[ensembl-dev] EnsemblGenomes bacteria couldn't startup

ek ek at ebi.ac.uk
Tue May 14 12:36:52 BST 2013


On 2013-05-14 11:58, 陈岗 wrote:
> Hi Ensembl developers
> 
> I couldn't startup bacteria service correctly, the other services
> work perfectly.
> 
> When first time run the command: /usr/local/apache2/bin/httpd -d
> /usr/local/ensembl_bacteria
> The server infor shows up as normal, but the file ensembl.httpd.pid
> doesn't exist in the directory logs and can't open the home page.

try using ctrl_scripts/restart_server


> The start process takes almost 2 hours.
indeed, at the very first attempt to start the browser caches some data 
that stored in the databases and frequently used by the webserver
it takes about 2 hours to run this process for ~ 6000 bacteria
once the cache files are created ( in conf/packed folder ) the restart 
of the server will be much quicker



> 
> So I have to start web server again. The second round returns a error 
> message:
> ' (98)Address already in use: make_sock: could not bind to address
> 0.0.0.0:8899 [1] '
> In this time, the file ensembl.httpd.pid is created, and home page 
> shows up.

' (98)Address already in use: make_sock: could not bind to address
indicates that the second attempt failed, and the server started just 
fine after the first attempt

i think you were just too quick to try and access the web page
when the server start up command returns it still takes some time 
before the server is available

you can monitor the error log to see when the server is fully 
operational

# ctrl_scritps/taillog
[Tue May 14 12:29:35 2013] [notice] caught SIGTERM, shutting down
[Tue May 14 12:30:45 2013] [notice] Apache/2.2.15 (Unix) mod_perl/2.0.4 
Perl/v5.10.1 configured -- resuming normal operations




> 
> However, only gene info can display,other data totally dispear.

what do you mean ? what is the page you are looking at , and what data 
are missing ?

> In error_log, there are two major error messages:
> 1.
>  For ensemblgenomes_ontology_18_71 there is a difference in the
> software release (71) and the database release (18). You should update
> one of these to ensure that your script does not crash.
this is expected , you can ignore the warning

> We keep both of Ensembl and Genomes databases on a same DB server.
> Does it cause the problem?
no

> 
> 2.
> 
> [Tue May 14 18:25:15 2013] (6126) Apache2::SizeLimit httpd process
> too big, exiting at SIZE=1117712 KB SHARE=4156 KB UNSHARED=1113556
> REQUESTS=2 LIFETIME=0 seconds
> 
> The entire error_log is attached with this mail.

you can increase the limit in conf/perl.startup
change the line
$Apache2::SizeLimit::MAX_PROCESS_SIZE = 1000000;


> need youe help.
> Thanks million!
> 
> --
> 
> Gang Chen
> TILSI
> Taicang Institute For Life Science Information
>  Address: A2/162, Renmin South Road, Taicang, 215400, Jiangsu
> Province, P.R.China
> Phone:(+86)512-82782588
> 
> Links:
> ------
> [1] http://0.0.0.0:8899
> 
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