Hi Jack, 1. Now running the script from de biomart home (./dist/scripts/biomart-server.sh) the command works, but only as root or another user, no using sudo. In this case I get the error that JAVA_HOME is not set. I've tried several things to keep JAVA_HOME set when using sudo but no way. Could you advise me on this?
2. I still have the problem that server shuts down when logging out as root or another user. Another biomart user told me that he is using sudo to start the server and it keeps alive after logging but I cannot confirm it because the above problem. Thanks for your help! Isaac 2011/7/5 Jack Hsu <[email protected]> > Hi Isaac, > > 1. How are you running the script? Can you try running it from within the > "dist" directory? > > ./scripts/biomart-server.sh restart > > I would also check the logs under "dist/logs" for any errors that may have > occurred. Look for a file starting with stdouterr. > > 2. The biomart-server.sh script should be running the server as a daemon > process, so screen is not necessary. Logging out from your SSH session > should be affect the process. Can you check that the process has indeed been > killed? "ps aux | grep biomart" > > Also, the session.timeout is for a user session in the > browser (cookie-based). It will not affect server operations. :) > > -jack > > > From: Isaac cano <[email protected]> > Date: Tue, 5 Jul 2011 03:50:16 -0400 > To: BioMart Users <[email protected]> > > Subject: [BioMart Users] biomart-server.sh start problem > > Dear Biomart Users, > > I'm trying to set up a prototype using Biomart over a mysql database and > I'm facing some problems when starting the server and trying to keep the > server up for a long time (As an operating system I'm using Suse 10 and the > Biomart version is 0.8 release candidate 6): > > 1. The first thing I would like to ask you is why I can run the server > through martconfigurator (loading the registry file and then starting the > server) but if I try to do the same using the "biomart-server.sh > start/restart" command the server doesn't start I get the following message > in the web browser: > > HTTP ERROR: 404 > > Problem accessing /. Reason: > > NOT_FOUND > > ------------------------------ > > *Powered by Jetty://* > > > The output of the "biomart-server.sh start" command is the following: > > Shutting down BioMart: 24945 > > Starting BioMart: > > nohup: appending output to `nohup.out' > > BioMart running pid=25125 > > > I've checked that the application settings point to the correct registry > file (test): > > ################################################## > > # BIOMART APPLICATION SETTINGS > > ################################################## > > biomart.debug = false > > biomart.registry.file=/root/test > > biomart.registry.key.file=/root/.test > > biomart.sidebar = true > > > 2. The other issue is how to keep the server up. I'm connecting to the > server via ssh and I'm using the screen command to start the server (via > martconfigurator) and then I detach the screen to keep the process running. > Then I realised that when closing the ssh connection (putty) the server is > usually down. Could you advice me about this issue? > Just one additional thing, I realised that the is a session.timeout setting > that I commented to prevent the server to go down after the specified amount > of seconds. > > I really appreciate your help, > > > Isaac Cano > -- Isaac Cano Bioinformatics Linkcare Health Services SL C/Villarroel 170 08036 - Barcelona Tel.: (+34)932 275 400, ext. 4182\4523 Mobile: (+34) 666 186 748 Fax: (+34) 932 275 455 [email protected]
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