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Why was the website so slow for so long?

The cause of the slowdown was a change to the ZFS dataset. In conjunction with the database server, very little caching was being done. This combination resulted in increased disk I/O as the system churned through the database. Details in the blog post which outlines the various things which changed. Many graphs.

Sanity Test Failure
Fri, 11 Nov 2016
[ 11:24 tijl ] Original commit   Revision:425884
linux-c6-flashplugin11 11.2r202.644 www  Deleted files touched by this commit  An older version of this port was marked as vulnerable. Restricted Adobe Flash Player NPAPI Plugin
MFH: r425840

Update flash plugin to 11.2r202.644.

Security:	https://helpx.adobe.com/security/products/flash-player/apsb16-37.html
Approved by:	ports-secteam (junovitch)

Sanity Test Results

www/linux-c7-flashplugin11:

I did not find a Makefile for this port, and none was mentioned in the
commit.  If a repocopy has been done, please ignore this message.This
command (FreshPorts code 1):

/usr/local/bin/sudo /usr/sbin/chroot -u dan /usr/FreshPorts/ports-jail
/make-port.sh /usr/local/PORTS-2016Q4 www/linux-c7-flashplugin11
2>/tmp/FreshPorts.www.linux-c7-flashplugin11.make-error.2016.11.11.11.24.56
.40435

produced this error:

Error message is: cd: /usr/local/PORTS-2016Q4/www/linux-c7-flashplugin11:
No such file or directory
make: cannot open
/usr/local/PORTS-2016Q4/www/linux-c7-flashplugin11/Makefile.
Make results are : 
make: stopped in /

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