The Musings of Chris Samuel

After El Reg’s article on HPC going down the gurgler at Oracle/Sun now HPC Wire are suggesting the same:

I, myself, have spoken with two credible sources that told me HPC engineering talent is also being axed. Although this has been rumored to have been going on for some time, the recent RIF last week was said to cut particularly deep.

One thing I hadn’t noticed though was:

If I still haven’t convinced you that Oracle is cutting HPC from its lineup, consider that the company has no exhibit at the Supercomputing Conference (SC10) in November, and as far as I can tell, is offering no presentations. Given that this is the largest HPC exhibition of the year, this should be a clear signal that Oracle is going to be leaving the teraflopping and petaflopping to others.

Now back at SC’09 in Portland I asked the Sun folks (whilst the whole Sun/Oracle deal was going through) what they thought, and they said they reckoned it would be OK because Oracle had already told them they would have a booth at SC10. Well sadly it seems that’s not the case and to me that is the clearest indication that Oracle are exiting the HPC market. Of course they won’t say that (Oracle don’t seem to say much at all, even to the OpenSolaris folks, and when they do it doesn’t see to be very nice).

Interesting take on why China may well dominate technology in the near future at BusinessWeek:

In China, eight of the nine members of the Standing Committee of the Political Bureau, including the Chinese president, Hu Jintao, have engineering degrees; one has a degree in geology.

Contrast that with the US:

Of the 15 U.S. cabinet members, six have law degrees. Only one cabinet member has a hard-science degree — Secretary of Energy Steven Chu, who won the Nobel Prize in physics in 1997, has a doctorate in physics. President Barack Obama and Vice President Joe Biden have law degrees.

Basically it comes down to political will and understanding on the part of the people with the power.

(Via the ever excellent InsideHPC)

Please note: enquiry and application information at the URL below, no agencies please!

Executive summary

Want to work with hundreds of TB of storage, HPC clusters and a Blue Gene supercomputer and have an aptitude for storage and data ?

http://jobs.unimelb.edu.au/jobDetails.asp?sJobIDs=624151

Background

To give you an idea of what this job relates to, VLSCI currently has in production:

• 136 node, 1088 core SGI cluster (Intel Nehalem CPUs)
• ~110TB usable of Panasas storage

Shortly arriving (< 1 month away):

• 2048 node, 8192 core IBM Blue Gene/P supercomputer
• 80 node, 640 core IBM iDataplex cluster (Intel Nehalem CPUs)
• ~300TB usable of IBM GPFS storage plus tape libraries

2012 – more!

Both Intel clusters are CentOS 5, the front end and service nodes for the Blue Gene are SuSE SLES 10. The GPFS servers are RHEL5. Panasas runs FreeBSD under the covers.
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After almost six and a half years working at VPAC it’s time to move on, in January I’ll be taking up the position of Senior Systems Administrator in the University of Melbourne for the Victorian Life Sciences Computational Initiative (VLSCI). For those who’ve not come across the VLSCI it describes itself thus:

Under the Victorian Life Sciences Computation Initiative, The University of Melbourne will host a $100 million supercomputing program and facility, with $50 million provided by the State Government. The goal of the initiative is for Victoria to retain its standing and enhance its leadership in world life sciences. This will lead to major improvements in public health outcomes in the areas such as cancer, cardiovascular and neurological disease, chronic inflammatory diseases, bone diseases and diabetes.

Their ambitions aren’t what you could call small, they want to be a supercomputing facility ranking in the top 5 in life sciences world-wide. It’s going to be a fun ride and a lot more than just going from a 4 letter acronym to a 5 letter one.

I’ve really enjoyed my time at VPAC over the years and I’m really going to miss the people there, but it’s gotten to the point where I want to be able to focus on running large HPC systems without distraction and the opportunity at VLSCI was too good to ignore!

Don’t panic, this isn’t about me.. No agencies please!

The Victorian Partnership for Advanced Computing (VPAC) is looking for an Operations Manager:

We are looking for a dynamic leader with excellent IT knowledge to lead and manage our High Performance Computing (HPC) team based at VPAC (housed at RMIT University in Carlton).

Your ideal background would include management of similar teams and the provision of strong hands-on experience, coupled with full responsibility for technical infrastructure. The Operations Manager will build and maintain strategic relationships with key stakeholders such as Victorian Universities and national initiatives such as ARCS, NCI and ANDS.

Reporting to the Chief Executive Officer you will be a key member of the VPAC Management Team and lead a growing team of around 15 Systems Administrators and Developers. As VPAC is aiming for industry best practice and holds ISO accreditation it will be expected that you will have worked in similar environments that provide a process based approach to IT service management.

A senior level remuneration package will be negotiated with the successful applicant. To obtain a copy of the position description and/or to apply for this exciting opportunity please email recruitment@vpac.org

There is also a copy of the PD on the VPAC employment positions web page.

As ever please contact VPAC recruitment, not me, about this position..

A few weeks ago Martin Sevior and Tom Ffield of the University of Melbourne did a talk at VPAC called “Belle Monte-Carlo production on the Amazon EC2 cloud” based on a paper they’d presented at the International Conference of Computing in High Energy and Nuclear Physics. The presentation is now available on the VPAC website.

It’s all about testing the cloud computing model via Amazon EC2 for Monte Carlo production for the SuperBelle experiment at the KEK collider in Japan. My favourite comment is that for a real full production run on Amazon EC2 to be useful it would need to be able to return data from S3 to the KEK collider at 600MB/s (~4.7Gb/s) sustained.

I don’t know what Amazon would say to that – well, apart from maybe “no”.

NB: This is the talk I mentioned in the comments on Joe Landman’s blog post called “Cloudy Issues“.

I’m just testing out the Fortran 90 compilers on our AMD quad core cluster Tango based on some code that Joe Landman wrote as a test case in January 2008, using the same input file as him. The compilers I’m using are GCC 4.3.3, Intel 11.0.81 and PGI 8.0-3.

For the unoptimised (-O0) version I get:

• GCC: 1.884s
• Intel: 3.891s
• PGI: 1.170s

For basic optimisation (-O) I get:

• GCC: 1.617s
• Intel: 3.515s
• PGI: 0.954s

Cranking up the optimisation to -O2 sees no change:

• GCC: 1.610s
• Intel: 3.514s
• PGI: 0.954s

Now we add compiler specific flags:

• GCC (-march=amdfam10 -O3): 0.956s
• Intel (-fast): 3.507s
• PGI (-fast -tp shanghai-64): 0.997s

That got me wondering which had the greater impact, -O3 or the -march=amdfam10 and the result was surprising:

• GCC (-O3): 1.611s
• GCC (-march=amdfam10 -O0): 1.238s

So that’s pretty conclusive, just enabling the AMD k10h CPU (i.e. Barcelona/Shanghai processors) with no optimisations gives a better speedup than the highest level of optimisation! Of course it’s better with both, as you can see from the previous set of results.

I’m *really* impressed by GCC’s performance there, as well as the PGI unoptimised speed, and disappointed by the Intel compilers general lack of performance. I suspect Intels answer would be (not unreasonably) that they don’t necessarily target performance for their competitors CPUs.

VPAC is looking for someone to join the systems team here to work on grid computing, including things like Shibboleth, SSL certificates, Globus and the like.
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As a member of the technical program committee for VTDC 2007 I present the following Call for Papers, please feel free to pass on the text version to others that you know who may have an interest in this workshop.

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Tango, the new AMD Opteron cluster that’s getting built at VPAC to replace the now 4 year old Brecca is taking shape nicely!