Transcript Characterisation Virtual Laboratory - Confluence

The Characterisation Virtual Laboratory
James Wettenhall
Clayton Campus
20th June 2012
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
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1 Introduction
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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.
• https://www.nectar.org.au/characterisation-virtual-laboratory
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2 How to launch a CVL instance
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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 ([email protected]:pt-610)
and secret key (Settings, EC2 Credentials).
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How to launch a CVL instance
1. Log into the NeCTAR Dashboard, using your AAF credentials.



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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.
[email protected]:pt-610 and secret key (Settings, EC2
Credentials).
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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.
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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”
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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.
[email protected]:pt-610 and secret key (Settings, EC2
Credentials).
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3 How to run a MASSIVE / CVL Desktop
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How to run a MASSIVE / CVL Desktop
 Instructions for logging into the MASSIVE Desktop can be found here:
– https://www.massive.org.au/userguide/massivedesktop
 Launching the MASSIVE Desktop requires multiple steps:
1.
2.
3.
4.
5.
Connect to the login node using SSH.
Set desired display size (“geometry”) in ~/.vnc/turbovncserver.conf
Request a visnode, using qsub.
Create an SSH tunnel to the visnode via the login node.
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.
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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).
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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
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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
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4 NeCTAR disk space
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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
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5 NeCTAR / MASSIVE file system
integration, backups and snapshots
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How to mount MASSIVE on NeCTAR
 wget
http://apt.sw.be/redhat/el6/en/x86_64/rpmforge/RPMS/fusesshfs-2.2-1.el6.rf.x86_64.rpm
 sudo rpm -ivh fuse-sshfs-2.2-1.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 [email protected]:/home/wettenhj
~/mnt/MASSIVE_home
 sshfs [email protected]:/home/projects/Desc002
~/mnt/MASSIVE_project
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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.
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6 Useful Links
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Useful Links
• CVL wiki: https://confluence-vre.its.monash.edu.au/display/CVL/
• CVL tasks/bugs: https://jira-vre.its.monash.edu.au/
• CVL SVN repository: https://svn-vre.its.monash.edu.au/cvl/
• CVL & MASSIVE package repository: repo.massive.org.au
• NeCTAR Technical Guides:
• http://support.rc.nectar.org.au/technical_guides.html
• NeCTAR Support Forums:
• http://support.rc.nectar.org.au/forum/
• NeCTAR Research Cloud Wiki:
• https://wiki.rc.nectar.org.au/wiki/Main_Page
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