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Setting Up an EC2 AMI for Scientific Computing in Python and R

This guide details the process of launching an EC2 instance for scientific computing using Python and R. It covers installing a VNC server for remote access, configuring a lightweight window manager like IceWM, and installing necessary packages such as GCC and LAPACK. Security configurations for SSH access, user management, and EBS volume setups are also included, along with troubleshooting connectivity issues in the US-EAST-1 region. Ideal for researchers and data scientists needing HPC capabilities in the cloud.

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Setting Up an EC2 AMI for Scientific Computing in Python and R

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  1. HPC in the Cloud Guy Tel-Zur

  2. http://aws.amazon.com/console/

  3. Sign In

  4. EC2 Dashboard

  5. EC2 AMI for scientific computing in Python and R AMI ID: ami-84bd41ed Source: http://www.r-bloggers.com/ec2-ami-for-scientific-computing-in-python-and-r/

  6. Launching Instance

  7. Connect using PuTTY

  8. Install VNC serverfrom the following packages: * xtightvncviewer* xvnc4viewer

  9. Add a user As root: useraddtelzur mkdir /home/telzur chown –R telzur /home/telzur sutelzur

  10. Passwordlessssh ssh-keygen -t dsa cd .ssh cat ./id_dsa.pub >> authorized_keys2 Use a lightweight window manager such as icewm

  11. Open ports 5800,5900-5901…in the security group for VNC to work

  12. Install a light window manager apt-get install icewm

  13. HPC Cluster

  14. 16 cores

  15. EBS /dev/sdh /volchange made in /etc/fstab

  16. Installations • yum install • gcc • gcc-c++ • gcc-gfortran • Lapsck • Python-devel • Need more repositories: • rpm -Uvhhttp://download.fedora.redhat.com/pub/epel/5/x86_64/epel-release-5-4.noarch.rpm • yum install atlas.x86_64 blas.x86_64 lapack.x86_64 • yum groupinstall XFCE (startxfce4) • yum install glibc-devel.i386

  17. Test MPI

  18. Quality of Service ???? 1:41 AM PDT We are currently investigating latency and error rates with EBS volumes and connectivity issues reaching EC2 instances in the US-EAST-1 region. 2:18 AM PDT We can confirm connectivity errors impacting EC2 instances and increased latencies impacting EBS volumes in multiple availability zones in the US-EAST-1 region. Increased error rates are affecting EBS CreateVolume API calls. We continue to work towards resolution. 2:49 AM PDT We are continuing to see connectivity errors impacting EC2 instances, increased latencies impacting EBS volumes in multiple availability zones in the US-EAST-1 region, and increased error rates affecting EBS CreateVolume API calls. We are also experiencing delayed launches for EBS backed EC2 instances in affected availability zones in the US-EAST-1 region. We continue to work towards resolution. 3:20 AM PDT Delayed EC2 instance launches and EBS API error rates are recovering. We're continuing to work towards full resolution. 4:09 AM PDT EBS volume latency and API errors have recovered in one of the two impacted Availability Zones in US-EAST-1. We are continuing to work to resolve the issues in the second impacted Availability Zone. The errors, which started at 12:55AM PDT, began recovering at 2:55am PDT 5:02 AM PDT Latency has recovered for a portion of the impacted EBS volumes. We are continuing to work to resolve the remaining issues with EBS volume latency and error rates in a single Availability Zone. 6:09 AM PDT EBS API errors and volume latencies in the affected availability zone remain. We are continuing to work towards resolution.

  19. BBC

  20. Who is affected by EC2? Source: http://ec2disabled.com/ (partial list)

  21. Saving the computer as an AMI

  22. 2 X 16cores !

  23. Add graphical WM (xfce4) using remote desktop (VNC) – Open port

  24. Price $1.60/hour for this xlarge machine $4,290 for 1 year $6,590 for 3 years This is the TCO !

  25. vi /etc/ssh/sshd_config Change: password authentication from no to yes Rloadsshd by /etc/init.d/sshd reload

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