I follow this steps to run the Metamap Java API 2014 on Linux platform
(Main page from metamap)
After start Metamap server, I run some main class in Metamap JavaAPI pakages, but it raises Error when querying Prolog Server: Connection refused
Then I check if the Metamap server is running on port 8066 by using the command:
sudo netstat -tulpn | grep 8066
but I receive nothing.
Did anyone had the same problem before and knows solution for this?
After running skrmedpostctl (and the optional word sense diambiguation server wsdserverctl), you need to run the mmserver executable in order to use the Java API for Metamap. This can be run by running the command
./bin/mmserver{two-digit-year}
Also, be sure to include the two jar files for metamap and prolog-beans in your classpath (in your IDE, this can be done by adding a dependency to these jars).
The issue may reside with the timeout: when the timeout parameter is not specified for the MetaMapImpl, it is set to 0, so the instance interprets any latency as failure and reports an error.
Increase the timeout to a reasonable value (for me 500 msec was enough).
I was getting this error after getting error SPIO_E_TOO_MANY_OPEN_FILES and losing the connection to the mmserver. I was tryig to construct instances of MetaMapApiImpl in a loop and calling processCitationsFromString for thousands of times. Therefore, I was getting error SPIO_E_TOO_MANY_OPEN_FILES after around a hundred repeats.
What I did to fix this error was to simply disconnect the api at the end of the loop, by calling the function disconnect().
Related
Every time I try to debug one of my tests (junit 5), I get an exception:
2019-12-20 10:40:53,776 [4972237] WARN - .ExternalSystemTaskDebugRunner - Interrupted function call: accept failed
java.net.SocketException: Interrupted function call: accept failed
at java.base/java.net.PlainSocketImpl.accept0(Native Method)
at java.base/java.net.PlainSocketImpl.socketAccept(PlainSocketImpl.java:159)
at java.base/java.net.AbstractPlainSocketImpl.accept(AbstractPlainSocketImpl.java:458)
at java.base/java.net.ServerSocket.implAccept(ServerSocket.java:551)
at java.base/java.net.ServerSocket.accept(ServerSocket.java:519)
at com.intellij.openapi.externalSystem.service.execution.ForkedDebuggerThread.run(ForkedDebuggerThread.java:103)
I've done quite a bit of searching through SO here, and have found several people that had similar problems. Most of them were resolve simply by upgrading (to 2013 or whatever, these questions aren't exactly spring chickens). The rest required some special sauce relevant to their system (android stuff mostly). Or they're getting a different exception (being disconnected, where I'm never getting the connection in the first place).
These tests (unit tests for the most part) are attached to a module with no "main".
I've tried launching gradlew -DtestDebug.test=true cleanTest test, and then connect with a remote debug session. I get an error: Unable to open debugger port (localhost:5005); java.net.ConnectException "Connection refused: connect", which I believe is just what IntelliJ's gui shows when it receives the aforementioned exception.
Ideally, I'd like to set my breakpoints, debug-launch my test task (perhaps specifying a class or individual #Test), and it'd Just Work.
Does anyone have any other ideas I could try? Logs I could look at?
The workaround is to switch the build/run actions to IntelliJ IDEA instead of using Gradle.
But if you still have this issue in the current IDE version, please consider reporting it with the sample project and the logs (Help | Compress Logs and Show in ...) attached.
I recently switched over from using a PC to a Mac and now for whatever reason one of my Impala drivers that worked fine is no longer found when run in Python. I keep receiving this error every time I run the script : "java.lang.RuntimeException: Class com.cloudera.impala.jdbc41.Driver not found". Please see code snippet for my connection below.
c = jaydebeapi.connect
(jclassname='com.cloudera.impala.jdbc41.Driver',
url='jdbc:impala://cloudera-impala-proxy.live.bi.xxx/;AuthMech=3;ssl=1;',
driver_args=['xxx', self.dwh_password], jars='/Users/xxx/Desktop/ImpalaJDBC41 2.jar')
Any help or suggestions are appreciated, I feel like I'm going crazy trying to get this to work.
Did you check do you have the ImpalaJDBC***.jar in your new machine.
Please check properly weather it's available at classpath/build path or not.
Edit:
You can use hive jdbc jar as well to connect with impala , just use the port of impala rather hive in jdbc url.
Looking at this error means your jar is corrupt.
First check your impalaJDBC jar
java -jar ImpalaJDBC<version>.jar
If it gives you error that means your jar is corrupt.
Download the correct jar from cloudera
I have a problem with Glassfish 4 that occurs when I try to start it.
I have searched for this error only but I haven't found a similar case.
Here's the error log:
Unable to update http port. Server shut down.
org.eclipse.core.runtime.CoreException:
Could not save to L/Servers/GlassFish 4 at localhost [myDomain].server.
But even though I've had this error, in Eclipse, the state of the Glassfish server is said to [Started, Republish] and I can access the Glassfish admin console.
Have any idea about what is going on there ?
Thanks for your consideration.
It's an old question but the issue still happens on Eclipse 2019-09 so here's what I found and a workaround for it.
It's caused by hitting the Switch Location button on server properties
That will remove this element on <workspace>/.metadata/.plugins/org.eclipse.wst.server.core/servers.xml
<server auto-publish-setting="1"
glassfish.adminserverportnumber="4948"
glassfish.debugport="4909"
glassfish.serverportnumber="4980"
glassfish.domainpath="/home/luis.munoz/projects/bin/glassfish3/glassfish/domains/domain-test/domain-test-1"
hostname="localhost"
id="GlassFish 3.1 [domain-test-1]"
name="GlassFish 3.1 [domain-test-1]"
runtime-id="GlassFish 3.1"
server-type="glassfish.server"
server-type-id="glassfish.server"
start-timeout="240" stop-timeout="240" timestamp="0" />
runtime-id must match the one in .plugins/org.eclipse.core.runtime/.settings/org.eclipse.wst.server.core.prefs
WORKAROUND:
Close Eclipse since servers.xml is cached.
Add the element back on servers.xml to fix the error. Change details as needed.
Start Eclipse
Server properties will show Location: [workspace metadata] again and the error message will not appear when starting Glassfish.
are you using 8080 port ?
ensure that no other processes are listening, if yes - kill em.
netstat -a -n -o | find "8080"
I was attempting to use Streamsets to query an Oracle database and publish the data into Kafka. I downloaded Streamsets' tarball on my Mac and unzipped it into my home directory. Running $HOME/streamsets-datacollector-2.1.0.2/bin/streamsets dc started up on my first try, then I followed the instructions here to add the jdbc driver, then the instructions here to configure my streamsets job. However, I got an error: JDBC_00 - Cannot connect to specified database: com.streamsets.pipeline.api.StageException: JDBC_06 - Failed to initialize connection pool: java.sql.SQLRecoverableException: IO Error: Bad file descriptor.
This wound up having something to do with the limit on the number of files a process can have open. When I ran ulimit -n on the laptop, it showed 4864, then I set it to 10,000 via ulimit -n 10000, restarted the streamsets server, and it worked! If I need to keep running this, I will find a more procedural way of setting the ulimit for this process to work around this issue.
you definitely want need increase ulimit -n. To permanently change for all users in Ubuntu try the following:
echo "* soft nofile 60000" > /etc/security/limits.d/*_limits.conf && echo "* hard nofile 60000" >> /etc/security/limits.d/*_limits.conf
substitute 60000 with whatever number you want. I've never had a problem in streamsets using 60k. you should be able to do something similar in bsd.
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.