Tag Archives: NeCTAR

GPU Flavors on R@CMon

We’re pleased to announce we now have GPGPU accelerated cloud instances working, a first for the NeCTAR Research Cloud!

If you’re not as excited by SSH session logs as I am you might like the following screenshots captured by Juptier Hu from the CVL team, which illustrate the CVL running on both a new GPU flavor and a standard non-GPU flavor. The CVL uses TurboVNC to achieve remote hardware accelerated rendering (care of VirtualGL), so the framerates here show CPU versus GPU rendering speeds.

CPU Render - 9 fps

CVL Desktop + CPU Rendering

GPU Render - 380 fps

CVL Desktop + GPU Rendering

And to really prove it, here’s the obligatory mono-spaced console dump you’d expect from a technical blog:

01:47:51 blair@bethwaite:~$ nova show f44cad73-40e1-4e83-8699-dd3f7f2e9ead | grep flavor
| flavor | cg1.medium (19) |
01:47:54 blair@bethwaite:~$ nova show f44cad73-40e1-4e83-8699-dd3f7f2e9ead | grep network
| monash-test network | 11x.xxx.255.20 |

01:48:39 blair@bethwaite:~$ sshrc root@11x.xxx.255.20
root@ubuntu:~# lshw | grep -C 2 NVIDIA
description: 3D controller
product: GF100GL [Tesla M2070-Q]
vendor: NVIDIA Corporation
physical id: 6
bus info: pci@0000:00:06.0
root@ubuntu:~# nvidia-smi
Mon Jan 13 01:52:22 2014
| NVIDIA-SMI 5.319.76   Driver Version: 319.76         |
| GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr. ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute M. |
|   0  Tesla M2070-Q       Off  | 0000:00:06.0     Off |                    0 |
| N/A   N/A    P0    N/A /  N/A |       10MB /  5375MB |      0%      Default |

| Compute processes:                                               GPU Memory |
|  GPU       PID  Process name                                     Usage      |
|  No running compute processes found                                         |

root@ubuntu:~# cd NVIDIA_CUDA-5.5_Samples/7_CUDALibraries/MersenneTwisterGP11213/
root@ubuntu:~/NVIDIA_CUDA-5.5_Samples/7_CUDALibraries/MersenneTwisterGP11213# ./MersenneTwisterGP11213 ./MersenneTwisterGP11213 Starting...

GPU Device 0: "Tesla M2070-Q" with compute capability 2.0
Allocating data for 2400000 samples...
Seeding with 777 ...

Generating random numbers on GPU...
Reading back the results...

Generating random numbers on CPU...
Comparing CPU/GPU random numbers...

Max absolute error: 0.000000E+00
L1 norm: 0.000000E+00

MersenneTwister, Throughput = 3.1591 GNumbers/s, Time = 0.00076 s, Size = 2400000 Numbers

Shutting down...

Currently these are available as cg1.* flavors in the monash-test cell, so not open for general consumption – and they won’t be for a while until we purchase and deploy more GPU nodes. The allocation process also needs to be tweaked to deal with this new capability. So currently GPU flavors are only accessible by special arrangement with the R@CMon team.

We’ll be deploying a considerable GPU capability as part of R@CMon in order to support, e.g., GPU accelerated rendering and GPGPU accelerated viz processing for the CVL. GPU capabilities can also be useful for on-demand development work, such as providing hardware rendering for the CAVE2 development environment.

At the moment we have a handful of NVIDIA Tesla M2070-Q’s, with Kepler K2’s coming as part of R@CMon phase2. If you’re keen to get access or try this out then drop us a line.

Software Carpentry Bootcamp for Bioinformaticians (Adelaide/Melbourne) – UPDATE

Last September 24-26 and October 1-3, the latest Software Carpentry Bootcamps were held in University of Adelaide and Monash University.

These Software Carpentry Bootcamps were designed for Bioinformaticians to enhance their knowledge and skills in programming and software development practices.The bootcamps were delivered using the NeCTAR Research Cloud where each trainee has been given dedicated access to a specific virtual workstation.


With the use of an automatic provisioning system, each virtual workstations have been preconfigured with the required tools, training materials and computing resources to perform the hands-on exercises.


On the first day of the bootcamp, the Software Carpentry instructors including the R@CMon team introduced the trainees to Python. The second day was mostly about software testing and documentation. The last day was when the trainees applied their knowledge from the previous sessions into collaborative group exercises.


Photos taken by Nathan Watson-Haigh (ACPFG).

“Thanks a lot for this information and also your kind efforts in running such a  useful and informative workshop” – Fariborz Sobhanmanesh (Research Engineer, Bioinformatician with CSIRO Animal, Food and Health Sciences Centre)

“I recently attended the SWC bootcamp in Adelaide and found it incredibly useful. Sure there was a lot of information in a short amount of time but the topics covered were practical and very relevant to my daily work. Thanks must go to the presenters and organisers who kept things moving along brilliantly.” – Terry Bertozzi (Research Scientist with the South Australian Museum)

Using the NeCTAR Research Cloud for Delivering Hands-on Bioinformatics Training (Adelaide)

A 1-day training workshop is scheduled for September 27, 2013 in Adelaide.

The training workshop aims to provide attendees relevant hands-on experience in using the NeCTAR Research Cloud for Bioinformatics.
The R@CMon team will be helping in the delivery of this workshop.

For more detailed information (contacts, venue, registration) on the training workshop, visit this BIG SA page.

Upcoming Software Carpentry Bootcamp for Bioinformaticians (Adelaide/Melbourne)

Two Software Carpentry Bootcamps are scheduled for September/October 2013.

The bootcamps are designed for Bioinformaticians to improve their productivity through good programming and software development practices.
The bootcamps will be held in Adelaide on September 2013. and Melbourne on October 2013.
It will be delivered using the NeCTAR Research Cloud and we, the R@CMon team, will be assisting in these bootcamps.

The bootcamps are supported by the following organisations:

Visit the Australian Bioinformatics Network site for details on the bootcamps

More information about the Adelaide bootcamp can be found here.
More information about the Melbourne bootcamp can be found here.

Visit the Software Carpentry site for more information about Software Carpentry and future international bootcamps.