If you use Windows and MS Office a lot use Skydrive and don’t read on There are posts which describe how to map the Skydrive like a local harddisk using MS Word.

On the long run I would like to mount a EBS storage like a local file tree, probably using WebDAV, but this is my first successful preliminary solution. s3cmd does not work for me.

Using Ubuntu/Linux rsync is a well established, reliable and easy to use tool to keep data between locations in sync. The following post marries rsync with an Elastic Cloud (EC2) server instance for an hour or some. One has to set up the so called rsync daemon and attach a persistent Elastic Block Storage.

This is another post. I will link to it later. There will also be a small script. There are some holes in this tutorial, only the direct configuration of the rsync daemon (including the script) is complete and working. I filled in some hints how to get to this stage. But will write follow ups on that.

System Out provided a nice tutorial of how to set up the rsync in demon mode on a server which listens for clients to sync their data.

Here is my version of it, with a short script at the end which should do the job.

Prerequisites

Of course you need to have rsync on both machines (the server and the client); since both are Ubuntu this is the case.

I will write another post on how to start the server. It is completely possible and quite intuitive to achieve it in the Amazon web interface. When the server is running and an extra EBS harddisk is attached you have to connect to the server using ssh
ssh -i PATH/TO/YOUR/PEM-KEY-FILE ubuntu@ec2-xxx-xx-xxx-xxx.compute-1.amazonaws.com

Mount the persistent drive

There are some posts about the advantages of the xfs filesystem, so I sticked to it. Alestic recommends it for all persistent EC2 cloud disks and I trust they know what they are doing. But xfs is not per default included in the Ubuntu micro instance I use for my backups. That said, in the SSH shell:

sudo apt-get install -y xfsprogs
sudo modprobe xfs

If the backup volume is newly created then format it:
sudo mkfs.xfs /dev/xvdb
Note: Only the first time. Otherwise you wipe your data, of course. Note also the device name. I attached it as /dev/sdb. Though it showed up in the Ubuntu Oneiric i386 t1.micro instance as /dev/xvdb.

Now mount the volume
echo "/dev/xvdb /media/backup xfs noatime 0 0" | sudo tee -a /etc/fstab
sudo mkdir /media/backup
sudo mount /media/backup
sudo chown ubuntu:ubuntu /media/backup
sudo chmod 777 /media/backup

Configuration files

On the server machine you need to set up a daemon to run in the background and host the rsync services.

Before you start the daemon you need to create some rsync daemon configuration files in the /etc directory.

Three files are necessary:

1. /etc/rsyncd.conf, the actual configuration file,
2. /etc/rsyncd.motd, Message Of The Day file (the contents of this file will be displayed by the server when a client machine connects) and
3. /etc/rsyncd.scrt, the username and password pairs.

To create the files on the server:
sudo nano /etc/rsyncd.conf

Now enter the following information into the rsyncd.conf file:

motd file = /etc/rsyncd.motd
[backup]
path = /media/backup
comment = the path to the backup directory on the server
uid = ubuntu
gid = ubuntu
read only = false
auth users = ubuntu
secrets file = /etc/rsyncd.scrt

Hit Ctrl-o to save and Ctrl-x to close nano.

The uid, gid, auth users are the users on the server. In the ssh session on the ec2 instance the user is ubuntu.

The format for the /etc/rsync.scrt file is
username:whatever_password_you_want

Use nano to put some arbitrary text into the /etc/rsync.motd.

Now you should have all the configuration information necessary, all that’s left to do is open the rsync port and start the daemon.

To open the port, open the /etc/default/rsync file, i.e.,

sudo nano /etc/default/rsync

and set RSYNC_ENABLE=true.

Here you might also specify another port than the default 873. Remember to open the port in the security group. Either with the AWS web interface in your browser or in the shell using the ec2-api-tools:
ec2-authorize default -p 873

Now to start the daemon,
sudo /etc/init.d/rsync restart
and exit the SSH session.

Syncing a folder

Now you can use your local shell to push some folders or files to the server. Update the server side from the client machine with ec2-api-tools installed:
EXIP=`ec2din | grep INSTANCE | grep -v terminated |awk '{print $4}'`
rsync -auv /home/rforge/articles ubuntu@$EXIP::backup/
$EXIP would be the server ip address

This gets the IP of the server from the ec2-api-tool and passes it to RSYNC.

Otherwise you have to remember the IP of your instance from the web interface and substitut it for xxx.xxx.xxx.xxx:
rsync -auv /PATH/TO/FOLDER/ ubuntu@$xxx.xxx.xxx.xxx::backup/

::backup has to match [backup] in the /etc/rsyncd.conf file. You will see the rsyncd.motd message and get prompted for the password in the rsyncd.scrt file. Then rsync starts the upload.

A Script

The following script should do the daemon setup after connecting to the server via ssh and mounting the volume. Keep me posted if something does not work.

echo "motd file = /etc/rsyncd.motd
[backup]
path = /media/backup
comment = the path to the backup directory on the server
uid = ubuntu
gid = ubuntu
read only = false
auth users = ubuntu
secrets file = /etc/rsyncd.scrt" > rsyncd.conf
sudo mv rsyncd.conf /etc/
#
sudo echo "Greetings! Give me the right password! Me want's it!" > rsyncd.motd
sudo mv rsyncd.motd /etc/
#
sudo echo "ubuntu:YourSecretPassword" > rsyncd.scrt
sudo mv rsyncd.scrt /etc/
#
sudo chmod 640 /etc/rsyncd.*
sudo chown root:root /etc/rsyncd.*
#
## enable demon mode in the /etc/default/rsync file
sudo cat /etc/default/rsync | sed 's/RSYNC_ENABLE=false/RSYNC_ENABLE=true/g' > rsync
sudo mv rsync /etc/default/
sudo chown root:root /etc/default/rsync
sudo chmod 644 /etc/default/rsync
#
sudo /etc/init.d/rsync restart # start the demon

This is not very newbee friendly and if included into a model-call nearly ufnreadable.

The function in the code box cut.at.n.tile() does the job.


cut.at.n.tile <- function(X , n = 4){ cut( X , breaks = quantile( X , probs = (0:n)/n , na.rm = TRUE ) , include.lowest = TRUE )}


In order to cut the continuous variable Creatinine in the dataset Patients into deciles (n=10) the syntax is:
cut.at.n.tile( Patients$Creatinine , n = 10 )

No big deal, but maybe useful…

The –type 0 option restricts the output to BIOS specific information and grep fishes for the revision number.

On my X61s Thinkpad the resulting output is
BIOS Revision: 2.19
Firmware Revision: 1.3

tr '[:upper:]' '[:lower:]' output.txt

I needed to clean up a messy old scriptfile where I lost track of my variable naming convention.

Very useful indeed

I got the idea from the answer of Phil Bradley on the superuser.com forum. He claimed that this would be fixed in Natty, but it isn’t although the configuration file he mentions has the port80 specification added by default, apt-key does not use it. The above snippet solves that.

For those Ubuntu users who have no idea what I am talking about:

Installing the newest R-version in Ubuntu requires to append the CRAN repository to you /etc/apt/sources.list. One might hit Alt+F2 and enter
gksu gedit /etc/apt/sources.list

With Xubuntu you would use mousepad instead of gedit. In any distro you can use
sudo nano /etc/apt/sources.list
in a terminal.

Usually I add the line
deb http://cran.uib.no/bin/linux/ubuntu natty/
at the end of the file and update with
sudo apt-get update.

CRAN at University of Bergen is closest to me. You might want another one (check the r-project.org site for mirrors).

apt-get update answers with a warning
GPG error: http://cran.uib.no nat/ Release: The folowing signatures coldn't be verified because the public key is not abailable

That is not a problem. One can install R and packages anyway, but it is better to have the public key.

Behind a firewall (and many public and open hotspots block several ports) it is not possible to use

sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-key E084DAB9

since the port through which the keyserver is contacted is blocked on most firewalls. You have to force port 80 by:
sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80/ --recv-key E084DAB9

After the key is added
sudo apt-get update
sudo apt-get install R-recommended emacs ess
proceeds without warning nor error.

Alter table can be used to move tables from one db to another.

alter table old_db.foo rename new_db.foo

mysql

Indeed

echo $PATH

To set the $PATH variable inside emacs one can append the following lines to the .emacs file (found on github, hattip Alex Payne):

; sane path
(setq path "/bin:/usr/bin:/sbin:/usr/sbin:/usr/local/bin:/usr/local/mysql/bin")
(setenv "PATH" path)

Next time Emacs starts one can go to the shell and

mysql

Back up your MySQL Database with Compress

If your mysql database is very big, you might want to compress the output of mysqldump. Just use the mysql backup command below and pipe the output to gzip, then you will get the output as gzip file.

$ mysqldump -u [uname] -p[pass] [dbname] | gzip -9 > [backupfile.sql.gz]
If you want to extract the .gz file, use the command below:

$ gunzip [backupfile.sql.gz]

Restoring your MySQL Database

Above we backup the Tutorials database into tut_backup.sql file. To re-create the Tutorials database you should follow two steps:

Create an appropriately named database on the target machine
Load the file using the mysql command:
$ mysql -u [uname] -p[pass] [db_to_restore] < [backupfile.sql]
Have a look how you can restore your tut_backup.sql file to the Tutorials database.

$ mysql -u root -p Tutorials < tut_backup.sql
To restore compressed backup files you can do the following:

gunzip < [backupfile.sql.gz] | mysql -u [uname] -p[pass] [dbname]

Removing empty lines from a file containing code in plain text (like .csv, .html, .php, etc…) is very easy with SED in a UNIX/ MAC OS shell and even possible in the Windows CMD (after installing SED). The following is a blockquote from ZoneO-tips for Mandriva Linux which I found really useful and well written:

So, open up a konsole and move into the directory where your file resides (cd MyDirectory). And here we go with the two lines that’ll do the job

sed '/^$/d' myFile > tt
mv tt myFile

Here is what happens:

sed '/^$/d' myFile removes all empty lines from the file myFile and outputs the result in the console, > tt redirects the output into a temporary file called tt,
mv tt myFile moves the temporary file tt to myFile.

Now, you may have 100 html files to correct at the same time. That’s where foreach comes in… Let’s say you want to correct all files ending with .html, here is what you should do:

Open up a konsole, move into the directory where your html files reside, type the following commands:

foreach file (*html)
sed '/^$/d' $file > tt
mv tt $file
end

Finished!

To give the conclusion first:

1. Always create indexes for each key-variable in each and every MySQL table, no matter how small or big.
   ALTER TABLE MyTable ADD INDEX(MyID)
   where MyTable is a Table in the database and MyID is one of the key variables.

2. Never use brackets in consecutive joint statements! The right way is:
   select * from Table_A A inner join Table_B B on A.id = B.id inner join Table_C on A.id = C.id;
   Brackets force the creation of temporary tables and increase execution time

The first one is the most important. It reduced the time for a join from more then 10 hours to a couple of minutes.


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