[InterMine Dev] Any suggestions on this error message when creating a new list?

Yo Yehudi yoyehudi at gmail.com
Tue Jul 12 11:12:40 BST 2016

Hey Sam,

Is this happening on the live mines? I've still been having performance
issues in general whilst trying to browse the beany mines (this is after
you upgraded the server instance), with a lot of timeouts and 500s. I've
tried to replicate the situation on the beany mines to see if I can find
out any more myself but I can't actually get that far - might it be that
the front end is simply reflecting the back end performance issues? I
suspect Joe's suggestion may be the way forward.



On 11 July 2016 at 18:06, Joe Carlson <jwcarlson at lbl.gov> wrote:

> On 07/11/2016 09:02 AM, Sam Hokin wrote:
>> I do not. You mean a JVM debugger? Or something that spits client-side
>> stuff out? Either way I'm all ears.
> I have found this to be essential.
> I work in eclipse. I know other people may like intellij or netbeans
> better, but they're not for me. So I can only give the recipe for eclipse
> but I suspect the other IDEs have similar capabilities.
> First, import the intermine codebase into eclipse. It is not necessary to
> get everything absolutely perfect. I still have some places where the
> classpaths are not completely set up; but that's OK. I don't use eclipse to
> build or deploy the code. Intermine must be built with debugging
> information - check that imbuild/library.xml has <property
> name="javac.debug" value="on"/> and <property name="javac.debuglevel"
> value="lines,vars,source"/> and that the source you're looking at agrees
> with what was used to build the deployed code.
> I'm using tomcat-7 on the webserver. On the server side, take whatever
> script you use for starting tomcat and define the environment variable
> JDPA_OPTS. For me I use
>> export JPDA_OPTS=-agentlib:jdwp=transport=dt_socket,address=<web server
>> host>:8069,server=y,suspend=y
> (Obviously replace <web server host> with the name of your host. I'm using
> 8069 as the debug port. You can use any free port)
> and start tomcat with:
>     $CATALINA_HOME/bin/catalina.sh jpda start
> After you issue that command, you'll probably get a 503 response if you
> point your browser to the webapp. You need to get eclipse to connect first.
> You do not need to be on the same host as the web server.
> Select Debug -> Debug Configuration -> Remote Java Application.
> Enter the name of the project (Intermine), Connection Type: Standard
> (Socket Attach) The connection properties are Host: <web server host> and
> port 8069. Then click debug.
> Now the web server will respond, a bit slower than normal, but certainly
> usable. Browse over the the bag creation code and set a breakpoint by right
> clicking on the line number or ctrl-shift-B. As soon as the hit this code,
> eclipse should automatically switch into the debug perspective and you can
> step through the code line by line.
> Hours of fun!
> Joe
>> On 07/09/2016 01:13 PM, Joe Carlson wrote:
>>> Do you know how to attach a debugger to the web app?
>>> Works for me. Many, many times.
>>> Joe
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