Debugging the TAIR GBrowse hang problem

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Debugging the TAIR GBrowse hang problem

Bob Muller
Scott,

With the help of Eric Lyons of iPlant and Vivek Krishnakumar of JCVI, we've debugged the GBrowse 2 problem we're having at TAIR and made some progress, but we don't understand why it's doing what it's doing. Specifically, it seems to be losing context and trying to reestablish it after successfully parsing a simple request, then it's getting the wrong session or something.

First, we debugged the fact that the problem happened for some browsers and not for others. Eric and I tried various things, then did an anonymous window session in my Chrome, which previously had successfully executed the request. That one failed. We cleared everything from my browser (cookies etc., not just cache, which I'd cleared previously) and that caused my Chrome to consistently fail. So whatever was being preserved in my browser was definitely avoiding the problem.

We then worked through the error trace from the Apache error log:

[Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] RUN(): GET: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/ name=AT1G01040 at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 239., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
[Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] session id = b20d5eec0c44fdffa5b8ee751f58fca8 at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 243., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
[Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] add_user_tracks() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 272., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
[Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] testing for asynchronous event() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 275., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
[Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] init() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 286., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
[Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] update_state() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 289., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
[Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] render() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 296., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
[Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] cleanup at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 300., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
[Wed Oct 16 07:44:26 2013] [error] [client 171.66.71.53] [12599] session flush at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 304., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
[Wed Oct 16 07:44:26 2013] [error] [client 171.66.71.53] [12599] synchronous exit at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 309., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
[Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] [12606] RUN(): POST: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/ action=navigate;navigate=left%200;view_start=NaN;view_stop=NaN;snapshot=false at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 239., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] [12606] session id = 45a76058f092dd69404635c055c98c04 at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 243., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] [12606] add_user_tracks() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 272., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] [12606] testing for asynchronous event() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 275., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2818., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2874., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2046., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] Premature end of script headers: gbrowse, referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040

We found the line with the view_start=NaN;view_stop=NaN that you noted before. Note also that it is after "synchronous exit". Vivek and I then spent quite a bit of time working through the Perl code trying to figure out what it was doing, and ultimately failing. Also note in line 2 the session id = b20d5eec0c44fdffa5b8ee751f58fca8, and in line 12, session id = 45a76058f092dd69404635c055c98c04--it's using a completely different session id. This is just after the line with the view_start/stop problem. Vivek verified with the image script that GBrowse can produce the image for the URL just fine. But what it seems to be doing is going back for some kind of asynchronous event involving a "navigate" action  in Render.pm, where it goes through a series of calls that fail due to the bad values for view_start and view_stop, presumably because it has lost its session context. What we don't know is why it is doing that. Do you have any insight into this?

We've set up a separate virtual machine at iPlant, and we're going to install the latest GB2 from scratch and import data and configuration to see if we can get a cleanly working system that way. If so, we'll replace the current gbrowse with it and move on. But if you can help us to debug the problem, it would save a lot of work!

Thanks!

   --Bob Muller, TAIR


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Re: Debugging the TAIR GBrowse hang problem

Scott Cain
Hi Bob,

I am baffled.  The only thing that occurs to me that I don't think I've asked about before is whether there is javascript in your configuration file that is getting included in the GBrowse page that might be interfering with the way GBrowse loads tracks.  I can't see how that would be the case given the symptoms, but it's all I've got.  I'm curious how the fresh install will go.

Scott



On Wed, Oct 16, 2013 at 9:08 AM, Bob Muller <[hidden email]> wrote:
Scott,

With the help of Eric Lyons of iPlant and Vivek Krishnakumar of JCVI, we've debugged the GBrowse 2 problem we're having at TAIR and made some progress, but we don't understand why it's doing what it's doing. Specifically, it seems to be losing context and trying to reestablish it after successfully parsing a simple request, then it's getting the wrong session or something.

First, we debugged the fact that the problem happened for some browsers and not for others. Eric and I tried various things, then did an anonymous window session in my Chrome, which previously had successfully executed the request. That one failed. We cleared everything from my browser (cookies etc., not just cache, which I'd cleared previously) and that caused my Chrome to consistently fail. So whatever was being preserved in my browser was definitely avoiding the problem.

We then worked through the error trace from the Apache error log:

[Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] RUN(): GET: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/ name=AT1G01040 at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 239., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
[Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] session id = b20d5eec0c44fdffa5b8ee751f58fca8 at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 243., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
[Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] add_user_tracks() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 272., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
[Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] testing for asynchronous event() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 275., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
[Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] init() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 286., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
[Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] update_state() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 289., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
[Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] render() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 296., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
[Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] cleanup at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 300., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
[Wed Oct 16 07:44:26 2013] [error] [client 171.66.71.53] [12599] session flush at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 304., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
[Wed Oct 16 07:44:26 2013] [error] [client 171.66.71.53] [12599] synchronous exit at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 309., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
[Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] [12606] RUN(): POST: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/ action=navigate;navigate=left%200;view_start=NaN;view_stop=NaN;snapshot=false at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 239., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] [12606] session id = 45a76058f092dd69404635c055c98c04 at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 243., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] [12606] add_user_tracks() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 272., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] [12606] testing for asynchronous event() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 275., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2818., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2874., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2046., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] Premature end of script headers: gbrowse, referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040

We found the line with the view_start=NaN;view_stop=NaN that you noted before. Note also that it is after "synchronous exit". Vivek and I then spent quite a bit of time working through the Perl code trying to figure out what it was doing, and ultimately failing. Also note in line 2 the session id = b20d5eec0c44fdffa5b8ee751f58fca8, and in line 12, session id = 45a76058f092dd69404635c055c98c04--it's using a completely different session id. This is just after the line with the view_start/stop problem. Vivek verified with the image script that GBrowse can produce the image for the URL just fine. But what it seems to be doing is going back for some kind of asynchronous event involving a "navigate" action  in Render.pm, where it goes through a series of calls that fail due to the bad values for view_start and view_stop, presumably because it has lost its session context. What we don't know is why it is doing that. Do you have any insight into this?

We've set up a separate virtual machine at iPlant, and we're going to install the latest GB2 from scratch and import data and configuration to see if we can get a cleanly working system that way. If so, we'll replace the current gbrowse with it and move on. But if you can help us to debug the problem, it would save a lot of work!

Thanks!

  --Bob Muller, TAIR




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Debugging the TAIR GBrowse hang problem

Bob Muller-2
In reply to this post by Bob Muller
We have resolved this problem by installing a completely new GBrowse version on a new VM and importing the databases and configuration files from our old server. Everything works as expected. It's now public on the TAIR site.

We were not able to resolve the problem any further on the original server, which we're decommissioning.

   --Bob Muller, TAIR

On 10/16/13 6:08 AM, Bob Muller wrote:

> Scott,
>
> With the help of Eric Lyons of iPlant and Vivek Krishnakumar of JCVI, we've debugged the GBrowse 2 problem we're having at TAIR and made some progress, but we don't understand why it's doing what it's doing. Specifically, it seems to be losing context and trying to reestablish it after successfully parsing a simple request, then it's getting the wrong session or something.
>
> First, we debugged the fact that the problem happened for some browsers and not for others. Eric and I tried various things, then did an anonymous window session in my Chrome, which previously had successfully executed the request. That one failed. We cleared everything from my browser (cookies etc., not just cache, which I'd cleared previously) and that caused my Chrome to consistently fail. So whatever was being preserved in my browser was definitely avoiding the problem.
>
> We then worked through the error trace from the Apache error log:
>
> [Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] RUN(): GET: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/ name=AT1G01040 at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 239., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
> [Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] session id = b20d5eec0c44fdffa5b8ee751f58fca8 at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 243., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
> [Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] add_user_tracks() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 272., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
> [Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] testing for asynchronous event() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 275., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
> [Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] init() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 286., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
> [Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] update_state() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 289., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
> [Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] render() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 296., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
> [Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] cleanup at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 300., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
> [Wed Oct 16 07:44:26 2013] [error] [client 171.66.71.53] [12599] session flush at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 304., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
> [Wed Oct 16 07:44:26 2013] [error] [client 171.66.71.53] [12599] synchronous exit at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 309., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
> [Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] [12606] RUN(): POST: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/ action=navigate;navigate=left%200;view_start=NaN;view_stop=NaN;snapshot=false at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 239., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
> [Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] [12606] session id = 45a76058f092dd69404635c055c98c04 at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 243., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
> [Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] [12606] add_user_tracks() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 272., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
> [Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] [12606] testing for asynchronous event() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 275., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
> [Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2818., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
> [Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
> [Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
> [Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
> [Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2874., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
> [Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2046., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
> [Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] Premature end of script headers: gbrowse, referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
>
> We found the line with the view_start=NaN;view_stop=NaN that you noted before. Note also that it is after "synchronous exit". Vivek and I then spent quite a bit of time working through the Perl code trying to figure out what it was doing, and ultimately failing. Also note in line 2 the session id = b20d5eec0c44fdffa5b8ee751f58fca8, and in line 12, session id = 45a76058f092dd69404635c055c98c04--it's using a completely different session id. This is just after the line with the view_start/stop problem. Vivek verified with the image script that GBrowse can produce the image for the URL just fine. But what it seems to be doing is going back for some kind of asynchronous event involving a "navigate" action  in Render.pm, where it goes through a series of calls that fail due to the bad values for view_start and view_stop, presumably because it has lost its session context. What we don't know is why it is doing that. Do you have any insight into this?
>
> We've set up a separate virtual machine at iPlant, and we're going to install the latest GB2 from scratch and import data and configuration to see if we can get a cleanly working system that way. If so, we'll replace the current gbrowse with it and move on. But if you can help us to debug the problem, it would save a lot of work!
>
> Thanks!
>
>     --Bob Muller, TAIR
>
>
> ------------------------------------------------------------------------------
> October Webinars: Code for Performance
> Free Intel webinars can help you accelerate application performance.
> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
> the latest Intel processors and coprocessors. See abstracts and register >
> http://pubads.g.doubleclick.net/gampad/clk?id=60135031&iu=/4140/ostg.clktrk
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>



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Re: Debugging the TAIR GBrowse hang problem

Bob Muller
In reply to this post by Bob Muller
We have resolved this problem by installing a completely new GBrowse version on a new VM and importing the databases and configuration files from our old server. Everything works as expected. It's now public on the TAIRsite.

We were not able to resolve the problem any further on the original server, which we're decommissioning.

   --Bob Muller, TAIR

On 10/16/13 6:08 AM, Bob Muller wrote:

> Scott,
>
> With the help of Eric Lyons of iPlant and Vivek Krishnakumar of JCVI, we've debugged the GBrowse 2 problem we're having at TAIR and made some progress, but we don't understand why it's doing what it's doing. Specifically, it seems to be losing context and trying to reestablish it after successfully parsing a simple request, then it's getting the wrong session or something.
>
> First, we debugged the fact that the problem happened for some browsersand not for others. Eric and I tried various things, then did an anonymous window session in my Chrome, which previously had successfully executed the request. That one failed. We cleared everything from my browser (cookies etc., not just cache, which I'd cleared previously) and that causedmy Chrome to consistently fail. So whatever was being preserved in my browser was definitely avoiding the problem.
>
> We then worked through the error trace from the Apache error log:
>
> [Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] RUN():GET: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/ name=AT1G01040 at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 239., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
> [Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] session id = b20d5eec0c44fdffa5b8ee751f58fca8 at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 243., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
> [Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] add_user_tracks() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 272., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
> [Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] testing for asynchronous event() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 275., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
> [Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] init()at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 286., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
> [Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] update_state() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 289., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
> [Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] render() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 296., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
> [Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] cleanup at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 300., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
> [Wed Oct 16 07:44:26 2013] [error] [client 171.66.71.53] [12599] session flush at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 304., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
> [Wed Oct 16 07:44:26 2013] [error] [client 171.66.71.53] [12599] synchronous exit at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line309., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
> [Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] [12606] RUN():POST: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/ action=navigate;navigate=left%200;view_start=NaN;view_stop=NaN;snapshot=false at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 239., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
> [Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] [12606] session id = 45a76058f092dd69404635c055c98c04 at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 243., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
> [Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] [12606] add_user_tracks() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 272., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
> [Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] [12606] testing for asynchronous event() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 275., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
> [Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2818., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
> [Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
> [Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
> [Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
> [Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2874., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
> [Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2046., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
> [Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] Premature end of script headers: gbrowse, referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
>
> We found the line with the view_start=NaN;view_stop=NaN that you noted before. Note also that it is after "synchronous exit". Vivek and I then spent quite a bit of time working through the Perl code trying to figure out what it was doing, and ultimately failing. Also note in line 2 thesession id = b20d5eec0c44fdffa5b8ee751f58fca8, and in line 12, sessionid = 45a76058f092dd69404635c055c98c04--it's using a completely different session id. This is just after the line with the view_start/stop problem. Vivek verified with the image script that GBrowse can produce the image for the URL just fine. But what it seems to be doing is going back forsome kind of asynchronous event involving a "navigate" action  in Render.pm, where it goes through a series of calls that fail due to the bad values for view_start and view_stop, presumably because it has lost its session context. What we don't know is why it is doing that. Do you have any insight into this?
>
> We've set up a separate virtual machine at iPlant, and we're going to install the latest GB2 from scratch and import data and configuration to see if we can get a cleanly working system that way. If so, we'll replace the current gbrowse with it and move on. But if you can help us to debug the problem, it would save a lot of work!
>
> Thanks!
>
>     --Bob Muller, TAIR
>
>
> ------------------------------------------------------------------------------
> October Webinars: Code for Performance
> Free Intel webinars can help you accelerate application performance.
> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
> the latest Intel processors and coprocessors. See abstracts and register >
> http://pubads.g.doubleclick.net/gampad/clk?id=60135031&iu=/4140/ostg.clktrk
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>



------------------------------------------------------------------------------
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Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
the latest Intel processors and coprocessors. See abstracts and register >
http://pubads.g.doubleclick.net/gampad/clk?id=60135991&iu=/4140/ostg.clktrk
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Re: Debugging the TAIR GBrowse hang problem

Scott Cain
In reply to this post by Bob Muller-2
Hi Bob,

Well, I'm glad it's working correctly now anyway.  I'm sorry about the time poured into trying to debug it.

Scott



On Mon, Oct 21, 2013 at 3:25 PM, Bob Muller <[hidden email]> wrote:
We have resolved this problem by installing a completely new GBrowse version on a new VM and importing the databases and configuration files from our old server. Everything works as expected. It's now public on the TAIR site.

We were not able to resolve the problem any further on the original server, which we're decommissioning.

   --Bob Muller, TAIR

On 10/16/13 6:08 AM, Bob Muller wrote:
> Scott,
>
> With the help of Eric Lyons of iPlant and Vivek Krishnakumar of JCVI, we've debugged the GBrowse 2 problem we're having at TAIR and made some progress, but we don't understand why it's doing what it's doing. Specifically, it seems to be losing context and trying to reestablish it after successfully parsing a simple request, then it's getting the wrong session or something.
>
> First, we debugged the fact that the problem happened for some browsers and not for others. Eric and I tried various things, then did an anonymous window session in my Chrome, which previously had successfully executed the request. That one failed. We cleared everything from my browser (cookies etc., not just cache, which I'd cleared previously) and that caused my Chrome to consistently fail. So whatever was being preserved in my browser was definitely avoiding the problem.
>
> We then worked through the error trace from the Apache error log:
>
> [Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] RUN(): GET: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/ name=AT1G01040 at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 239., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
> [Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] session id = b20d5eec0c44fdffa5b8ee751f58fca8 at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 243., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
> [Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] add_user_tracks() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 272., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
> [Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] testing for asynchronous event() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 275., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
> [Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] init() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 286., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
> [Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] update_state() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 289., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
> [Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] render() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 296., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
> [Wed Oct 16 07:44:25 2013] [error] [client 171.66.71.53] [12599] cleanup at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 300., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
> [Wed Oct 16 07:44:26 2013] [error] [client 171.66.71.53] [12599] session flush at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 304., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
> [Wed Oct 16 07:44:26 2013] [error] [client 171.66.71.53] [12599] synchronous exit at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 309., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
> [Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] [12606] RUN(): POST: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/ action=navigate;navigate=left%200;view_start=NaN;view_stop=NaN;snapshot=false at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 239., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
> [Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] [12606] session id = 45a76058f092dd69404635c055c98c04 at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 243., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
> [Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] [12606] add_user_tracks() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 272., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
> [Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] [12606] testing for asynchronous event() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 275., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
> [Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2818., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
> [Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
> [Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
> [Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
> [Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2874., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
> [Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2046., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
> [Wed Oct 16 07:44:27 2013] [error] [client 171.66.71.53] Premature end of script headers: gbrowse, referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
>
> We found the line with the view_start=NaN;view_stop=NaN that you noted before. Note also that it is after "synchronous exit". Vivek and I then spent quite a bit of time working through the Perl code trying to figure out what it was doing, and ultimately failing. Also note in line 2 the session id = b20d5eec0c44fdffa5b8ee751f58fca8, and in line 12, session id = 45a76058f092dd69404635c055c98c04--it's using a completely different session id. This is just after the line with the view_start/stop problem. Vivek verified with the image script that GBrowse can produce the image for the URL just fine. But what it seems to be doing is going back for some kind of asynchronous event involving a "navigate" action  in Render.pm, where it goes through a series of calls that fail due to the bad values for view_start and view_stop, presumably because it has lost its session context. What we don't know is why it is doing that. Do you have any insight into this?
>
> We've set up a separate virtual machine at iPlant, and we're going to install the latest GB2 from scratch and import data and configuration to see if we can get a cleanly working system that way. If so, we'll replace the current gbrowse with it and move on. But if you can help us to debug the problem, it would save a lot of work!
>
> Thanks!
>
>     --Bob Muller, TAIR
>
>
> ------------------------------------------------------------------------------
> October Webinars: Code for Performance
> Free Intel webinars can help you accelerate application performance.
> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
> the latest Intel processors and coprocessors. See abstracts and register >
> http://pubads.g.doubleclick.net/gampad/clk?id=60135031&iu=/4140/ostg.clktrk
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>



------------------------------------------------------------------------------
October Webinars: Code for Performance
Free Intel webinars can help you accelerate application performance.
Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
the latest Intel processors and coprocessors. See abstracts and register >
http://pubads.g.doubleclick.net/gampad/clk?id=60135991&iu=/4140/ostg.clktrk
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
October Webinars: Code for Performance
Free Intel webinars can help you accelerate application performance.
Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
the latest Intel processors and coprocessors. See abstracts and register >
http://pubads.g.doubleclick.net/gampad/clk?id=60135991&iu=/4140/ostg.clktrk
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