I had already tried Project -> Clean… and closing Eclipse, deleting all the built class files and restarting Eclipse to no avail as was the original question author. The right answer lies in deleting the corrupted search index which is explained in Eclipse bug’s #269820 comment.

How to delete the search index:

1. Close Eclipse
2. Delete workspace/.metadata/.plugins/org.eclipse.jdt.core/*.index
3. Delete workspace/.metadata/.plugins/org.eclipse.jdt.core/savedIndexNames.txt
4. Start Eclipse again

This fixed the issue for me.

Luckily it is easy to tell the system to redirect the traffic from some port to other. Just define some new xinetd services in /etc/xinetd.d/tomcat.

# vim /etc/xinetd.d/tomcat
# Redirects any requests on port 80 to port 8080 (where Tomcat is listening)
service tomcat-http
{
        disable                 = no
        flags                   = REUSE
        wait                    = no
        user                    = root
        socket_type         = stream
        protocol                = tcp
        port                    = 80
        redirect                = localhost 8080
        log_on_success  -= PID HOST DURATION EXIT

        #per_source = UNLIMITED
        #instances = UNLIMITED
}

# Redirects any requests on port 443 to port 8443 (where Tomcat is listening)
service tomcat-https
{
        disable                 = no
        flags                   = REUSE
        wait                    = no
        user                    = root
        socket_type         = stream
        protocol                = tcp
        port                    = 443
        redirect                = localhost 8443
        log_on_success  -= PID HOST DURATION EXIT

        #per_source = UNLIMITED
        #instances = UNLIMITED
}

(via Securing Linux for Java services: The port dilemma)

Xinetd puts a connection limit per source IP, by default and this causes the service to become unresponsive when there are dozens of queries a second. You see the following kind of line in your messages log file: “xinetd[2049]: FAIL: tomcat-https per_source_limit from=123.456.789.123″. To correct this, uncomment the per_source and instances lines in your xinet.d file and restart it.

Also add those xinetd services to /etc/services.

# vim /etc/services
http        80/tcp     www www-http tomcat-http # WorldWideWeb http
http        80/udp     www www-http tomcat-http # WorldWideWeb HTTP
http        443/tcp    tomcat-https # WorldWideWeb HTTPS
http        443/udp    tomcat-https # WorldWideWeb HTTPS

And now just restart the xinetd and admire how your traffic is redirected to Tomcat’s ports.

# service xinetd restart

Force everything to transmit through HTTPS
If you also want to redirect all HTTP traffic to HTTPS you can add the following section to you Tomcat web.xml:

     <web-resource-collection>
        <web-resource-name>Protected Context</web-resource-name>
          <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <<!-- auth-constraint goes here if you requre authentication -->
      user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
    </security-constraint>

If you are using this redirection of all traffic to HTTPS with JIRA and want to attachments working also with Internet Explorer then you must add the following to your jira.xml (f. ex. /opt/tomcat/conf/Catalina/localhost/jira.xml). This is a Internet Explorer bug, for more information see http://jira.atlassian.com/browse/JRA-8179.

<Context ...>
...
<!-- for IE bug, see http://jira.atlassian.com/browse/JRA-8179-->
<Valve className="org.apache.catalina.authenticator.NonLoginAuthenticator"
disableProxyCaching="false" />

...
</Context ...>

Simply say in the command line of domU:

echo 1 > /proc/sys/xen/independent_wallclock

Or if you have noclobber on:

echo 1 >! /proc/sys/xen/independent_wallclock

To reenable tracking of Xen wallclock:

echo 0 > /proc/sys/xen/independent_wallclock

And to keep the setting between reboots, just add it to the /etc/sysctl.conf:

xen.independent_wallclock = 1

Although, it is better if the Xen dom0 syncs the clock frequently so all the domains (domU) don’t need to do it by themselves and thus wasting resources. Why do things multiple times when it could be done just once.

My Samba service had worked fine for a long time but after a kernel update and a reboot, the performance was horrible. It was really slow to do anything. Fortunately I wasn’t the only one to come by with this problem and there was a topic Samba Performance Problem Due to Changing Linux Kernel in Samba Performance Tuning -guide which provided a solution to my problem. Just restarted the network interface and the performance was as good as before.

Earlier this month Samba Team Received Microsoft Protocol Docs so maybe in the near future we will get better and faster software.

The Protocol Freedom Information Foundation (PFIF), signed an agreement with Microsoft to receive the protocol documentation needed to fully interoperate with the Microsoft Windows workgroup server products and to make them available to Free Software projects such as Samba.

Microsoft was required to make this information available to competitors as part of the European Commission March 24th 2004 Decision in the antitrust lawsuit, after losing their appeal against that decision on September 17th 2007.
- Samba Team

After some googling I found a Spanish-blog which explained the “bug” and provided a solution. Unfortunately I don’t speak Spanish but the solution was clear with pieces of code to show the way. After I knew what to look for I found some discussions about this topic on WordPress Trac and an entry 2 weeks ago with a patch gettext-64-without-bitwise-ops.diff seems to get the thing fixed.

The problem is in the PHP-gettext which is used for translating strings. The file is located at wp-includes/gettext.php and in that file the problem is created by fixing a bug in PHP 5.0.2 on 64-bit systems. The counterfix is luckily an easy one and you just have to remove some bitwise operators.

The solution with problematic line on red and the fix on green:

wp-includes/gettext.php
line
115	$this->STREAM = $Reader;
116	$magic = $this->readint();
117    	if ($magic == ($MAGIC1 & 0xFFFFFFFF) || $magic == ($MAGIC3 & 0xFFFFFFFF)) { // to make sure it works for 64-bit platforms
117	if ($magic == $MAGIC1 || $magic == $MAGIC3) { // to make sure it works for 64-bit platforms
118		$this->BYTEORDER = 0;
119	} elseif ($magic == ($MAGIC2 & 0xFFFFFFFF)) {
120		$this->BYTEORDER = 1;

The search engines <3

Update, 2008-02-05:
With WordPress 2.3.3 this bug is finally closed with some other minor bug fixes and security fix for xmlrpc.php.

The problem is that /usr/lib/libaprutil-0.so.0.9.12 which belongs to apr-util is still broken. But how can that be broken when you just ran the revdep-rebuild which should have fixed the problem. The reason is that by executing eix apr-util, you see that there are two versions of apr-util installed.

After re-emergeing the apr-util-0.9.12-r1, apache2 starts normally.

The problem is actually caused by the “-X” option of revdep-rebuild command, which emerges the best (currrently is the latest stable) packages available. In this apr-util case, it will emerge apr-util-1.2.8.

So for slotted packages, don’t use “-X” option for revdep-rebuild command.
- Shaochun Wang

SNMP and MRTG graphs

Statistics and graphs are nice way to follow what the machine is doing. Just a little bit of configuration and scripts you can use f. ex. servers’, routers’ and firewalls’ operational statistical data from their Object Identifiers (OID) with the help of Simple Network Management Protocol (SNMP) and Management Information Base (MIB) which define the available OID functions.

For more detailed how-to, check out: http://www.siliconvalleyccie.com/linux-hn/mrtg.htm#_Toc92809393 or a bit Gentoo specific guide http://forums.gentoo.org/viewtopic-t-105865-highlight-mrtg+rrdtool.html

Tools for the job

From Gentoo package-format:

* [net-analyzer/net-snmp]
* [net-analyzer/mrtg]
* [net-analyzer/rrdtool]
* [net-www/apache]

SNMP

We want to restrict the use of SNMP to local network so we edit SNMP’s config file which contains the community string and other parameters. Our selected community string here is “humppa”.

/etc/snmp/snmpd.conf

com2sec    local    localhost    humppa
com2sec    network_1    172.168.1.0/24    humppa
com2sec    network_2    192.168.1.0/24    humppa

group    MyROGroup    v1    local
group    MyROGroup    v1    network_1
group    MyROGroup    v1    network_2

view    all-mibs    included    .1    80

access   MyROGroup  ""  v1  noauth  0  all-mibs  none  none

So now:

• only 3 networks (localhost, 172.168.1.0/24, and 192.168.1.0/24) are allowed to use SNMP with humppa community string.
• Every network is on the MyROGroup and defined to use SNMP version 1 protocol with all MIBs.
• Only Reading the MIBs is allowed and thus the write section is “none”.

Start the SNMP service:

root@pikseli ~ # /etc/init.d/snmpd start
* Starting net-snmpd ... [ ok ]

Add the service to always start after reboots:

 ~ # rc-update add snmpd default
 * snmpd added to runlevel default
 * rc-update complete.

Test that the SNMP works with snmpwalk

~ # snmpwalk -v 1 -c humppa localhost system
SNMPv2-MIB::sysDescr.0 = STRING: Linux pikseli 2.6.11-ck1 #1 Fri Mar 4 01:59:56 EET 2005 x86_64
SNMPv2-MIB::sysObjectID.0 = OID: NET-SNMP-MIB::netSnmpAgentOIDs.10
SNMPv2-MIB::sysUpTime.0 = Timeticks: (13374) 0:02:13.74
SNMPv2-MIB::sysContact.0 = STRING: xyz@qwe.fi
SNMPv2-MIB::sysName.0 = STRING: mysupercomputer
...
...
~ # snmpwalk -v 1 -c humppa localhost interface
IF-MIB::ifNumber.0 = INTEGER: 3
IF-MIB::ifIndex.1 = INTEGER: 1
IF-MIB::ifIndex.2 = INTEGER: 2
IF-MIB::ifIndex.3 = INTEGER: 3
IF-MIB::ifDescr.1 = STRING: eth0
IF-MIB::ifDescr.2 = STRING: lo
IF-MIB::ifDescr.3 = STRING: eth1
...
...
~ #

MRTG

MRTG (Multi-Router Traffic Grapher) is a tool to draw some graphs from different statistical sources and they can look like the image on the right.

Configuring MRTG

MRTG’s config file is usually found in /etc/mrtg/mrtg.cfg and the resulting files are usually found under the Web Server’s root (f. ex. /var/www/mrtg/).

Mrtg Config:

LogFormat: rrdtool
EnableIPv6: no
Options[_]: bits,growright

# System: My Super Computer
# Description: Linux mysupercomputer
# Contact: -
# Location: Finland

# Global configuration
LoadMIBs: /usr/share/snmp/mibs/UCD-SNMP-MIB.txt, \
/usr/share/snmp/mibs/TCP-MIB.txt, \
/usr/share/snmp/mibs/HOST-RESOURCES-MIB.txt

Title[server.net]: a 10MB line to Internet
PNGTitle[server.net]: Internet Traffic
PageTop[server.net]: <H1>Link to the Internet</H1>
Target[server.net]: 1:humppa@localhost
MaxBytes[server.net]: 10000000
YLegend[server.net]: kbps
Options[server.net]: growright

# Established TCP Connections
Target[server.estabcons]: tcpCurrEstab.0&tcpCurrEstab.0:humppa@localhost
Title[server.estabcons]: Currently Established TCP Connections
PNGTitle[server.estabcons]: Currently Established TCP Connections
PageTop[server.estabcons]: <H1>Established TCP Connections</H1>
MaxBytes[server.estabcons]: 10000000000
ShortLegend[server.estabcons]:
YLegend[server.estabcons]: Connections
LegendI[server.estabcons]: In
LegendO[server.estabcons]:
Legend1[server.estabcons]: Established connections
Legend2[server.estabcons]:
Options[server.estabcons]: growright,nopercent,gauge

# New TCP Connection Monitoring (per minute)
Target[server.newconns]: tcpPassiveOpens.0&tcpActiveOpens.0:humppa@localhost
Title[server.newconns]: Newly Created TCP Connections
PNGTitle[server.newconns]: Newly Created TCP Connections
PageTop[server.newconns]: <H1>New TCP Connections
MaxBytes[server.newconns]: 10000000000
ShortLegend[server.newconns]: c/s
YLegend[server.newconns]: Conns / Min
LegendI[server.newconns]: In
LegendO[server.newconns]: Out
Legend1[server.newconns]: New inbound connections
Legend2[server.newconns]: New outbound connections
Options[server.newconns]: growright,nopercent,perminute

Target[server.cpu]:ssCpuRawUser.0&ssCpuRawUser.0:humppa@localhost + \
ssCpuRawSystem.0&ssCpuRawSystem.0:humppa@localhost + \ 
ssCpuRawNice.0&ssCpuRawNice.0:humppamachine@localhost
RouterUptime[server.cpu]: humppa@localhost
MaxBytes[server.cpu]: 100
Title[server.cpu]: CPU Load
PNGTitle[server.cpu]: CPU Load
PageTop[server.cpu]: <H1>Active CPU Load %</H1>
Unscaled[server.cpu]: ymwd
ShortLegend[server.cpu]: %
YLegend[server.cpu]: CPU Utilization
Legend1[server.cpu]: Active CPU in % (Load)
Legend2[server.cpu]:
Legend3[server.cpu]:
Legend4[server.cpu]:
LegendI[server.cpu]:  Active
LegendO[server.cpu]:
Options[server.cpu]: growright,nopercent

Target[server.rootdisk]:hrStorageSize.4&hrStorageUsed.4:humppa@localhost * 4000
MaxBytes[server.rootdisk]: 12000000000
Unscaled[server.rootdisk]: dwym
Title[server.rootdisk]: Disk / Usage ( / )
PNGTitle[server.rootdisk]: Disk / Usage ( / )
PageTop[server.rootdisk]: <H1>Disk / Usage ( / )</H1>
ShortLegend[server.rootdisk]: B
kilo[server.rootdisk]: 1024
YLegend[server.rootdisk]: disk utilization
Legend1[server.rootdisk]: / disk size
Legend2[server.rootdisk]: / disk used
Legend3[server.rootdisk]:
Legend4[server.rootdisk]:
LegendI[server.rootdisk]:  / disk size
LegendO[server.rootdisk]:  / disk used
Options[server.rootdisk]: growright, gauge,nopercent

Target[server.usrsys]: ssCpuRawUser.0&ssCpuRawSystem.0:humppa@localhost
Title[server.usrsys]: CPU usr sys
PNGTitle[server.usrsys]: CPU usr sys
MaxBytes[server.usrsys]: 100
PageTop[server.usrsys]: <H1>Active CPU Load (usr sys) %</H1>
Unscaled[server.usrsys]: ymwd
ShortLegend[server.usrsys]: %
YLegend[server.usrsys]: CPU Utilization
Legend1[server.usrsys]: % (usr)
Legend2[server.usrsys]: % (sys)
Legend3[server.usrsys]:
Legend4[server.usrsys]:
LegendI[server.usrsys]: % (usr)
LegendO[server.usrsys]: % (sys)
Options[server.usrsys]: growright, nopercent

Checking the MRTG config

Execute the script env LANG=C /usr/bin/mrtg /etc/mrtg/mrtg.cfg 3 times. You get some errors but don’t worry.

Create or uncomment the following line in your cron.d so you get regularly updated graps (once in a 5 minutes)

/etc/cron.d/mrtg

0-59/5 * * * * root env LANG=C /usr/bin/mrtg /etc/mrtg/mrtg.cfg > /dev/null 2>&1

Finally create a index page for MRTG (f. ex. http://localhost/mrtg/index.html) with

~ # indexmaker --output=/var/www/mrtg/index.html \
 --title="Power of Tech Under Control :)" \
 --sort=name \
 --enumerate \
 /etc/mrtg/mrtg.cfg

MRTG ja RRDtool

MRTG can log data with RRDtool which is better than the default log format. Just use the “LogFormat: rrdtool” line and you’re done. There is more information about RRDtool and MRTG on Oetiker’s site.

mrtg-rrd

“The mrtg-rrd.cgi is a CGI/FastCGI script for displaying MRTG graphs from data in the RRDtool format. It can make your monitoring system faster because MRTG does not have to generate all the PNG files with graphs every 5 minutes or so. Instead of this the graphs are generated on-demand when the user wants to see them.” http://www.fi.muni.cz/~kas/mrtg-rrd/

To use Mrtg-rrd.cgi just download it from the link above and place it on Apache’s cgi-bin -directory.

Extra scripts for extra statistics

Memory and Swap usage

The script: mem.pl

Lines for the mrtg.cfg:

Target[server.mem-swap]: `/usr/local/sbin/mem.pl`
Title[server.mem-swap]: Mem and Swap Usage
Unscaled[server.mem-swap]: dwym
MaxBytes[server.mem-swap]: 300000000
PageTop[server.mem-swap]: <H1>Mem and Swap Usage</H1>
#kMG[server.mem-swap]: k,M,G,T,P
LegendI[server.mem-swap]: Swap
LegendO[server.mem-swap]: Mem
Legend1[server.mem-swap]: Swap
Legend2[server.mem-swap]: Mem
YLegend[server.mem-swap]: Mem and Swap Usage
ShortLegend[server.mem-swap]:  
Options[server.mem-swap]: gauge,nopercent

Ping Round Trip Time

The script: ping.sh

Lines for the mrtg.cfg:

# Ping
Title[server.ping]: Round Trip Time
PNGTitle[server.ping]: Round Trip Time
PageTop[server.ping]: <H1>Round Trip Time</H1>
Target[server.ping]: `/usr/local/sbin/ping.sh`
MaxBytes[server.ping]: 2000
Options[server.ping]: growright,unknaszero,nopercent,gauge
LegendI[server.ping]: Pkt loss %
LegendO[server.ping]: Avg RTT
Legend1[server.ping]: Maximum Round Trip Time in ms
Legend2[server.ping]: Minimum Round Trip Time in ms
Legend3[server.ping]: Maximal 5 Minute Maximum Round Trip Time in ms
Legend4[server.ping]: Maximal 5 Minute Minimum Round Trip Time in ms
YLegend[server.ping]: RTT (ms)

Uptime in days

The script: uptime.pl

And the lines for the mrtg.cfg:

Title[server.uptime]: System Uptime
PNGTitle[server.uptime]: System Uptime
PageTop[server.uptime]: <H1>System Uptime</H1>
Target[server.uptime]: `/usr/local/sbin/uptime.pl`
MaxBytes[server.uptime]: 1000
ShortLegend[server.uptime]: days
Options[server.uptime]: growright,unknaszero,nopercent,gauge
LegendI[server.uptime]: Uptime
LegendO[server.uptime]:
Legend1[server.uptime]: Maximum uptime in days
YLegend[server.uptime]: Time (days)
 

Apache hits and traffic

I googled for some scripts to get Apache statistics but found none. Luckily I had one on my harddrive which does the trick. Just don’t remember where I got it.

The trick is to enable “server-status” -information in Apache’s configuration. Your httpd.conf needs to include something like the following:

<Location /server-status>
    SetHandler server-status
    Order allow,deny
    Allow from localhost
</Location>
ExtendedStatus On

After that you can see Apache status in http://localhost/server-status.

Next step is the script: webstats.pl.

The lines for the MRTG are:

# Apache bytes
# server-info gives us kBytes, original script outputs bytes
Target[server.apache-tkbytes]: `/usr/local/sbin/webstats.pl bytes`
Title[server.apache-tkbytes]: Apache Traffic
PNGTitle[server.apache-tkbytes]: kBytes per second
MaxBytes[server.apache-tkbytes]: 256000
PageTop[server.apache-tkbytes]: <h2>Apache traffic</h2>
#Unscaled[server.apache-tkbytes]: ymwd
ShortLegend[server.apache-tkbytes]: kB/s
YLegend[server.apache-tkbytes]: kBytes/second
LegendI[server.apache-tkbytes]:
LegendO[server.apache-tkbytes]:  
Options[server.apache-tkbytes]: growright, nopercent, noinfo, nobanner, integer,noi

# Apache hits
Target[server.apache-thits]: `/usr/local/sbin/webstats.pl hits`
PageTop[server.apache-thits]: <h2>Apache Hits</h2>
Title[server.apache-thits]: Apache Hits
Options[server.apache-thits]:  growright, nopercent, perhour,nobanner, noinfo, integer, noi
MaxBytes[server.apache-thits]: 12000
YLegend[server.apache-thits]: hits/hour
ShortLegend[server.apache-thits]: hits/hour
WithPeak[server.apache-thits]: wmy
LegendI[server.apache-thits]:
LegendO[server.apache-thits]:  
Legend2[server.apache-thits]: Hits per hour
Legend4[server.apache-thits]: 5 minute Peak

Postfix stats: mails sent and received

Joel Knight at packetmischief.ca has a nice script for getting stats from Postfix. The idea is to “determine the number of email messages delivered locally and abroad per unit time and to graph that data.” There is also Craig Sanders’s script to provide same kind of results but I found the Joel Knight’s script to be little better.

The whole thing is documented on those pages so check them out and get some nice statistics. The difference between Joel’s and Craig’s scripts is that with Joel’s script you can also draw graphs of rejected mails.

Gongrats! You’re all done;

There is a great series of three articles on IBM’s developerWorks -site about Tuning LAMP systems. First article is about “Understanding the LAMP architecture”, second article concentrates on “Optimizing Apache and PHP” and final part is for “Tuning your MySQL server”.

More practical example is on Disruptive Library Technology Jester -blog which writes about WordPress/MySQL Tuning on a Pentium III with 512M RAM box which runs a mail server (IMAP, ClamScan, Spam) and an Apache (WordPress and stuff).

Article contains setting up Alternative PHP Cache and some options for database tuning focusing on memory management. About MySQL tuning the article points out Peter Zaitsev’s “What to tune in MySQL Server after installation” and ez.no documentation on Optimizing for read performance.

If you have app-admin/syslog-ng-2.0.4 and get errors like

syslog-ng[8827]: Number of allowed concurrent connections exceeded; num=’10′, max=’10′

to the syslog then read this helpfull topic from Gentoo forums.

There was also note in Changelog:

2.0.4:
Mon, 14 May 2007 11:47:48 +0200

IMPORTANT NOTES:
* This version of syslog-ng fixes a bug in enforcing the max-connections() limit for various stream-like sources (unix-stream and tcp). Previously this limit was not enforced, thus production environments may use an inadequate value. Validate your max-connection() settings before upgrading and check your logs for rejected connections.

In short, just change one line in /etc/syslog-ng/syslog-ng.conf to match with:
source src { unix-stream("/dev/log" max-connections(20)); internal(); pipe("/proc/kmsg"); };