code.cytoscape.org down?

80 views
Skip to first unread message

Victor Cassen

unread,
Jan 27, 2013, 11:07:56 PM1/27/13
to cytoscap...@googlegroups.com
Hi, 

I'm trying to do a compile using maven against the 3.0 code, on a fresh install.  When I execute 'mvn install', the build hangs (sorta; see below) with the following message:


(Actually, it doesn't fully hang; it pauses at this stage for a minute or two, then attempts to download the next target, with a similar result).

When I try to load http://code.cytoscape.org in a browser, I get a 502 (bad gateway) error.

Am I doing something wrong, or is there a problem with the server at code.cytoscape.org?

Thanks in advance,
-Victor

Jason Montojo

unread,
Jan 28, 2013, 10:19:37 AM1/28/13
to cytoscap...@googlegroups.com
Hi Victor,

I think the downtime was temporary.  I'm not sure what happened but it seems to be up now.  Can you try again?

Thanks,
Jason



--
You received this message because you are subscribed to the Google Groups "cytoscape-discuss" group.
To post to this group, send email to cytoscap...@googlegroups.com.
To unsubscribe from this group, send email to cytoscape-disc...@googlegroups.com.
Visit this group at http://groups.google.com/group/cytoscape-discuss?hl=en.
For more options, visit https://groups.google.com/groups/opt_out.
 
 

Barry Demchak

unread,
Jan 28, 2013, 12:27:50 AM1/28/13
to cytoscap...@googlegroups.com
Victor --

That's what I get, too.

I think the service (University of Toronto) is down. This happened last week, too ... we'll take a closer look tomorrow (Monday) morning. Sorry for the trouble.

--
You received this message because you are subscribed to the Google Groups "cytoscape-discuss" group.
To post to this group, send email to cytoscap...@googlegroups.com.
To unsubscribe from this group, send email to cytoscape-disc...@googlegroups.com.
Visit this group at http://groups.google.com/group/cytoscape-discuss?hl=en.
For more options, visit https://groups.google.com/groups/opt_out.
 
 



--
vvvvvvvvvvvvvvvvvvvvvvvvvvvv
: Barry Demchak, PhD
: UC San Diego, Department of Medicine
: https://sosa.ucsd.edu/confluence/display/~bdemchak/Home
: (858) 452-8700
vvvvvvvvvvvvvvvvvvvvvvvvvvvv

Victor Cassen

unread,
Jan 29, 2013, 3:08:38 AM1/29/13
to cytoscap...@googlegroups.com
It appears to be back up now.  Yay!

-Victor

-Victor Cassen
------------------------------------------------------------
Let's play motorcycle tag! CRASH! You're it!

Simone Zorzan

unread,
Mar 6, 2014, 7:06:08 AM3/6/14
to cytoscap...@googlegroups.com
Hi, is the service down again? I get a "Connection timed out" exception from Maven when I try to compile a template sample.
I can ping http://code.cytoscape.org/ but no response on port 80

Thanks,
Simone.

Lennaert van den Brink

unread,
Mar 6, 2014, 7:29:10 AM3/6/14
to cytoscap...@googlegroups.com
You are not the only one, I can't reach it either...

Op donderdag 6 maart 2014 13:06:08 UTC+1 schreef Simone Zorzan:

piet molenaar

unread,
Mar 6, 2014, 7:32:07 AM3/6/14
to Cytoscape-Discuss
Apparently several Cytoscape servers are down; sys admins are working on it.
We'll keep you posted, sorry for the inconvenience.
Cheers,
Piet


To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-disc...@googlegroups.com.

To post to this group, send email to cytoscap...@googlegroups.com.

For more options, visit https://groups.google.com/groups/opt_out.



--
Piet Molenaar
piet...@gmail.com
Department of Oncogenomics, M1-131
Academic Medical Center
University of Amsterdam
Meibergdreef 9
1105 AZ Amsterdam
the Netherlands

tel (+31) 20-5666592
fax (+31) 20-6918626

Igor Rodchenkov

unread,
Mar 6, 2014, 9:38:39 AM3/6/14
to cytoscap...@googlegroups.com
Aye, sorry, we're here waiting for sysadmins (looks like a router failure, since yesterday about 8pm; one particular IP subnetwork affected...)
Wait...

Jason Montojo

unread,
Mar 6, 2014, 10:33:12 AM3/6/14
to cytoscap...@googlegroups.com
Hi everyone,

code.cytoscape.org should be back up again.  We apologize for the inconvenience.  One of our switches became unresponsive and had to be restarted.  Not all of the services came back online automatically so we had to manually restart a number of them.  Please let me know if you notice any issues.

Thanks,
Jason

Lennaert van den Brink

unread,
Mar 10, 2014, 7:58:06 AM3/10/14
to cytoscap...@googlegroups.com
I am having problems again accessing the javadoc on code.cytoscape.org . Am I the only one, or is it down once more?

Op donderdag 6 maart 2014 16:33:12 UTC+1 schreef Jason Montojo:

piet molenaar

unread,
Mar 10, 2014, 8:09:49 AM3/10/14
to Cytoscape-Discuss
I can't access the javadocs either.
Piet


For more options, visit https://groups.google.com/d/optout.

piet molenaar

unread,
Mar 10, 2014, 8:11:06 AM3/10/14
to Cytoscape-Discuss
jenkins, nexus and sonar links are offline also; only redmine link is working.

Lennaert van den Brink

unread,
Mar 10, 2014, 9:49:08 AM3/10/14
to cytoscap...@googlegroups.com
Appears to be up again!

Op maandag 10 maart 2014 13:11:06 UTC+1 schreef Piet:

Jason Montojo

unread,
Mar 10, 2014, 9:51:50 AM3/10/14
to cytoscap...@googlegroups.com
Hi everyone,

The application server hosting Jenkins, Nexus and Sonar ran out of memory.  I had to restart it.  It's up and running now but we'll probably need to tweak the configuration.  Sorry for the inconvenience!

Thanks,
Jason

Oriol Guitart Pla

unread,
Mar 11, 2014, 6:29:05 AM3/11/14
to cytoscap...@googlegroups.com
Hi Jason,

I think it is down again. I can't connect to nexus.
Thanks,


oriol

Jason Montojo

unread,
Mar 11, 2014, 8:45:59 AM3/11/14
to cytoscap...@googlegroups.com
Hi Oriol,

Thanks for letting me know.  I've restarted the application server again.  It should be up now.  I think I need to bump the memory settings even higher.

Thanks,
Jason

Oriol Guitart Pla

unread,
Mar 11, 2014, 9:00:51 AM3/11/14
to cytoscap...@googlegroups.com
Thanks Jason! It seems to work now.


oriol

Oriol Guitart Pla

unread,
Mar 13, 2014, 7:17:30 AM3/13/14
to cytoscap...@googlegroups.com
Hi Jason,


I think Nexus has a problem again.
Thanks,

oriol

Jason Montojo

unread,
Mar 13, 2014, 9:46:09 AM3/13/14
to cytoscap...@googlegroups.com
Hi Oriol,

I'm sorry for the inconvenience.  I thought I had all the issues fixed.  The root cause was a file descriptor leak in Jenkins.  Every time someone visited one of the pages there, Jenkins would leak 2 descriptors.  For some reason, we had a huge spike in overnight (eastern time) page hits starting March 7.  I increased the open file limit, but the following night, the limit got breached again.  I updated Jenkins to a version that no longer leaks file descriptors but now it seems Sonar got corrupted and crashed the application server.  I've reinstalled Sonar.  I'll check the logs again tonight to see if the problem still persists.  It should be working for now.

Access logging was disabled by default so I've enabled it.  That should tell us if we're getting hammered by search engines, hackers, or other bots.

Thanks,
Jason

Oriol Guitart Pla

unread,
Mar 13, 2014, 11:08:22 AM3/13/14
to cytoscap...@googlegroups.com
Thanks Jason, it works again.


oriol

Oriol Guitart Pla

unread,
Mar 17, 2014, 6:42:26 AM3/17/14
to cytoscap...@googlegroups.com
Hi Jason,


Nexus seems to be down again.

oriol

Jason Montojo

unread,
Mar 17, 2014, 1:42:55 PM3/17/14
to cytoscap...@googlegroups.com
Hi Oriol,

Sorry for the delay!  I'm between flights right now in San Francisco.  Looks like we'll need to bump up the memory on the server.  It's just running out of memory at this point.  I've restarted the services so it should be up again.  I'll try to have this addressed more permanently soon.  Thanks for your patience!

Thanks,
Jason

Tim Hull

unread,
Mar 19, 2014, 2:23:49 PM3/19/14
to cytoscap...@googlegroups.com
It seems that Nexus, Jenkins, and Sonar are down (or at least not responding) right now. Redmine is working, though. Might this be the same issue again?

Tim

Jason Montojo

unread,
Mar 19, 2014, 2:32:59 PM3/19/14
to cytoscap...@googlegroups.com
Hi Tim,

The app server ran out of heap space.  I've increased the amount of RAM allocated to it from 1GB to 4GB.  Let's hope this will be enough...  On the plus side, I think the Google Bot has stopped indexing us.

Thanks,
Jason
Reply all
Reply to author
Forward
0 new messages