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Websphere works when run but fails when debug

I'm using Intellij with WebSphere 8. When I run from within IDE the server works normally. When I try to run it in debug mode however, it fails with the following error:
C:\IBM\WebSphere\AppServer\profiles\AppSrv01\bin\generated_websphere_server_start_script.cmd
C:\IBM\WebSphere\AppServer\java\bin\java -Dfile.encoding=windows-1252 -classpath "C:\IBM\WebSphere\AppServer\runtimes\com.ibm.ws.admin.client_8.5.0.jar;C:\IBM\WebSphere\AppServer\plugins\com.ibm.ws.security.crypto.jar;C:\Program Files (x86)\JetBrains\IntelliJ IDEA 13.1.3\plugins\webSphereIntegration\lib\webSphereIntegration.jar;C:\Program Files (x86)\JetBrains\IntelliJ IDEA 13.1.3\plugins\JavaEE\lib\javaee-impl.jar;C:\Program Files (x86)\JetBrains\IntelliJ IDEA 13.1.3\lib\openapi.jar;C:\Program Files (x86)\JetBrains\IntelliJ IDEA 13.1.3\plugins\webSphereIntegration\lib\specifics\webSphereClientImpl.jar" com.intellij.javaee.oss.process.JavaeeProcess 62847 com.intellij.j2ee.webSphere.agent.WebSphereAgent
Error: JDWP agent already loaded - please check java command line options
[2014-08-11 01:58:59,248] Artifact x.ear: Server is not connected. Deploy is not available.
JVMJ9TI064E Agent initialization function Agent_OnLoad failed for library jdwp, return code -1
Detected server admin port: 8880
JVMJ9VM015W Initialization error for library j9jvmti26(-3): JVMJ9VM009E J9VMDllMain failed
Detected server http port: 9080
Disconnected from server
I tried almost everything I have no idea what the problem is. I did google it for several hours with no luck.
Do anyone know what this all is about and how can it be fixed?
Here is my server configuration:

Solution 1
unchecked the Pass environment variables check box and restart the server in debug mode. it should work properly.
Run --> Edit Configuration --> websphere server --> Startup/Conections tab
select debug, you will see the Pass environment variables check box. it need to be unchecked for debug to work.
Solution 2
if debug mode of websphere is working in eclipse and not working in intellij that reason i found out is debugging serverice on the websphere is already started and intellij is again trying to start the debggin service. so stop the service from websphere console (Servers > Server Types > WebSphere application servers > [serverName] > Debugging Service) and all the default configurations in intellij should work.

I had the same problem. Finally I figure it out. I hope this solution helps. I'm using Intellij idea 2019.1.3.. and WebSphere 8.5.5.13
check WebSphere start server script find debug env variable name (in my script (WebSphere\AppServer\bin\startServer.bat)
WAS_DEBUG)
add same debug option name to intelliJ IDEA
run- debug configuration environment tab.
Since default env variable is debug and cannot be overridden
check pass env variables
add WAS_DEBUG option as I did
or you can update WAS_DEBUG as DEBUG (same as default in IntelliJ) in server startup.bat script.
Both should work.

Pretty old, but i was able to experience too!
They will try to fix this now in: https://youtrack.jetbrains.com/issue/IDEA-193580

firstly, sorry if the translation is not good, I am Brazilian and I would like to share the solution I made.
First: Locate the file "startServer.bat in "WebSphere\AppServer\bin" and open it with any text editor.
Second: Search for the second incidence of the word "WAS_DEBUG" and replace it with "DEBUG", as shown in the image...
Third: In Intellij, go to the server settings and in the "Startup/Connection" tab, select debug.
Fourth: Now uncheck the "use default" checkbox in "Startup script" and point to the location of the "startServer.bat" file in the webSphere directory.
Fifth: Right on the left side of the checkbox, there is an option to enter a parameter. Click and a "Program Arguments" field will appear. Enter the server name, in my case it was "server1".
Okay, now just test
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Debugging JNLP started application

I created a Java desktop-application (using Swing) and am now trying to make it work by starting it from the net using JNLP. The application works fine when I start it from the terminal, but as soon as I launch it from JNLP, it does not close. I have to manually kill the process every time.
I read that there might be a problem if my JFrame uses DISPOSE_ON_CLOSE as the default close-operation, but it doesn't. It uses DO_NOTHING_ON_CLOSE (implicitly). Also, I'm explicitly calling System.exit(0) after releasing all my objects:
f = new JFrame("Pacman");
f.addWindowListener(new WindowAdapter() {
#Override
public void windowClosing(WindowEvent e) {
// Terminate the Game-loop:
GameLoop.INSTANCE.stopLoop();
// Close the application:
System.exit(0);
}
});
I guess that there might be an exception thrown when I close the application, but I can't find a way to get the console-output (e.g. the Stack-Trace) of a running application started with JNLP. Here's what I tried:
Start javaws with the debugging parameters and connect with jconsole (works but I can't find any exception- or console-ouput).
Start javaws with the debugging parameters and attach IntelliJ debugger to it (also works but does not give me any output)
So, how can I start the application with JNLP and get the output (written to the default out- and error-streams), as if I would do with a normal desktop application?

Solution #1 - Enable Java Console, and look for exceptions.
You can do it via Java Control Panel. Switch to Advanced tab, and in the Java Console make sure Show console is selected.
Then, run your application and monitor the console for exceptions. Fix the exception.
Solution #2 - Debug your running application (properly).
Start the Web Start app like this (for Java 1.6 and newer):
javaws -verbose -J-Xdebug -J-Xnoagent -J-Xrunjdwp:transport=dt_socket,server=n,suspend=y,address=8123 http://myserver.com/path/to/myapp.jnlp
If using earlier java versions (1.4.2, 1.5) set the environment variable, like this:
set JAVAWS_VM_ARGS="-Xdebug -Xnoagent -Xrunjdwp:transport=dt_socket,server=n,suspend=y,address=8123"
and run the app via:
javaws http://myserver.com/path/to/myapp.jnlp
When the app runs:
Attach a debugger (Eclipse will do - use Run => Debug Configurations => Remote Java Application, and in Connection Properties panel enter the port passed in the parameters to javaws (in this case: 8123).
Set a breakpoint inside your windowClosing method.
Try to close your application - Eclipse should break the execution on your breakpoint
Step into the GameLoop.INSTANCE.stopLoop() method to see where/when it hangs.
Don't expect to see a solutions in the console, just step through the code with a debugger - if the application hangs, it will show you where.

There are times when even the console doesn't show anything, for example when there is a problem with the TLS/SSL handshake (i.e. a close_notify or handshake_failure). In these cases you need to do the following:
Enable the Java logs and tracing in the Java Control Panel > Advanced.
Enable parameters for debugging Java & launching the JNLP, there are two ways you can do it:
2.a. Download the JNLP file and execute it from command line (the SET command is not required in this particular case).
set JAVA_TOOL_OPTIONS=-Djavax.net.debug=all
javaws -wait jnlp.jnlp
2.b. Add arguments (i.e. -Djavax.net.debug=all) for the JVM in the Java Control Panel > Java > View (this is not required in this particular), and launch the JNLP file from browser:
The logs and traces are located in the log directory from the Java Deployment Home from where I paste these locations:
a. Windows XP: %HOME%\Application Data\Sun\Java\Deployment
b. Windows 7/Vista: %APPDATA%\..\LocalLow\Sun\Java\Deployment
c. Linux/Solaris: %HOME%/.java/deployment

This answer is an alternative to npe answer to enable the remote debug (Windows).
Go to Control Panel;
Click on Java, to open Java Control Panel;
Inside of Java Control Panel, go to Java tab, and click "View";
This will open a window with installed java versions. On runtime parameters put "-Xdebug -Xrunjdwp:transport=dt_socket,address=8123,server=y,suspend=n" (if you want to debug when application is starting, change to "suspend" to "y", that will make the application stop until an editor connect remotely);
Afer that, configure you editor to debug remotely to the configured port (localhost:8123 in this case).

Eclipse : Failed to connect to remote VM. Connection refused. [duplicate]

This question already has answers here:
Eclipse Error: "Failed to connect to remote VM"
(26 answers)
Closed 9 years ago.
When ever i tried to launch my eclipse debug(for server side code) i'm getting the following error Failed to connect to remote VM. Connection refused.
What's the problem may be? I already tried with most of the solutions out in the web but none of that solved my issue. Could any one can assist me to fix this? Advance thanks..

when you have Failed to connect to remote VM Connection refused error, restart your eclipse

Which server are you using?
Like already said:
In your debug configuration you'll have to define the right port of your server (GF:9009 / Tomcat:8000)
You'll have to set the JVM property of the server to debug
For Glassfish:
Log in to admin-console > Configurations > server-config > JVM-Settings > check DEBUG checkbox > restart server
For Tomcat:
create file debug.bat/.sh (depending on your OS) in %TOMCAT_HOME%/bin directory and write
set JPDA_ADDRESS=8000
set JPDA_TRANSPORT=dt_socket
catalina.bat jpda start
in it.
After you've created this file start server by executing debug.bat/.sh.
Now you should be able to debug remotely in Eclipse after you set the necessary properties in your debug configuration.
Hope this helped! Have Fun!
EDIT
If you're running tomcat in a Win environment as a service you don't have a catalina.bat file in the bin-directory of your tomcat installation.
To set your server into debug-mode please try the following:
Run the Configuration option in Windows Menu or run %catalina_home%/bin/tomcat6w.exe
In Java tab, add this line to Java:
options:-Xrunjdwp:transport=dt_socket,address=8000,server=y,suspend=n

Sometimes the port which you are trying to access, gets occupied and won't be released.
Try some tools to find whether the port is in use or not.
I also faced the same issue. I tried giving different port numbers but unfortunately it didn't work. I tried restarting the system (not the application server), and it worked :)

I faced the same issue. But i resolved it by changing my port numbers to different one.

The port number in the Eclipse configuration and the port number of
your application might not be the same.
You might not have been started your application with the right
parameters.
Those are the simple problems when I have faced "Connection refused" error.

As suat said, most of the time the connection refused is due to the fact that the port you set up is in use or there is a difference between the port number in your remote application debugging configuration in Eclipse and the port number used in the address attribute in
-Xrunjdwp:transport=dt_socket,address=1044,server=y,suspend=n.
Check those things. Thanks!

If you need to debug an application working on Tomcat, make sure that your Tomcat-folder/bin/startup.bat (if using windows) contains the following lines:
set JPDA_TRANSPORT="dt_socket"
set JPDA_ADDRESS=8000
call "%EXECUTABLE%" jpda start %CMD_LINE_ARGS%

I ran into this problem debugging play framework version 2.x, turned out the server hadn't been started even though the play debug run command was issued. After a first request to the webserver which caused the play framework to really start the application at port 9000, I was able to connect properly to the debug port 9999 from eclipse.
[info] play - Application started (Dev)
The text above was shown in the console when the message above appeared, indicating why eclipse couldn't connect before first http request.

Cannot run project from IntelliJ IDEA because of jdwp error

I have a project in IntelliJ IDEA I want to run locally. When I click its debug button it says:
ERROR: Cannot load this JVM TI agent twice, check your java command line for duplicate jdwp options.
Disconnected from server
Error occurred during initialization of VM
agent library failed to init: jdwp
When I click the run button it works. What is the matter?

This is probably too late to help you, but maybe it will help somebody else. The answer is based on a support forum posting by Aleksei Sosnovski.
This can happen when your JAVA_OPTS contains two -Xrunjdwp arguments. E.g., one of these arguments might come from the server start script invoked by IntelliJ to start the container, and another may be added by IntelliJ itself. You can check by looking at JAVA_OPTS in the log when launching the container without debug. If you see an -Xrunjdwp argument, just find where it is set in the container startup script, and remove it.

I guess you already are debugging the server app? In this case it's not possible to connect another instance of debugger.

Most likely the problem happens because you have specified the debugging options in the "VM parameters" field of your run configuration. Everything will work if you remove them.

I had the same problem in my case -Xrunjdwp was set twice: one in the IDEA debug configuration and again in the system variables in CATAALINA_OPTS.
once I removed it from system variables (inside the IDEA it is read only) problem was fixed

Thanks for the tips, it helped me work out the problem too. Mine was due to having
set DEBUG_OPTS=-agentlib:jdwp=transport=dt_socket,server=y,suspend=n,address=5005
In my catalina.bat

check server.xml if you have jvmEntries get rid of that entry from server.xml
<!-- <jvmEntries xmi:id="JavaVirtualMachine_1" classpath="" bootClasspath="" verboseModeClass="false" verboseModeGarbageCollection="false" verboseModeJNI="false" runHProf="false" hprofArguments="" debugMode="false" debugArgs="-Djava.compiler=NONE -Xdebug -Xnoagent -Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=7777" genericJvmArguments="">
Open admin console (http://localhost:9060/ibm/console/login.do)
Application servers > server1 > Debugging service
un-check Enable service at server startup if checked restart server.

On Intellij uncheck the 'Pass environment variables' box in Run/Debug configuration

Remote debugging using Eclipse - How to set breakpoints?

I asked this question about how to debug server side applications and I think I was looking for Java remote Debugging.
I have configured my server side startup script:
JAVA_OPTS="-Xmx2G -server -Xdebug -Xnoagent -Xrunjdwp:transport=dt_socket,address=1044,server=y,suspend=n"
By this, I assume the remote java app should be available on localhost:1044 (try it first using localhost)
But, what do I do next? I have configured the debug options to the class to be debugged via Run-->Debug Configurations. But it asks me to click Debug. But my class does not have a main() method.
Say, I want to debug getValue() in Methods.java, now getValue() is invoked from a client (via tcp).
So, how do I attach the java process to eclipse remote debugger when that method is invoked? Am I missing out on something basic about remote debugging?
UPDATE: (I can see this in my debug view, that means, the remote app is connected and in the debug mode, now how do I put a breakpoint in the file where I want)

Add the line below:
-agentlib:jdwp=transport=dt_socket,address=1044,server=y,suspend=n
to run eclipse in debug mode
For eclipse, click on debug as icon > debug configurations > add a new remote java application > change the project to the project that you need and port to 1044 and click on apply and debug.
Put your breakpoint and access the remote application