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is there any way to show jmap dump progress in executing

Is there any possible way to show jmap dump progress? I am using this command to dump stack:
/opt/dabai/tools/jdk1.8.0_211/bin/jmap -F -dump:format=b,file=my.dump 5307
the output is:
[root#log001 ~]# /opt/dabai/tools/jdk1.8.0_211/bin/jmap -F -dump:format=b,file=my.dump 5307
Attaching to process ID 5307, please wait...
Debugger attached successfully.
Server compiler detected.
JVM version is 25.211-b12
Dumping heap to my.dump ...
stay dump more than 5 minites,how to known what happen in dump progress?should I waiting?

Extracting information from a a java core dump with jmap(1.5)

Long story short, some coworkers are running a pretty old setup(oc4j jdk1.5.6 in x86_64) with an application which happens to be mission critical. They recently have tried to deploy a new version of the application, but as soon as they do the java process(es) throw a core dump and die.
The problem is, the core dumps seem to be fine, gdb can open them, but jmap and other tools refuse to process them:
# /usr/java/jdk1.5.0_06/bin/jmap /usr/java/jdk1.5.0_06/bin/java core
Attaching to core core from executable /usr/java/jdk1.5.0_06/bin/java, please wait...
Error attaching to core file: Can't attach to the core file
And newer versions throw a exception:
# jdk1.6.0_45/bin/jmap /usr/java/jdk1.5.0_06/bin/java core
Attaching to core core from executable /usr/java/jdk1.5.0_06/bin/java, please wait...
Exception in thread "main" java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at sun.tools.jmap.JMap.runTool(JMap.java:179)
at sun.tools.jmap.JMap.main(JMap.java:110)
Caused by: sun.jvm.hotspot.runtime.VMVersionMismatchException: Supported versions are 20.45-b01. Target VM is 1.5.0_06-b05
at sun.jvm.hotspot.runtime.VM.checkVMVersion(VM.java:224)
at sun.jvm.hotspot.runtime.VM.<init>(VM.java:287)
at sun.jvm.hotspot.runtime.VM.initialize(VM.java:357)
at sun.jvm.hotspot.bugspot.BugSpotAgent.setupVM(BugSpotAgent.java:594)
at sun.jvm.hotspot.bugspot.BugSpotAgent.go(BugSpotAgent.java:494)
at sun.jvm.hotspot.bugspot.BugSpotAgent.attach(BugSpotAgent.java:348)
at sun.jvm.hotspot.tools.Tool.start(Tool.java:169)
at sun.jvm.hotspot.tools.PMap.main(PMap.java:67)
... 6 more
gdb offers little information without symbols:
Reading symbols from /usr/java/jdk1.5.0_06/bin/java...(no debugging symbols found)...done.
[New Thread 9841]
[New Thread 31442]
[New Thread 31441]
...
Core was generated by `/usr/java/jdk1.5.0_06/bin/java -server -XX:+UseConcMarkSweepGC -XX:MaxHeapFreeR'.
Program terminated with signal 6, Aborted.
#0 0x0000003bbf030285 in ?? ()
(gdb) bt
#0 0x0000003bbf030285 in ?? ()
#1 0x0000003bbf031d30 in ?? ()
#2 0x0000000000000000 in ?? ()
The only valuable information I've gathered from the core is that most threads
are blocked(I'm far from being a gdb guru):
35 Thread 10093 0x0000003bbfc0b1c0 in pthread_cond_timedwait##GLIBC_2.3.2 ()
from /lib64/libpthread.so.0
34 Thread 10097 0x0000003bbfc0b1c0 in pthread_cond_timedwait##GLIBC_2.3.2 ()
from /lib64/libpthread.so.0
33 Thread 10099 0x0000003bbfc0b1c0 in pthread_cond_timedwait##GLIBC_2.3.2 ()
from /lib64/libpthread.so.0
Besides, I don't know if it's really relevant. The app is almost always heavily loaded, and my bet is that there were some lock contention already but since it's another's team app my knowledge about it it's pretty shallow.
I guess this is a long shot, but is there something that we can do to get a java thread dump or something like that? Do Sun used to offer debuginfo of the jdk as I guess is avalaible now with openjdk?
Thanks in advance.
UPDATE: The other team has resolved the issue without getting info from the core dump, just by trial and error after successfully replicating the problem in a test system. I'm still intrigued about the thing: how to debug an ancient java core dump which jmap can't process, it might be valuable info for the future, althought it seems is that there is no solution to that problem. Probably the JVM memory got corrupted and that's why jmap can't process it.

You can add the following JVM option when starting your application, that will allow you to run any command you specify if a fatal JVM error occurs:
-XX:OnError="<cmd args>"
For instance, you could run a command (or a script) that will perform certain actions like get a heap or thread dump.

Jmap and other JVM utilities are extremely version sensitive. From your error, it is self explanatory that hopefully the same jvm is not used in your case.
Java VisualVM can load core dumps directly. But you must use the same jvm that created the core file.
Resource Link:
https://stackoverflow.com/a/9981498/2293534
Suggestion#1:
kjkoster has given a solution here in this tutorial.
You need to use the jmap that comes with the JVM. From your error
message I gather that you are using a different version of jmap than
of the JVM.
Please check what JVMs are installed on your machine and ensure than
when you run jmap, you use the right version.
To solve such issues I never rely on path. Instead I set JAVA_HOME to
be the one that the JVM uses and then invoke both the JVM and jmap
like so:
Code:
$ JAVA_HOME=/usr/local/jdk1.6.0
$ export JAVA_HOME
$ ${JAVA_HOME}/bin/java ...
...
$ ${JAVA_HOME}/bin/jmap ...
Hope this helps.
Suggestion#2:
It is a full solution step by step is given by Chamilad. Hope it will clarify your root cause and solution procedure.
Almost every Java developer knows about jmap and jstack tools that come with the JDK. These provide functionality to extract heap and thread information of a running JVM instance. Easy.
What if there’s a running JVM that has produced a deadlock and you want to take a thread dump while the process is running? You go in and run the following.
jstack pid >> thread_dump.txt
Turns out the system doesn’t know what jstack is. You don’t panic, but you get a tiny sensation at the back of your head saying you’re not leaving early this Friday.
What has happened is the running JVM is based on a JRE and not a JDK. The JRE is a minimal runtime that doesn’t pack the monitoring and analysis tools that the JDK packs.
So what are our options here?
Stop the process. Download JDK, start the process again on top of
JDK and hope the deadlock happens again. Nope.
Start JVisualVM on your laptop and hope the process has JMX enabled. Nope.
tools.jar TO THE RESCUE!
Functionalities such as jstack are implemented in the tools.jar file which is packed inside <JDK_HOME>/lib folder. We can use this to invoke the JStack class and get a thread dump of the running process.
So we march on to download and extract the JDK, and then to run the following.
java -classpath <JDK_HOME>/lib/tools.jar sun.tools.jstack.JStack <pid> >> thread_dump.txt
..and come across the following error.
Exception in thread "main" java.lang.UnsatisfiedLinkError: no attach in java.library.path
at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1867)
at java.lang.Runtime.loadLibrary0(Runtime.java:870)
at java.lang.System.loadLibrary(System.java:1122)
at sun.tools.attach.LinuxVirtualMachine.<clinit>(LinuxVirtualMachine.java:342)
at sun.tools.attach.LinuxAttachProvider.attachVirtualMachine(LinuxAttachProvider.java:63)
at com.sun.tools.attach.VirtualMachine.attach(VirtualMachine.java:208)
at sun.tools.jstack.JStack.runThreadDump(JStack.java:163)
at sun.tools.jstack.JStack.main(JStack.java:116)
Darn it! Spoiled again!
How do we solve this? The above error is caused when the process can’t find libattach.so file which is related to the Dynamic Attach function related to JStack. Setting the following environment variable will help the JVM to find the libattach.so file.
export LD_LIBRARY_PATH=<JDK_HOME>/jre/lib/amd64/
Now let’s run JStack again, this time with results!
java -classpath <JDK_HOME>/lib/tools.jar sun.tools.jstack.JStack <pid> >> thread_dump.txt
Now that we have the thread dump, we move on to the heap dump. The tool we normally use is jmap but that too is not available on the JRE. So what? We can use the binary in the JDK’s bin directory right? right?
root#snowflake1 latest]# <JDK_HOME>/bin/jmap -heap <pid>
Attaching to process ID <pid>, please wait…
Error attaching to process: sun.jvm.hotspot.runtime.VMVersionMismatchException: Supported versions are 25.102-b14. Target VM is 25.91-b14
sun.jvm.hotspot.debugger.DebuggerException: sun.jvm.hotspot.runtime.VMVersionMismatchException: Supported versions are 25.102-b14. Target VM is 25.91-b14
at sun.jvm.hotspot.HotSpotAgent.setupVM(HotSpotAgent.java:435)
at sun.jvm.hotspot.HotSpotAgent.go(HotSpotAgent.java:305)
at sun.jvm.hotspot.HotSpotAgent.attach(HotSpotAgent.java:140)
at sun.jvm.hotspot.tools.Tool.start(Tool.java:185)
at sun.jvm.hotspot.tools.Tool.execute(Tool.java:118)
at sun.jvm.hotspot.tools.HeapSummary.main(HeapSummary.java:49)
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 sun.tools.jmap.JMap.runTool(JMap.java:201)
at sun.tools.jmap.JMap.main(JMap.java:130)
Caused by: sun.jvm.hotspot.runtime.VMVersionMismatchException: Supported versions are 25.102-b14. Target VM is 25.91-b14
at sun.jvm.hotspot.runtime.VM.checkVMVersion(VM.java:227)
at sun.jvm.hotspot.runtime.VM.<init>(VM.java:294)
at sun.jvm.hotspot.runtime.VM.initialize(VM.java:370)
at sun.jvm.hotspot.HotSpotAgent.setupVM(HotSpotAgent.java:431)
… 11 more
Nope! Unless you match the JDK version with the exact version the JRE is at you get the above issue (which is pretty self-explanatory). So we download the JDK of the JRE of on top our process is running and run jmap again.
<JDK_HOME>/bin/jmap -dump:file=heap_dump.hprof <pid>
Resource Link:
Extracting memory and thread dumps from a running JRE based JVM

jmap is not going to help you debug a core dump. The JVM dumps core when either it has a bug or you have JNI code with a problem. Organizations with mission-critical applications should, sadly, see upgrading from unsupported versions of the JVM as mission-critical, or be prepared to pay Oracle a fortune for help.

Error while starting GoldFish server: Ubuntu 13.10

I consulted here and here but could not get my problem solved.
When I type this on terminal /opt/glassfish4/glassfish/bin/asadmin start, I get the following result:
Remote server does not listen for requests on [localhost:4848]. Is the server up?
Unable to get remote commands.
Closest matching local command(s):
restart-domain
restart-local-instance
start-database
start-domain
start-local-instance
Command start failed.
Similarly, when I type this /opt/glassfish4/glassfish/bin/asadmin --port 5656 start-domain, I get
java.io.IOException: Couldn't get lock for /opt/glassfish4/glassfish/domains/domain1/logs/server.log
at java.util.logging.FileHandler.openFiles(FileHandler.java:389)
at java.util.logging.FileHandler.<init>(FileHandler.java:287)
at com.sun.enterprise.admin.launcher.GFLauncherLogger.addLogFileHandler(GFLauncherLogger.java:98)
at com.sun.enterprise.admin.launcher.GFLauncher.setup(GFLauncher.java:191)
at com.sun.enterprise.admin.servermgmt.cli.StartDomainCommand.createLauncher(StartDomainCommand.java:220)
at com.sun.enterprise.admin.servermgmt.cli.StartDomainCommand.executeCommand(StartDomainCommand.java:117)
at com.sun.enterprise.admin.cli.CLICommand.execute(CLICommand.java:321)
at com.sun.enterprise.admin.cli.AdminMain.executeCommand(AdminMain.java:360)
at com.sun.enterprise.admin.cli.AdminMain.doMain(AdminMain.java:298)
at org.glassfish.admin.cli.AsadminMain.main(AsadminMain.java:56)
Waiting for domain1 to start .Error starting domain domain1.
The server exited prematurely with exit code 1.
Before it died, it produced the following output:
Launching GlassFish on Felix platform
Exception in thread "main" java.lang.RuntimeException: the domain directory is not writable.
at com.sun.enterprise.glassfish.bootstrap.MainHelper.verifyDomainRoot(MainHelper.java:244)
at com.sun.enterprise.glassfish.bootstrap.MainHelper.findInstanceRoot(MainHelper.java:347)
at com.sun.enterprise.glassfish.bootstrap.GlassFishMain.main(GlassFishMain.java:78)
at com.sun.enterprise.glassfish.bootstrap.ASMain.main(ASMain.java:54)
Command start-domain failed.
I sense there is something problem in path /opt/glassfish4/glassfish/bin/asadmin. I am working on my first JSF web application and cannot run glassfish server. I am using Netbeans and ubuntu 13.10.
Can anyone show me the way?
Thank you!

The error messages
java.io.IOException: Couldn't get lock for
/opt/glassfish4/glassfish/domains/domain1/logs/server.log
and
Exception in thread "main" java.lang.RuntimeException: the domain
directory is not writable.
indicate that the user account you use to start the server doesn't have write permissions in your Glassfish domain folder.
To solve the problem either change the permissions or start the asadmin command with a user who has sufficient permissions.
If this doesn't solve the problem, there may be another process which has a lock on your server.log file, but I guess you would have noticed that. To make sure you can run
lsof /opt/glassfish4/glassfish/domains/domain1/logs/server.log
to see if any process is using the file.
See also:
Failed to start glassfish server because Couldn't get lock for /opt/glassfishv3/glassfish/domains/domain1/logs/server.log

How does jstack -F affect a running Java process?

I am trying to diagnose a problem where a Java web application I'm using (Jenkins) becomes unresponsive. If I run jstack without the -F flag it doesn't give me anything, but if I put the flag in to force a thread dump not only do I get a result, but the application starts responding and goes on as if nothing had happened until it eventually stops responding again.
What does jstack -F flag do that would affect a running JVM and cause an unresponsive application to start responding again?

You can see the source to jstack here. The -F argument changes how jstack connects to the jvm. With -F (or -m) JStack connects to the jvm using the java debugger interface. If a pid is specified, JStack connects with the SA PID Attaching Connector which says,
The process to be debugged need not have been started in debug
mode(ie, with -agentlib:jdwp or -Xrunjdwp). It is permissable for the
process to be hung.
I don't know why it would cause an unresponsive application to start responding again, but the link above also says,
The process is suspended when this connector attaches and resumed when
this connector detaches.
This may have an effect.

jstack -F -l pid is similarly to (assume working dir is JAVA_HOME)
bin/java -Dsun.jvm.hotspot.debugger.useWindbgDebugger -Dsun.jvm.hotspot.debugger.useProcDebugger -cp lib/sa-jdi.jar;lib/tools.jar sun.tools.jstack.JStack -F -l pid
and in the sun.tools.jstack.JStack code
if (arg.equals("-F")) {
useSA = true;
}
.....
// now execute using the SA JStack tool or the built-in thread dumper
if (useSA) {
// parameters (<pid> or <exe> <core>
...
runJStackTool(mixed, locks, params);
} else {
// pass -l to thread dump operation to get extra lock info
String pid = args[optionCount];
...
runThreadDump(pid, params);
}
and since -F is passed in, runJStackTool is called to load sun.jvm.hotspot.tools.JStack, it have same effect of invoking directly
bin\java -Dsun.jvm.hotspot.debugger.useWindbgDebugger -Dsun.jvm.hotspot.debugger.useProcDebugger -cp lib/sa-jdi.jar;lib/tools.jar sun.jvm.hotspot.tools.JStack pid
and sun.jvm.hotspot.tools.JStack will call sun.jvm.hotspot.bugspot.BugSpotAgent attach -> go ->setupVM method
Maybe below code is the magic
jvmdi = new ServiceabilityAgentJVMDIModule(debugger, saLibNames);
if (jvmdi.canAttach()) {
jvmdi.attach();
jvmdi.setCommandTimeout(6000);
debugPrintln("Attached to Serviceability Agent's JVMDI module.");
// Jog VM to suspended point with JVMDI module
resume();
suspendJava();
suspend();
debugPrintln("Suspended all Java threads.");
}
it will suspend all Java threads in the target process. if your application is hang for thread starvation, the suspend method call may relax them.

How to automatically get thread dumps from tomcat

We had some issues of thread pile ups with production tomcat server so I wanted to setup some cron to to periodically check thread dumps and send alert email if something is wrong. To do this we need to take thread dumps in file from shell script but I am unable to do that. From shell I can issue KILL -3 <PID> at periodic intervals but the problem is that dump goes to catalina.out which contains GBs of data because of which pulling out only thread dump is painful process. Some discussion threads suggested usage of "jstack" and redirect output to a file but that also is not working and giving this error:
-bash-3.2# java -version
java version "1.6.0_26"
Java(TM) SE Runtime Environment (build 1.6.0_26-b03)
Java HotSpot(TM) 64-Bit Server VM (build 20.1-b02, mixed mode)
-bash-3.2# uname -a
Linux ip-10-130-225-20 2.6.16.33-xenU #2 SMP Wed Aug 15 17:27:36 SAST 2007 x86_64 x86_64 x86_64 GNU/Linux
-bash-3.2# sudo /usr/java/jdk1.6.0_24/bin/jstack -F 15668
Attaching to process ID 15668, please wait...
Debugger attached successfully.
Server compiler detected.
JVM version is 19.1-b02
Deadlock Detection:
No deadlocks found.
Thread 8183: (state = BLOCKED)
Error occurred during stack walking:
sun.jvm.hotspot.debugger.DebuggerException: sun.jvm.hotspot.debugger.DebuggerException: get_thread_regs failed for a lwp
at sun.jvm.hotspot.debugger.linux.LinuxDebuggerLocal$LinuxDebuggerLocalWorkerThread.execute(LinuxDebuggerLocal.java:152)
at sun.jvm.hotspot.debugger.linux.LinuxDebuggerLocal.getThreadIntegerRegisterSet(LinuxDebuggerLocal.java:466)
at sun.jvm.hotspot.debugger.linux.LinuxThread.getContext(LinuxThread.java:65)
at sun.jvm.hotspot.runtime.linux_amd64.LinuxAMD64JavaThreadPDAccess.getCurrentFrameGuess(LinuxAMD64JavaThreadPDAccess.java:92)
at sun.jvm.hotspot.runtime.JavaThread.getCurrentFrameGuess(JavaThread.java:256)
at sun.jvm.hotspot.runtime.JavaThread.getLastJavaVFrameDbg(JavaThread.java:218)
at sun.jvm.hotspot.tools.StackTrace.run(StackTrace.java:76)
at sun.jvm.hotspot.tools.StackTrace.run(StackTrace.java:45)
at sun.jvm.hotspot.tools.JStack.run(JStack.java:60)
at sun.jvm.hotspot.tools.Tool.start(Tool.java:221)
at sun.jvm.hotspot.tools.JStack.main(JStack.java:86)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at sun.tools.jstack.JStack.runJStackTool(JStack.java:118)
at sun.tools.jstack.JStack.main(JStack.java:84)
Caused by: sun.jvm.hotspot.debugger.DebuggerException: get_thread_regs failed for a lwp
at sun.jvm.hotspot.debugger.linux.LinuxDebuggerLocal.getThreadIntegerRegisterSet0(Native Method)
This bug seems to be open with java team.
Any other suggestion to intelligently take and analyze thread dumps? Or script to parse huge catalina.out and get just thread dumps out of it?

Checkout this article about scheduling thread dumps. I think it is exactly what you are trying to do.

Another option could be JMX - ThreadMXBean. This was discussed at SO question How do I create a thread dump via JMX?

One quick way I figured out was (mis)using javamelody. We use it to monitor various aspects of application and it also provides visual & usual ways to look at current threads so I wrote small shell script to hit "http://IP:PORT/SERVICE/monitoring?part=threadsDump" every minute and dump response in a file. If response contains any blocked thread script will take thread dumps every 5 seconds. This helps upto some extent but when problem worsens and server stalls, javamelody also stop responding.