gav's questions

All e-mail sent from a yahoo.com server to my domain fails to be correctly received. The difference between yahoo.com and other domains is that they open with HELO rather than EHLO and therefore attempt to send the data in one part rather than in chunks (as I understand it).

Looking at the wikipedia example communication it seems that we are conforming to the protocol our side. When we expect data to arrive with us however the yahoo server fails to reply leading to a timeout.

2010-10-27T09:17:15.52...-,,Local
2010-10-27T09:17:18.11...+,,
2010-10-27T09:17:18.11...*,SMTPSubmit SMTPAcceptAnySender SMTPAcceptAuthoritativeDomainSender AcceptRoutingHeaders,Set Session Permissions
2010-10-27T09:17:18.11...>,"220 remote.ourserver.co.uk Microsoft ESMTP MAIL Service ready at Wed, 27 Oct 2010 10:17:17 +0100",
2010-10-27T09:17:18.13...<,HELO omp1009.mail.ukl.yahoo.com,
2010-10-27T09:17:18.13...>,250 remote.ourserver.co.uk Hello [xxx.xxx.xxx.xxx],
2010-10-27T09:17:18.14...<,MAIL FROM:<[email protected]>,
2010-10-27T09:17:18.14...*,08CD4019188CB09A;2010-10-27T09:17:18.111Z;1,receiving message
2010-10-27T09:17:18.14...>,250 2.1.0 Sender OK,
2010-10-27T09:17:18.16...<,RCPT TO:<[email protected]>,
2010-10-27T09:17:18.16...>,250 2.1.5 Recipient OK,
2010-10-27T09:17:18.17...,<,DATA,
2010-10-27T09:17:18.17...,>,354 Start mail input; end with <CRLF>.<CRLF>,
2010-10-27T09:19:08.19...

I am stumped as to what to try, I attempted to manually telnet and send an e-mail but I get rejected as I don't have a valid server to send from (I get refused as potential junk).

I have access to the logs of the box but not easy access to the config. Any advice would be greatly appreciated.

Running python from my terminal currently uses the packaged Cygwin install;

$ which python
/usr/bin/python

But I want it to point at;

C:\Python27

in other words;

/cygdrive/c/Python27/python

I could add an alias in my ~/.profile but this feels hacky to me, the latter python is on my path but the Cygwin bundled version overrides it.

I am actually using xrvt if it makes any difference.

Many thanks in advance!

I'm read up a bit about this tool and obviously looked at the man pages. The trouble is that ddrescue takes so long I need to get the command right first time. I wasn't sure how to improve on the vanilla;

$ sudo ./ddrescue -v /dev/disk0s5 MyVolImage.dmg MyVolRescue.log
$ sudo ./ddrescue -v MyVolImage.dmg /dev/disk1s3 MyVolRestore.log

• From HSF+ to HSF+ drives
• Source (Broken) HDD is connected via USB 2.0
• Dest HDD is inside MacBook
• I would choose accuracy over speed

There seem to be a lot of options but I'm not sure how they impact quality and speed of recovery.

Thanks,

Gav

I have a 2.5" SATA hard drive on an employee's MacBook which is in a lot of pain. I can hear it trying to read when I boot and it fails without an error.

If I take this drive out and attach it to another box using a caddy what tools are there for recovering data? The tools can be on Windows or Linux (I don't have another Mac!).

I don't usually work with OSX, is there anything I need to know about the file format before I start the job?

Thanks,

Gav

I am running Ubuntu and am ultimately trying to connect Tomcat to my MySQL database using JDBC.

It has worked previously but after a reboot the instance now fails to connect.

• Both Tomcat 6 and MySQL 5.0.75 are on the same machine
• Connection string: jdbc:mysql:///localhost:3306
• I can connect to MySQL on the command line using the mysql command
• The my.cnf file is pretty standard (Available on request) has bind address: 127.0.0.1
• I cannot Telnet to the MySQL port despite netstat saying MySQL is listening
• I have one IpTables rule to forward 80 -> 8080 and no firewall I'm aware of.

I'm pretty new to this and I'm not sure what else to test. I don't know whether I should be looking in etc/interfaces and if I did what to look for. It's weird because it used to work but after a reboot it's down so I must have changed something.... :).

I realise a timeout indicates the server is not responding and I assume it's because the request isn't actually getting through. I installed MySQL via apt-get and Tomcat manually.

MySqld processes

root@88:/var/log/mysql#  ps -ef | grep mysqld
root     21753     1  0 May27 ?        00:00:00 /bin/sh /usr/bin/mysqld_safe
mysql    21792 21753  0 May27 ?        00:00:00 /usr/sbin/mysqld --basedir=/usr --datadir=/var/lib/mysql --user=mysql --pid-file=/var/run/mysqld/mysqld.pid --skip-external-locking --port=3306 --socket=/var/run/mysqld/mysqld.sock
root     21793 21753  0 May27 ?        00:00:00 logger -p daemon.err -t mysqld_safe -i -t mysqld
root     21888 13676  0 11:23 pts/1    00:00:00 grep mysqld

Netstat

root@88:/var/log/mysql# netstat -lnp | grep mysql
tcp        0      0 0.0.0.0:3306            0.0.0.0:*               LISTEN      21792/mysqld
unix  2      [ ACC ]     STREAM     LISTENING     1926205077 21792/mysqld        /var/run/mysqld/mysqld.sock

Toy Connection Class

root@88:~# cat TestConnect/TestConnection.java

import java.sql.Connection;
import java.sql.DriverManager;
import java.sql.SQLException;

public class TestConnection {

  public static void main(String args[]) throws Exception {
    Connection con = null;

    try {
      Class.forName("com.mysql.jdbc.Driver").newInstance();
      System.out.println("Got driver");
      con = DriverManager.getConnection(
                "jdbc:mysql:///localhost:3306",
                "uname", "pass");
      System.out.println("Got connection");

      if(!con.isClosed())
        System.out.println("Successfully connected to " +
          "MySQL server using TCP/IP...");

    } finally {
        if(con != null)
          con.close();
    }
  }
}

Toy Connection Class Output

Note: This is the same error I get from Tomcat.

root@88:~/TestConnect# java -cp mysql-connector-java-5.1.12-bin.jar:. TestConnection
Got driver
                Exception in thread "main" com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure

The last packet sent successfully to the server was 1 milliseconds ago. The driver has not received any packets from the server.
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
        at com.mysql.jdbc.Util.handleNewInstance(Util.java:409)
        at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1122)            
        at TestConnection.main(TestConnection.java:14)
Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure

The last packet sent successfully to the server was 0 milliseconds ago. The driver has not received any packets from the server.
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
        at com.mysql.jdbc.Util.handleNewInstance(Util.java:409)
        at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1122)
        at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:344)
        at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2181)
        ... 12 more
Caused by: java.net.ConnectException: Connection timed out
        at java.net.PlainSocketImpl.socketConnect(Native Method)
        ... 13 more

Telnet Output

root@88:~/TestConnect# telnet localhost 3306
Trying 127.0.0.1...
telnet: Unable to connect to remote host: Connection timed out

Iptables

NOTE: I did have a rule setup in for NAT but I've removed it and the problem persists.

root@88:~# iptables -nL
Chain INPUT (policy ACCEPT)
target     prot opt source               destination

Chain FORWARD (policy ACCEPT)
target     prot opt source               destination

Chain OUTPUT (policy ACCEPT)
target     prot opt source               destination

root@88:~# iptables -t nat -nL
Chain PREROUTING (policy ACCEPT)
target     prot opt source               destination

Chain POSTROUTING (policy ACCEPT)
target     prot opt source               destination

Chain OUTPUT (policy ACCEPT)
target     prot opt source               destination

Command used to setup iptables

iptables -t nat -I PREROUTING --src 0/0 --dst 88.198.31.14 -p tcp --dport 80 -j REDIRECT --to-ports 8080

I have since removed the rule this setup for the NAT so unbless there's a side effect to this command it's not relevant.

UPDATE -I can't ping localhost

ip a

root@88:~/TestConnect# ip a
1: lo: <LOOPBACK> mtu 16436 qdisc noop state DOWN
    link/loopback 00:00:00:00:00:00 brd 00:00:00:00:00:00
3: venet0: <BROADCAST,POINTOPOINT,NOARP,UP,LOWER_UP> mtu 1500 qdisc noqueue state UNKNOWN
    link/void
    inet 127.0.0.1/32 scope host venet0
    inet 88.198.31.14/32 scope global venet0:0

ip r

root@88:~/TestConnect# ip r
    192.0.2.1 dev venet0  scope link
    default via 192.0.2.1 dev venet0

ip rule

root@88:~/TestConnect# ip rule
0:      from all lookup local
32766:  from all lookup main
32767:  from all lookup default

ping -c 1 localhost

root@88:~/TestConnect# ping -c 1 localhost
PING localhost.localdomain (127.0.0.1) 56(84) bytes of data.

--- localhost.localdomain ping statistics ---
1 packets transmitted, 0 received, 100% packet loss, time 0ms

cat /etc/hosts

root@88:~/TestConnect# cat /etc/hosts
127.0.0.1 localhost.localdomain localhost
# Auto-generated hostname. Please do not remove this comment.
88.198.31.14 88.198.31.14  88 88

ifconfig

root@88:/var/log/mysql# ifconfig
venet0    Link encap:UNSPEC  HWaddr 00-00-00-00-00-00-00-00-00-00-00-00-00-00-00-00
          inet addr:127.0.0.1  P-t-P:127.0.0.1  Bcast:0.0.0.0  Mask:255.255.255.255
          UP BROADCAST POINTOPOINT RUNNING NOARP  MTU:1500  Metric:1
          RX packets:144432 errors:0 dropped:0 overruns:0 frame:0
          TX packets:153825 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:0
          RX bytes:37896766 (37.8 MB)  TX bytes:28722595 (28.7 MB)

venet0:0  Link encap:UNSPEC  HWaddr 00-00-00-00-00-00-00-00-00-00-00-00-00-00-00-00
          inet addr:88.198.31.14  P-t-P:88.198.31.14  Bcast:0.0.0.0  Mask:255.255.255.255
          UP BROADCAST POINTOPOINT RUNNING NOARP  MTU:1500  Metric:1

Thanks to pQd I think we've narrowed down the error, I need to go read up about what this all means and why localhost isn't ping-able.

I missed a payment for my server and hey suspended my account for a day or so. When they brought the server back up all my data was in tact but for some reason Tomcat can't make a JDBC connection to my MySql server. They both run on the same machine and hence I have a bind address of 127.0.0.1.

It's strange because I have reset the machine of my own accord before without issue but clearly something has been reset in the downtime.

I followed this guide (Just the bits which don't concern S3, I am not on Amazon infrastructure) originally and everything worked as expected.

I'm very new to being a SysAdmin and I'm not sure what to try, how would you go about diagnosing this issue? The stack trace I get is as follows;

INFO: Deploying web application archive myapp-1.1.war
2010-05-26 22:07:22,221 [main] ERROR context.ContextLoader  - Context initialization failed
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'messageSource': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager': Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Cannot resolve reference to bean 'hibernateProperties' while setting bean property 'hibernateProperties'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'hibernateProperties': Cannot resolve reference to bean 'dialectDetector' while setting bean property 'properties' with key [hibernate.dialect]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'dialectDetector': Invocation of init method failed; nested exception is org.springframework.jdbc.support.MetaDataAccessException: Could not get Connection for extracting meta data; nested exception is org.springframework.jdbc.CannotGetJdbcConnectionException: Could not get JDBC Connection; nested exception is org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (Communications link failure

The last packet sent successfully to the server was 0 milliseconds ago. The driver has not received any packets from the server.)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:519)
        at org.codehaus.groovy.grails.commons.spring.ReloadAwareAutowireCapableBeanFactory.doCreateBean(ReloadAwareAutowireCapableBeanFactory.java:129)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450)
        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:287)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
        at org.springframework.context.support.AbstractApplicationContext.initMessageSource(AbstractApplicationContext.java:714)
        at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:404)
        at org.codehaus.groovy.grails.commons.spring.GrailsWebApplicationContext.refresh(GrailsWebApplicationContext.java:153)

...

I get this error for a number of 'beans'.

If I type mysql at my command prompt then I can easily login with the same credentials as my grails app which uses GORM and Hibernate to persist objects to the DB.

I might not have given enough info to start with but I'm really interested to learn and will certainly provide it if asked, I just really don't know where to start on this one.

UPDATE: I can connect to mysql by running the binary at the command line. I also ran mysql over tcp and couldn't connect, does this spread any light on the issue?

root@88:~# mysql -u grails --protocol=tcp -p
Enter password:
ERROR 2003 (HY000): Can't connect to MySQL server on 'localhost' (110)

I have bind-address as 127.0.0.1 as previously discussed so maybe it's not a surprise this doesn't work. Is there anything I need to check in my hosts file?

Thanks,

Gav

I installed Tomcat 6 using the tar-ball via wget. Startup of the server is fine but on shutdown I get a timeout exception.

root@88:/usr/local/tomcat/logs# /usr/local/tomcat/bin/shutdown.sh 
Using CATALINA_BASE:   /usr/local/tomcat
Using CATALINA_HOME:   /usr/local/tomcat
Using CATALINA_TMPDIR: /usr/local/tomcat/temp
Using JRE_HOME:        /usr
Using CLASSPATH:       /usr/local/tomcat/bin/bootstrap.jar
30-Mar-2010 17:33:41 org.apache.catalina.startup.Catalina stopServer
SEVERE: Catalina.stop: 
java.net.ConnectException: Connection timed out
    at java.net.PlainSocketImpl.socketConnect(Native Method)
    at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:333)
    at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:195)
    at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:182)
    at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366)
    ...

I read that this might be because I have a firewall blocking incoming connections on the shutdown port (8005). I have a default Ubuntu 9.04 installation running on a VPS with no rules in my iptables. How can I tell if that port is blocked? How can I check that the server is listening for connections on 8005?

Bizarrely pinging localhost or the IP of my server fails from the server itself, whereas pinging the IP of my server from another machine succeeds.

-------- EDIT -------- (In reply to Davey)

Thanks for all the tips and suggestions!

netstat -nlp

Active Internet connections (only servers)
Proto Recv-Q Send-Q Local Address           Foreign Address         State       PID/Program name
tcp        0      0 127.0.0.1:8005          0.0.0.0:*               LISTEN      9611/java       
tcp        0      0 127.0.0.1:3306          0.0.0.0:*               LISTEN      28505/mysqld    
tcp        0      0 0.0.0.0:8080            0.0.0.0:*               LISTEN      9611/java       
tcp        0      0 0.0.0.0:22              0.0.0.0:*               LISTEN      

...

So we can see that tomcat is listening, I just don't seem to be able to reach it.

root@88:/usr/local/tomcat# telnet localhost 8005
Trying 127.0.0.1...

Trying to telnet to the port Hangs indefinitely. I have no rules in my iptables so I don't think it's a firewall thing.

root@88:/usr/local/tomcat# iptables --list
Chain INPUT (policy ACCEPT)
target     prot opt source               destination         

Chain FORWARD (policy ACCEPT)
target     prot opt source               destination         

Chain OUTPUT (policy ACCEPT)
target     prot opt source               destination 

This is the contents of /etc/hosts

127.0.0.1 localhost.localdomain localhost
# Auto-generated hostname. Please do not remove this comment.
88.198.31.14 88.198.31.14  88 88

But I still can't ping localhost... do I need to check a loopback device is enabled properly or something? (I'm unsure how to do that if you do say yes :)).

root@88:/usr/local/tomcat# ping localhost
PING localhost (127.0.0.1) 56(84) bytes of data.

--- localhost ping statistics ---
7 packets transmitted, 0 received, 100% packet loss, time 5999ms

Trying to find out what the loop back is configured as;

root@88:~# ifconfig lo
lo        Link encap:Local Loopback  
          LOOPBACK  MTU:16436  Metric:1
          RX packets:0 errors:0 dropped:0 overruns:0 frame:0
          TX packets:0 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:0 
          RX bytes:0 (0.0 B)  TX bytes:0 (0.0 B)

SOLUTION THANKS TO DAVEY

I needed to bring up the interface (Not sure why it wasn't running). ifconfig lo up did the trick.

root@88:~# ifconfig lo up
root@88:~# ifconfig lo
lo        Link encap:Local Loopback  
          inet addr:127.0.0.1  Mask:255.0.0.0
          inet6 addr: ::1/128 Scope:Host
          UP LOOPBACK RUNNING  MTU:16436  Metric:1
          RX packets:0 errors:0 dropped:0 overruns:0 frame:0
          TX packets:0 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:0 
          RX bytes:0 (0.0 B)  TX bytes:0 (0.0 B)

root@88:~# ping localhost
PING localhost.localdomain (127.0.0.1) 56(84) bytes of data.
64 bytes from localhost.localdomain (127.0.0.1): icmp_seq=1 ttl=64 time=0.025 ms

Thanks again,

Gav

I installed Tomcat6 on a Ubuntu 9.04 server using apt-get install tomcat6. I uploaded a WAR using the manager interface and tried to start the application but get a pretty generic error on the Web interface saying it couldn't be started.

I am trying to find the logs to determine why my war won't start (I suspect low memory as i'm on a small VPS) but I don't know where they are.

/var/lib/tomcat6/logs is empty. My Tomcat splash page reliably informs me of the following;

Tomcat is installed with CATALINA_HOME in /usr/share/tomcat6 
CATALINA_BASE in /var/lib/tomcat6, 
following the rules from /usr/share/doc/tomcat6-common/RUNNING.txt.gz.

UPDATE

I tried running;

$ ps -ax 
/usr/bin/jsvc -user tomcat6 -cp /usr/share/java/commons-daemon.jar:/usr/share/tomcat6/bin/bootstrap.jar -outfile SYSLOG -errfile SYSLOG -pidfile /var/run/tomcat6.pid

But there is nothing in /var/log/syslog

Also runing

$ losof -p PID

didn't show any log files...

$  for PID in $(pgrep jsvc);do sudo ls -l /proc/$PID/fd|grep ' 1 -> ';done
l-wx------ 1 root 500 64 2010-03-30 13:29 1 -> pipe:[301470406]
lrwx------ 1 root 500 64 2010-03-30 13:29 1 -> /dev/null
l-wx------ 1 root root 64 2010-03-30 13:29 1 -> pipe:[301470406]

Thanks,

Gav

tl;dr - I have a rooted linux box that I want to run tomcat on as a server (No Apache Web Server) how would you set this up avoiding common security pitfalls?

I've written a Grails App that I want to run on a VPS I rent. The VPS has very little memory and I am using it for the sole purpose of running this application so I don't need the apache web server.

This is my first venture into Server administration and I'm sure to fall into some well known traps.

• Should I use iptables to redirect requests from port 80 to 8080?
• Should I run tomcat as root or as its own user?
• What configuration settings would be good for a low memory system expecting less than 10 concurrent users?

Hopefully an easy one for you! Anyone who could link to a tutorial would be a personal hero destined for great things no doubt.

Gav