Creating an AMI on EC2

Notes About Creating a New EC2 AMI

Back to parent: GotCloud

The following are notes taken when creating the Amazon Machine Instance used for the CSG pipeline process.

These notes assume you have already created an EC2 account and have the certificates and keys set up properly.

Launch an instance

 Login to https://console.aws.amazon.com/ec2       # EC2 Management Console

Pay attention to the region you are using, at least for now it seems any StarCluster activity must be in us-east-1.

Launch a new instance starting from a StarCluster AMI. We will use set up the software on this instance and ultimately save it as an AMI.

1. EC2 DashBoard -> Launch Instance
2. Select: Community AMIs
   1. Enter in the search box: starcluster-base-ubuntu
   2. Select: starcluster-base-ubuntu-12.04-x86_64 - ami-765b3e1f
3. Select the Instance Type: Micro t1.micro
   • Since we are just using this instance to setup the system, pick the smallest/cheapest machine.
4. Click: Review and Launch
   1. Select: Make General Purpose (SSD) the boot volume for this instance.
   2. Select: Next
5. Scroll down to the Storage section
6. Click: Edit storage
   1. Update the Size: 30
      • We use 30G to fit the GotCloud code and reference files. Make it larger if you want additional space.
   2. Click: Review and Launch
7. Click: Launch
8. Select the key/pair you want to use & Launch

Setup the instance with GotCloud

This assumes you have already logged onto the instance.

1. Get the latest version of GotCloud:
   • Multiples ways to do this, one way is to do:
     1. git clone https://github.com/statgen/gotcloud.git gc_src
2. Download cmake (required to build premo)
   • sudo apt-get update
   • sudo apt-get upgrade (takes a while, may be able to skip this step)
   • sudo apt-get install cmake
   1. Build the source (if you obtained the source code).
      1. cd gc_src/src
      2. make
      3. cd ..
   2. Generate the installation.
      1. cd gc_src/
      2. ./debian/makedeb.sh bin =
      3. cd
3. Install: sudo dpkg -i gc_src/gotcloud-bin_1.14.3_amd64.deb
4. Move installation to home so will be on all nodes: sudo mv /usr/local/gotcloud .
5. Remove source: rm -rf gc_src/ (required since not enough storage space.)
6. Get the reference files
   1. wget ftp://anonymous@share.sph.umich.edu/gotcloud/ref/h37-db135-v3.tgz
7. Untar: tar xvf h37-db135-v3.tgz
8. Move reference to gotcloud directory: sudo mv gotcloud.ref gotcloud
9. Remove tar file: rm h37-db135-v3.tgz
10. Add aliases for GotCloud and tabix: vi .bash_aliases
    1. alias gotcloud='/home/ubuntu/gotcloud/bin/gotcloud'
    2. alias tabix='/home/ubuntu/gotcloud/bin/tabix'

Set Up Swap Space

Issue the command swapon -s to see if there is swap space. If there is only a header line, you need to add a swap file like this:

 df -h          # Be sure there's enough space, decide on swap size
 #  Create a file /swap to use (assuming / is large enough)
 sudo bash      # Run these commands as root
 swap=/swap
 dd if=/dev/zero of=$swap bs=524288 count=16384     # 8GB swap on t1.micro   15G=bs=1073741824 count=15
 chown root:root $swap
 mkswap $swap
 chmod 0600 $swap
 swapon $swap
 echo "$swap  none swap sw  0  0" >> /etc/fstab

 swapon -s       # Should show the swap device

Install the Software

(1) There are a number of additional Debian packages that you may well need, so we make sure they are all installed.

 sudo apt-get update
 sudo apt-get upgrade           # Apply maintenance

 sudo apt-get install java-common default-jre make libssl0.9.8 
 sudo apt-get install libnet-amazon-ec2-perl s3cmd
 sudo apt-get install make g++ libcurl4-openssl-dev libssl-dev libxml2-dev libfuse-dev

(2) S3fs allows one to access S3 storage as a conventional file system. This can be quite handy, if it is set up properly. Our recent experience is that the 1000 Genomes data is has many files with incorrect permissions. Still if you're lucky, your data will be useful. Install the software like this:

 mkdir -p ~/src
 cd ~/src
 wget  http://s3fs.googlecode.com/files/s3fs-1.68.tar.gz
 tar xzvf s3fs-1.68.tar.gz
 cd s3fs*
 ./configure
 sudo make install

(3) Configure s3cmd. This will ask for your AWS ID and Secret Key. If creates a file in ~/.s3cfg

 s3cmd --configure

 Enter new values or accept defaults in brackets with Enter.
 Refer to user manual for detailed description of all options.

 Access key and Secret key are your identifiers for Amazon S3
 Access Key: AKI1234QEUWZ3YCZF2Q
 Secret Key: ft1eJa1234NE8iitNlbA08x/G8iMqkMI1234IGf

 Encryption password is used to protect your files from reading
 by unauthorized persons while in transfer to S3
 Encryption password: password_you_do_not_need_to_know
 Path to GPG program [/usr/bin/gpg]: 

 When using secure HTTPS protocol all communication with Amazon S3
 servers is protected from 3rd party eavesdropping. This method is
 slower than plain HTTP and can't be used if you're behind a proxy
 Use HTTPS protocol [No]: 

 On some networks all internet access must go through a HTTP proxy.
 Try setting it here if you can't conect to S3 directly
 HTTP Proxy server name: 

 New settings:
   Access Key: AKI1234QEUWZ3YCZF2Q
   Secret Key: ft1eJa1234NE8iitNlbA08x/G8iMqkMI1234IGf
   Encryption password: password_you_do_not_need_to_know
   Path to GPG program: /usr/bin/gpg
   Use HTTPS protocol: False
   HTTP Proxy server name: 
   HTTP Proxy server port: 0

 Test access with supplied credentials? [Y/n] 
 Please wait...
 Success. Your access key and secret key worked fine :-)

 Now verifying that encryption works...
 Success. Encryption and decryption worked fine :-)

 Save settings? [y/N] y
 Configuration saved to '/home/ubuntu/.s3cfg'

(4) Follow the instructions to install the GotCloud Debian packages Run the tests to be sure everything is OK.

Configure the Host to be Usable

It is useful to configure /etc/rc.local to do most things you need at boot time. There are many other ways to do this, but here's one simple way - create the file /etc/rc.local (as root). The following example sets up access details for s3cmd and s3fs (use your own credentials).

ubuntu@ip-10-254-60-210:~$ sudo more /etc/rc.local

#!/bin/sh 
#
# rc.local
#
# This script is executed at the end of each multiuser runlevel.
# Make sure that the script will "exit 0" on success or any other
# value on error.
#
# In order to enable or disable this script just change the execution
# bits.
#
# By default this script does nothing.
USER=ubuntu
THOUSANDG=/mnt/1000g
FILES3=/etc/passwd-s3fs     # Where s3fs access info will live
S3ERR=/tmp/s3fs.err
#   These are needed for s3fs access
AWSACCESSKEYID=AKIAxxxxxxZ3YCZF2Q
AWSSECRETACCESSKEY=ft1eJa3WxxxxxxxNlbA08x/G8iMqkMIkJjFCIGf


#    Check that we have swap set up
a=`swapon -s | grep -v File`
if [ "$a" = "" ]; then
  echo "#######################################################"
  echo "#   You have no SWAP file set up"
  echo ""
  echo "#  swap=/mnt/swapfile"
  echo "#  sudo dd if=/dev/zero of=$swap bs=1073741824 count=20"
  echo "#  sudo chown root:root $swap"
  echo "#  sudo mkswap $swap"
  echo "#  sudo chmod 0600 $swap"
  echo "#  sudo swapon $swap"
  echo ""
  echo "#  If need be, add to /etc/fstab"
  echo "#  echo "$swap  none swap sw  0  0" >> /etc/fstab"
  echo "#######################################################"
fi

#    Set up for GotCloud
gc=/gotcloud.mnt
if [ ! -r $gc/release_version.txt ]; then
  mkdir -p $gc
  mount /dev/xvdg $gc
  if [ -d $gc/gotcloud.ref ]; then
    echo "#######################################################"
    echo "#   GotCloud is set up on $gc"
    echo "#######################################################"
  fi
fi

#    Set up access to S3 storage as normal filesystem 
echo "${AWSACCESSKEYID}:$AWSSECRETACCESSKEY" > $FILES3
chown root.root $FILES3
chmod 640 $FILES3

usermod -aG fuse $USER

#    Setup 1000genomes
mkdir -p $THOUSANDG
if [ ! -r $THOUSANDG/release ]; then
  chown $USER.$USER $THOUSANDG
  /usr/local/bin/s3fs -o allow_other 1000genomes $THOUSANDG > $S3ERR 2>&1
  if [ ! -r $THOUSANDG/alignment.index ]; then
    echo "#######################################################"
    echo "#   1000genomes is not set up on $THOUSANDG"
    echo "#   See S3FS errors in $S3ERR"
    echo "#######################################################"
  fi
  df -h
fi
exit 0

Test the new AMI

Launch a new AMI instance and check that files are in the correct places. In the EC2 Management Console do:

 EC2 DashBoard -> AMIs -> Select CSG instance -> Launch Instance
 Launch Instances  (take defaults)
 Advanced Instance Options  (take defaults)
 Storage Device Configuration -> Edit
 Change volume to 30G or larger -> Continue     # Defaults are OK
 Instance Details
   Key Name = test of instance
 Create Key/Pair if you need to, most likely you can use one you have created
 Choose a Security Group -> sg-a098e9c8 - quick-start-1
 Review -> Launch