Re: [Myhadoop-users] Start Hadoop, ERROR security.UserGroupInformation: PriviledgedActionException

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Sorry,  the log corresponds to $HADOOP_HOME/bin/start-all.sh
I tried to run following command instead of  $HADOOP_HOME/bin/start-all.sh
$HADOOP_HOME/bin/hadoop name node
$HADOOP_HOME/bin/hadoop datanode

Here is the log:
myHadoop: Using HADOOP_HOME=/home/hpc-ruhua/hadoop-stack/hadoop-1.2.1
myHadoop: Using MH_SCRATCH_DIR=/tmp/hpc-ruhua/4178
myHadoop: Using JAVA_HOME=/usr
myHadoop: Generating Hadoop configuration in directory in /home/hpc-ruhua/hadoop/conf/hadoop-conf.4178...
myHadoop: Using directory /home/hpc-ruhua/hadoop/hdfs for persisting HDFS state...
myHadoop: Designating cn53 as master node (namenode, secondary namenode, and jobtracker)
myHadoop: The following nodes will be slaves (datanode, tasktracer):
cn53
cn54
cn55
cn56
Linking /home/hpc-ruhua/hadoop/hdfs/0 to /tmp/hpc-ruhua/4178/hdfs_data on cn53
Linking /home/hpc-ruhua/hadoop/hdfs/1 to /tmp/hpc-ruhua/4178/hdfs_data on cn54
Linking /home/hpc-ruhua/hadoop/hdfs/2 to /tmp/hpc-ruhua/4178/hdfs_data on cn55
Linking /home/hpc-ruhua/hadoop/hdfs/3 to /tmp/hpc-ruhua/4178/hdfs_data on cn56
15/01/16 15:35:14 INFO namenode.NameNode: STARTUP_MSG: 
/************************************************************
STARTUP_MSG: Starting NameNode
STARTUP_MSG:   host = cn53/192.168.100.53
STARTUP_MSG:   args = []
STARTUP_MSG:   version = 1.2.1
STARTUP_MSG:   build = https://svn.apache.org/repos/asf/hadoop/common/branches/branch-1.2 -r 1503152; compiled by 'mattf' on Mon Jul 22 15:23:09 PDT 2013
STARTUP_MSG:   java = 1.7.0_71
************************************************************/
15/01/16 15:35:14 INFO impl.MetricsConfig: loaded properties from hadoop-metrics2.properties
15/01/16 15:35:14 INFO impl.MetricsSourceAdapter: MBean for source MetricsSystem,sub=Stats registered.
15/01/16 15:35:14 INFO impl.MetricsSystemImpl: Scheduled snapshot period at 10 second(s).
15/01/16 15:35:14 INFO impl.MetricsSystemImpl: NameNode metrics system started
15/01/16 15:35:14 INFO impl.MetricsSourceAdapter: MBean for source ugi registered.
15/01/16 15:35:14 INFO impl.MetricsSourceAdapter: MBean for source jvm registered.
15/01/16 15:35:14 INFO impl.MetricsSourceAdapter: MBean for source NameNode registered.
15/01/16 15:35:14 INFO util.GSet: Computing capacity for map BlocksMap
15/01/16 15:35:14 INFO util.GSet: VM type       = 64-bit
15/01/16 15:35:14 INFO util.GSet: 2.0% max memory = 932184064
15/01/16 15:35:14 INFO util.GSet: capacity      = 2^21 = 2097152 entries
15/01/16 15:35:14 INFO util.GSet: recommended=2097152, actual=2097152
15/01/16 15:35:15 INFO namenode.FSNamesystem: fsOwner=hpc-ruhua
15/01/16 15:35:15 INFO namenode.FSNamesystem: supergroup=supergroup
15/01/16 15:35:15 INFO namenode.FSNamesystem: isPermissionEnabled=true
15/01/16 15:35:15 INFO namenode.FSNamesystem: dfs.block.invalidate.limit=100
15/01/16 15:35:15 INFO namenode.FSNamesystem: isAccessTokenEnabled=false accessKeyUpdateInterval=0 min(s), accessTokenLifetime=0 min(s)
15/01/16 15:35:15 INFO namenode.FSNamesystem: Registered FSNamesystemStateMBean and NameNodeMXBean
15/01/16 15:35:15 INFO namenode.FSEditLog: dfs.namenode.edits.toleration.length = 0
15/01/16 15:35:15 INFO namenode.NameNode: Caching file names occuring more than 10 times 
15/01/16 15:35:15 INFO common.Storage: Start loading image file /tmp/hpc-ruhua/4178/namenode_data/current/fsimage
15/01/16 15:35:15 INFO common.Storage: Number of files = 28
15/01/16 15:35:15 INFO common.Storage: Number of files under construction = 1
15/01/16 15:35:15 INFO common.Storage: Image file /tmp/hpc-ruhua/4178/namenode_data/current/fsimage of size 2996 bytes loaded in 0 seconds.
15/01/16 15:35:15 INFO namenode.FSEditLog: Start loading edits file /tmp/hpc-ruhua/4178/namenode_data/current/edits
15/01/16 15:35:15 INFO namenode.FSEditLog: Invalid opcode, reached end of edit log Number of transactions found: 32.  Bytes read: 2579
15/01/16 15:35:15 INFO namenode.FSEditLog: Start checking end of edit log (/tmp/hpc-ruhua/4178/namenode_data/current/edits) ...
15/01/16 15:35:15 INFO namenode.FSEditLog: Checked the bytes after the end of edit log (/tmp/hpc-ruhua/4178/namenode_data/current/edits):
15/01/16 15:35:15 INFO namenode.FSEditLog:   Padding position  = 2579 (-1 means padding not found)
15/01/16 15:35:15 INFO namenode.FSEditLog:   Edit log length   = 1048580
15/01/16 15:35:15 INFO namenode.FSEditLog:   Read length       = 2579
15/01/16 15:35:15 INFO namenode.FSEditLog:   Corruption length = 0
15/01/16 15:35:15 INFO namenode.FSEditLog:   Toleration length = 0 (= dfs.namenode.edits.toleration.length)
15/01/16 15:35:15 INFO namenode.FSEditLog: Summary: |---------- Read=2579 ----------|-- Corrupt=0 --|-- Pad=1046001 --|
15/01/16 15:35:15 INFO namenode.FSEditLog: Edits file /tmp/hpc-ruhua/4178/namenode_data/current/edits of size 1048580 edits # 32 loaded in 0 seconds.
15/01/16 15:35:15 INFO common.Storage: Image file /tmp/hpc-ruhua/4178/namenode_data/current/fsimage of size 3745 bytes saved in 0 seconds.
15/01/16 15:35:15 INFO namenode.FSEditLog: closing edit log: position=4, editlog=/tmp/hpc-ruhua/4178/namenode_data/current/edits
15/01/16 15:35:15 INFO namenode.FSEditLog: close success: truncate to 4, editlog=/tmp/hpc-ruhua/4178/namenode_data/current/edits
15/01/16 15:35:16 INFO namenode.NameCache: initialized with 0 entries 0 lookups
15/01/16 15:35:16 INFO namenode.FSNamesystem: Finished loading FSImage in 1162 msecs
15/01/16 15:35:16 INFO namenode.FSNamesystem: dfs.safemode.threshold.pct          = 0.9990000128746033
15/01/16 15:35:16 INFO namenode.FSNamesystem: dfs.namenode.safemode.min.datanodes = 0
15/01/16 15:35:16 INFO namenode.FSNamesystem: dfs.safemode.extension              = 30000
15/01/16 15:35:16 INFO namenode.FSNamesystem: Number of blocks excluded by safe block count: 0 total blocks: 0 and thus the safe blocks: 0
15/01/16 15:35:16 INFO namenode.FSNamesystem: Total number of blocks = 0
15/01/16 15:35:16 INFO namenode.FSNamesystem: Number of invalid blocks = 0
15/01/16 15:35:16 INFO namenode.FSNamesystem: Number of under-replicated blocks = 0
15/01/16 15:35:16 INFO namenode.FSNamesystem: Number of  over-replicated blocks = 0
15/01/16 15:35:16 INFO hdfs.StateChange: STATE* Safe mode termination scan for invalid, over- and under-replicated blocks completed in 7 msec
15/01/16 15:35:16 INFO hdfs.StateChange: STATE* Leaving safe mode after 1 secs
15/01/16 15:35:16 INFO hdfs.StateChange: STATE* Network topology has 0 racks and 0 datanodes
15/01/16 15:35:16 INFO hdfs.StateChange: STATE* UnderReplicatedBlocks has 0 blocks
15/01/16 15:35:16 INFO util.HostsFileReader: Refreshing hosts (include/exclude) list
15/01/16 15:35:16 INFO namenode.FSNamesystem: ReplicateQueue QueueProcessingStatistics: First cycle completed 0 blocks in 0 msec
15/01/16 15:35:16 INFO namenode.FSNamesystem: ReplicateQueue QueueProcessingStatistics: Queue flush completed 0 blocks in 0 msec processing time, 0 msec clock time, 1 cycles
15/01/16 15:35:16 INFO namenode.FSNamesystem: InvalidateQueue QueueProcessingStatistics: First cycle completed 0 blocks in 0 msec
15/01/16 15:35:16 INFO namenode.FSNamesystem: InvalidateQueue QueueProcessingStatistics: Queue flush completed 0 blocks in 0 msec processing time, 0 msec clock time, 1 cycles
15/01/16 15:35:16 INFO impl.MetricsSourceAdapter: MBean for source FSNamesystemMetrics registered.
15/01/16 15:35:16 INFO ipc.Server: Starting SocketReader
15/01/16 15:35:16 INFO impl.MetricsSourceAdapter: MBean for source RpcDetailedActivityForPort54310 registered.
15/01/16 15:35:16 INFO impl.MetricsSourceAdapter: MBean for source RpcActivityForPort54310 registered.
15/01/16 15:35:16 INFO namenode.NameNode: Namenode up at: cn53/192.168.100.53:54310
15/01/16 15:35:16 INFO mortbay.log: Logging to org.slf4j.impl.Log4jLoggerAdapter(org.mortbay.log) via org.mortbay.log.Slf4jLog
15/01/16 15:35:16 INFO http.HttpServer: Added global filtersafety (class=org.apache.hadoop.http.HttpServer$QuotingInputFilter)
15/01/16 15:35:16 INFO http.HttpServer: dfs.webhdfs.enabled = false
15/01/16 15:35:16 INFO http.HttpServer: Port returned by webServer.getConnectors()[0].getLocalPort() before open() is -1. Opening the listener on 50070
15/01/16 15:35:16 INFO http.HttpServer: listener.getLocalPort() returned 50070 webServer.getConnectors()[0].getLocalPort() returned 50070
15/01/16 15:35:16 INFO http.HttpServer: Jetty bound to port 50070
15/01/16 15:35:16 INFO mortbay.log: jetty-6.1.26
15/01/16 15:35:16 INFO mortbay.log: Started SelectChannelConnector@0.0.0.0:50070
15/01/16 15:35:16 INFO namenode.NameNode: Web-server up at: 0.0.0.0:50070
15/01/16 15:35:16 INFO ipc.Server: IPC Server Responder: starting
15/01/16 15:35:16 INFO ipc.Server: IPC Server listener on 54310: starting
15/01/16 15:35:16 INFO ipc.Server: IPC Server handler 0 on 54310: starting
15/01/16 15:35:16 INFO ipc.Server: IPC Server handler 1 on 54310: starting
15/01/16 15:35:16 INFO ipc.Server: IPC Server handler 2 on 54310: starting
15/01/16 15:35:16 INFO ipc.Server: IPC Server handler 3 on 54310: starting
15/01/16 15:35:16 INFO ipc.Server: IPC Server handler 4 on 54310: starting
15/01/16 15:35:16 INFO ipc.Server: IPC Server handler 5 on 54310: starting
15/01/16 15:35:16 INFO ipc.Server: IPC Server handler 6 on 54310: starting
15/01/16 15:35:16 INFO ipc.Server: IPC Server handler 8 on 54310: starting
15/01/16 15:35:16 INFO ipc.Server: IPC Server handler 7 on 54310: starting
15/01/16 15:35:16 INFO ipc.Server: IPC Server handler 9 on 54310: starting

Best.
Ruhua

On Jan 20, 2015, at 12:14 PM, Ruhua Jiang <ruh...@gm...> wrote:

> Hello 
> 
> I am trying to run Hadoop (1.2.1) on top of a HPC infrastructure using myHadoop(0.30).  The HPC uses SLURM. 
> First I tried the word counting example using non-persist mode, here is the script, I did some modification based on example code of Dr. Lockwood.  The result seems good. 
> 
> However, when I try to run the persist mode, there are some problems. We are using GPFS. Here is the script:
> #!/bin/bash
> ################################################################################
> #  slurm.sbatch - A sample submit script for SLURM that illustrates how to
> #    spin up a Hadoop cluster for a map/reduce task using myHadoop
> #
> #  Glenn K. Lockwood, San Diego Supercomputer Center             February 2014
> ################################################################################
> #SBATCH -p Westmere
> #SBATCH -n 4
> #SBATCH --ntasks-per-node=1
> #SBATCH -t 1:00:00
> 
> ### If these aren't already in your environment (e.g., .bashrc), you must define
> ### them.  We assume hadoop and myHadoop were installed in $HOME/hadoop-stack
> export HADOOP_HOME=$HOME/hadoop-stack/hadoop-1.2.1
> export PATH=$HADOOP_HOME/bin:$HOME/hadoop-stack/myhadoop-0.30/bin:$PATH:$PATH
> export JAVA_HOME=/usr
> 
> export HADOOP_CONF_DIR=$HOME/hadoop/conf/hadoop-conf.$SLURM_JOBID
> export MH_SCRATCH_DIR=/tmp/$USER/$SLURM_JOBID
> export MH_PERSIST_DIR=$HOME/hadoop/hdfs
> myhadoop-configure.sh -s $MH_SCRATCH_DIR -p $MH_PERSIST_DIR
> 
> if [ ! -f ./pg2701.txt ]; then
>   echo "*** Retrieving some sample input data"
>   wget 'http://www.gutenberg.org/cache/epub/2701/pg2701.txt'
> fi
> 
> ##$HADOOP_HOME/bin/start-all.sh
> $HADOOP_HOME/bin/hadoop namenode
> $HADOOP_HOME/bin/hadoop datanode
> $HADOOP_HOME/bin/hadoop dfs -mkdir data
> $HADOOP_HOME/bin/hadoop dfs -put ./pg2701.txt data/
> $HADOOP_HOME/bin/hadoop dfs -ls data
> $HADOOP_HOME/bin/hadoop jar $HADOOP_HOME/hadoop-examples-*.jar wordcount data wordcount-output
> $HADOOP_HOME/bin/hadoop dfs -ls wordcount-output
> $HADOOP_HOME/bin/hadoop dfs -get wordcount-output ./
> 
> $HADOOP_HOME/bin/stop-all.sh
> 
> myhadoop-cleanup.sh
> 
> 
> Here is the log:
> ===
> myHadoop: Using HADOOP_HOME=/home/hpc-ruhua/hadoop-stack/hadoop-1.2.1
> myHadoop: Using MH_SCRATCH_DIR=/tmp/hpc-ruhua/4128
> myHadoop: Using JAVA_HOME=/usr
> myHadoop: Generating Hadoop configuration in directory in /home/hpc-ruhua/hadoop/conf/hadoop-conf.4128...
> myHadoop: Using directory /home/hpc-ruhua/hadoop/hdfs for persisting HDFS state...
> myHadoop: Designating cn53 as master node (namenode, secondary namenode, and jobtracker)
> myHadoop: The following nodes will be slaves (datanode, tasktracer):
> cn53
> cn54
> cn55
> cn56
> Linking /home/hpc-ruhua/hadoop/hdfs/0 to /tmp/hpc-ruhua/4128/hdfs_data on cn53
> Linking /home/hpc-ruhua/hadoop/hdfs/1 to /tmp/hpc-ruhua/4128/hdfs_data on cn54
> Linking /home/hpc-ruhua/hadoop/hdfs/2 to /tmp/hpc-ruhua/4128/hdfs_data on cn55
> Warning: Permanently added 'cn55,192.168.100.55' (RSA) to the list of known hosts.
> Linking /home/hpc-ruhua/hadoop/hdfs/3 to /tmp/hpc-ruhua/4128/hdfs_data on cn56
> Warning: Permanently added 'cn56,192.168.100.56' (RSA) to the list of known hosts.
> starting namenode, logging to /tmp/hpc-ruhua/4128/logs/hadoop-hpc-ruhua-namenode-cn53.out
> cn53: starting datanode, logging to /tmp/hpc-ruhua/4128/logs/hadoop-hpc-ruhua-datanode-cn53.out
> cn54: starting datanode, logging to /tmp/hpc-ruhua/4128/logs/hadoop-hpc-ruhua-datanode-cn54.out
> cn55: starting datanode, logging to /tmp/hpc-ruhua/4128/logs/hadoop-hpc-ruhua-datanode-cn55.out
> cn56: starting datanode, logging to /tmp/hpc-ruhua/4128/logs/hadoop-hpc-ruhua-datanode-cn56.out
> cn53: starting secondarynamenode, logging to /tmp/hpc-ruhua/4128/logs/hadoop-hpc-ruhua-secondarynamenode-cn53.out
> starting jobtracker, logging to /tmp/hpc-ruhua/4128/logs/hadoop-hpc-ruhua-jobtracker-cn53.out
> cn53: starting tasktracker, logging to /tmp/hpc-ruhua/4128/logs/hadoop-hpc-ruhua-tasktracker-cn53.out
> cn56: starting tasktracker, logging to /tmp/hpc-ruhua/4128/logs/hadoop-hpc-ruhua-tasktracker-cn56.out
> cn55: starting tasktracker, logging to /tmp/hpc-ruhua/4128/logs/hadoop-hpc-ruhua-tasktracker-cn55.out
> cn54: starting tasktracker, logging to /tmp/hpc-ruhua/4128/logs/hadoop-hpc-ruhua-tasktracker-cn54.out
> mkdir: cannot create directory data: File exists
> put: Target data/pg2701.txt already exists
> Found 1 items
> -rw-r--r--   3 hpc-ruhua supergroup          0 2015-01-07 00:09 /user/hpc-ruhua/data/pg2701.txt
> 15/01/14 12:21:08 ERROR security.UserGroupInformation: PriviledgedActionException as:hpc-ruhua cause:org.apache.hadoop.ipc.RemoteException: org.apache.hadoop.mapred.JobTrackerNotYetInitializedException: JobTracker is not yet RUNNING
> 	at org.apache.hadoop.mapred.JobTracker.checkJobTrackerState(JobTracker.java:5199)
> 	at org.apache.hadoop.mapred.JobTracker.getNewJobId(JobTracker.java:3543)
> 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
> 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> 	at java.lang.reflect.Method.invoke(Method.java:606)
> 	at org.apache.hadoop.ipc.RPC$Server.call(RPC.java:587)
> 	at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:1432)
> 	at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:1428)
> 	at java.security.AccessController.doPrivileged(Native Method)
> 	at javax.security.auth.Subject.doAs(Subject.java:415)
> 	at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1190)
> 	at org.apache.hadoop.ipc.Server$Handler.run(Server.java:1426)
> 
> org.apache.hadoop.ipc.RemoteException: org.apache.hadoop.mapred.JobTrackerNotYetInitializedException: JobTracker is not yet RUNNING
> 	at org.apache.hadoop.mapred.JobTracker.checkJobTrackerState(JobTracker.java:5199)
> 	at org.apache.hadoop.mapred.JobTracker.getNewJobId(JobTracker.java:3543)
> 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
> 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> 	at java.lang.reflect.Method.invoke(Method.java:606)
> 	at org.apache.hadoop.ipc.RPC$Server.call(RPC.java:587)
> 	at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:1432)
> 	at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:1428)
> 	at java.security.AccessController.doPrivileged(Native Method)
> 	at javax.security.auth.Subject.doAs(Subject.java:415)
> 	at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1190)
> 	at org.apache.hadoop.ipc.Server$Handler.run(Server.java:1426)
> 
> 	at org.apache.hadoop.ipc.Client.call(Client.java:1113)
> 	at org.apache.hadoop.ipc.RPC$Invoker.invoke(RPC.java:229)
> 	at org.apache.hadoop.mapred.$Proxy2.getNewJobId(Unknown Source)
> 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
> 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> 	at java.lang.reflect.Method.invoke(Method.java:606)
> 	at org.apache.hadoop.io.retry.RetryInvocationHandler.invokeMethod(RetryInvocationHandler.java:85)
> 	at org.apache.hadoop.io.retry.RetryInvocationHandler.invoke(RetryInvocationHandler.java:62)
> 	at org.apache.hadoop.mapred.$Proxy2.getNewJobId(Unknown Source)
> 	at org.apache.hadoop.mapred.JobClient$2.run(JobClient.java:944)
> 	at org.apache.hadoop.mapred.JobClient$2.run(JobClient.java:936)
> 	at java.security.AccessController.doPrivileged(Native Method)
> 	at javax.security.auth.Subject.doAs(Subject.java:415)
> 	at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1190)
> 	at org.apache.hadoop.mapred.JobClient.submitJobInternal(JobClient.java:936)
> 	at org.apache.hadoop.mapreduce.Job.submit(Job.java:550)
> 	at org.apache.hadoop.mapreduce.Job.waitForCompletion(Job.java:580)
> 	at org.apache.hadoop.examples.WordCount.main(WordCount.java:82)
> 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
> 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> 	at java.lang.reflect.Method.invoke(Method.java:606)
> 	at org.apache.hadoop.util.ProgramDriver$ProgramDescription.invoke(ProgramDriver.java:68)
> 	at org.apache.hadoop.util.ProgramDriver.driver(ProgramDriver.java:139)
> 	at org.apache.hadoop.examples.ExampleDriver.main(ExampleDriver.java:64)
> 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
> 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> 	at java.lang.reflect.Method.invoke(Method.java:606)
> 	at org.apache.hadoop.util.RunJar.main(RunJar.java:160)
> ls: Cannot access wordcount-output: No such file or directory.
> get: null
> stopping jobtracker
> cn54: stopping tasktracker
> cn55: stopping tasktracker
> cn53: stopping tasktracker
> cn56: stopping tasktracker
> stopping namenode
> cn53: no datanode to stop
> cn54: no datanode to stop
> cn56: no datanode to stop
> cn55: no datanode to stop
> ===
> The error is “ERROR security.UserGroupInformation: PriviledgedActionException as:hpc-ruhua cause:org.apache.hadoop.ipc.RemoteException:” it says JobTracker is not yet running. 
> 
> Any idea about that? Thanks
> 
> Best,
> Ruhua Jiang
> Graduate Student at University of Connecticut
> HORNET Cluster Technical Support 