gbrowse crashing with too many open mysql queries

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gbrowse crashing with too many open mysql queries

Nathan Liles
The past couple of days, our GBrowse instance (v2.52) has been crashing with the following message: 

 Error: Could not open user account database. If you are the administrator, run gbrowse_metadb_config.pl

I think I pinpointed the problem. It appears gbrowse is opening multiple redundant connections. After running show processlist, I can see dozens of these queries like so:

+------+--------------+-----------+-----------------+---------+------+-------+------------------+
| Id   | User         | Host      | db              | Command | Time | State | Info             |
+------+--------------+-----------+-----------------+---------+------+-------+------------------+
|  281 | gbrowse_user | localhost | gb_BW2952       | Sleep   | 1509 |       | NULL             |
|  285 | gbrowse_user | localhost | gbrowse_login   | Sleep   | 1509 |       | NULL             |
|  286 | gbrowse_user | localhost | gbrowse_login   | Sleep   | 1509 |       | NULL             |
|  287 | gbrowse_user | localhost | gbrowse_login   | Sleep   | 1509 |       | NULL             |
|  315 | gbrowse_user | localhost | gbrowse_login   | Sleep   | 1508 |       | NULL             |
|  316 | gbrowse_user | localhost | gbrowse_login   | Sleep   | 1508 |       | NULL             |
|  317 | gbrowse_user | localhost | gbrowse_login   | Sleep   | 1508 |       | NULL             |
|  329 | gbrowse_user | localhost | gb_W3110        | Sleep   |  169 |       | NULL             |
|  331 | gbrowse_user | localhost | gb_BW2952       | Sleep   |  169 |       | NULL             |
|  332 | gbrowse_user | localhost | gb_DH10B        | Sleep   |   41 |       | NULL             |
+------+--------------+-----------+-----------------+---------+------+-------+------------------+

These sleeping queries seem to persist until eventually the connection limit is saturated and GBrowse won't load because it cannot access the gbrowse_login database. Has anyone seen this behavior before? Can it be fixed by an upgrade? Or is it something we're doing on our end?

Thanks,
Nathan

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Re: gbrowse crashing with too many open mysql queries

Lincoln Stein
I do not know. Are you using built in authentication with named user accounts?

Lincoln

On Wednesday, February 20, 2013, Nathan Liles wrote:
The past couple of days, our GBrowse instance (v2.52) has been crashing with the following message: 

 Error: Could not open user account database. If you are the administrator, run gbrowse_metadb_config.pl

I think I pinpointed the problem. It appears gbrowse is opening multiple redundant connections. After running show processlist, I can see dozens of these queries like so:

+------+--------------+-----------+-----------------+---------+------+-------+------------------+
| Id   | User         | Host      | db              | Command | Time | State | Info             |
+------+--------------+-----------+-----------------+---------+------+-------+------------------+
|  281 | gbrowse_user | localhost | gb_BW2952       | Sleep   | 1509 |       | NULL             |
|  285 | gbrowse_user | localhost | gbrowse_login   | Sleep   | 1509 |       | NULL             |
|  286 | gbrowse_user | localhost | gbrowse_login   | Sleep   | 1509 |       | NULL             |
|  287 | gbrowse_user | localhost | gbrowse_login   | Sleep   | 1509 |       | NULL             |
|  315 | gbrowse_user | localhost | gbrowse_login   | Sleep   | 1508 |       | NULL             |
|  316 | gbrowse_user | localhost | gbrowse_login   | Sleep   | 1508 |       | NULL             |
|  317 | gbrowse_user | localhost | gbrowse_login   | Sleep   | 1508 |       | NULL             |
|  329 | gbrowse_user | localhost | gb_W3110        | Sleep   |  169 |       | NULL             |
|  331 | gbrowse_user | localhost | gb_BW2952       | Sleep   |  169 |       | NULL             |
|  332 | gbrowse_user | localhost | gb_DH10B        | Sleep   |   41 |       | NULL             |
+------+--------------+-----------+-----------------+---------+------+-------+------------------+

These sleeping queries seem to persist until eventually the connection limit is saturated and GBrowse won't load because it cannot access the gbrowse_login database. Has anyone seen this behavior before? Can it be fixed by an upgrade? Or is it something we're doing on our end?

Thanks,
Nathan


--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

------------------------------------------------------------------------------
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Download AppDynamics Lite for free today:
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