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[protege-discussion] Trying to Start Protege 3.3.1 server on Linux

Samuel Lee samlee at ncmir.ucsd.edu
Fri Jul 24 09:50:02 PDT 2009


I changed the port, and I changed the run_protege_server.sh file, and  
I get a similar error.

First, here's the run_protege_server.sh file:

#!/bin/sh

# ------------------- Where is Java? -------------------

# Change to the script' working directory, should be the Protege root  
directory
cd /usr/local/Protege_3.3.1/

DARWIN="false"

if [  -x /usr/bin/uname ]
then
   if [ "x`/usr/bin/uname`" = "xDarwin" ]
   then
     DARWIN="true"
   fi
fi

if [ ${DARWIN} = "true" ]
then
   JAVA_PATH=/usr/bin
else
   # Attempt to use the bundled VM if none specified
   if [ "$JAVA_HOME" = "" ]; then
         JAVA_HOME=.
   fi

   JAVA_PATH=$JAVA_HOME/jre/bin
fi

# Check if the Java VM can be found
if [ ! -e $JAVA_PATH/java ]; then
         echo Java VM could not be found. Please check your JAVA_HOME  
environment variable.
         exit 1
fi
# ------------------- Where is Java? -------------------


CLASSPATH 
= 
protege 
.jar:looks 
-2.1.3 
.jar:unicode_panel 
.jar:driver.jar:driver0.jar:driver1.jar:driver2.jar:plugins/ 
edu.stanford.smi.protegex.changes/change-model.jar
MAINCLASS=edu.stanford.smi.protege.server.Server


# ------------------- JVM Options -------------------
MAX_MEMORY=-Xmx200M
HEADLESS=-Djava.awt.headless=true
CODEBASE_URL=file:$PWD/protege.jar
CODEBASE=-Djava.rmi.server.codebase=$CODEBASE_URL
HOSTNAME_PARAM=-Djava.rmi.server.hostname=$HOSTNAME
TX="-Dtransaction.level=READ_COMMITTED"

OPTIONS="$MAX_MEMORY $HEADLESS $CODEBASE $HOSTNAME_PARAM ${TX}"

#
# Instrumentation debug, delay simulation,  etc
#
#DELAY="-Dserver.delay=80"
PORTOPTS="-Dprotege.rmi.server.port=5200 - 
Dprotege.rmi.registry.port=5100"
#DEBUG_OPT="-Xdebug - 
Xrunjdwp:transport=dt_socket,address=8000,server=y,suspend=n"

OPTIONS="${OPTIONS} ${DELAY} ${PORTOPTS} ${DEBUG_OPT}"
# ------------------- JVM Options -------------------

# ------------------- Cmd Options -------------------
# If you want automatic saving of the project,
# setup the number of seconds in SAVE_INTERVAL_VALUE
# SAVE_INTERVAL=-saveIntervalSec=120
# ------------------- Cmd Options -------------------

METAPROJECT=examples/server/metaproject.pprj

$JAVA_PATH/rmiregistry &
$JAVA_PATH/java -cp $CLASSPATH $TX $OPTIONS $MAINCLASS $SAVE_INTERVAL  
$METAPROJECT



Next, the error output.

java.rmi.server.ExportException: Port already in use: 1099; nested  
exception is:
	java.net.BindException: Address already in use
	at sun.rmi.transport.tcp.TCPTransport.listen(Unknown Source)
	at sun.rmi.transport.tcp.TCPTransport.exportObject(Unknown Source)
	at sun.rmi.transport.tcp.TCPEndpoint.exportObject(Unknown Source)
	at sun.rmi.transport.LiveRef.exportObject(Unknown Source)
	at sun.rmi.server.UnicastServerRef.exportObject(Unknown Source)
	at sun.rmi.registry.RegistryImpl.setup(Unknown Source)
	at sun.rmi.registry.RegistryImpl.<init>(Unknown Source)
	at sun.rmi.registry.RegistryImpl.main(Unknown Source)
Caused by: java.net.BindException: Address already in use
	at java.net.PlainSocketImpl.socketBind(Native Method)
	at java.net.PlainSocketImpl.bind(Unknown Source)
	at java.net.ServerSocket.bind(Unknown Source)
	at java.net.ServerSocket.<init>(Unknown Source)
	at java.net.ServerSocket.<init>(Unknown Source)
	at  
sun 
.rmi.transport.proxy.RMIDirectSocketFactory.createServerSocket(Unknown  
Source)
	at  
sun 
.rmi.transport.proxy.RMIMasterSocketFactory.createServerSocket(Unknown  
Source)
	at sun.rmi.transport.tcp.TCPEndpoint.newServerSocket(Unknown Source)
	... 8 more
CONFIG: fixed port=5200
CONFIG: local port: 5200
SEVERE: java.rmi.ConnectException: Connection refused to host:  
198.202.94.231; nested exception is:
	java.net.ConnectException: Connection refused
	at sun.rmi.transport.tcp.TCPEndpoint.newSocket(Unknown Source)
	at sun.rmi.transport.tcp.TCPChannel.createConnection(Unknown Source)
	at sun.rmi.transport.tcp.TCPChannel.newConnection(Unknown Source)
	at sun.rmi.server.UnicastRef.newCall(Unknown Source)
	at sun.rmi.registry.RegistryImpl_Stub.rebind(Unknown Source)
	at edu.stanford.smi.protege.server.Server.bindName(Unknown Source)
	at edu.stanford.smi.protege.server.Server.initialize(Unknown Source)
	at edu.stanford.smi.protege.server.Server.<init>(Unknown Source)
	at edu.stanford.smi.protege.server.Server.startServer(Unknown Source)
	at edu.stanford.smi.protege.server.Server.startServer(Unknown Source)
	at edu.stanford.smi.protege.server.Server.main(Unknown Source)
Caused by: java.net.ConnectException: Connection refused
	at java.net.PlainSocketImpl.socketConnect(Native Method)
	at java.net.PlainSocketImpl.doConnect(Unknown Source)
	at java.net.PlainSocketImpl.connectToAddress(Unknown Source)
	at java.net.PlainSocketImpl.connect(Unknown Source)
	at java.net.SocksSocketImpl.connect(Unknown Source)
	at java.net.Socket.connect(Unknown Source)
	at java.net.Socket.connect(Unknown Source)
	at java.net.Socket.<init>(Unknown Source)
	at java.net.Socket.<init>(Unknown Source)
	at  
edu 
.stanford 
.smi.protege.server.ServerRmiSocketFactory.createSocket(Unknown Source)
	... 11 more
  -- Server.bindName()
SEVERE: server startup failed -- java.rmi.ConnectException: Connection  
refused to host: 198.202.94.231; nested exception is:
	java.net.ConnectException: Connection refused
	at sun.rmi.transport.tcp.TCPEndpoint.newSocket(Unknown Source)
	at sun.rmi.transport.tcp.TCPChannel.createConnection(Unknown Source)
	at sun.rmi.transport.tcp.TCPChannel.newConnection(Unknown Source)
	at sun.rmi.server.UnicastRef.newCall(Unknown Source)
	at sun.rmi.registry.RegistryImpl_Stub.rebind(Unknown Source)
	at edu.stanford.smi.protege.server.Server.bindName(Unknown Source)
	at edu.stanford.smi.protege.server.Server.initialize(Unknown Source)
	at edu.stanford.smi.protege.server.Server.<init>(Unknown Source)
	at edu.stanford.smi.protege.server.Server.startServer(Unknown Source)
	at edu.stanford.smi.protege.server.Server.startServer(Unknown Source)
	at edu.stanford.smi.protege.server.Server.main(Unknown Source)
Caused by: java.net.ConnectException: Connection refused
	at java.net.PlainSocketImpl.socketConnect(Native Method)
	at java.net.PlainSocketImpl.doConnect(Unknown Source)
	at java.net.PlainSocketImpl.connectToAddress(Unknown Source)
	at java.net.PlainSocketImpl.connect(Unknown Source)
	at java.net.SocksSocketImpl.connect(Unknown Source)
	at java.net.Socket.connect(Unknown Source)
	at java.net.Socket.connect(Unknown Source)
	at java.net.Socket.<init>(Unknown Source)
	at java.net.Socket.<init>(Unknown Source)
	at  
edu 
.stanford 
.smi.protege.server.ServerRmiSocketFactory.createSocket(Unknown Source)
	... 11 more


Thanks,

Sam

On Jul 17, 2009, at 1:21 PM, Bhaskar Ghosh wrote:

> Hi Sam,
>
> Protege Server needs the RMI Registry to run. 1099 is the default  
> RMI port. The error message indicate that the port 1099 is already  
> in use. you can start RMI server on a different port (edit the  
> corresponding line inside the run_protege_server.sh file)
>
> thanks
> Bhaskar
>
> "Ignorance is Bliss... Knowledge never brings Peace!!!"
>
>
> From: Samuel Lee <samlee at ncmir.ucsd.edu>
> To: protege-discussion at mailman.stanford.edu
> Sent: Friday, 17 July, 2009 11:33:31 PM
> Subject: [protege-discussion] Trying to Start Protege 3.3.1 server  
> on Linux
>
> When trying to start the Protege Server 3.3.1, I'm getting the  
> following errors:
>
> Any ideas?
>
> Sam
>
>
> [root at protege33 Protege_3.3.1]# ./run_protege_server.sh
> java.rmi.server.ExportException: Port already in use: 1099; nested  
> exception is:
>     java.net.BindException: Address already in use
>     at sun.rmi.transport.tcp.TCPTransport.listen(TCPTransport.java: 
> 310)
>     at  
> sun.rmi.transport.tcp.TCPTransport.exportObject(TCPTransport.java:218)
>     at  
> sun.rmi.transport.tcp.TCPEndpoint.exportObject(TCPEndpoint.java:393)
>     at sun.rmi.transport.LiveRef.exportObject(LiveRef.java:129)
>     at  
> sun.rmi.server.UnicastServerRef.exportObject(UnicastServerRef.java: 
> 190)
>     at sun.rmi.registry.RegistryImpl.setup(RegistryImpl.java:92)
>     at sun.rmi.registry.RegistryImpl.<init>(RegistryImpl.java:78)
>     at sun.rmi.registry.RegistryImpl.main(RegistryImpl.java:322)
> Caused by: java.net.BindException: Address already in use
>     at java.net.PlainSocketImpl.socketBind(Native Method)
>     at java.net.PlainSocketImpl.bind(PlainSocketImpl.java:359)
>     at java.net.ServerSocket.bind(ServerSocket.java:319)
>     at java.net.ServerSocket.<init>(ServerSocket.java:185)
>     at java.net.ServerSocket.<init>(ServerSocket.java:97)
>     at  
> sun 
> .rmi 
> .transport 
> .proxy 
> .RMIDirectSocketFactory 
> .createServerSocket(RMIDirectSocketFactory.java:27)
>     at  
> sun 
> .rmi 
> .transport 
> .proxy 
> .RMIMasterSocketFactory 
> .createServerSocket(RMIMasterSocketFactory.java:333)
>     at  
> sun.rmi.transport.tcp.TCPEndpoint.newServerSocket(TCPEndpoint.java: 
> 649)
>     at sun.rmi.transport.tcp.TCPTransport.listen(TCPTransport.java: 
> 299)
>     ... 7 more
> CONFIG: Protege 3.3.1 Build 430, JVM 1.6.0_13-b03, memory=208M,  
> Linux, encoding=UTF-8, language=en, country=US
> CONFIG: Loaded plugin org.algernon - Algernon
> CONFIG: Loaded plugin edu.stanford.smi.protegex.owl - OWL Plugin
> CONFIG: Loaded plugin uk.ac.man.cs.mig.coode.owlindividualstab
> CONFIG: Loaded plugin uk.ac.man.cs.mig.coode.owldoc
> CONFIG: Loaded plugin edu.stanford.smi.protegex.rdf_backend - RDF  
> Backend
> CONFIG: Loaded plugin edu.stanford.smi.protegex.wordnet - WordNet Tab
> CONFIG: Loaded plugin edu.stanford.smi.protegex.datamaster -  
> DataMaster Tab
> CONFIG: Loaded plugin edu.stanford.smi.protegex.facets_tab
> CONFIG: Loaded plugin edu.stanford.smi.protegex.changes - Changes tab
> CONFIG: Loaded plugin ca.uvic.cs.chisel.jambalaya - Jambalaya
> CONFIG: Loaded plugin edu.stanford.smi.protegex.instance_tree
> CONFIG: Loaded plugin edu.stanford.smi.protegex.pal_tabs - PAL Tabs
> CONFIG: Loaded plugin edu.stanford.smi.protegex.ezpal - EZPal Tab
> CONFIG: Loaded plugin edu.stanford.smi.protegex.standard_extensions  
> - Graph Widget, Table Widget
> CONFIG: Loaded plugin edu.stanford.smi.protegex.chatPlugin
> CONFIG: Loaded plugin edu.stanford.smi.protege.collab -  
> Collaborative Protege
> CONFIG: Loaded plugin uk.ac.man.cs.mig.coode.protege.wizard - Basic  
> Wizards
> CONFIG: Loaded plugin uk.ac.man.cs.mig.coode.protege.wizard.owl -  
> OWL Wizards
> CONFIG: Loaded plugin edu.stanford.smi.protegex.xml_tab - XML Tab
> CONFIG: Loaded plugin uk.ac.man.cs.mig.coode.debugger
> CONFIG: Loaded plugin edu.stanford.smi.protegex.prompt - PROMPT Tab
> CONFIG: Loaded plugin edu.stanford.smi.protege.stringsearch - String  
> Search Tab
> CONFIG: Loaded plugin uk.ac.man.cs.mig.coode.owlviz
> CONFIG: Loaded plugin edu.stanford.smi.protegex.umls_tab - UMLS Tab
> CONFIG: Loaded plugin edu.stanford.smi.protege.script - Script Plugin
> CONFIG: Loaded plugin dfki.protege.ontoviz
> CONFIG: Loaded plugin uk.ac.man.cs.mig.coode.manchesterowlsyntaxeditor
> CONFIG: Loaded plugin uk.ac.iam.soton.akt.tgviztab - TGVizTab
> CONFIG: Loaded plugin se.liu.ida.JessTab - JessTab Plugin
> SEVERE: java.rmi.ConnectException: Connection refused to host:  
> 198.202.95.113; nested exception is:
>     java.net.ConnectException: Connection refused
>     at sun.rmi.transport.tcp.TCPEndpoint.newSocket(TCPEndpoint.java: 
> 601)
>     at  
> sun.rmi.transport.tcp.TCPChannel.createConnection(TCPChannel.java:198)
>     at  
> sun.rmi.transport.tcp.TCPChannel.newConnection(TCPChannel.java:184)
>     at sun.rmi.server.UnicastRef.newCall(UnicastRef.java:322)
>     at sun.rmi.registry.RegistryImpl_Stub.rebind(Unknown Source)
>     at edu.stanford.smi.protege.server.Server.bindName(Unknown Source)
>     at edu.stanford.smi.protege.server.Server.initialize(Unknown  
> Source)
>     at edu.stanford.smi.protege.server.Server.<init>(Unknown Source)
>     at edu.stanford.smi.protege.server.Server.startServer(Unknown  
> Source)
>     at edu.stanford.smi.protege.server.Server.startServer(Unknown  
> Source)
>     at edu.stanford.smi.protege.server.Server.main(Unknown Source)
> Caused by: java.net.ConnectException: Connection refused
>     at java.net.PlainSocketImpl.socketConnect(Native Method)
>     at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:333)
>     at  
> java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:195)
>     at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:182)
>     at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366)
>     at java.net.Socket.connect(Socket.java:519)
>     at java.net.Socket.connect(Socket.java:469)
>     at java.net.Socket.<init>(Socket.java:366)
>     at java.net.Socket.<init>(Socket.java:180)
>     at  
> edu 
> .stanford 
> .smi.protege.server.ServerRmiSocketFactory.createSocket(Unknown  
> Source)
>     at sun.rmi.transport.tcp.TCPEndpoint.newSocket(TCPEndpoint.java: 
> 595)
>     ... 10 more
> -- Server.bindName()
> SEVERE: server startup failed -- java.rmi.ConnectException:  
> Connection refused to host: 198.202.95.113; nested exception is:
>     java.net.ConnectException: Connection refused
>     at sun.rmi.transport.tcp.TCPEndpoint.newSocket(TCPEndpoint.java: 
> 601)
>     at  
> sun.rmi.transport.tcp.TCPChannel.createConnection(TCPChannel.java:198)
>     at  
> sun.rmi.transport.tcp.TCPChannel.newConnection(TCPChannel.java:184)
>     at sun.rmi.server.UnicastRef.newCall(UnicastRef.java:322)
>     at sun.rmi.registry.RegistryImpl_Stub.rebind(Unknown Source)
>     at edu.stanford.smi.protege.server.Server.bindName(Unknown Source)
>     at edu.stanford.smi.protege.server.Server.initialize(Unknown  
> Source)
>     at edu.stanford.smi.protege.server.Server.<init>(Unknown Source)
>     at edu.stanford.smi.protege.server.Server.startServer(Unknown  
> Source)
>     at edu.stanford.smi.protege.server.Server.startServer(Unknown  
> Source)
>     at edu.stanford.smi.protege.server.Server.main(Unknown Source)
> Caused by: java.net.ConnectException: Connection refused
>     at java.net.PlainSocketImpl.socketConnect(Native Method)
>     at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:333)
>     at  
> java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:195)
>     at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:182)
>     at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366)
>     at java.net.Socket.connect(Socket.java:519)
>     at java.net.Socket.connect(Socket.java:469)
>     at java.net.Socket.<init>(Socket.java:366)
>     at java.net.Socket.<init>(Socket.java:180)
>     at  
> edu 
> .stanford 
> .smi.protege.server.ServerRmiSocketFactory.createSocket(Unknown  
> Source)
>     at sun.rmi.transport.tcp.TCPEndpoint.newSocket(TCPEndpoint.java: 
> 595)
>     ... 10 more
>
>
>
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