The Characterisation Virtual Laboratory James Wettenhall Clayton Campus 20 th June 2012

Characterisation Virtual Laboratory2 Outline 1 Introduction 2 How to launch a CVL instance 3 How to run a MASSIVE / CVL Desktop 4 NeCTAR disk space 5 NeCTAR / MASSIVE file system integration and backup 6 Useful Links

20 th June 2012Characterisation Virtual Laboratory3 1 Introduction

20 th June 2012Characterisation Virtual Laboratory4 Introduction The Characterisation Virtual Laboratory (CVL) will: (i)Integrate Australia’s imaging equipment with specialised HPC capabilities provided by MASSIVE and NCI and with data collections provided by RDSI nodes, (ii)Provide scientists with a common environment for analysis and collaboration, the Characterisation VL Desktop, and (iii)Produce three exemplar platforms for multi-modal or large-scale imaging in neuroscience, structural biology, and energy materials.

20 th June 2012Characterisation Virtual Laboratory5 2 How to launch a CVL instance

20 th June 2012Characterisation Virtual Laboratory6 How to launch a CVL instance 1.Log into the NeCTAR Dashboard, using your AAF credentials. 2.Create an SSH key pair 3.Select the CVL image/snapshot (not yet available*), and click “Create Instance” * We can create this by starting with the generic CentOS 6.2 amd64 image, installing our software, and creating a snapshot. Alternatively, we can provide a cross-platform client-side application which can launch the instance using the Python Boto API. This would require the user to log into the NeCTAR Dashboard at least once to obtain their EC2 username ( and secret key (Settings, EC2 Credentials).

20 th June 2012Characterisation Virtual Laboratory7 How to launch a CVL instance 1.Log into the NeCTAR Dashboard, using your AAF credentials.   

20 th June 2012Characterisation Virtual Laboratory8 How to launch a CVL instance 1.Log into the NeCTAR Dashboard, using your AAF credentials. 2.Create an SSH key pair 3.Select the CVL image/snapshot (not yet available*), and click “Create Instance” * We can create this by starting with the generic CentOS 6.2 amd64 image, installing our software, and creating a snapshot. Alternatively, we can provide a cross-platform client-side application which can create the instance using the Python Boto API. This would require the user to log into the NeCTAR Dashboard at least once to obtain their EC2 username, e.g. and secret key (Settings, EC2 Credentials).

20 th June 2012Characterisation Virtual Laboratory9 How to launch a CVL instance 1.Log into the NeCTAR Dashboard, using your AAF credentials. 2.Create an SSH key pair If you wish to use PuTTY to connect to your CVL instance, you will need to convert the private key to PuTTY format, using PuTTY’s Key Generator.

20 th June 2012Characterisation Virtual Laboratory10 How to launch a CVL instance 1.Log into the NeCTAR Dashboard, using your AAF credentials. 2.Create an SSH key pair 3.Select the CVL image/snapshot (not yet available), and click “Launch”

20 th June 2012Characterisation Virtual Laboratory11 How to launch a CVL instance Alternatively, we can provide a cross-platform client-side application which can create the instance using the Python Boto API. This would require the user to log into the NeCTAR Dashboard at least once to obtain their EC2 username, e.g. and secret key (Settings, EC2 Credentials).

20 th June 2012Characterisation Virtual Laboratory12 3 How to run a MASSIVE / CVL Desktop

20 th June 2012Characterisation Virtual Laboratory13 How to run a MASSIVE / CVL Desktop  Instructions for logging into the MASSIVE Desktop can be found here: –  Launching the MASSIVE Desktop requires multiple steps: 1.Connect to the login node using SSH. 2.Set desired display size (“geometry”) in ~/.vnc/turbovncserver.conf 3.Request a visnode, using qsub. 4.Create an SSH tunnel to the visnode via the login node. 5.Launch TurboVNC and connect to localhost:1  These steps have recently been automated in a cross-platform wxPython GUI, known as the MASSIVE Launcher (still in prototyping phase).  The Launcher can be adapted to connect to a NeCTAR virtual machine, and can make use of the Python Boto API to access OpenStack data.

20 th June 2012Characterisation Virtual Laboratory14 The MASSIVE Launcher prototype Implemented in wxPython (Python interface to the wxWidgets GUI toolkit). Runs on multiple operating systems, including Windows and Mac OS X. Python shared libraries and Python module dependencies can be packaged up into an application bundle using py2app (Mac OS X) or py2exe (Windows). The application bundle can be distributed as a DMG (Mac OS X), or as an InnoSetup installation wizard (Windows).

20 th June 2012Characterisation Virtual Laboratory15 The MASSIVE Launcher prototype Source code is under version control – SVN The Launcher automatically checks its version number against the official version number on the MASSIVE Launcher webpage. The launcher refuses to run if it is not up-to-date. It advises the user to download the latest version from the Launcher webpage

20 th June 2012Characterisation Virtual Laboratory16 How to run a CVL / NeCTAR Desktop  If starting from NeCTAR’s CentOS 6.2 amd64 image, –yum groupinstall "X Window System" –yum groupinstall "KDE desktop” –yum install tigervnc-server No point in installing TurboVNC server yet, because the current NeCTAR infrastructure lacks GPUs. –vi /etc/sysconfig/vncservers –service vncserver start –Run “ vncpasswd ” as non-root user.  Create SSH tunnel : –ssh –L 5901:localhost:5901 nectar_vm_ip_address  Launch TurboVNC or other VNC client app and connect to localhost:1

20 th June 2012Characterisation Virtual Laboratory17 4 NeCTAR disk space

20 th June 2012Characterisation Virtual Laboratory18 NeCTAR disk space  Each NeCTAR virtual machine has a 10 GB primary partition for OS and core software. –This won’t be large enough for the CVL. We can request more. –Only this primary partition will be saved in a snapshot.  The user data partition will not be mounted automatically when a new virtual machine is instantiated. It can be mounted by running the following as root : fdisk –l mkfs.ext4 /dev/vdb mkdir /disk2 e2label /dev/vdb /disk2 echo "LABEL=/disk2 /disk2 ext4 defaults 1 2" >> /etc/fstab mount /disk2/ df -h

20 th June 2012Characterisation Virtual Laboratory19 5 NeCTAR / MASSIVE file system integration, backups and snapshots

20 th June 2012Characterisation Virtual Laboratory20 How to mount MASSIVE on NeCTAR  wget sshfs el6.rf.x86_64.rpm sshfs el6.rf.x86_64.rpm  sudo rpm -ivh fuse-sshfs el6.rf.x86_64.rpm  sudo chmod a+x /bin/fusermount  sudo usermod -a -G fuse wettenhj  mkdir ~/mnt/MASSIVE_home  mkdir ~/mnt/MASSIVE_project  sshfs ~/mnt/MASSIVE_home  sshfs ~/mnt/MASSIVE_project

20 th June 2012Characterisation Virtual Laboratory21 Backing up NeCTAR virtual machines  NeCTAR Research Cloud Wiki : –“ backup of user data, including images and running VMs is the responsibility of the users. ”  A temporary solution is to backup to a MASSIVE project directory, e.g. MASSIVE’s /home/projects/Desc002/. Each project on MASSIVE is allocated 1 TB of disk space.  A Cron Job can be set up for the NeCTAR VM’s root user, which regularly runs rsync to back up files to a MASSIVE project directory.  Taking a snapshot of a running virtual machine only saves the 10 GB primary partition (OS and core software); it does not save the user data partition.

20 th June 2012Characterisation Virtual Laboratory22 6 Useful Links

20 th June 2012Characterisation Virtual Laboratory23 Useful Links CVL wiki: CVL tasks/bugs: CVL SVN repository: CVL & MASSIVE package repository: repo.massive.org.au NeCTAR Technical Guides: NeCTAR Support Forums: NeCTAR Research Cloud Wiki: