02-22 06:06:00,419] WARN - BlockingConditionRetriever Failed retrieving Blocking Conditions from remote endpoint: Connection refused. Retrying after 15 seconds...
[2017-02-22 06:06:00,421] WARN - KeyTemplateRetriever Failed retrieving throttling data from remote endpoint: Connection refused. Retrying after 15 seconds...
[2017-02-22 06:06:15,422] WARN - BlockingConditionRetriever Failed retrieving Blocking Conditions from remote endpoint: Connection refused. Retrying after 15 seconds...
[2017-02-22 06:06:15,423] WARN - KeyTemplateRetriever Failed retrieving throttling data from remote endpoint: Connection refused. Retrying after 15 seconds...
[2017-02-22 06:06:17,531] WARN - AppDeployerServiceComponent Waiting for required OSGi services: org.wso2.carbon.application.deployer.synapse.service.SynapseAppDeployerService,
[2017-02-22 06:06:17,546] WARN - StartupFinalizerServiceComponent Waiting for required OSGi services: org.wso2.carbon.application.deployer.service.CappDeploymentService,org.wso2.carbon.server.admin.common.IServerAdmin,org.wso2.carbon.throttling.agent.ThrottlingAgent,
[2017-02-22 06:06:30,425] WARN - BlockingConditionRetriever Failed retrieving Blocking Conditions from remote endpoint: Connection refused. Retrying after 15 seconds...
[2017-02-22 06:06:30,426] WARN - KeyTemplateRetriever Failed retrieving throttling data from remote endpoint: Connection refused. Retrying after 15 seconds...
[2017-02-22 06:06:44,926] WARN - SynapseAppDeployerDSComponent Waiting for required OSGi services: org.wso2.carbon.message.processor.service.MessageProcessorDeployerService,org.wso2.carbon.message.store.service.MessageStoreDeployerService,org.wso2.carbon.proxyadmin.service.ProxyDeployerService,
[2017-02-22 06:06:45,428] WARN - BlockingConditionRetriever Failed retrieving Blocking Conditions from remote endpoint: Connection refused. Retrying after 15 seconds...
[2017-02-22 06:06:45,428] WARN - KeyTemplateRetriever Failed retrieving throttling data from remote endpoint: Connection refused. Retrying after 15 seconds...
[2017-02-22 06:07:00,430] WARN - BlockingConditionRetriever Failed retrieving Blocking Conditions from remote endpoint: Connection refused. Retrying after 15 seconds...
[2017-02-22 06:07:00,431] WARN - KeyTemplateRetriever Failed retrieving throttling data from remote endpoint: Connection refused. Retrying after 15 seconds...
[2017-02-22 06:07:15,434] WARN - BlockingConditionRetriever Failed retrieving Blocking Conditions from remote endpoint: Connection refused. Retrying after 15 seconds...
[2017-02-22 06:07:15,434] WARN - KeyTemplateRetriever Failed retrieving throttling data from remote endpoint: Connection refused. Retrying after 15 seconds...
[2017-02-22 06:07:17,531] WARN - AppDeployerServiceComponent Waiting for required OSGi services: org.wso2.carbon.application.deployer.synapse.service.SynapseAppDeployerService,
[2017-02-22 06:07:17,545] WARN - StartupFinalizerServiceComponent Waiting for required OSGi services: org.wso2.carbon.application.deployer.service.CappDeploymentService,org.wso2.carbon.server.admin.common.IServerAdmin,org.wso2.carbon.throttling.agent.ThrottlingAgent,
[2017-02-22 06:07:30,438] WARN - BlockingConditionRetriever Failed retrieving Blocking Conditions from remote endpoint: Connection refused. Retrying after 15 seconds...
[2017-02-22 06:07:30,438] WARN - KeyTemplateRetriever Failed retrieving throttling data from remote endpoint: Connection refused. Retrying after 15 seconds...
[2017-02-22 06:07:36,930] INFO - SynapseTaskManager Shutting down the task manager
[2017-02-22 06:07:44,926] WARN - SynapseAppDeployerDSComponent Waiting for required OSGi services: org.wso2.carbon.message.processor.service.MessageProcessorDeployerService,org.wso2.carbon.message.store.service.MessageStoreDeployerService,org.wso2.carbon.proxyadmin.service.ProxyDeployerService,
[2017-02-22 06:07:45,440] WARN - BlockingConditionRetriever Failed retrieving Blocking Conditions from remote endpoint: Connection refused. Retrying after 15 seconds...
[2017-02-22 06:07:45,442] WARN - KeyTemplateRetriever Failed retrieving throttling data from remote endpoint: Connection refused. Retrying after 15 seconds...
[2017-02-22 06:08:00,444] WARN - KeyTemplateRetriever Failed retrieving throttling data from remote endpoint: Connection refused. Retrying after 15 seconds...
[2017-02-22 06:08:00,445] WARN - BlockingConditionRetriever Failed retrieving Blocking Conditions from remote endpoint: Connection refused. Retrying after 15 seconds...
[2017-02-22 06:08:15,452] WARN - KeyTemplateRetriever Failed retrieving throttling data from remote endpoint: Connection refused. Retrying after 15 seconds...
[2017-02-22 06:08:15,452] WARN - BlockingConditionRetriever Failed retrieving Blocking Conditions from remote endpoint: Connection refused. Retrying after 15 seconds...
[2017-02-22 06:08:17,531] WARN - AppDeployerServiceComponent Waiting for required OSGi services: org.wso2.carbon.application.deployer.synapse.service.SynapseAppDeployerService,
[2017-02-22 06:08:17,545] WARN - StartupFinalizerServiceComponent Waiting for required OSGi services: org.wso2.carbon.application.deployer.service.CappDeploymentService,org.wso2.carbon.server.admin.common.IServerAdmin,org.wso2.carbon.throttling.agent.ThrottlingAgent,
[2017-02-22 06:08:30,456] WARN - KeyTemplateRetriever Failed retrieving throttling data from remote endpoint: Connection refused. Retrying after 15 seconds...
[2017-02-22 06:08:30,456] WARN - BlockingConditionRetriever Failed retrieving Blocking Conditions from remote endpoint: Connection refused. Retrying after 15 seconds...
[2017-02-22 06:08:44,927] WARN - SynapseAppDeployerDSComponent Waiting for required OSGi services: org.wso2.carbon.message.processor.service.MessageProcessorDeployerService,org.wso2.carbon.message.store.service.MessageStoreDeployerService,org.wso2.carbon.proxyadmin.service.ProxyDeployerService,
[2017-02-22 06:08:45,458] ERROR - BlockingConditionRetriever Exception when retrieving Blocking Conditions from remote endpoint
java.net.ConnectException: Connection refused
at java.net.PlainSocketImpl.socketConnect(Native Method)
at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:589)
at sun.security.ssl.SSLSocketImpl.connect(SSLSocketImpl.java:668)
at org.apache.http.conn.ssl.SSLSocketFactory.connectSocket(SSLSocketFactory.java:522)
at org.apache.http.conn.ssl.SSLSocketFactory.connectSocket(SSLSocketFactory.java:401)
at org.apache.http.impl.conn.DefaultClientConnectionOperator.openConnection(DefaultClientConnectionOperator.java:178)
at org.apache.http.impl.conn.AbstractPoolEntry.open(AbstractPoolEntry.java:144)
at org.apache.http.impl.conn.AbstractPooledConnAdapter.open(AbstractPooledConnAdapter.java:131)
at org.apache.http.impl.client.DefaultRequestDirector.tryConnect(DefaultRequestDirector.java:610)
at org.apache.http.impl.client.DefaultRequestDirector.execute(DefaultRequestDirector.java:445)
at org.apache.http.impl.client.AbstractHttpClient.doExecute(AbstractHttpClient.java:863)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:82)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:106)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:57)
at org.wso2.carbon.apimgt.gateway.throttling.util.BlockingConditionRetriever.retrieveBlockConditionsData(BlockingConditionRetriever.java:79)
at org.wso2.carbon.apimgt.gateway.throttling.util.BlockingConditionRetriever.loadBlockingConditionsFromWebService(BlockingConditionRetriever.java:105)
at org.wso2.carbon.apimgt.gateway.throttling.util.BlockingConditionRetriever.run(BlockingConditionRetriever.java:51)
at java.util.TimerThread.mainLoop(Timer.java:555)
at java.util.TimerThread.run(Timer.java:505)
[2017-02-22 06:08:45,458] ERROR - KeyTemplateRetriever Exception when retrieving throttling data from remote endpoint
java.net.ConnectException: Connection refused
at java.net.PlainSocketImpl.socketConnect(Native Method)
at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:589)
at sun.security.ssl.SSLSocketImpl.connect(SSLSocketImpl.java:668)
at org.apache.http.conn.ssl.SSLSocketFactory.connectSocket(SSLSocketFactory.java:522)
at org.apache.http.conn.ssl.SSLSocketFactory.connectSocket(SSLSocketFactory.java:401)
at org.apache.http.impl.conn.DefaultClientConnectionOperator.openConnection(DefaultClientConnectionOperator.java:178)
at org.apache.http.impl.conn.AbstractPoolEntry.open(AbstractPoolEntry.java:144)
at org.apache.http.impl.conn.AbstractPooledConnAdapter.open(AbstractPooledConnAdapter.java:131)
at org.apache.http.impl.client.DefaultRequestDirector.tryConnect(DefaultRequestDirector.java:610)
at org.apache.http.impl.client.DefaultRequestDirector.execute(DefaultRequestDirector.java:445)
at org.apache.http.impl.client.AbstractHttpClient.doExecute(AbstractHttpClient.java:863)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:82)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:106)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:57)
at org.wso2.carbon.apimgt.gateway.throttling.util.KeyTemplateRetriever.retrieveKeyTemplateData(KeyTemplateRetriever.java:83)
at org.wso2.carbon.apimgt.gateway.throttling.util.KeyTemplateRetriever.loadKeyTemplatesFromWebService(KeyTemplateRetriever.java:111)
at org.wso2.carbon.apimgt.gateway.throttling.util.KeyTemplateRetriever.run(KeyTemplateRetriever.java:54)
at java.util.TimerThread.mainLoop(Timer.java:555)
at java.util.TimerThread.run(Timer.java:505)
Exception in thread "Timer-5" java.lang.NullPointerException
at java.util.Objects.requireNonNull(Objects.java:203)
at java.util.Arrays$ArrayList.<init>(Arrays.java:3813)
at java.util.Arrays.asList(Arrays.java:3800)
at org.wso2.carbon.apimgt.gateway.throttling.util.KeyTemplateRetriever.loadKeyTemplatesFromWebService(KeyTemplateRetriever.java:111)
at org.wso2.carbon.apimgt.gateway.throttling.util.KeyTemplateRetriever.run(KeyTemplateRetriever.java:54)
at java.util.TimerThread.mainLoop(Timer.java:555)
at java.util.TimerThread.run(Timer.java:505)
[2017-02-22 06:09:16,963] INFO - BinaryDataReceiverServiceComponent Binary Data Receiver server shutting down...
[2017-02-22 06:09:16,964] INFO - BinaryDataReceiver Stopping Binary Server..
[2017-02-22 06:09:17,531] WARN - AppDeployerServiceComponent Waiting for required OSGi services: org.wso2.carbon.application.deployer.synapse.service.SynapseAppDeployerService

I was running Java 17 SDK and got this same problem. Solved this by running the WSO2 script with Java 11 SDK instead.
You can either :
Change your JAVA_HOME variable value
Create a new environment variable pointing to Java 11 SDK and replace recursively inside the WSO2 directory JAVA_HOME with the new environment variable you have created

This is because port 5672 is occupied at the time when the API Manager server starts up. You can have 2 options I can think of to proceed with,
Change the default port offset.
You can either start the API manager server with -DportOffset=[offset] (ex- -DportOffset=1) or change the value in /repository/conf to a value other than 0 and start the server.
Stop the existing process of already occupied server
Without worrying about port offset, you can run the API Manager server on 5672 port for AMQP transport.
Search the process of occupied port (5672 in this case)
netstat -nlp|grep 5672
Output should looks like something below
tcp 0 0 0.0.0.0:5672 0.0.0.0:* LISTEN 6187/java
Kill the process
kill -9 [Process_ID]
(here, 6187)
Then start the server and you won't see the exception anymore.

I was trying from long time. RMQ was running in my system.
Got to C:\Program Files (x86)\RabbitMQ Server\rabbitmq_server-3.3.4\sbin and run
rabbitmq-service.bat stop

Port 5672 is needed for API Manager, from your exception trace, that port is occupied by another process.
Normally RabbitMQ uses 5672, if that's the case you have to shut down that process. If you have another API Manager running on the physical node, then you have to offset the port with -DportOffset=1

There's a problem with your port 5672,this port is already in use by some other process. So shutdown your wso2 process by ps -ef|grep wso2 and then kill -9 .
Then change your port by following this link and start wso2 api manager again.
https://docs.wso2.com/display/AM200/Changing+the+Default+Ports+with+Offset

As Tanvi and Abimaran said, Port 5672 is used for queuing. It's very common to get this error when configuring two nodes in one machine for trying cluster. If this port has been used by another application, and you can't shut that application down, then you can change
connectionfactory.TopicConnectionFactory = amqp://admin:admin#clientid/carbon?brokerlist='tcp://localhost:5672'
connectionfactory.QueueConnectionFactory = amqp://admin:admin#clientID/test?brokerlist='tcp://localhost:5672'
to another port for API manager in (/repository/config/jndi.properties).

You could change the default ports with an offset. So go to :
deployment.toml
and for example change the following config:
[server]
offset=1
so port no 5672 will be change to 5673.

Spark & SparkR Configuration on EC2 - Java Timeout

I'm trying to get Spark, and SparkR, running on a small EC2 cluster using the provided scripts and directions. Whenever I ask for an operation that would require computation on an RDD (e.g., collect(), reduce()), I get the error logged below. Workers do appear to startup correctly -- if I only parallelize, I see the workers running via the master's web ui.
The error I get is similar to the one in Intermittent Timeout Exception using Spark and I've been through all of the solutions there (modifying the conf file for URL's, disabling the firewall, etc.), no luck.
Here is the error log, thank you in advance for your help:
15/02/17 19:10:22 INFO executor.CoarseGrainedExecutorBackend: Registered signal handlers for [TERM, HUP, INT]
15/02/17 19:10:22 INFO spark.SecurityManager: Changing view acls to: root,-
15/02/17 19:10:22 INFO spark.SecurityManager: Changing modify acls to: root,-
15/02/17 19:10:22 INFO spark.SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users with view permissions: Set(root, -); users with modify permissions: Set(root, -)
15/02/17 19:10:23 INFO slf4j.Slf4jLogger: Slf4jLogger started
15/02/17 19:10:23 INFO Remoting: Starting remoting
15/02/17 19:10:23 INFO Remoting: Remoting started; listening on addresses :[akka.tcp://driverPropsFetcher#-.ec2.internal:60218]
15/02/17 19:10:23 INFO util.Utils: Successfully started service 'driverPropsFetcher' on port 60218.
15/02/17 19:10:53 ERROR security.UserGroupInformation: PriviledgedActionException as:- cause:java.util.concurrent.TimeoutException: Futures timed out after [30 seconds]
Exception in thread "main" java.lang.reflect.UndeclaredThrowableException: Unknown exception in doAs
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1134)
at org.apache.spark.deploy.SparkHadoopUtil.runAsSparkUser(SparkHadoopUtil.scala:59)
at org.apache.spark.executor.CoarseGrainedExecutorBackend$.run(CoarseGrainedExecutorBackend.scala:115)
at org.apache.spark.executor.CoarseGrainedExecutorBackend$.main(CoarseGrainedExecutorBackend.scala:161)
at org.apache.spark.executor.CoarseGrainedExecutorBackend.main(CoarseGrainedExecutorBackend.scala)
Caused by: java.security.PrivilegedActionException: java.util.concurrent.TimeoutException: Futures timed out after [30 seconds]
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:415)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1121)
... 4 more
Caused by: java.util.concurrent.TimeoutException: Futures timed out after [30 seconds]
at scala.concurrent.impl.Promise$DefaultPromise.ready(Promise.scala:219)
at scala.concurrent.impl.Promise$DefaultPromise.result(Promise.scala:223)
at scala.concurrent.Await$$anonfun$result$1.apply(package.scala:107)
at scala.concurrent.BlockContext$DefaultBlockContext$.blockOn(BlockContext.scala:53)
at scala.concurrent.Await$.result(package.scala:107)
at org.apache.spark.executor.CoarseGrainedExecutorBackend$$anonfun$run$1.apply$mcV$sp(CoarseGrainedExecutorBackend.scala:127)
at org.apache.spark.deploy.SparkHadoopUtil$$anon$1.run(SparkHadoopUtil.scala:60)
at org.apache.spark.deploy.SparkHadoopUtil$$anon$1.run(SparkHadoopUtil.scala:59)
... 7 more

This was ultimately resolved by a combination of
- Updates to SparkR, which have resolved a number of serialization issues.
- Recognizing that the Spark-ec2 scripts require that the control node and master node be the same machine.
and
- Replacing calls to parallelize() with distributing and then loading the data by hadoop.
I am writing an intro to SparkR for R programmers that I hope will help people with things like this in the future.

Resources