Discussion:
[Gmod-gbrowse] Very slow rendering when using MySQL database, Can't store GLOB items at ../../lib/Storable.pm
L Shen
2015-10-07 02:38:30 UTC
Permalink
OS: RHEL 6, SELinux enforced, but running at permissive mode
Server: 24 CPU, 32GB RAM, behind firewall in DMZ.
GBrowse: 2.5.5 installed with MCPAN
GD: 2.3.9, bioperl 1.6.9

Data: from MySQL database, remote, accessing in PHP is very fast
Session Lock: mysql
Slave enabled, 32
fast-cgi and fcgid enabled.


The speed with demo yeast is fine.
http://104.193.218.155/cgi-bin/gb2/gbrowse/yeast_advanced/


The speed with human (mysql) is very slow, rendering time out error for
almost any track, even for 5-bp region.
http://104.193.218.155/cgi-bin/gb2/gbrowse/human/


Change my Full name or change email: it took 2 seconds to show the name or
email in the text box


Thank you,

Lishuang


# some /var/log/httpd/error_log:

# change my Full name:

[Tue Oct 06 12:22:42 2015] [error] [client xx.xxx.xx.xx] Can't store GLOB
items at ../../lib/Storable.pm (autosplit into ../../lib/auto/Storable/_
store.al) line 264, at /usr/local/share/perl5/Bio/Graphics/FeatureFile.pm
line 445., referer: http://104.193.218.155/cgi-bin/gb2/gbrowse/human/
[Tue Oct 06 12:22:42 2015] [error] [client xx.xxx.xx.xx] Use of
uninitialized value in numeric ge (>=) at
/usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 769.,
referer: http://104.193.218.155/cgi-bin/gb2/gbrowse/human/
[Tue Oct 06 12:22:42 2015] [error] [client xx.xxx.xx.xx] Use of
uninitialized value in numeric ge (>=) at
/usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 769.,
referer: http://104.193.218.155/cgi-bin/gb2/gbrowse/human/

# change my email:
[Tue Oct 06 12:22:49 2015] [error] [client xx.xxx.xx.xx] Can't store GLOB
items at ../../lib/Storable.pm (autosplit into ../../lib/auto/Storable/_
store.al) line 264, at /usr/local/share/perl5/Bio/Graphics/FeatureFile.pm
line 445., referer: http://104.193.218.155/cgi-bin/gb2/gbrowse/human/
[Tue Oct 06 12:22:49 2015] [error] [client xx.xxx.xx.xx] Use of
uninitialized value in numeric ge (>=) at
/usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 769.,
referer: http://104.193.218.155/cgi-bin/gb2/gbrowse/human/
[Tue Oct 06 12:22:49 2015] [error] [client xx.xxx.xx.xx] Use of
uninitialized value in numeric ge (>=) at
/usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 769.,
referer: http://104.193.218.155/cgi-bin/gb2/gbrowse/human/



# view 1kb region, one gene track only, " Track rendering error: timeout;
try viewing smaller region


[Tue Oct 06 12:21:00 2015] [error] [client xx.xxx.xx.xx] Can't store GLOB
items at ../../lib/Storable.pm (autosplit into ../../lib/auto/Storable/_
store.al) line 264, at /usr/local/share/perl5/Bio/Graphics/FeatureFile.pm
line 445., referer:
http://104.193.218.155/cgi-bin/gb2/gbrowse/yeast_advanced/
[Tue Oct 06 12:21:00 2015] [error] [client xx.xxx.xx.xx] Use of
uninitialized value in numeric ge (>=) at
/usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 769.,
referer: http://104.193.218.155/cgi-bin/gb2/gbrowse/yeast_advanced/
[Tue Oct 06 12:21:00 2015] [error] [client xx.xxx.xx.xx] Use of
uninitialized value in numeric ge (>=) at
/usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 769.,
referer: http://104.193.218.155/cgi-bin/gb2/gbrowse/yeast_advanced/
[Tue Oct 06 12:21:02 2015] [error] [client xx.xxx.xx.xx] Can't store GLOB
items at ../../lib/Storable.pm (autosplit into ../../lib/auto/Storable/_
store.al) line 264, at /usr/local/share/perl5/Bio/Graphics/FeatureFile.pm
line 445., referer:
http://104.193.218.155/cgi-bin/gb2/gbrowse/yeast_advanced/
[Tue Oct 06 12:21:02 2015] [error] [client xx.xxx.xx.xx] Use of
uninitialized value in numeric ge (>=) at
/usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 769.,
referer: http://104.193.218.155/cgi-bin/gb2/gbrowse/yeast_advanced/
[Tue Oct 06 12:21:02 2015] [error] [client xx.xxx.xx.xx] Use of
uninitialized value in numeric ge (>=) at
/usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 769.,
referer: http://104.193.218.155/cgi-bin/gb2/gbrowse/yeast_advanced/
[Tue Oct 06 12:21:03 2015] [error] [client xx.xxx.xx.xx] Can't store GLOB
items at ../../lib/Storable.pm (autosplit into ../../lib/auto/Storable/_
store.al) line 264, at /usr/local/share/perl5/Bio/Graphics/FeatureFile.pm
line 445., referer: http://104.193.218.155/cgi-bin/gb2/gbrowse/human/
[Tue Oct 06 12:21:03 2015] [error] [client xx.xxx.xx.xx] Use of
uninitialized value in numeric ge (>=) at
/usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 769.,
referer: http://104.193.218.155/cgi-bin/gb2/gbrowse/human/
[Tue Oct 06 12:21:03 2015] [error] [client xx.xxx.xx.xx] Use of
uninitialized value in numeric ge (>=) at
/usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 769.,
referer: http://104.193.218.155/cgi-bin/gb2/gbrowse/human/

...

Tue Oct 06 12:21:05 2015] [error] [client xx.xxx.xx.xx] [20903] rendering
error track: Timeout; Try turning off tracks or looking at a smaller
region. at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line
3693., referer: http://104.193.218.155/cgi-bin/gb2/gbrowse/human/
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