VOLUME 7 ISSUE 2
MICA (P) No. 177/02/2012
January 2013
A Publication Of The Institute Of High Performance Computing
2
4/5
8/9
News
News
Research
Happenings in IHPC
Conference
Reports
The mystery of Nitrogen
embedment in Zirconium
IHPC
Milestones
Prof Alfred Huan, ED IHPC, chatting with Lloyd Register’s Singapore GTC managing
director, Claus Myllerup, during the press conference and signing ceremony.
IHPC to set up Joint Lab with Lloyd’s Register
A big thumbs all from everyone at the CEL celebration.
First Anniversary of Computational Engineering
Laboratory (CEL)
By Sean Ang
[email protected]
In December 2012, IHPC colleagues held a simple celebration with
partners from the Computational Engineering Laboratory (CEL) formed
with Rolls Royce.
ED IHPC Prof Alfred Huan, and Dr Kurichi Kumar, Rolls Royce’s Director
of Research & Technology for Asia, joined in the celebrations with
researchers from both organizations.
The CEL is the collaborative platform through which IHPC interacts
with Rolls-Royce on research & development projects across a range
of technical areas of mutual interest, with a focus on intelligent data
analytics.
Here’s to another great year of collaboration at the CEL in 2013!
By Corporate Communications
[email protected]
A press conference held in Fusionopolis in September 2012, Lloyd’s
Register of London announced the establishment of its Group Technology
Centre (GTC) in Singapore, and also signed an agreement with A*STAR
to collaborate on R&D projects under the GTC’s activities.
The intent is to set up a Joint Lab facility with IHPC to co-develop applications
and solutions in the marine and offshore sectors. This arrangement will
promote R&D activities in computational modelling and simulation,
providing bespoke technical solutions for companies in the relevant sectors.
news
IHPC
Happenings
Research Agreement With ICAM
With the New Year comes good tidings and more good news for IHPC.
Prof. Alfred Huan, Executive Director of the A*STAR Institute of High
Performance Computing (IHPC), recently signed a research agreement
with Prof. Wang Tie Jun from the International Centre for Applied
Mechanics (ICAM) at Xi’an Jiaotong University.
(From Left) Prof. Wang from ICAM with Prof. Huan, ED IHPC.
Prof. Wang is the Dean of the School of Aerospace Engineering, and
Director of the State Key Lab for Strength and Vibration of Mechanics
Structures, at the university.
ICAM is described as the first-of-its-kind major research center for applied
mechanics in China, and is located in the Shanxi province. ICAM also
serves as a “special zone” for the reformation of research and educational
activities in mechanics in China, and aims to foster the growth of young
scientists and students in interdisciplinary areas.
Prof. Wang and his colleague, Dr. Liu Zishun, visited IHPC in December
2012 to call on Prof Alfred Huan. They had a friendly exchange of ideas
before signing the agreement.
Under the auspices of the three-year research agreement, IHPC’s
Dr. Zhang Yong-Wei (EM Department) and Dr. Liu from ICAM will
coordinate the research activities that underscore the collaboration
between IHPC and ICAM.
Three key research topics will be pursued over the next three years:
• Energy harvest using soft materials
• Mechanics of load-bearing biological materials
• Thermal transport of 2D materials.
This collaboration will strengthen the research capabilities in fundamental
research in applied mechanics for both institutions.
Guest starring Dr Wang Zhaoxia (right) and Dr Gary Lee as the Scientists in Attendance.
Scientist for a Day – Scientist-in-Attendance
By Chan Hoong Maeng
[email protected]
Dr Wang Zhaoxia and Dr Gary Lee were the Scientists-in-Attendance
at Science Centre Singapore on Saturday, 3 November 2012 to present
their work on the epidemiological model of the Dengue disease in
collaboration with the Genome Institute of Singapore (GIS) and Science
Centre Singapore. Students from secondary schools participating in
this project also talked about their involvement and their learning
experiences during the event.
Various equipment and mosquito larvae were also on display to educate
the visitors on how the Dengue virus and its host were tracked in this
study. This event attracted over 50 visitors over two sessions.
This collaboration was made possible by an A*STAR Joint Council Office
(JCO) grant, and this event forms part of the educational outreach
initiatives under the grant.
2
news
SMI Forum 2012 Panel discussion chaired by Mr Heng Chiang Gnee, Executive Director of SMI
SMI Forum 2012
By Sean Ang
[email protected]
IHPC was invited to the recent conference organised by the Singapore
Maritime Institute (SMI). The SMI Forum 2012 brought together insights
from both the academic and industry perspectives, for the benefit of
the maritime sector.
More than 200 distinguished guests from the maritime and offshore
industry, Institutes of Higher Learning (IHLs) and SMI’s partners attended
the event, including Executive Director of IHPC, Prof Alfred Huan and
Amy Foo, Director of Industry Development.
Together, they discussed topics that included maritime education &
training, research & development and policy research for the maritime
and offshore industry in Singapore.
The networking lunch also provide a good avenue for IHPC to interact
with the Maritime community.
Dr Lu Xin from Fluid Dynamics Department presented Computational
Fluid Dynamics (CFD) posters for an exhibition in this forum. He was
invited based on his expertise and wealth of experience in fluid dynamics
modeling, in particular, in complex marine offshore studies involving
free surface, nonlinear waves, and structure impact.
The posters describe some of the maritime related projects successfully
conducted by IHPC in the following areas:
• Offshore Structure Hydrodynamics
• Jack-up hydrodynamic loading, wave loading,
aerodynamic loading
• Jack-up drag analysis at chord, bay and unit level
• Free Surface Simulation
• LNG tank sloshing
• Green water analysis
• Wave Dynamics
• Numerical towing tank
• Numerical wave generator, nonlinear random waves
• Sea keeping study
• Nonlinear ship wave
• Wave impact on structure
• Green Shipping
• Marine propeller performance analysis
• New efficient Kort nozzle design
• Propeller tip vortex, cavitation inception and noise control
• Propeller downwash impact to ocean environment
• Exhaust dispersion and safety from FPSO
We are looking forward to the next SMI Forum and more workshops in
2013, on a wide range of topics covering maritime and offshore activities.
IHPC will be working with partners like SMI, the Maritime Port Authority
(MPA) and the Economic Development Board to engage the maritime
industry and to promote innovation in the maritime sector.
Dr. Liu Xin (Right) from Fluid Dynamics Department and Sean Ang (left) from Industry
Development manning the IHPC booth.
3
news
Conference
Reports
We take a look back at some of the notable conferences in
the second half of 2012, in which IHPC researchers played
a leading role.
International Symposium on Cavitation (CAV 2012)
By Ohl Siew-Wan
[email protected]
The 8th International Symposium on Cavitation was held in Novotel
Clark Quay, Singapore in August last year.
It was jointly organized by IHPC, NUS and NTU. A wide range of topics
was covered, including supercavitation, propellers and pumps, and
cavitations in biology and medicine.
We had over 250 participants from more than 30 countries. The conference
ran for three full days with 3 parallel sessions every day, and 6 invited
speakers in total.
Executive Director of IHPC, Prof Alfred Huan, gave the welcome address
on the first day.
Prof Alfred Huan giving the welcome address at CAV2012.
Among the invited speakers were prominent scientists like Professor K.
Suslick, Professor B. Fox, and Professor S. Takagi, and active industrial
researchers such as Dr F. Holstyens from Lam Research and A. Wilson
from Rolls Royce.
To provide additional networking opportunities, participants were
treated to an evening reception every day, and a conference dinner
at Peony Jade restaurant with traditional Singaporean cuisine. These
dining treats provided ample opportunities for scientific discussions
and interactions on top of the conference proper.
The symposium also saw good support from industrial sponsors. Seven
commercial companies took up sponsorship and booths during the
conference. Their participation signified the importance of the study
of cavitation bubble dynamics to a wide range of industry applications.
The conference was a big success and concluded on a high note with
the announcement of the next CAV conference: CAV 2015 will be hosted
by Dr. Mohamed Farhat in Lausanne, Switzerland.
4
news
International Conference on Electronic Commerce
(ICEC)
By Yang Yinping
[email protected]
The 1st International Conference on Electronic Commerce (ICEC) was held
in Seoul, Korea in 1999, and since then the conference has been held all
around in the world in far-flung cities.
Dr. Raj. Thampuran (left) MD A*STAR, and Dr. Terence Hung, Deputy ED IHPC,
speaking to the participants of BSCI@A*STAR Day.
This past year’s ICEC (www.icec2012.net) was hosted by Singapore
Management University, and included a series of three events in August
2012:
1) The Summer Institute Workshop on Analytics for Business,
Consumer and Social Insights (BCSI 2012)
2) The A*STAR Day for the Workshop on Analytics for Business,
Consumer and Social Insights (BCSI 2012 @ A*STAR Day)
3) The 14th International Conference on Electronic Commerce
(ICEC 2012)
We also had a special opportunity to organise the programme of the
“BCSI@A*STAR Day,” and hosted a total of forty highly prolific academic
and industry delegates. This was their first visit to A*STAR. The programme
featured six research sharing and demo sessions presented by eight
researchers from IHPC, I2R (Institute of Infocomm Research), and IMCB
(Institute of Molecular and Cell Biology). A*STAR’s Managing Director,
Dr. Raj. Thampuran, gave an address to welcome the participants to
A*STAR, and IHPC’s Deputy Executive Director, Dr. Terence Hung,
introduced the research goals and activities of IHPC.
The quality of this year’s ICEC was very high, owing to the organisation
and participation by world-class scholars in a number of different fields.
Two key features of the conference impressed the participants. One was
the interdisciplinary intellectual exchange among computer scientists,
information systems researchers, and business leaders. The other was the
significant participation from industry delegates, including IBM, SingTel,
Citibank, and DHL.
We created a strong presence for IHPC, and further generated a great
number of potential collaboration opportunities for the institute.
Colleagues in the Computing Science Department are also having
active follow-up discussions with contacts we established from ICEC,
including two collaborations that were formalized by late December
2012. We believe that this team-based presence strengthened the
visibility of IHPC in the global research community, and can be a model
for future team participation at international conferences.
Topics covered included electronic commerce technologies, data analytics
and data mining, “big data”, artificial intelligence and machine learning,
supply chain management, social media, online gaming, Internet search
and online recommendations, and consumer behavior and electronic
market mechanisms.
As the ICEC 2012 main conference’s programme co-chair in charge of
special research tracks, I am glad that the conference went off well and
resulted in many fruitful interactions among the participants. My
involvement in the overall planning began in December 2011. I worked
closely with the General Chair, Professor Rob Kauffman, to coordinate the
organization of eight special research tracks, including the identification
of and invitations to the special track chairs, and management of the
overall review process. The resulting conference proceedings, co-edited
by Rob Kauffman, Martin Bichler, Hoong Chuin Lau, Yinping Yang and
Chris Yang, was published by ACM in August 2012 in its International
Conference Proceedings Series.
Comments and Accolades
“Thank you for introducing me to your distinguished colleagues in A*STAR.
I am very impressed with the breadth and depth of talents in A*STAR. I look
forward to the opportunity to collaborate with you and your other
colleagues.”
Dr. Jamshid Vayghan, IBM Distinguished Engineer and Director of CTO Sales
Transformation
“Please accept my warm thanks for all that you did to put on an outstanding
day of scientific briefings at A*STAR for the attendees of the 2012 Workshop
on Analytics for Business, Consumer and Social Insights (BCSI) last week.
The visit gave them a great impression of your organisation, its people
and its scientific research projects — and opportunities to think out loud
about the issues we all share in common in research.”
Professor Robert Kauffman, the Lee Kuan Yew Faculty Fellow for Research
Excellence, Professor of Information Systems and Associated Dean (Research)
at the Singapore Management University’s School of Information Systems and
ICEC 2012 General Chair
The BCSI Co-Chairs Team (Photo courtesy of ICEC official site)
5
research
Molecular
Dynamics
Simulations at the
Length Scales of
Experiments
By Wu Zhaoxuan
[email protected]
Computational simulations are helping researchers at IHPC
to better understand the complexities of nanomaterial
research beyond what physical experiments can yield. Here
is one example presented by Dr. Wu Zhaoxuan.
Materials and their behavior are always more complex than what we
can simulate using computers.
This complexity is multifaceted. At the atomistic level, materials consist
of atoms with interatomic spacing as small as a few angstroms (10 -10 m).
Typically, crystalline material of 1 cm3 contains ~1023 atoms. The atoms
are bonded together through a force field created by their interatomic
interactions.
The full description of such interactions requires the knowledge of the
density of electronic states. Quantum mechanics methods, such as
Density Functional Theory (DFT), are useful in calculating such electronic
states and properties.
In Molecular Dynamics (MD) simulations, the time step used is typically
on the order of femtoseconds (10 -15 second).
While a tiny time step is necessary to capture atomic vibrations during
simulations, it also limits most simulation (even using empirical potentials)
periods to a few nanoseconds or shorter.
There are additional complexities which often arise in modeling materials
under experimental conditions. Materials rarely exist in pure form. Oxide
formation at surfaces and impurity segregation to internal boundaries
can strongly alter material properties and behavior.
Such microstructural effects become increasingly important in nanomaterials
and are often difficult to be isolated from intrinsic material properties
under laboratory conditions. Separation of material properties from
testing artifacts becomes increasingly challenging with decreasing
experimental length scales, especially in nanomaterials research.
Decreases in experimental sample and device sizes and increases in
computational capability now present a unique opportunity for an
integrated approach combining both simulations and experiments in
nanomaterials research.
As we demonstrate below for the case of platinum nanopillars, the
combined approach is not only indispensable, but also provides an indepth understanding of the deformation and mechanical properties
of nanomaterials.
In the current study, nanocrystalline platinum nanopillars were synthesized
by electroplating into patterned templates and tested using custombuilt devices at Caltech [1].
Platinum is especially good for the study of intrinsic material property
because of its minimal oxide formation under laboratory conditions.
In addition, its metallic bonding nature allows us to use efficient semiempirical potentials so that we can simulate samples with large sizes
comparable to experimental ones.
However, they are formidably expensive to compute and typically scale
as O(n3) or worse.
Therefore, the state-of-the-art quantum mechanical simulations are
limited to a few hundreds of atoms representing a tiny fraction of the
amount usually exists in experiments.
Semi-empirical and empirical force fields/potentials use functional
approximation fitted to quantum mechanical calculations or experimental
measurements. They typically scale as O(n2) and O(n).
Because of their computational efficiency, they are frequently used
in material modeling simulations where the electronic details can be
approximated or implicitly treated.
However, these potentials cannot be used to reliably reproduce processes
involving chemical reactions, such as bond breaking and formation.
The mismatches between simulations and experiments are not only
in physical accuracy and length scales, there are mismatches in time
scales as well.
6
FIG. 1: Stress-strain behavior of nanocrystalline platinum nanopillars in experiments
(A-B) and simulations (C-D).
The experimental nanopillars are of similar grain sizes of 12 nm and
have different diameters varying from 60 nm to 1 µm.
research
Transmission electron microscopy analysis suggests the platinum
nanopillars contained few or no initial dislocations.
As shown in Fig. 1 A-B, uniaxial compression tests show a “smaller
is weaker” trend in nanopillar yield strength, contrary to the widely
observed “smaller is stronger” size effect in single crystal nanopillars.
In addition, the simulations also revealed that the atomistic origin
responsible for the observed size effects is associated with the distinct
plastic deformation mechanisms operating in interior and surface
grains, i.e., dislocation plasticity and plasticity dominated by grain
boundary sliding.
Unfortunately, the small nanopillar sizes make it difficult to identify the
underlying mechanism responsible for this unusual size effect.
Therefore, MD simulations were performed on an overlapping range of
pillar diameters (22 to 64 nm) and with similar pillar height to diameter
aspect ratio.
The MD samples contain 2.5 to 44 million atoms. The simulations were
performed using LAMMPS [2] and a platinum EAM interatomic potential [3].
FIG. 3: Plastic deformation mechanisms of platinum nanopillars under compressive
loading in MD simulations. (A) Grain boundary sliding at surface grains and (B)
dislocation nucleation and propagation in interior grains.
In detail, our simulations suggest grain boundary mediated deformation
mechanisms are actively operating during nanopillar compression.
Grain boundary plasticity in dislocation starved samples leads to
softening in their yield strengths.
Grains at the free surfaces are less constrained than those in pillar interior.
Therefore, grain boundary plasticity (mainly sliding) is more active for
grains close to the free surfaces and as a result, further reduces yield
strengths.
Grain boundary plasticity at pillar interior results in stress concentrations
at their triple junctions which in turn lead to dislocation nucleations
there (see Fig.3).
This is the mechanistic origin of the “smaller is weaker” size effect in our
current study. Our previous study on nanocrystalline Ni nanopillars with
grain diameter of 60 nm also suggests the same size effect.
FIG. 2: Plastic deformation of platinum nanopillars under compressive loading. (A-B)
show a nanopillar before loading and at 25% strain in experiments. (C-F) show plastic
deformation process of nanopillars in MD simulations; the images correspond to
strain of 0, 4, 8 and 12%, respectively. The same deformation mode is observed in
experiments and in MD simulations.
By carrying out simulations with similar sample sizes and nanostructures
as experimental ones, we obtained excellent qualitative agreement
between experiments and simulations in several aspects (see Fig. 1
and Fig. 2).
Both simulations and experiments show:
(i) a trend of “smaller is weaker” in yield strength with decreasing
pillar diameters,
(ii) the strength asymptotically approaches the bulk nanocrystalline
strength with increasing pillar diameters,
(iii) an increasingly oscillatory stress-strain curves with decreasing
pillar diameters and
(iv) a similar deformation pattern where plastic yield is followed
by plastic bending.
Because the length scales involved in these atomistic processes are of
the size of atomic spacing (i.e., a few angstroms), it is difficult to identify
them under laboratory conditions.
Hence our large scale simulations are currently the only way to get
the requisite level of detail about the deformation of nanocrystalline
nanopillars.
In summary, our simulations demonstrate the importance of an
integrated approach in understanding nanomaterial properties. By
employing a semi-empirical EAM potential fitted to platinum, we were
able to simulate materials with similar sizes and nanostructure details
as experimental ones.
Our large scale simulations not only reveal the atomistic origin for the
experimentally observed size effects, but also show the potential of
such computer simulations in current nanomaterial research.
References:
[1] Gu, X. W.; Loynachan, G. N; Wu, Z. X.; Zhang, Y. W.; Srolovitz, D. J. and Greer,
J. R. Nano Letters, 12 (12), 6385–6392, 2012.
[2] Plimpton, S. J. Journal of Computational Physics, 117, 1, 1995.
[3] Sheng, H.W.; Kramer, M. J.; Cadien, A.; Fujita, T.; Chen, M.W. Physical Review B, 83,
134118, 2011.
7
research
The mystery
of Nitrogen
embedment in
Zirconium
We doped NO molecule at the oxygen site, and it was found that the
final energetic state is a split defect at oxygen site as shown in Fig.1 after
full atomic relaxation fixing the supercell lattice constants.
We analyzed the final configuration, and considered that the NO split
into the oxygen vacancy (NO)O in fourfold coordination.
By Yu Zhigen
[email protected]
How does nitrogen embed in zirconium? Dr Yu Zhigen from
IHPC’s Materials Science and provides an explanation with
his research findings, which are relevant to the design and
construction of nuclear reactors.
The stability of zirconium cladding alloys, which is used for hosting
nuclear fuels, has been in the media focus ever since the ongoing
radiation disaster at Japan’s Fukushima nuclear reactors that resulted
from the massive earthquake-caused tsunami that hit the country back
in March 2011.
But the alloy oxidation mechanism, especially the effect of nitrogen
which originated from the sponge zirconium, is still not well understood.
Commercial zirconium cladding alloys are designed based on the
assumption that nitrogen will substitute lattice oxygen in Zirconia.
Therefore, alloy elements like tin and niobium were introduced to
control the nitrogen effect and slow down oxidation [1,2].
Unintentional doping of N in ZrO2 was reported either at the fabrication
or operation stage, which would further impact the performance of
ZrO2 devices.
However, to date, theoretical and experimental mechanism investigations
on N-related defects have led to controversial results, although it was
suspected that N2 would replace two oxygens and create one additional
oxygen vacancy in cubic zirconia.
However, it seems that N will likely not prefer to replace oxygen site
based on its reported formation energy.
A very systematic theoretical investigation on nitrogen substitution in
cubic ZrO2 has been conducted by Bredow and the reported formation
enthalpy is 5.48-6.35 eV, (electron voltage, which describes an energy
unit) depending on its configuration [3].
It is impossible to lead to a measurable N concentration by so low a
solubility [4]. But it was found that there was NO adsorption on ZrO2
surface even at room temperature [5].
In a recent study, we investigated native defects as well as all possible
N-related defects in ZrO2 by using first principles calculations [6].
8
Fig. 1. Atomic structure and calculated electron density of embedded NO as well
as NO free molecule. The yellow represents positive value as well electron density
increase (bonding state) and light blue represents negative value as well as electron
density decrease (anti-bonding state).
The formation energies of (NO)O as a function of the Fermi level are
shown in Fig. 2.
Under oxygen-rich growth conditions [Fig. 2(a)], the formation energy
of neutral (NO)O is 5.03 eV and the calculated transition energies are
0.91 eV (+/0) and 0.49 eV (++/+) above the VBM.
(NO)O is likely to be a very deep donor, which cannot contribute to
electronic conduction in ZrO2.
We find that
is the most stable state and its formation energy
decreases with increase in Fermi level.
The transition energy is 1.35 eV (0/−) above the top of the valence band.
Hence, self-compensation may pin the Fermi level between 0.91 and
1.35 eV. When the chemical potential of oxygen decreases [Fig. 2(b)], all
lines would shift down and the relative formation energies decrease.
research
Fig.2. Formation energies of (NO)O defects as a function of Fermi level in ZrO2 under
oxygen-rich (
) and oxygen-poor conditions (
). The charge states
are denoted by number, while transition energies
are the kinks in each line.
The valence band maximum (VBM) is set to zero.
Based on our results for the charge state, for every two nitrogen atoms
introduced, three lattice-site oxygens would be removed, of which
two would combine with N to form NO split diatomic defects and the
remaining one leaves (presumably as O2).
Interestingly, the formation energy of embedded NO is −0.11 eV when
the Fermi level is pinned by N doping under the oxygen-poor growth
conditions, and the formation energy would be lower if the Fermi level
decreases further.
Similarly, N evolved from the Zr or Zircaloy into the ZrO2 would be
expected to produce (NO)O defects and oxygen vacancies. Such vacancies
provide paths for O diffusion, which can affect corrosion.
This means that NO would be spontaneously involved in ZrO2 under
oxygen-poor growth conditions. Based on our simulation results, we
demonstrate a novel chemical reaction mechanism of N in ZrO2 for
forming anion vacancies:
Our theory clears up the long-term misunderstandings on the substitution
mechanism of N-involved zirconia and builds the basis to understand
and develop novel Zr-based nuclear fuel cladding alloys, where multialloying elements, may be used to stabilize lattice oxygen.
When nitrogen enters ZrO2, e.g., into voids formed by radiation damage,
it would tend to react with the lattice O, especially under extreme
conditions of operation (T and radiation). This would form split (NO)O
defects and an oxygen vacancy following the neutralization rule.
As a consequence, the negative effect of nitrogen impurity originating
from the sponge raw Zr metal can be efficiently controlled. Based on
our simulation results, N as well as NO must be controlled in the Zr
metal fabrication process.
In conclusion, we present theoretical evidence for the existence of NO
units in ZrO2 and associate their formation with O vacancy formation.
We will continue to investigate N formation in ZrO2 grain boundary.
References:
[1] Y. B. Cheng, J. Am. Ceram. Soc. 76, 683-688 (1993).
[2] A.M. Garde, S. R. Pati, M. A. Krammen, G. P. Smith and R. K. Endter, Corrosion Behavior
of Zircaloy-4 Cladding with Varying Tin Content in High-temperature Pressurized
Water Reactors, Zirconium in the nuclear Industry: Tenth International Symposium,
ASTM STP 1245, A. M. Garde and E. R. Bradley, Eds., American Society for Testing
and Materials, Philadelphia, 1994, pp. 760-778.
[3] T. Bredow, Phys. Rev. B 75, 144102 (2007).
[4] J.-S. Lee, M. Lerch, and J. Maier, J. Solid State Chem. 179, 270 (2006).
[5] M. Kantcheva and E. Z. Ciftlikli, J. Phys. Chem. B 106,3941-3949 (2002).
[6] Z. G. Yu, J. Zhang, P. Wu and D. J. Singh, Phys. Rev. B 85, 144106 (2012)
9
updates
Having A
Wild Time
By Mark Jhon
[email protected]
It was a swinging good time for all as IHPC celebrated its first Family
Day on a lovely Saturday in September 2012 at the Singapore Zoological
Gardens. Over one hundred staff members from IHPC, S3 and A*CRC
attended together with their families.
In the morning, staff and family members had the opportunity to meet
and mingle. The children were greatly entertained by the ice-cream,
popcorn snacks, and handicraft stations – as were the adults!
The Social Committee organized an entertainment programme which
included game stalls, stage games and an impressive comedy juggling
demonstration that thrilled both young and old. The programme
concluded with a lucky draw for IHPC staff.
The rest of the day was free-and-easy for all to enjoy the call of the
wild. Everyone had a wild time viewing the animals and enjoying the
park attractions.
The Family Day was organized by the IHPC Social Committee: Sharon
Ee, Mark Jhon, Iris Teo, Zhang Jia, Matthew Price, Iftikhar Ahmed, Li
Dongying, Kayo Sakamoto and Loganathan Ponnambalam.
Enjoy the snapshots from the fun and exciting IHPC Family Day 2012!
10
A*CRC Updates
By Marek Michalewicz
[email protected]
NWChem Workshop
Between 25th and 27th October, A*CRC organised an intense, hands-on
workshop on NWChem Quantum Chemistry package. The instructors
were two of the developers of the code from the Pacific Northwest
National Laboratory, USA: Computer scientist, Dr. Edoardo Apra, and
Quantum Chemist, Dr. Karol Kowalski.
More than 70 researchers and students from several A*STAR Institutes
and Universities in Singapore participated in the three-day workshop,
with a long tutorial and hand-on sessions.
NWChem is an open source quantum chemistry package designed
for supercomputers. It was designed to be massively scalable, parallel
program for the most difficult problems in Quantum Chemistry. It
achieved 1.31 PetaFlops, at 57% of the peak performance, on 224,196
processors on ORNL’s Jaguar supercomputer.
This package has been implemented with most modern ab initio and
molecular mechanics methods and algorithms. It’s range of methods
span from ground state Hartree-Fock theory to excited states calculations
in equation-of-motions coupled cluster (EOMCC) methods; from atomic
scale density functional theory (DFT) calculations to large scale plane
wave calculations; and from static molecular properties to quantum
molecular dynamics (MD) simulations.
Modelling for large scale bimolecular systems are also enabled by
various solvation models and QM/MM algorithms.
The tutorial covered the use of NWChem to perform calculations in DFT,
coupled cluster (CC), and excited state EOMCC methods. Plane wave DFT,
MD and QM/MM calculations had also been discussed in the tutorial.
Participants practiced the use of these applications with exercises during
the hand-on sessions, and had discussions with the instructors on the
existing features and future developments of NWChem.
A*CRC welcomes all users who plan to carry out larger scale molecular
modelling and simulations to explore this software. NWChem version
6.1.1 has been installed at all A*CRC x86 computer platforms. Support and
detailed information are available from the A*CRC Quantum Chemistry
software expert, Dr. Dominic Chien.
Cumulus: The New 100 TFLOPS Computer System
at A*CRC
A*CRC is continually striving to ensure that A*STAR researchers have
access to adequate and most modern computational resources. We
have just completed a tender assessment process for a new machine:
The 100 TFLOPS (TeraFlops) IBM BlueGene/Q system.
With the code name Cumulus, it will be the fastest and most powerefficient computer system in Southeast Asia known to date.
Cumulus will consume approximately 48kW of electrical power, compared
with about 120kW for a typical 100 TFLOPS Intel or AMD x86 cluster.
The high-level specifications of the system are:
• Processor: PowerPC A2 CPU, 1.6GHz, 18 cores
(16 for computation, 1 for OS and 1 warm spare)
• Memory: 1GB per compute core
• Number of single socket nodes: 512
• Network topology: 5D torus HPC network
• Latency: 80n
• Bandwidth per link: 40GB/s
• Scratch disk: > 60TB GPFS available from Day 1.
The BlueGene/Q system is extremely suitable for very large problems
typically requiring thousands of cores. However, codes that do not scale
well beyond small number of cores are not suitable for this massively
parallel system.
All A*STAR researchers whose codes scale-up well and who wish to exploit
this very fast parallel architecture will be given access and support.
We encourage all current users of our older systems to move their
parallel codes to Cumulus. This will release resources on Aurora, Axle,
Cirrus and Fuji for the rest of the users whose codes do not scale and
are not sufficiently parallel.
After installation and tests, we expect Cumulus to be released to users
in mid-March 2013. More details will be released nearer the date.
A*CRC has recently converted its
meeting room to a multi-function
seminar room for hosting tutorial
sessions and workshops. NWchem
workshop was the first event which
was held in this venue.
11
research
Supercomputing
2012
By Corporate Communications
[email protected]
IHPC and A*CRC colleagues share their experience at the
recent Supercomputing international conference held in
Utah, USA.
Supercomputing is arguably the most important annual international
event that attracts the best and the brightest in the high performance
computing (HPC) industry. There were 10,000 attendees representing
more than 50 countries and 366 exhibitors.
IHPC and A*CRC (A*STAR Computational Resource Centre) colleagues
took part in the Supercomputing 2012 (SC12) conference held in Utah’s
Salt Lake City in the U.S., with a joint exhibition booth on the show floor.
Sean Ang, IHPC’s Industry Development Manager, said: “IHPC’s capabilities
in simulation and modeling were showcased at SC12. The roundtable
discussions & networking events also provided us opportunities to link
up with the key players in the industry.”
A*CRC and IHPC booth at SC12. Marek Michalewicz (left) and Pierre-Yves Aquilanti
(second left) discussing new technologies with Allinea developers.
participants to learn the best practices and new trends, and to network
with leaders and trend-setters in our industry.”
His take on the most notable new technologies presented this year:
Xeon Phi, ScaleMP solutions, Cray Cascade, IBM’s BlueGene/Q.
“The trending hot topic that surfaced this year was Big Data, and how
Big Data and HPC are merging and are not two separate playing fields
anymore.”
Sean added that the conference helped IHPC to strength relationships
with existing partners, while at the same time, aiding the institute in
garnering new project leads and discovering a new pool of potential
collaborators.
Some highlights, according to Dr Michalewicz, came from:
• YarcData, a Cray company, which presented its new Big Graph Data Analytics appliance - uRICA.
• Pittsburgh Supercomputer Centre, which showed their recently acquired uRICA sytem called “Sherlock” at their expo booth.
According to Dr Huynh Phung Huynh, HPC Capability group manager
Computing Science Department, the poster IHPC presented at the
conference was well-received.
The joint booth was also a highlight: It was visited by a large number
of attendees who were intrigued and interested in the HPC-powered
R&D developments here.
He said: “There was a lot of interest in our poster on ‘Mapping Streaming
Applications onto GPU Systems’.”
Dr Michalewicz added: “We held many meetings and discussions at
our booth. Our presence has been noticed by many attendees, and
showed the international community that Singapore is a serious player
in the HPC field.”
“The poster elaborates our framework on automated generation of
GPU code for most streaming applications that can be run efficiently
and scalable on a single or multi-GPU. IHPC research work is put on the
international stage.”
Find out more about SC12 at http://sc12.supercomputing.org/.
For Dr Marek Michalewicz, Director of A*CRC, Supercomputing 2012
was indeed the place to be.
He said: “We were able to discover the newest trends in HPC technologies,
processors and systems, storage, networking, visualisation and HPC
research. It was the ideal platform to exchange ideas with other
Dr. Huynh Phung Huynh (centre) from Computing Science Department sharing his
research at SC12.
12
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