Refined Solution How HPC Is Changing the Face of Oil and Gas

www.scientific-computing.com April/May 2013 issue 129

Informatics in petrochemicals Geological applications Data retrieval

Refined solution How HPC is changing the face of oil and gas

COMPUTING SOLUTIONS FOR SCIENTISTS AND ENGINEERS

Issue 129 April/May 2013 CONTENTS Laboratory Informatics News and products 4 Laboratory informatics systems are fuelling efficiency 6 Fuel the future Tom Wilkie reports on laboratory informatics in the petrochemicals industry As I write this, details of Pangea, Total’s new 2.3-petaflop supercomputer based at Statistical Science the company’s Jean Feger Scientific and Computing Centre (CSTJF) in southwest Retrieving data day queries 10 France, have been released. Felix Grant takes on the challenge of data retrieval and explores the issues Touted as the largest commercial HPC surrounding ballooning volumes system in the world, Pangea represents a valuable resource in the exploration of oil High-Performance Computing and gas reserves and will enable Total’s in- News and products 14 house engineers and geologists to develop more complete visualisations of seismic Digging for black gold 16 landscapes, while concurrently running HPC is a vital part of the oil and gas industry, simulations at 10 times the resolution as Warren Clark discovers of existing oil and gas reservoir models. From laboratory informatics and HPC Modelling and Engineering to modelling and simulation, computing technologies are playing fundamental Technology in Turin 23 roles within petrochemicals and oil and The 6th European Altair Technology Conference is coming gas industries. Our features on pages 6, 16 to Italy in April. We preview the event and 30 provide further perspectives. Within our statistical science section, Simulation software simplifies stress 27 Felix Grant turns his attention to data Tom Wilkie investigates why design engineers are turning retrieval (p10) while we offer a preview to simulation software more often of the upcoming European Altair Technology Conference (p23). Rounding Earth, wind and fire 30 out the issue are a feature on computer- The natural world is increasingly the subject of modelling aided design (p27) and our regular inside and simulation, as Warren Clark discovers view column.

Resources Beth Harlen Suppliers’ directory 32 Editor

Inside view 34

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www.scientific-computing.com l @scwmagazine April/MAy 2013 3 news and products LABORATORY For regular news updates, please visit INFORMATICS www.scientific-computing.com/news

Products in brief Careful consolidation? ACD/Labs and SORD Beth Harlen looks more than 400 organisations were from discrete informatics products has capture ‘lost chemistry’ identified within the informatics market, led to mergers and acquisitions. The Selected Organic Reactions at recent changes each with annual revenues of $1 million Accelrys’ purchase of Vialis has Database (SORD) is tapping into within the informatics or more: ‘The vendor community two noteworthy aspects. Firstly, it the vast reserves of chemical has become far too fragmented and exemplifies a push by informatics reaction information from academic market it’s impossible for users to stitch providers to add a services element research that has been locked together all these little, best-of-breed, to their offerings. But this may be away for half a century. Using hen Accelrys aquired point-products and come up with an problematic for the industry. According technology by Advanced Chemistry Vialis earlier this year, it environment and set of capabilities that to Elliott, one of the challenges that Development (ACD/Labs) marked the company’s will meet needs in the longer term. comes with vendors expanding their millions of these reactions will be W fourth such deal in a ‘There’s not a week that goes by service offering is a perception that processed into an electronic format year. Other companies have also been where I don’t get a phone call, email the services are there simply to sell that is accessible over the internet. out shopping – in 2011, for example, or FedEx packet from one of those product. ‘Historically, there really hasn’t Perkin Elmer bought CambridgeSoft, 400 informatics companies looking been a software vendor in this space O3Lims & O3LimsXpress Caliper Life Sciences, Labtronics and to sell itself. Some of those are great that’s been successful in having a truly Bytewize has released version ArtusLabs. opportunities, but most are distressed independent services offering that can 4.3 of its LIMS-systems, O3Lims Insiders believe there will be more situations, where these companies have help customers go through workflow and O3LimsXpress. The systems mergers and acquisitions. What is seen the writing on the wall. They can analysis and determine which products are constantly developing and driving this trend and what are the no longer continue as they have been, fit best,’ he said. customers are automatically implications for scientists? One factor due to the shift in customer behaviours.’ Elliott added that the decision to updated to the latest version is the nature of the vendor community He also noted the financial meet the high valuation of $5 million for without any extra cost. itself, while another is the behaviour and imperatives from higher management Vialis was unexpected, given that for In version 4.3, it is possible expectations of customers. to configure the system to The market is fragmented – there COMPANIES canNOT continue as automatically send status mails are many small companies supplying to the laboratory´s customers as informatics products – so we are seeing they have been, due to the shift the sample passes certain defined a consolidation. But users want to move in customer behaviours steps in the testing process. away from a laboratory that has many ‘siloed’ applications and towards an driving technological consolidation the same level of investment Accelrys Paradigm Scientific integrated, single-solution laboratory. within the laboratory, remarking that, for could have built up its own capability Search Software In part, this convergence is driven example, 10 years ago, a computational within that area. However, Carnecchia Waters has announced it by the needs of scientists, but their chemist in a life sciences company maintained that, rather than trying to ‘roll is expanding its laboratory bosses also want their laboratories to would have had a decent budget and up the space’, Accelrys is attempting informatics offerings with the be more efficient. Michael Elliott, CEO of the freedom to use different systems to assemble a portfolio of capabilities addition of Paradigm Scientific Atrium Research and Consulting, said: for in silico modelling and simulation. both through acquisitions and also Search Software, an information ‘Companies that rely on informatics ‘Fast forward, and half that team has organically, through its own internal access platform. The company are facing substantial cutbacks in been laid off, and the company has had R&D engineering efforts. He pointed out says it takes search beyond basic both capital and expenditure, and the to standardise on one system.’ that while Accelrys has invested more keywords by enabling users to consolidation and closure of sites Convergence can be seen in the than $100 million on acquisitions, it has perform object-based searches throughout the organisation. Generally, behaviour of large vendors such as also spent 22 per cent of revenues on across both structured and when this occurs within the user Waters, which has launched products internal activities. With regards to the unstructured data, and across community, it is mirrored by a level of that no longer fit the traditional category acquisitions, he is keen to emphasise different data platforms. supplier consolidation as companies of a laboratory information management that the company is adding domain attempt to address customers in a system, or an electronic laboratory expertise and that many employees, For more products, please visit more concentrated fashion.’ notebook, but include a combination of including the founders, of recently www.scientific-computing.com/products Max Carnecchia, Accelrys’ CEO, technologies rolled into one solution. purchased Contur, VelQuest and Aegis noted that, when he joined the firm, For other companies, this shift away have remained part of Accelrys.

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Enabling Science

SCW April 2013.indd 1 19/03/2013 16:01:55 Laboratory informatics systems are fuelling efficiency Shell/Qatar Petroleum

The petrochemicals industry is finding that laboratory manufacturing units to maximise safety, product grade, and yield. informatics can save money and improve product quality, In some ways, then, the demands on a laboratory informatics system in the as Tom Wilkie discovers petrochemicals sector appear similar to those of the pharmaceutical industry – globalised and mission-critical. But there nwittingly and unwillingly but Out of necessity, the petrochemicals are important differences: petrochemicals very publically, British motorists business is global in its reach, so its quality is not a ‘regulated’ industry; and, in many provided an object lesson in the control laboratories lie in different areas of instances, its production processes are Uimportance of quality control in the world and often use differing languages. continuous rather than batch-oriented. It’s the petrochemicals industry, almost exactly Laboratory informatics needs to feed data possible, therefore, to use many differing six years ago. Newspapers and television and reports into other software, often systems, because the laboratory informatics reported mysterious engine failures by up massive, company-wide management systems do not need to be validated to to 10,000 cars in the southern UK requiring information and control systems. The standards set by an external body such as expensive engine repairs, all as a result of informatics reports are mission-critical the US Food and Drug Administration. damage caused by silicon-contaminated – mistakes are very costly, but so too is Cost-saving and a desire to have an unleaded petrol sold by some supermarket any delay in getting results out to plant ‘integrated’ software system may incline petrol stations. operations that use the data to tune the some companies towards an ERP-based

6 SCIENTIFIC COMPUTING WORLD @scwmagazine l www.scientific-computing.com informatics in petrochemicals

The Pearl GTL (gas to liquids facility) at Ras Laffan Industrial City in Qatar Shell/Qatar Petroleum

Mansoor Al-Shamri, laboratory manager, and Ajith Kumar, senior business analyst, in the Pearl GTL laboratory

itself, leads to errors and thus more costs as as a whole, he continued. There is usually these have to be traced and corrected. ‘It’s a local implementation. ‘In the pharma easier to get to the data with a LIMS than to world, they would use a more centralised customise data-gathering from SAP,’ he said. approach partly because of the validation costs associated with each site having The challenges of continuous its own instance, customisations, and processes processes.’ In the regulated environment of Most companies, he continued, are going the pharmaceutical industry, it is usually down the route of building in quality at cheaper to bring in a single, pre-validated every stage of the process. This means that system for the entire enterprise across all between 50 and 90 per cent of the samples labs and countries than to pay separately for going to the analytical laboratory are from individual validation. in-process testing, rather than raw materials In petrochemicals, by contrast, each or output. ‘That tells you a lot about the site will adapt the LIMS to meet the focus of the company,’ he said. He also requirements of its own workflows. believes it is appropriate to the continuous Mergers and acquisitions have also lead to a proliferation of LIMS from different vendors Ultimately, at different sites, he said. ‘It’s only when there’s a corporate upgrade that you’d see a companies avoid platform rationalisation and simplification system, but such software tends to be batch- disruption in project.’ oriented, and so a dedicated LIMS may be production, which better suited to the huge volume of samples improves cost- Efficiency and product quality being taken and, if instrument integration is The payoff between investing in a LIMS possible, there are huge savings to be made effectiveness and improvements in efficiency and quality in eliminating manual data entry. of product are just as evident in northern For Yves Dupont, senior manager for nature of the process: ‘You don’t have a Europe, in the view of Adam Wahlund, oil and gas at informatics consultancy batch so it’s difficult to do finished-product Marketing Manager for Bytewize. Over the LabAnswer, a dedicated LIMS will not only testing, but you can tap the pipeline.’ In past decade, he said, ‘we have experienced an reduce costs but increase revenues ‘because contrast, he feels that for most ERP systems increased need for LIMS in petrochemical you can provide data that is more real- and their quality control modules, ‘the basic laboratories. I think companies have learned time to the manufacturing process, so they transaction is creating a batch’ even though how much time and money they can save can take action quicker to increase plant with continuous processes, you never finish by regular analysis. Thanks to a LIMS, efficiency or decrease variance and thus the batch. the laboratory work is more efficient and produce more, higher-quality products.’ In ‘Generally speaking, what we see accurate. If, for example, there is water contrast, even though enterprise resource because of history is a LIMS system at in insulating oil, the quality of the oil is planning software such as SAP has a quality each site potentially with local reports decreased. Gas in transformer oil means control module built in, he believes that or workflows, rather than a global that the transformer isn’t working properly. the manual data entry required is costly in centralised LIMS’ serving the company By regularly taking samples and sending www.scientific-computing.com l @scwmagazine APRIL/MAY 2013 7 informatics in petrochemicals them to the laboratory, plants can decrease The same themes – integration with pre- systems. Instead of sending test results the wear on machines and also the oil costs. existing software, immediate access to data, manually to operations, technologists and Ultimately, companies avoid disruption and the efficiencies that come from using a process engineers, at Pearl GTL results in production, which improves cost- LIMS – are evident at Ras Laffan Industrial become available to all relevant parties within effectiveness.’ City in Qatar. Here, the world’s largest gas to the PI system as soon as they are authorised Bytewize has been supplying informatics liquids facility, Pearl GTL, was established in SampleManager. software to the petrochemicals industry, by Shell and Qatar Petroleum in 2006. It Colin Thurston, director of product predominantly in the Nordic countries, since currently processes 1.6 billion cubic feet of strategy, process industries, at Thermo Fisher 1999. Its first such customer, VP Diagnose, wellhead gas each day, using Shell’s Middle Scientific, cites an example of the benefits could not find a system that fitted its needs Distillate Synthesis process to convert the gas of this integration: when panel operators as they had to save a lot of information about need to move oil to new tanks in preparation the source of the sample (in their case, the data management for shipping, they do not have to wait to be transformer from where they take the oil notified of test results, minimising demurrage sample). This led to customising O3Lims was a major priority. charges for loading delays that can cost for the specific needs of a petrochemical We needed as much as $35,000 per day. ‘Since Pearl laboratory. condensed, accurate GTL opened, the facility has incurred no Direct input from instruments and tight information at demurrage charges, an outstanding feat for an integration with existing company software operation so large,’ he said. are common themes here too: ‘When we get our fingertips But there are benefits from integration a new customer it is very likely that it already in the other direction – with the has other software installed, something that into fuels, lubricants and other products. instrumentation, Thurston continued. increases the demand of developing a flexible According to Ajith Kumar, senior business Sample points in the field are marked with LIMS that is easy to integrate. Connecting analyst for Qatar Shell GTL: ‘With billions radio frequency identification tags so that LIMS to the instrument software can save of investor dollars and tens of thousands of when field staff perform sample rounds: ‘A a lot of time as you decrease the need for jobs at stake, data management was a major handheld computer guides them to each manual handling; results and other data can priority. We needed condensed, accurate sample point and then automatically records get imported automatically.’ information at our fingertips at all times.’ the required information. The data are then Wahlund said that even replacing an For its testing laboratories, Shell opted for instantly transferred to SampleManager from older system puts pressure on the flexibility a Thermo Scientific SampleManager LIMS. the field, saving Pearl GTL an estimated of the LIMS: ‘Many laboratories want to At Pearl GTL, this LIMS is integrated with 2,400 man-hours a year.’ Mansoor Al-Shamri, import historical data into the new system an operations management system (known laboratory manager for Qatar Shell GTL, and instead of typing in data manually from as OTTER), process historian (PI), the stressed the benefits: ‘Field operators can do maybe 10 years back, we write a script and oil movement and batch tracking system, their jobs faster and also more accurately, transfer it automatically.’ laboratory instruments and other production since they’re not recording readings by hand.’

Lessons from life sciences?

It is not only in process quality control but also luxury in the life sciences,’ O’Brien said. ‘People IP may be the process rather than the product itself in research and technology development that access and make decisions on data across multiple but the challenge to the informatics system is the petrochemical companies have a need for departments, and we see the same model now same – ensuring that everything is documented informatics software to manage the huge amounts being applied to petrochemicals.’ Williams added: and recorded in a way that will stand up in patent of data that they generate and produce knowledge ‘We do see a lot of commonality. There may be litigation, if need be. IP protection is one of the that is useful for scientific and business decisions. different emphases, but research is research.’ major things that electronic lab notebooks do, And these other applications also face similar Users do not need a complicated system, he said, which is why the biofuels companies are problems of accommodating data generated by O’Brien continued. Dotmatics offers an off-the-shelf interested in such solutions. legacy systems, of crossing geographical and web-based ‘dashboard’ that is data-agnostic. It The structure of the biofuels industry mirrors linguistic boundaries, and of integrating with existing connects with disparate data sources, retrieves that of biotechnology, with lots of small companies software. and presents the information in a format that the carrying out early stage work and hoping to sell For Shikha O’Brien, VP business development end-user wants. The petrochemicals industry is a on to the big oil majors (or, indeed, sell the entire USA for Dotmatics, the aim is a fully integrated challenge, she went on, because it has a lot of data, company and its intellectual property portfolio). system that can be accessed piecemeal in order to often held on legacy or in-house systems from as Their need is to have ‘systems that are flexible enable scientists to collaborate. ‘Irrespective of how far back as the 1980s and it is only recently, in her and track the decision making processes -- what users have captured their data, scientists should view, that the industry has started looking at the life they have done and the results, to see if they are have access to it in a format that makes sense to sciences model to see how it can bring in a proper successful -- and then move on to the stage of “can them,’ she said. informatics solution to capture and retrieve data. you scale it up?”.’ Both she and Glyn Williams, VP of product For Glyn Williams, one very big growth area, Although the emphasis is often on novel delivery at IDBS, see parallels with the where he sees parallels with the life sciences, is in procedures, he sees the whole enterprise as very pharmaceutical and life sciences industries, more biofuels. There is a similarity to early-stage pharma, similar to pharmaceuticals, where once a compound so perhaps than is evident in the quality-control he said, where the companies need to protect their is developed the challenge is to scale that up area. ‘Today, collaboration is a necessity, not a intellectual property (IP). In the case of biofuels, the efficiently and cost effectively.

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This advertisement prepared by: Magnitude 9.6 345 W. 13th Street New York, NY 10014 240-362-7079 Edwin [email protected] Retrieving data day queries Felix Grant tackles data retrieval challenges

erhaps the most famous data retrieval case in the history of science comes from 16th century orbital mechanics. PCopernicus had laid the foundations for a viable heliocentric system; Kepler stood ready to finalise it. Between the two, both problem and solution, lay the mysteries of Pedro Miguel Sousa/Shutterstock.com Pedro Mars, ‘the wanderer planet’. The data that Kepler needed already existed, in a database of naked eye observations painstakingly constructed over two decades by Danish philosopher Tycho Brahe. The problem was twofold. Brahe had nailed his colours to a mixed system at odds with that of Copernicus; and his data was his claim to posterity. He employed Kepler as an assistant, but jealously guarded access to the full observational data set. Kepler did, eventually, gain access to the data. It wasn’t easy, nor always amicable (though allegations that he murdered Brahe to achieve it have been discounted) – but it was done. He still had to learn how to retrieve it productively, but six years of mining and analysis finally bridged the gap to produce a final, successful, validated model. Things have changed almost unrecognisably over the four or five more carefully curated, can sometimes be centuries since Copernicus, Kepler and DIGITAL harder to reach than older analogue stores. Brahe, but some features recognisably INFORMATION CAN Reusing information after it has passed remain amid the new. Investment in SOMETIMES BE HARDER its initial shelf life is a bigger issue than it research is balanced against the advantages ought to be. As a recent case of my own of shared access. Boundaries, proprietary TO REACH THAN OLDER shows (see box ‘Retrieving the recent past’), or otherwise, remain between researchers ANALoGUE STORES multiple rapidly changing factors combine and data repositories. Murder and less to deny retrievability remarkably quickly extreme espionage methods may be rare becoming cheaper. The headache often and opaquely. The most future-proof data (though not unheard of) as means of gaining becomes how to ensure that one retrieves storage option is probably plain text CSV access to data stores, but Kepler would no the right data for particular purposes from (comma separated value) files, stored online; doubt recognise in essence the processes of the ever-ballooning volumes that are thus but even that is not guaranteed, and frequent negotiation and persuasion that allow those becoming available. review is the only certain guarantee of boundaries to be permeated. And then there is the problem of storage posterity. Methods to provide transparent The biggest early 21st century data format obsolescence. Unlikely as it may access to contemporary but incompatible retrieval issue, however, is a different one. seem, digital information which is by databases (as described below) also suggest Acquisition in large quantity is becoming definition recent and (you might think) ways to retain access to older ones as new ever easier. Storage is, in relative terms, ought to be more easily accessible, and developments occur.

10 SCIENTIFIC COMPUTING WORLD @scwmagazine l www.scientific-computing.com statistical science: data retrieval

Some areas of scientific work generate more product, and correspondingly bigger headaches, than others: the life sciences, particularly the mapping of genomes, are particularly fecund for example. A scan of patents shows a marked rise in the number of applications relating to data retrieval methods since the blossoming of the Human Genome Project (HGP). Clinical research programmes increasingly accumulate and share data, with a concomitant need to manage its use efficiently. Few fields are slow to feed the flood, however. Whether probing the picoseconds after the Big Bang or seeking to map every fragment of rock in our solar system, the same pattern of explosive data growth is present everywhere. The key word so far, and not one The ability to retrieve sequence information for genes of interest is a powerful feature of the BioMart tool. universally common among statisticians, is Here a user can download the coding sequence for all genes on chromosome 22 as well as additional ‘database’. Data analysts (especially of my information about each gene and this can be exported in a useful format generation, but things are really only just beginning to change) tend to think in terms however, have been retrieved from an continually added to the database In essence, of lists, or tables, or worksheets of data, operational historian database currently it’s an idea that Kepler (who arrived at his rather than databases. In local terms, we containing more than 300 million cases (and elliptic orbit solution by progressing from are perhaps right to do so; most statistical growing) of just over 2,000 variables. They analysis of retrieved triplets on a mistaken tests are applied to quite small subsets of do not represent a randomised selection, nor circular assumption) would have understood the data available. When a subset contains a systematised extraction; they are the result perfectly 400 years ago; in detailed a few hundred cases from two variables, it of painstakingly developed queries based on execution, it can only happen in very recent looks like (and is) a pair of lists, just as much the hypotheses to be tested. They represent computerised methods. as if it were only the dozen or so cases in the concentrations of C1 and C2 at, and only While that example was an in situ a textbook. But these days the subset will at, all moments when a dozen other variables entomological observational study, historian probably have been retrieved from a very meet specific criteria: other concentrations, databases are mostly widely used in process much larger database – and the criteria for temperature range, light level, atmospheric analysis, fed by sensors and other data that retrieval will range far and wide through humidity, wind direction and the occurrence generators integrated into the machinery other variables, and intercase comparators, of a very specific and relatively infrequent of industrial contexts. Since they are time- not visible in the final subset itself. phenomenon in insect flight. Depending on series based, they are (in principle, at least) In an ongoing investigation which I’ve what this and previous tests show, the query very easy to link with other databases – not just pulled up, for instance, the comparative will be adjusted to extract different cases necessarily from the same or even similar concentrations in a scent of two specific from the same two variables; and so on. The context – to produce burgeoning data chemicals (call them C1 and C2) have queries also allow for switching between complexity. It would be perfectly feasible, been retrieved at 73 different time points inclusion or exclusion, as appropriate, from for example, to relate the database from for hypothesis testing. Those paired lists, any time frame, of the new entries being my insect habitat to that from a nearby

Retrieving the recent past

I was asked to revisit and reanalyse data from a were now able to decode the backups to yield sets chemistry models by Professor Tom O’Haver at the 20-year-old longitudinal study in the light of new of files created and saved by the spreadsheet Wingz. University of Maryland. I could load the epidemiology knowledge. Large and detailed, the data set was Wingz was a spreadsheet program from Informix, files into this and then save them as WK2 (middle backed up onto VHS video cassettes. ground-breaking in its day, far ahead of its time... but period Lotus 123) format. WK2 files are readable by Magnetic tape deteriorates with time, and the that day and time came to an end in 1994. GenStat, a number of current worksheet-oriented products, so stored signal also tends to ‘print through’ from layer from VSNi, has a well-deserved reputation for being could then be saved yet again in any form I wished. to layer. Finding a VHS cassette player that could able to import a wide range of file formats, so I (An alternative would have been to copy and paste be connected to a PC was a challenge. But a tried it. No dice: even GenStat was stumped. I sent via the Windows clipboard, but file saves were more university IT department was able to solve these a hopeful email off to VSNi (suppliers of GenStat), elegant and preserved fuller numerical precision.) problems, copying the content onto a backed-up asking if they had any suggestions, and their ‘expert After rigorously checking that the results were network. in NZ’ offered to develop a complete direct file format preserving the integrity of the original data, it then After investigating several defunct VHS backup import solution in a week or two, but also suggested became a fairly simple process to convert the whole systems, I was rescued by a helpful hobbyist in an immediate workaround. archive. But the fact that this degree of ingenuity Albania who had a copy of the necessary restore The immediate workaround involved a ‘player’ should be required to read information recorded only program and a 286 PC on which it would run. We application for Wingz files used for educational two decades ago does make you think.

www.scientific-computing.com l @scwmagazine APRIL/MAY 2013 11 statistical science: data retrieval

FlexPRO, whose central focus is time Geographical distribution is irrelevant: of the series and refers to variables as signals, 45 databases currently federated at the time of emphasises an uncompromisingly database writing, 30 are in Europe, 11 in the Americas view of its numerical content over the and four in Asia. Open source in structure, more usual worksheet approach. Again, a it is designed to ‘promote collaboration product specific automation model allows and code reuse’, provide ‘unified access to programmed retrieval of specified data disparate, geographically distributed data from this store, with the database approach sources’ and be ‘data agnostic and platform providing a rigorous environment for sample independent, such that existing databases design planning. can easily be incorporated’[1]. In this it offers The provision of automation methods hope of backward and forward compatibility sometimes obscures the fact that most for some of the storage format obsolescence heavyweight data analysis programs are, issues mentioned above, as well as addressing behind their graphical user interfaces, actually contemporary incompatibility problems. programming languages in their own right Ensembl is one of several genomic A database subset extracted by progressively designed SQL queries into a GenStat spreadsheet with automated data retrieval potential browsers designed to bring bioinformatic data for analysis of their own. There are also long-term retrieval and relational database principles developments, such as Microsoft’s ODBC under a single interface umbrella, providing factory, an adjacent motorway, an industrial (open database connectivity) standards, researchers with a unified retrieval view. dairy, a weather station – and that sort of which facilitate access to generic data stores Automated annotation of sequence data combinatorial multiple database approach is by analytic tools. becoming increasingly common. VSNi’s GenStat is a good example of this, Efficiency favours The retrieval tools do not necessarily have its present interactive graphical face being a to be in the same software as the analytic, relatively recent development on top of a data an integrated system, of course. Flexibility often argues for their analysis specific high-level language with a and this is reflected separation, in fact. Efficiency, however, long scientific pedigree. Logical structures by software favours an integrated system, and this is and expressions, loops and conditional increasingly reflected by software suppliers. branching, free (as well as fixed) field input, suppliers Statsoft’s Statistica analysis product, for ability to incorporate user programmes into instance, has long ago evolved into the core the main program resources as transparent produces a MySQL database, which Ensembl of much bigger aggregate solutions aimed extensions alongside native directives and then makes freely available to researchers. at specific purposes. There was built in procedures, all provide far more scope for Several levels are available, from a web-based database management from an early stage. automated responsively adaptive approaches GUI to large dataset retrieval through the Data mining has been a priority for a long to data retrieval than most users ever dream BioMart data mining tool or tightly defined time, leading to development of various of. It also has an unusually flexible and direct SQL queries. Developed in early product clusters including process control extensible file import facility which permits response to the HGP, it now includes other and investigation. Automation is handled users to design their own format templates or key model organisms (such as fruitfly, mouse by SVB, Statistica’s specific (see box: ‘Retrieving the recent and zebra fish) and an expanded range of implementation of VBA (Visual Further past’) draw on the experience genomic data. It focuses on vertebrates, Basic for Applications). For of a user community that may but a sister project, Ensembl Genomes, the Enterprise Edition there is information have already trodden the same has extended the scope to bacteria, fungi, a specific add-in for retrieving Adept Science or similar paths. invertebrate metazoa, plants and protists. analytic data from OSIsoft’s PI www.adeptscience. Genetics is, as I noted earlier, There are similar tools and approaches data historian product (which, com one of the drivers behind being developed in other areas of science, by comparison with my insect the flood of data which has though some are less open and distributed BioMart Project study’s collection rate of well made retrieval such a high than others. www.biomart.org under a million cases a day, can priority area. From it, and Mapping extreme orbit objects in the cope with a capture resolution Ensembl Project particularly from the rise of solar system to make them predictable is of half a million events per ensembl.org genome sequencing and the a particular case, crying out for a shared second) and also extends OSIsoft HGP, have developed two key database in which all positional ‘stranger’ retrieval to other VBA methods. www.osisoft.com practical coping concepts, observations can be logged for subsequent An interface provides for the Statsoft which point the way to more query based retrieval and analysis as the size defining the data repository general solutions: federated grows and patterns begin to be discerned. www.statsoft.co.uk and the method by which data database systems (FDBS) and Which brings us neatly full circle to Brahe erpconnect.umd. are to be retrieved, collections genome browsers, of which and Kepler. edu/~toh/models/ of queries specifying data to BioMart and Ensembl are good index.html be retrieved and analysed, and representative examples. References and Sources metadata specifying appropriate VSN International BioMart, like other FDBS, 1. BioMart project. www.biomart.org. [cited treatment of the retrieved data www.vsni.co.uk is a project designed to 2013 2013-03-01] for the analysis in hand. Weisang GmbH provide single entry point 2. Kinsella, R.J., et al., Ensembl BioMarts: a In a different direction, www.weisang.com access via portals to multiple hub for data retrieval across taxonomic space. Weisang’s analytic software, and disparate databases. Database (Oxford), 2011. 2011: p. bar030.

12 SCIENTIFIC COMPUTING WORLD @scwmagazine l www.scientific-computing.com Not to Miss at ISC: Top 10 Reasons to Attend ISC’13 NEW Industry track NEW Distinguished speakers series | @ A great networking event Human Brain Project | The largest HPC exhibition in Europe | @ Unmatched access to thought leaders TOP500 awarding @ Relevant and practical information @ Source of inspiration for new ideas and new ventures @ Sessions organized into new dynamic formats @ The latest information on the TOP500 systems Tutorials June 16, 2013 @ Your next customer could be here @ Meet with the specialists who can help solve your problems @ Full and half-day tutorials @ Gain insight to help advance your career @ Cover a broad range of HPC areas of interest @ Leipzig is the better Berlin

Exhibition June 17 – 19, 2013 Conference June 17 – 20, 2013 @ With almost 170 exhibitors from research institutions and industries representing supercomputing, storage and networking, ISC’13 will Conference Highlights stand out as the largest HPC exhibition in Europe in 2013. @ State of the Art in Petascale Applications @ Four-Day Research Track @ Parallel Programming Models and Tools @ Analysis of Big Data: Hard Problems for HPC The 2013 Keynotes @ Petascale Computing in the Cloud? @ HPC Centers Subject to Change @ Future Challenges of Large-Scale Computing @ Challenges for HPC Prof. Dr. Bill Dally, Willard R. and Inez Kerr Bell Professor, @ Panel: Long-Term Investments into Parallel Programming Stanford University & Chief Scientist and SVP of Research, NVIDIA @ Publication of the 41st TOP500 list @ Moore’s Law in the Year 2020 @ ISC Think Tank series on Big Data Stephen S. Pawlowski, Senior Fellow, Chief Technology Ofﬁ cer for the @ HPC in Asia Session Datacenter & Connected Systems Group (DCSG) & General Manager @ Analyst Crossfire for the Architecture Group & DCSG Pathﬁ nding, Intel NEW The Industry Track June 18 – 19, 2013 @ HPC Achievement & Impact 2013 Prof. Dr. Thomas Sterling, Professor, School of Informatics & Computing @ The goal of the Industry Track is to help commercial firms make informed and Chief Scientist & Associate Director, CREST, Indiana University decisions about acquiring and managing HPC systems. @ Fooling the Masses with Performance Results: Contributed Sessions Old Classics & Some New Ideas @ Research Papers & Posters Prof. Dr. Gerhard Wellein, Head of High Performance @ Birds-of-a-Feather Sessions (BoFs) Computing Group, Erlangen Regional Computing Center Vendor Sessions

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Products in brief Deglaciation secrets unfrozen Supercomputers initiative that has obtained a mean triggered its gradual warming as a CREC cooling system global temperature for the past 21,000 result of the large increase in high- A technique pioneered by have been used to years, enabling comparisons of carbon latitude spring/summer insolation and EcoCooling and described as decipher Earth’s dioxide levels and temperatures across strong sensitivity of the land-dominated ‘using the building as an air- the world. Jaguar, managed by the Oak northern high latitudes to insolation handler’ has been demonstrated last major period of Ridge Leadership Computing Facility forcing; from 19,000 to 17,000 years to free up space for an additional rising temperatures (OLCF), has since transitioned to Titan, ago the AMOC phenomenon primarily 200 revenue-generating racks in currently recognised as the fastest accounts for early southern hemisphere a typical 1,000-rack large data hree years of work – and computer in the world. warming and deglaciation; and the rise

centre – while cutting the energy 14 million processor Data shows that about 19,000 years in CO2 starting around 17,000 years requirement for cooling from more hours – using the Jaguar ago, northern hemisphere glaciers ago brought about the final stages. than 1,700kW to a mere 160kW. T supercomputer have unlocked began to melt, and sea levels rose. The simulations have consumed the secrets of Earth’s last major Glaciers released so much fresh water more than 14 million processor hours InfiniteStorage 5600 deglaciation. into the ocean that it slowed a system on Jaguar. Technical computing company SGI Our planet has experienced warming of currents known as the Atlantic The team’s weapon of choice was has introduced its InfiniteStorage and cooling throughout its history. meridional overturning circulation the Community Climate System Model 5600 product – a next- About 22,000 years ago Earth’s ice (AMOC). This ocean conveyor belt (CCSM), a model that includes coupled generation, high-performance sheets declined – slowly at first, but flows northward across the equator, atmospheric, land, ocean and sea ice storage platform suited to then more rapidly. Given concerns over taking southern hemisphere heat and models. high-performance computing today’s shrinking glaciers and ice caps, exporting it to the northern hemisphere. ‘The simulation reproduces the and Big Data workloads. Using knowledge of previous deglaciations are The AMOC then sinks in the North southern hemisphere proxy records modular architecture, SGI says the of great importance. Atlantic and returns south. A large pulse beautifully. A good model is the result of IS5600 delivers industry-leading While researchers agree that a rapid of glacial meltwater, however, can place many people’s efforts,’ said He.

performance. release of CO2 about 17,000 years ago led to a rise in temperatures, it The simulation reproduces ARM-as-a-Service was not known until recently what set Boston has unveiled its ARM-as-a- the ball rolling. Now researchers from the southern hemisphere proxy Service (AaaS), powered by Breeze the University of Wisconsin-Madison, records beautifully and ARM, at CeBIT 2013. Harvard University, Oregon State The Boston AaaS is hailed as the University, and the National Center for a ‘freshwater lid’ over the North Atlantic The OLCF has given the project world’s first commercially available Atmospheric Research (NCAR) have and block the entire conveyor belt. nearly four continuous years of access, cloud offerings based on the discovered the trigger for the beginning The simulations showed a weakening allowing the team to run climate Calxeda EnergyCore ARM-based of the last great deglaciation. of the AMOC and a decrease in ocean simulations over 22,000 years and processor technology. The team ran continuous simulations heat transport, keeping heat in the produce nearly 300 terabytes of data. on Oak Ridge National Laboratory’s southern hemisphere and cooling the ‘We have the resources to stage all DXi6800 (ORNL) Jaguar supercomputer over northern hemisphere – leading to a data online for analysis,’ said the OLCF’s Quantum, a provider of data three years to create the first physics- phenomenon known to climatologists as Valentine Anantharaj, who worked with protection and Big Data based test of hemispheric deglaciation. ‘the bipolar seesaw’. the team to make sure they got the management, has announced the They discovered an increase in This, in turn, led to an enormous most from their time on Jaguar.

new DXi6800 Series deduplication insolation (solar radiation reaching release of CO2 from primarily beneath Anantharaj now works with users on appliance, combining industry- Earth) caused by changes in Earth’s the ocean, which then greatly the 10-fold more powerful Titan system, leading performance, scalability orbit, and ocean circulation. accelerated the warming of the globe. and says the OLCF represents a

and efficiency with ‘pay-as-you- The simulations, by Feng He and ‘When the CO2 came out, everything valuable end-to-end resource capability: grow’ extensibility. Zhengyu Liu of UW-Madison and changed,’ explained He. ‘Our facility supports a scientific Bette Otto-Bliesner of NCAR, build on Essentially, said He, the timeline workflow that enables our users to run For more products, please visit simulations at ORNL and featured in for the Earth’s last deglaciation is as their simulations, do their analyses and www.scientific-computing.com/products Science in 2009 and Nature in 2012. follows: from 22,000 to 19,000 years visualise and archive the results.’ The research is part of a larger ago, northern hemisphere insolation Report by Tim Gillett

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The oil and gas industry pushes HPC capabilities Darren Foltinek, RTM product manager at Acceleware, adds: ‘The entire history of to their limits, as Warren Clark discovers geophysics has been a matter of approximating the physics so that a useful image can be s the earth’s natural resources compute- and data-intensive applications such produced on the computers of the day. As continue to be plundered, there are as seismic processing and reservoir simulation.’ computing power has grown, these physics fears that the pace at which oil and Supermicro’s Tau Leng believes that approximations have become more and more A gas can be extracted will slow up customers in oil and gas are major drivers in accurate, but there are still vastly simplifying imminently. Those fears have been with us for HPC development. ‘Money talks,’ says Leng. ‘Oil assumptions being made in order to keep more than a decade or so – but, thanks in part and gas has the highest refresh rate across all compute costs reasonable.’ to HPC, the pace of extraction is yet to slow up of the sectors that HPC addresses. Every year, McGarry adds: ‘The impact of modern at all. they keep upgrading the technology, and the HPC solutions hasn’t simply been about Dr Raymond McGarry, seismic research team lifecycle of a server might only be three or four making the same old applications run faster. lead at Acceleware, says: ‘HPC is absolutely years. HPC is playing a part in maintaining the The greater impact is in making completely indispensable within the oil and gas industry pace of oil and gas extraction by helping to find new things possible – which is timely, given today, particularly on the upstream side, with resources quicker.’ the advanced state of exploitation of “easily-

16 SCIENTIFIC COMPUTING WORLD @scwmagazine l www.scientific-computing.com method is reversemethod migration time (RTM). To example of acurrent state-of-the-art imaging computational of infrastructure day. the Agood required to make imaging possible at on all the grossin which over-simplifications were wave propagation than older the techniques more to fundamental the physics of seismic computational solutions that adhere much Gulf of Mexico, offshore andWest Africa Brazil. ofunder inmuch a body salt as is case the of the for example where hydrocarbons are contained require more advanced imaging techniques, regions with relatively complex that geology gas discoveries are increasingly confined to accessible” hydrocarbon deposits. New oil and www.scientific-computing.com ‘Imaging below requires such salt bodies

@scwmagazine

Huyangshu/Shutterstock.com it speculative, we because don’t know whether data the is interested. tosell whoever We call whereby awhole scan area, we will and then to We echoes. the doalot of speculative work, worldthe to vibrate and or listen sea earth the explains: ‘We out send and trucks boats around acquisition company. Global’s Menger Bill reducing cost the of HPC.’ are levelling playing the field by dramatically newer the sense, computethis architectures majorthe companies. oil and gas or In service user-base, rather than it of preserve the being has available made technology the to awide on GPUs and multi-core CPUs, Acceleware our solution on heterogeneous clusters based HPC.However,modern by implementing proofed against changing hardware trends. consideralso applications their as future- being appealing benefit to our clients that is can they are they in which ultimately interested. An owntheir efforts the high-level on application hardware developments concentrating while immediately advantage take latest of very the using our functions, library our clients can hardware and top-level the application. By gapthe massively the between multi-core to provide of alibrary functions bridge which Acceleware for model is needs meeting these tailoredbe to suitapplications. particular The performance out of hardware that may have to understanding of how maximum to squeeze geophysics and mathematics, as well as adeep inmanyexpertise different areas; including imaging projects requires teams specialist with another. during one wavefield simulationbe available in by requiring that data the volume produced of complexity to data the management problem challenge initself. RTM adds an additional level Simply withvolume dealing this of data is a volumes, into running easily many terabytes. to leads and huge beneath salt bodies data requiredsurveys to adequately image around burden, azimuth wide the nature of seismic the HPCtechnology.modern that simply would not possible without be This is a Earth. huge computational problem propagation of wavefield aseismic through the requires two simulations or three full of the tensbe of thousands RTM within asurvey), image shot asingle seismic (of there which may expertise inmanydifferentareas imaging projectsrequiresspecialistteamswith Global GeophysicalGlobal is primarily aseismic ‘RTM simply would without not practical be ‘Meeting computational the of needs current ‘Apart from extreme the computational Meeting thecomputational needsofcurrent balanced networkbalanced important. is very other for node I/Oaccess.every Having afair, one hasSo, node diskto contend file. every with I could have wanting all 50nodes to write to dynamic routing and balancing. load low latency,was very the and second the was featurestwo particular that appealed. The first Ethernet, on we of because decided Gnodal players and, having to stick decided with replacement, Ilooked at of leading the several to occasional lock-ups of system. the For a fabric was proving inadequate, to be leading core fabric from previous Gnodal. Our core in Houston feeding with 300nodes into a right now across Americas, including the one entire output image. alot needs ofalso inorder memory to store the 4ms wavenew is quite every I/Ointensive. It state solid toneeds be disk, as pushing out a a terabyte of node. Ideally, disk spaceper this intensive process, though, that requires about to fivedays. and threads. Atypical jobmight from run one MPI to communicate servers those between threads across any number using of servers, on 60and run between 600executive jobs will of to createall these image. afocused These sensors, and migration the process collapses soundthe waves from sources the back to the depth migration.tracksthe This ray paths of one Kirchhoff of is which called prestack of different majoralgorithms that a cluster,need split out among There nodes. the are a number algorithms ‘The we use are well suitedbeing to 100andbetween 500nodes,’ continues Menger. to have industry practice inthis clusters of makes HPCasensible option. ‘It is common and cavities.’ providesmethod an accurate map of rock the rockthat inthe and occur cause little pops. The place,is taking and listening for tiny cracks array of sensors around awell where fracking results;the microseismic involves placing an field crewsuse vibrateto earth theand collect and Active active seismic. is where seismic we requires HPC. 3Dimages.full It’s processing this of data that process it and show actually some results with so, inorder to make data the more attractive, we anyone buy will it. It’s quite expensive to dothat ‘Data management presents ahuge challenge. ‘Global Geophysical has fivedata centres ‘We RTM. use also It’s compute- avery The processing this data way of in collected ‘We two classes of collect data: microseismic APRIL/MA

HPC: oilandgas Y 2013 17

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HPC: oil and gas

‘A further challenge is that MPI transactions ‘Seismic analysis is all about processing need to be very quick and very predictable, as power, with very little communication required well as feature low jitter, low latency and high between nodes, so it scales very nicely to bandwidth. thousands of nodes. Reservoir simulation, Altair ‘The installation of the Gnodal fabric meant by contrast, requires very high-speed it could feed and draw from our data storage interconnects, so we develop systems that have much quicker than ever before, so we’ve ended Infiniband built in.’ up upgrading our storage significantly. Reservoir simulation is the process by which ‘The only other HPC user that comes close existing wells whose oil production is slowing to oil and gas in terms of compute intensity and are assessed for ongoing productivity. The data size is Nasa. We use so much memory and process enables the production company to take so much disk space that the cloud is simply not data from points underground, reconstruct the an option.’ underground in a 3D picture to help establish Subsurface topology with strata and faults Hardware specialists Supermicro, which where there is still oil, and run simulations that has several customers in the oil and gas space, will inform future extraction plans. centre power needs by 40 per cent. ‘We found builds its HPC solutions from the ground One of Supermicro’s recent projects has that CGGVeritas is a company that is always up, from the motherboard up to server been with CGGVeritas, a geophysical company open to new technology,’ says Leng. ‘We used configuration. delivering technologies and services to the a GPU-based solution for the computation. Dr Tau Leng, VP and general manager global oil and gas industry. Supermicro worked This is a high-density solution, and also draws of HPC at Supermicro, says his company is with Green Revolution Cooling to deliver a lot of power, which is why the submerged well set-up to deal with the demands of the an HPC solution at CGGVeritas’ centre in solution was particularly suitable. Some cost- oil and gas industry. ‘We have a very broad Houston. benefit analysis has been done on this, which range of products,’ he says. ‘And we specialise Supermicro’s 1U dual-GPU SuperServer is suggests that if the power is above 25kW, then a in providing application-optimised solutions, being used in conjunction with GRC’s CarnotJet submerged solution is often better.’ whether that be for seismic analysis or reservoir fluid submersion cooling system. Together, simulation. Each of these requires a very they create a high-density, high-capacity Workload management different solution. computing solution that has reduced data PBS Works is an HPC workload management suite, which is used extensively by the oil and gas industry. It includes a number of tools, A Total solution including PBS Professional, which optimises HPC resource usage, and PBS Analytics, a web-based portal that visualises historical usage Marc Simon, technical director, SGI and also through a cooling system that was able data by jobs, applications, users, projects, and to accept warm water cooling. other metrics so the user can capture trends for Total has been a customer of SGI in France for ‘For the most part, Total uses the system for capacity planning and what-if scenarios. more than 15 years. Marc Simon, technical seismic processing. The new algorithms, together ‘Oil and gas users generally have large director at SGI, says: ‘We supply them both the with the power of HPC, enable them to see clusters,’ says Rick Watkins, account manager at HPC and the storage – the two are very tightly what is under the earth much more clearly, and Altair, which produces PBS Works. ‘And clusters connected. They need to manage both the therefore determine whether oil or gas is present. need management! Both seismic processing and processes and the big data that the processes ‘In the future, Total will also use the set-up for reservoir simulation are compute-intensive, so create. reservoir simulation, which is a technique that oil and gas has always been an early adopter of ‘Our approach with them has always been helps oil and gas companies determine the most HPC technology. It’s also about ensuring that to get a full understanding of the customer’s efficient method of extraction. any task is using the right resources. We have workflow, their approach to R&D, and how they ‘SGI is a partner in terms of the support we alternative resources now, such as GPUs and use HPC. We have a team of people based at can offer Total, ensuring that what they want to other accelerators, which oil and gas codes are Total’s operation in the south of France, who do is able to run efficiently and reliably on our starting to utilise. So, it’s just simple business not only address HPC projects, but also other system. Around half of our dedicated team works sense to have cluster management software aspects of Total’s requirements, such as data on system administration, while the other half in place of a team of people allocating jobs to management or visualisation. concentrates on R&D support and development. resources. ‘Last year, we won the latest contract on This means helping the process move from a pure ‘The clusters used in the oil and gas offer from Total, which will enable them to take engineer’s algorithm to a smooth application of industry are very large and that size dictates the next step in terms of HPC usage, using new computer science on an HPC system.’ that functions such as health monitoring are algorithms, and also to allow it to cope with ‘By working with Total at the R&D stage, we are essential. bigger data. We supplied them with an integrated aware of the algorithms they are working on, and ‘HPC technology has improved research in cluster based on our Ice X architecture. It has can evaluate early on how to run these algorithms oil and gas. Jobs that used to take two or three 100,000 cores, more than 5400 terabytes on emerging systems and processors. In turn, this weeks to complete can now be done in two of memory, and 8 petabytes of disk space. helps Total select an appropriate configuration or three days. Processors are better, codes are Like any customer, they wanted the solution to the next time they upgrade their system. We have better optimised, and interconnects are faster. demonstrate a high level of performance, but it teams looking at Nvidia GPUs and Intel’s latest All of these component parts of an HPC setup also needed to be energy-efficient. We achieved chips all the time to assess their suitability to have had to improve to keep up with the size of this through the improved density our products, these new algorithms as they emerge. cluster demanded by oil and gas. ‘We have integrated PBS Works with a

18 SCIENTIFIC COMPUTING WORLD @scwmagazine l www.scientific-computing.com NWC13-FullNWC13-Full Page 3D Page Mag 3D Advert Mag Advertv3:NAFEMS v3:NAFEMS 27/02/2013 27/02/2013 18:57 18:57Page 1 Page 1 HPC: oil and gas

DDN Our customers are looking to bring the problem to the data, rather than the other way round, to save the costly effort of having to move the data in the first place.’ Noer believes that the application of HPC within oil and gas is growing beyond the data management side. ‘Until now, many oil and gas companies have a dedicated HPC department, which is entirely separate from their day-today IT department,’ he says. ‘However, we are seeing the adoption of HPC technologies even within the IT departments too. We see this trend continuing even beyond energy companies.’ DDN has years of experience in providing the storage behind HPC, and more recently has been supplying such products to the oil and gas market. ‘The real data-intensive part of oil and gas is seismic processing,’ says DDN’s James Coomer. ‘The data capture itself takes place in odd locations such as on ships in the middle of oceans The data-intensive part of oil and gas exploration is seismic processing or on vehicles in deserts. Storage has a major part to play here in two roles: first, in the ingestion number of specialised third party simulation and the scale of the storage required for the data rates – that is, collecting the highest resolution packages in the oil and gas industry, such as they’re creating.’ data possible from the sensors, which can be from Schlumberger’s Eclipse, which means that users Geoffrey Noer, senior director of product 1GB/s upwards; and second, the processing of of that software can access the functionality of marketing, adds: ‘Within seismic processing, that data into, for example, a 3D map. the PBS Works suite directly from the Eclipse there is a continuing push for ever-finer detail at ‘Our storage can cope with the high data rates interface. On the HPC side, PBS Professional a more granular level. As that happens, the drive during the ingestion period, and also in the is able to schedule jobs executing that software, is towards larger and larger compute clusters to processing part, when thousands of nodes may according to the number of licenses available.’ process the data, as well as the need for faster be accessing the storage at the same time. In oil and faster storage. The faster you can process the and gas, data rates in this latter part of the process The storage challenge data, the faster you can make a decision about can be typically 6GB/s and maybe much higher. Panasas has been involved in supplying the where to drill. This is why, in seismic processing It is easy to migrate from a traditional NAS oil and gas industry with storage solutions for deployments, you often see thousands of storage system to one of our parallel file systems, several years. Barbara Murphy, chief marketing compute nodes, rather than the tens or hundreds so users need make no changes within the officer, says: ‘Panasas has been operating in the many other HPC applications demand.’ application. This is important for industries such energy sector since our inception. Our scalable, as oil and gas, who can now take advantage of the high performance system suits the size and The faster you faster data rates offered by parallel file systems complexity of the data sets they are dealing with. without impacting the surrounding systems. ‘We’ve worked with third-party seismic can process the ‘The industry is becoming ever more software vendors to help them parallelise data, the faster complex; the acquisition and exploration process their applications for the workload, and that’s you can make a is becoming more precise and using more really helped us gain market share. It remains complicated algorithms. So both the compute our largest growth sector, as the energy decision about side and the amount of data being ingested is industry has moved from a long period of where to drill always going up.’ being in “extraction” mode to once again return to “discovery” mode. With the price As the years go by, data accumulates, and Looking ahead of oil and gas continuing to climb, it’s now this creates a challenge. Murphy continues: ‘All Acceleware’s McGarry concludes: ‘The current worth the investment in complex extraction. seismic data is valuable, and it is so expensive to HPC generation has, for the first time, given us We have installations in over 50 countries, in collect that no data is ever thrown away. Some the ability to base production seismic imaging environments as diverse as deserts, the Arctic of our customers are still referring to data that software on realistic physics. In the coming circle, mountains and so on. These are often in they extracted 20 years ago. The earth’s structure years we will see ever more complex physics very remote, inclement areas with minimal IT won’t have changed in that time, but the tools to being simulated, for example elastic RTM will facilities. The design of our units makes them pull out and analyse that data do evolve. Oil and supplement the current acoustic-based version particularly easy to service. gas, therefore, is an industry that has a massive to account for elastic deformation of the Earth ‘Oil and gas is one of the most mature scale out problem; we don’t talk about terabytes due to the seismic disturbance. Full Waveform industries when it comes to using HPC for its here, we talk about petabytes – and it’s tens of Inversion, which has long been the Holy Grail scientific workload. From that point of view, the petabytes of new storage every year. in terms of building structural Earth models, market was early to adopt parallel file systems ‘Seismic processing is compute intensive, will become increasingly common. And these and scale out architectures to manage both the network intensive and storage intensive. So, developments will require significantly more complexity of the simulations they are running moving data around becomes a real problem. computational power.’

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The 6th European Altair Technology Conference takes place in Turin, Italy from 22 to 24 April. Here’s a preview of the event and its exhibition

he 6th European Altair Technology and access, resulting in maximum software Conference (EATC) is set to attract utilisation, productivity and return on more than 500 European engineers investment. T and engineering managers, who will www.altairalliance.com Digimat’s holistic approach to model hear more than 100 keynote and technical advanced materials and structures, offers presentations on a wide range of topics within Click2Cast is a casting material suppliers and end-users the capability product lifecycle management technology in process simulation to: investigate and predict the behaviour of advanced manufacturing. software developed a large mix of composite materials; improve Keynote presentations are drawn from under an innovative user prediction of CAE analyses by accounting for a diverse range of industries, including experience, allowing the the influence of the manufacturing process automotive, heavy machinery, shipbuilding, complete simulation to in structural FEA; minimise the weight, cost and aerospace. be done in five simple steps and through a and time-to-market of high-performance Among the exhibitors will be Altair itself, completely new and user-friendly interface. composite parts; design and manufacture which will be showcasing how its HyperWorks Click2Cast allows users to enhance and innovative high-performance composite parts; platform applies a subscription-based licensing optimise their manufactured components and reduce material testing and prototyping model, where customers use floating licenses avoiding typical casting defects such as air by characterising material better, faster and to access a broad suite of Altair-developed as entrapment, porosity, cold shots, and more, cheaper. well as third-party software applications on- thanks to the simple and quick mould filling www.e-xstream.com demand. and solidification simulation. The Altair Partner Alliance effectively www.click2cast.com With more than 10 extends the HyperWorks Platform from 28 years in designing and internally developed solutions to more than 80 Digimat, the material modelling solution manufacturing applications with the addition of new partner from e-Xstream engineering, an MSC Software high-performance applications. Customers can invoke these third- Company, provides technology to predict systems, E4 Computer Engineering is an party applications at no incremental cost, using the properties of advanced materials, saving Italian vendor delivering a range of workstation, their existing HyperWorks licenses. design and testing time and resources for server, storage and solutions for HPC and Customers benefit from improved flexibility manufacturers. industry. www.scientific-computing.com l @scwmagazine APRIL/MAY 2013 23 Providing leading-edge products for research, pharmaceutical, automotive, fluid- Fluidon will be showcasing DSHplus, dynamics and prototyping applications, which offers 1D system simulation for E4 Computer Engineering focuses on complex hydraulic and pneumatic systems the development of the most advanced and components. DSHplus is a simulation technologies in order to deliver solutions. tool that offers advanced engineering At EATC, E4 will be showing performances technologies. The dynamic calculation and benchmarks resulting from the latest tests shows the physical behaviour of individual on Intel Xeon Phi as well as introducing its fluid power components and their exclusive ARKA Microcluster, a system based interactions. on ARM architecture ideal for a wide range of Different examples of models from various markets such as oil and gas, image analysis and application areas simplify and accelerate cloud computing. modelling processes. Within the shortest www.e4company.com time possible, engineers obtain high-quality the development area of automotive systems, development results from the simulations, off-highway and commercial vehicle systems, Eurotech is a global company which contribute substantially to ensuring manufacturing systems, mobile hydraulics, based in Italy and with their company’s long-term success. naval and railway systems, medical or subsidiaries in Europe, USA DSHplus applies to manufacturers, aerospace. and Asia. The Eurotech Group developers or users of fluid power systems in www.fluidon.com develops and markets miniaturised computers for special uses and high performance computers. Eurotech is a leader in the implementation of MultiMech will highlight durability and data analysis solutions, nCode the pervasive computing scenario in a variety its True Multiscale has been a leader in solutions to understand of market sectors. technology, which helps product performance, accelerate product The Eurotech HPC division is committed to engineers to think outside development and improve design. The power bringing value to customers providing energy the box when looking for and ease of use of nCode software is a direct efficient computational power that greatly the ideal composite result of its world-class development process, accelerates applications and allows customer material design to their specific applications. expertise and in-depth experience of a broad to save costs, increase revenues and leverage Even before the very first physical prototype range of industries. green IT policies. is ever made, the software allows designers www.ncode.com At EATC, Eurotech will introduce its GPU- to experiment with multiple composites, by based line of high-performance computing virtually combining constituents, such as fibre Novacast will showcase products, which provide CAE, EDA, CAD and resin, to build novel composites from the NovaFlow & Solid CV, a and rendering applications with the greatest ground up. mould-filling and acceleration and the most compact and The technology can then quickly and solidification simulation energy-efficient design on the market. accurately simulate composite structural package based on www.eurotech.com performance, as a function of microstructural advanced fluid flow and heat transfer theories. design variables. Ultimately, this saves costs With new meshing technology, new HP and Intel enable engineers’ by reducing material and structural testing advanced numeric models and control volume innovation according to three needs during product development, as well as meshing, it is an efficient simulation package. vectors: technologies to boost premature mechanical failure. A complete simulation including start-up, parallelisation and performance; MultiMech will keep pushing the envelope meshing and running can be set up in less than ‘smart’ job management to get of advanced materials simulation software to an hour and is extremely accurate in accordance more design cycles out of a given provide solutions aimed at the most innovative with 3D drawings. licence budget; and easier and and challenging structural designs. Most casting methods – gravity sand casting, more ‘democratic’ use of www.multimechrd.com gravity permanent mould, low and high pressure simulation. die casting, lost wax method, tilt pouring and At EATC, HP and Intel will nCode DesignLife lost foam process can be simulated. Commercial showcase recent examples that reflect their performs CAE-based alloys can be simulated – grey and ductile iron, collaborative work with Altair, including: fatigue analysis using steel, aluminium alloys, copper-, zinc- and parallelisation and performance – RADIOSS results from all leading magnesium-based alloys, super alloys, all types 12 SPH scalability study – simulation of FE codes, identifying of mould and core materials on the market and bird impact on an airplane wing airspeed critical locations and calculating fatigue lives. exothermic materials, as well as chills. sensor with 10 million SPH cells; smart job Users can go beyond simple stress analysis and Simulations visualise the consequences of management – HP Insight CMU – PBS Pro avoid under- or over-designing products by certain designs of gating systems and moulds. connector; and democratic use of simulation: predicting fatigue using actual loading Casting defects, such as oxide inclusions due cluster starter kit for small- and medium-sized conditions with nCode DesignLife for Altair to excessive turbulence, cold-shuts, shrinkage business to run explicit solvers, implicit solvers Partner Alliance. This provides a combination cavities and slag inclusions, can be avoided by and remote visualisation. of ease-of-use and powerful fatigue analysis – optimising the design of the gating and venting www.hp.com without additional investment for APA users. system. www.intel.com With more than 30 years of expertise in www.novacast.se

24 SCIENTIFIC COMPUTING WORLD @scwmagazine l www.scientific-computing.com event preview: EATC

SGI aims to deliver a unified SolidThinking aims to create, develop compute and storage solution to and market technology that helps its user its manufacturing customers, community bring the most desirable products reducing overall system to their customers faster. management requirements and SolidThinking Inspire allows design costs as well as simplifying data engineers and architects to generate and management and archival needs. investigate structurally efficient concepts quickly The company says its flexible x86 based (unstructured mesh), scSTREAM (cartesian and easily. Traditional structural simulations server portfolio can scale effortlessly to meet mesh), and HEAT Designer (cartesian mesh) allow engineers to learn if a design will support customer’s compute and I/O requirements as for electronics design. the required loads. Inspire assists by creating they evolve. Software Cradle is a leading provider of CFD a new geometry within the package space, The SGI UV 2 product family provides a software and related engineering services and using the loads as an input. SolidThinking says single-node, cache-coherent shared memory their solutions are used by companies such Inspire is easy to learn and works with existing platform that can start small and grow as Toyota, Ford, Honda, Nissan, Hyundai, tools to help seamlessly as needs develop. Samsung, Panasonic, Sony, Valeo, Bosch, Canon users reduce Built with Intel Xeon processors E5 family, and IBM. development SGI UV 2000 is capable of consolidating the The company’s CFD solutions are aimed at time, material entire CAE workflow onto a single platform. helping customers reduce their time to market consumption SGI ICE X and SGI Rackable servers provide by providing powerful and easy to use software and product weight. best-of-breed cluster computing. And finally, at an affordable price. SolidThinking Evolve combines the SGI Modular Infinite Storage provides the The main advantages are: Ease of use – modelling freedom of organic surfaces with the ability to store and access the vast amount intuitive navigation system guides you through control of parametric solids and construction of engineering data created by these CAE the modelling process, from importing CAD history. The company says Evolve’s integrated bandwidth-intensive applications. native geometry to executing the solution; rendering creates stunning photo-realistic www.sgi.com automatic mesh generator – the integrated images. pre-processor is one of the industry’s leading SolidThinking software is sold and supported Software Cradle was established in 1984 and flexible, controllable and robust mesh by a global network of distribution partners specialised in development of computational generators; and the product uses a small and is also available as part of the Altair fluid dynamics (CFD) and thermal-fluid amount of memory. HyperWorks simulation suite. analysis software including scTETRA www.cradle-cfd.com www.solidThinking.com

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Design engineers are Esteco increasingly turning to simulation software to ensure they make the best choices. Tom Wilkie reports

t is a commonplace of modern industrial society that products are getting ‘smarter’ – and therefore more complex. Whether Iit be the eponymous smartphone or an oil drilling rig, many more functions and capabilities are being built-in – often, in the consumer market, more than the customer can actually make use of. Esteco software is used to drive geometry modification and simulation processes But before complexity and ‘smartness’ can be built-in, they need to be designed-in; and this is to the surface for interpretation. ‘Twenty years disgruntled customer but will be tweeted posing multiple challenges for the providers of ago you would not have thought of electronics or otherwise disseminated on social media, computer-aided engineering (CAE) software. in a drill bit,’ he said. much more widely than before. Thus, he said, Where once individual aspects of physics The point about such complex systems, he engineers will want to evaluate lots of different could be evaluated sequentially – electronics went on, is that they do not fail individually; designs but it will be impracticable to build as and then structural mechanics for a phone; they fail as a system. Thus it is no longer many physically as they want to evaluate. The structural mechanics and fluid dynamics for possible to optimise a system by optimising only solution is simulation, in his view. But, an off-shore oil rig – now the demand is for the individual components – the system has Christenson continued, simulation is nowadays multi-physics packages to do it all at once. And being used not just to validate or troubleshoot a the people worrying about the antenna design single design but to study hundreds of designs of a smartphone need to talk to the people there was interest to make sure they are robust. designing the case, yet they come from two in simulating larger different disciplines – can the software allow models, requiring Complexity needs collaboration mechanical engineers and electronic engineers access to more Growth in demand was evident across all areas, to talk together effectively, even if they are on he said, although there was particularly strong different continents? computing power interest in simulating larger models, requiring This trend to more complex, smarter access to more powerful computing power such products is a key driver for the software to be evaluated, and optimised, as a whole: as high-performance computing (HPC). ‘You developers, according to Barry Christenson, ‘This creates complexity, and is one of the can evaluate designs very quickly on a large director of product management at Ansys, challenges that software developers must face cluster or network,’ he said. which specialises in engineering simulation and overcome.’ Complex designs necessitate large design software. Products have electronics in them A second driver for innovation and teams, with mixes of different scientific and that they never had before, he remarked, development in CAE software is that engineering disciplines. One further aspect citing the example of oil drill-bits. These engineering designers want their products of modern engineering simulation software, sometimes go down two miles and it would to be more robust and to work over a wider according to Christenson, is that it should be impracticable to use wires to communicate range of conditions. Partly, this is because facilitate communication between these with the drill-bit, so they are equipped with an in today’s age of publicity, the failure of one different people who may not be in the same electronics package that sends a sonogram back consumer product will not result in just one office together or may not even be in the same

www.scientific-computing.com l @scwmagazine APRIL/MAY 2013 27 modelling: computer-aided engineering

of aerodynamic performance at the same Ansys time as obtaining a four per cent reduction in the weight of the wing. ‘The optimised configurations, while still matching TLAR, determined substantial advantages compared to the initial wing profiles,’ she concluded.

Optimising train design Energy consumption is equally a concern for modern railways and, just as in aero- engineering, can be accomplished by optimising the aerodynamic shape of the train. But there are conflicting constraints: the best models for drag do not have a good stability against crosswinds. In addition, trying to accommodate a lot of passengers also conflicts with optimal aerodynamic shape. In an ideal world, form and function may go faultlessly hand in hand, but in the real world of trade-offs in engineering design, elegance and functionality do not always do so. These were some of the challenges faced by Bombardier, the Canadian transport Simulation of fluid–structure interaction to allow designers to assess the impact of waves on freshwater engineering company, in the development of and offshore systems Zefiro train, intended to be the world’s most economical and eco-friendly very high speed country. Added to that, companies want to Aircraft Requirements (TLAR). train, which can reach speeds of 380 km/hr. expand their in-house engineering resources by The problem is one of simulation and Bombardier used Esteco’s modeFrontier not getting more people to use simulation software optimisation while dealing with the structural only to integrate the various CAE tools that and take decisions which means that the mechanics of the wing design and the fluid it was using but also to drive the geometry creators of the software, such as Ansys, have to dynamics (CFD) of the airflow over it. Esteco’s modification and simulation process, and to make it easier to use and more accessible. The design automation process, employing its provide the necessary graphical tools for the key direction is to make it more ‘automatable’ ‘modeFrontier’ software, enabled 20,000 design statistical interpretation of results. so that people can customise their own profiles of the 2D wing shape to be evaluated, Bombardier’s engineers considered some workflows rather than making it ‘automatic’, while taking account of aerodynamic and 60 different design parameters in their which may be too restrictive. structural analysis via Alenia in-house software. models, including the train’s outer shell, the After the optimal 2D profile had been selected, cab, behaviour in the event of a crash, and The key direction CFD computations were validated against a ergonomic constraints. is to make it more parametric Catia 3D wing-body. According In the end, the company brought the to Enrica Marentino, CFD Specialist at Alenia aerodynamic resistance down by 20 per cent, ‘automatable’ so that Aermacchi, the process helped the design thereby reducing energy consumption by about people can customise team to achieve a 2.5 per cent enhancement 10 per cent. workflows Esteco For Esteco, the Italian-based company specialising in research and development of engineering software, an aircraft design project by Alenia Aermacchi exemplifies the benefits of a multiphyics, many-design evaluation. This study was performed in the framework of the Clean Sky Joint Technology Initiative, whose objective was to develop a new generation aircraft that generated less noise, particularly on take-off and landing, and had better fuel efficiency. One way to achieve this is to alter the profile of the wing, making it thinner – but there are counterbalancing drivers such as maintaining the structural integrity (and therefore safety) of the wing while reducing its weight, which would point to a thicker design. Any solution had to comply with the Top Level Esteco’s modeFrontier in action

28 SCIENTIFIC COMPUTING WORLD @scwmagazine l www.scientific-computing.com ® HyperWorks 12.0 A Platform for Innovation™

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improving knowledge, as J. Helgason/Shutterstock.com Warren Clark discovers

hether it’s up in the sky or under our feet, the natural world and all its complexities W are increasingly being modelled by software packages. The results are used to predict future movements of, for example, volcanic ash – or to identify the most productive process for mining coal.

Ashes to ashes At the Barcelona Supercomputing Center (BSC), Arnau Folch, has been working as part of the Environmental Simulations Group to provide numerical modelling of volcanic ash clouds. Explosive volcanic eruptions eject into the atmosphere enormous quantities of The Eyjafjallajokull eruption in May 2010 wreaked havoc with international flights particulate matter, globally known as tephra, that is dispersed by winds at scales from local strategies were not as good as could be,’ monitor and predict ground-level fallout,’ to continental. Millimetric particles sediment says Folch. ‘Moreover, different VAACs use says Folch. ‘But now, it is used mostly for and fall out, causing an array of impacts different codes and modelling strategies.’ predicting the concentration of ash in the air, on local communities, infrastructures and The BSC group develops and maintains which is why the civil aviation industry has ecosystems. In contrast, micrometric-size FALL3D, a parallel VATDM running at scales become interested in it.’ particles (volcanic ash) can remain airborne from local to continental, and used at the The code itself could run on a standard for days to weeks, in the form of ash clouds VAAC in Buenos Aires. Several other users PC – but, in order to achieve the results at that jeopardise aerial navigation. apply the model worldwide for a number of the speed at which they are useful, HPC is Volcanic Ash Advisory Centers (VAACs) purposes including operational forecast of required. ‘In an emergency, speed of the code are the official institutions tasked by the tephra fallout and ash clouds or generation is important,’ says Folch. ‘The problem is International Civil Aviation Organization of probabilistic maps for long-term hazard that there is still great uncertainty during an (ICAO) with monitoring and forecasting of eruption, since we are dependent on live data ash clouds within their assigned airspace. The code could being fed into the model in order for it to be Although the 2010 Iceland eruption was run on a PC, but IN accurate. It is very difficult to measure all the the most disruptive event in recent history, factors in an eruption in real time. We mainly VAACs have been around since the mid-90s. ORDER to achieve need to know how much ash has erupted, VAACs make use of satellite imagery useful results, and how it is distributed within the cloud. If and Volcanic Ash Transport and Dispersal HPC IS REQUIRED we are able to feed in satellite imagery and Models (VATDMs) to produce six-hourly data from ground-based systems, the model forecasts that are used by civil aviation and risk assessment (for example, Australia can be more accurate. So, in the early stages authorities to close contaminated airspace Geoscience or the members of the Latin- of an eruption, prediction is very difficult. and aircraft re-routing. The recent American thematic network CENIZA). In ‘Also, some volcanoes are very well disruptions caused by Eyjafjallajökull turn, the group is also developing a GIS- monitored, while others are in remote (Iceland, 2010) and Cordón Caulle (Chile, based tool for short- and long-term air traffic locations that may not even have proper 2011) volcanoes have evidenced some flaws management aimed at providing decision satellite coverage; that will clearly have an in the operational strategies and lead to an support to stakeholders, decision-makers and effect on the quality of the model we can examination of VATDMs. ‘The community other model end users. generate. realised that existing codes and modelling ‘Originally, we developed the code just to ‘HPC is still not widely used within the

30 SCIENTIFIC COMPUTING WORLD @scwmagazine l www.scientific-computing.com volcanology community. Very few of the essential part of our modelling efforts. I do codes have been adapted for parallel use. not think we would ever get a model of this It would be fantastic if there was more magnitude out without Minex.’ widespread use of HPC, but the community One person would take three to four weeks does not yet have the skills to take advantage to create a bench structure model for the of it.’ mine, according to Van Heerden. ‘When you reproduce something with the same data and Coal in the hole methodology, the software always renders Gemcom, part of Dassault Systemes, provides the same answer,’ he says. ‘If the output is a range of geology and mine planning different, you know that you are either doing software solutions, and has worked with something wrong, or something has changed major companies around the world. in the data or methodology. This high level Its Minex product has been used in of accuracy is especially important in view Exxaro’s Grootegeluk mine in South Africa’s of the stringent specifications and narrow Waterberg Coalfield, which produces 18 tolerances imposed by many of Grootegeluk’s million tonnes of coal per year from an clients.’ area of more than 740 hectares. It has been Van Heerden highlights the advantages of applied to model complex coal reserves the software’s 3D capabilities. ‘You can utilise in order to achieve maximum quality and the graphical display to check your work production. as you go along,’ he continues. ‘The results The amount of data generated in a mining of the behind-the-scenes mathematics are operation of this size is staggering. A recent displayed in the graphics window, so you geological model at Grootegeluk covered always have a feel for what is happening in 760 boreholes. A full succession borehole the modelling process.’ holds 12 coal zones and five interburden This will help the next stage, as Van waste seams, as well as an unweathered Heerden moves to a more complex seam and a weathered overburden horizon. This model. ‘The new model will have 58 seams equates to 17 different mining horizons, or in total, resulting from specific combinations benches. Each horizon has a roof, a floor, and of the 76 coal and non-coal samples,’ he a thickness grid, yielding a total of 81 grids in explains. ‘The sample qualities are combined the bench structure model. to yield seam qualities. Combining different The 12 coal and coal-bearing seams are seams to form new bench scenarios will modelled in 13 different density fractions for enable us to optimise production from the life-of-mine scheduling purposes, generating mine and product qualities from the plants.’ 1,560 quality grids for proximate analysis. This optimisation will enable Grootegeluk ‘Our bench quality model comprises 5,696 to expand the number of high-value products grids and counting,’ says Caille Van Heerden, that can be extracted from the same deposit. senior geologist at Grootegeluk. ‘The It will also mean that more tonnes can be complexity of the multi-seam geology and its mined with the same equipment, thereby associated quality parameters make Minex an saving money and increasing profitability.

Modelling coal reserves using Gemcom’s Minex software Gemcom

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www.scientific-computing.com l @scwmagazine APRIL/MAY 2013 33 inside view

The optimisation conundrum Thermo Scientific SampleManager 11 LIMS Put Control in the Hands of your LIMS Users and Transform Your Business opportunity to boost their innovation assets and Carlo Poloni, president of Esteco and take product development to the next level. Engineering Professor at University of Trieste, Upfront optimisation becomes a strategic driver and helps shape the new design argues in favour of optimisation process: simulation, analysis, decision making, prototyping and testing are optimised to cut To enable today’s laboratories to be more flexible, efficient and compliant costs, but the real competitive advantage starts at o optimise or not to optimise? This of encompassing multiple opposing objectives the product concept level. than ever, software must empower users and demonstrably improve is hardly the question anymore. within the same project. Targets like increasing Exploring and evaluating configurations Numerical optimisation has recently efficiency and durability while reducing weight before competitors is crucial for companies productivity across a connected enterprise. gained momentum among engineering and cost are easily achieved. The quest for best striving with the manufacturing of complex T and manufacturing companies, where such a compromises is identified along the so-called products, while understanding key factors and principle is now integrated in the product design Pareto Frontier, representing trade-offs between variables dependencies ahead of time allows for and development process. The overwhelming the considered objectives, and giving theT hermoa dramatic reduction of design Scientific cycle, cutting The SampleManagerhardest working LIMS in the industry now 11 LIMS question has rather become: does optimisation decision-maker a useful decision dashboard. down time and further lowering development has advanced new tools and user-interface still make a difference? Nowadays, we are in the middle of a multi- costs. enhancements that improve laboratory process In the humble opinion of this writer the disciplinary integration shift. Process complexity Does this not sound enough? If cost and time mapping management and automation. answer is ‘yes’. Coming from a long career is increasing as dispersed and sometimesPut Controlare not the only factors atin play, arethe we really sureHands of your LIMS Users and Transform Your Business in engineering, both as a professor and a global engineering teams concur to improve we can identify the best possible solution? SampleManager 11 puts decision-making power businessman, I keep considering optimisation as product performance metrics. Different domain Giving free rein to optimisation techniques where it belongs, in the hands of users who can a truly revolutionary tool to inspire innovation approaches and a large number of variables, and embracing them, starting from the product make logical choices about workflow, instrument in the product design process. constraints and objectives, related to different conception stage, opens up another substantial integration and data reporting for management To begin with, it represents a driving force disciplines, all compete in the hunt for the best advantage: the capability of pinpointing for ‘out of the box’ solutions. By increasing result. The solution comes from the integration solutions that are completely innovative and metrics or regulatory requirements. exploration efficiency, advanced optimisation of several powerful simulation tools and the have not been considered before. The most Workflow capabilities simplify implementation, algorithms lead to designs that would otherwise automation of sophisticated workflows into a advanced genetic and evolutionary algorithms allowing lab managers to easily model their remain hidden and that can save time and software platform, which can satisfy the need for allow the boundaries of research to be pushed money.How Bydo moving we deliver the simulation the safest phase to product the cost-effective on a global and repeatable design processes. even further by smartly exploring the design procesess in SampleManager. As laboratory beginningbasis — of using the product standardized life cycle, optimisation processes , meetingSuch scenarios set a demanding challenge space and identifying configurations that a needsT hermoevolve, workflows can Scientificbe modified to SampleManager 11 LIMS tools can reduce design and development time. for R&D teams, but can turn into a great traditional approach would not acknowledge. change with them. Theregulato result isry better guidelines, coordination ensur in producting workeropportunity safety for companies willing to embrace Further methods, like MORDO – multi- Put Control in the Hands of your LIMS Users and Transform Your Business strategiesand monitor and bettering planning. quality through the entirthe moste innovative technologies and a new objective robust design optimisation – are able The fascinating fact, though, is that it all supply chain? SampleManager 11 At a Glance: comes down to the organisation, the team, and that younger me would have been surprised ultimately to the individual inclination. In other • Configurable workflow and extended lifecycle words, the whole optimisation approach requires to see what simulation is capable of and what features aHow cultural do shift we in employ the engineering the mostattitude sustainableand is achievable within the field of optimisation • Simplified Sample Login user interface provid- theprocesses confidence in to ourlet simulation-driven business — designreducing energy How do we deliver the safest product on a global ing easy access to frequently used functions becomeusage ,optimisation-driven. reducing waste and employingengineering more philosophy. The design process to add real-lifebasis uncertainties — using standardized to the equation. processes , meeting But let us start at the beginning. Optimisation becomes an iterative practice performed Engineering redesigngulato optimisationry guidelines, problems ensuring often work er safety • Flexibility in splitting and merging aliquots techniques have been used in engineering for a efficiently using technology, while the engineer have parameters with uncontrollable variations, automation? and monitoring quality through the entire and samples decade – primarily to maximise a performance concentrates on the decision making, based on calling for solutionssupply chain?that in terms of objectives metric, or to minimise the cost of a product for trade-off solutions quantitatively determined or and feasibility are as good as possible and at • User-Friendly Search Syntax, new Internet a given performance. A younger me, in the early How do we do all this and still remainestimated protable with the software aid. the same timeHow are doleast we sensitive employ tothe parameter most sustainable Explorer® features and improved support for 90s, on a bus to the Von Karman Institute for And that is only the beginning of the variations. A robust design is able to maintain — making better use of all our resources, having processes in our business — reducing energy Windows® 7 and 8 For more information about SampleManager 11, Fluid Dynamics, was having a conversation with advantages arising from leveraging this powerful a certain performance level or quality even if usage, reducing waste and employing more amor Britishe harmonizedAerospace aerodynamic processes engineer, mitigating about technology. risks On the IT side, the increased ‘noise’, simulating sampled and unpredictable • Files, web links and attachments for any entity please visit us at www.thermoscientific.com/SM11 automation? thewhile optimisation continuously of a wing profile. looking We pointedfor p rocessavailability improve of distributed- computational external factors, is added to the process. available for inclusion in reports or email us at [email protected] out that such a calculation would have required resources, offered by multi-core CPU, HPC, and MORDO is used to keep such uncertainties How do we do all this and still remain protable theirments? entire CrayT3D parallel supercomputer. high-speed interconnections, allows for ever- under control, granting real world effectiveness — making better use of all our resources, having A few weeks later, the feasibility study of the complex optimisation campaigns. of the optimal solution. more harmonized processes, mitigating risks approach was started and in almost a month, the The next step up is moving optimisation Certainly that younger me of the 1990s would while continuously looking for process improve- vector-parallel computer was saturated, but our to the product concept phase. By interveningIN FOhave been surprisedTechnical to see Informationwhat simulation is Bulletins | Videos | Press & Articles | Case Studies theories were proved. at the earliest steps of the design process capable of andments? what is achievable within the field More recently, the research for powerful and evaluating the feasibility of certain of optimisation – but even now I still believe that algorithms has brought about the possibility configurations sooner, companies have theV isit wwwoptimisation.thermoscientific.com/samplemanager has a long way to go. 10 or ContactINFO us:Technical mark Informationeting.informatics@thermofisher Bulletins | Videos | Press & Articles |.com Case Studies

34 SCIENTIFIC COMPUTING WORLD @scwmagazine l www.scientific-computing.com Visit www.thermoscientific.com/samplemanager10 or Contact us: [email protected]

SM11 SC.indd 1 3/25/13 4:28 PM The optimisation conundrum Thermo Scientific SampleManager 11 LIMS Put Control in the Hands of your LIMS Users and Transform Your Business

To enable today’s laboratories to be more flexible, efficient and compliant than ever, software must empower users and demonstrably improve productivity across a connected enterprise.

Thermo Scientific The SampleManagerhardest working LIMS in the industry now 11 LIMS has advanced new tools and user-interface enhancements that improve laboratory process Put Control in the Hands of mappingyour management LIMS and automation. Users and Transform Your Business SampleManager 11 puts decision-making power where it belongs, in the hands of users who can make logical choices about workflow, instrument integration and data reporting for management metrics or regulatory requirements. Workflow capabilities simplify implementation, allowing lab managers to easily model their How do we deliver the safest product on a global procesess in SampleManager. As laboratory basis — using standardized processes, meeting needsT hermoevolve, workflows can Scientificbe modified to SampleManager 11 LIMS change with them. regulatory guidelines, ensuring worker safety Put Control in the Hands of your LIMS Users and Transform Your Business and monitoring quality through the entire supply chain? SampleManager 11 At a Glance: • Configurable workflow and extended lifecycle features How do we employ the most sustainable • Simplified Sample Login user interface provid- processes in our business — reducing energy How do we deliver the safest product on a global ing easy access to frequently used functions usage, reducing waste and employing more basis — using standardized processes, meeting regulatory guidelines, ensuring worker safety • Flexibility in splitting and merging aliquots automation? and monitoring quality through the entire and samples supply chain? • User-Friendly Search Syntax, new Internet How do we do all this and still remain protable How do we employ the most sustainable Explorer® features and improved support for — making better use of all our resources, having processes in our business — reducing energy Windows® 7 and 8 For more information about SampleManager 11, usage, reducing waste and employing more more harmonized processes, mitigating risks • Files, web links and attachments for any entity please visit us at www.thermoscientific.com/SM11 automation? while continuously looking for process improve- available for inclusion in reports or email us at [email protected] ments? How do we do all this and still remain protable — making better use of all our resources, having more harmonized processes, mitigating risks while continuously looking for process improve- INFO Technicalments? Information Bulletins | Videos | Press & Articles | Case Studies

Visit www.thermoscientific.com/samplemanager10 or ContactINFO us:Technical mark Informationeting.informatics@thermofisher Bulletins | Videos | Press & Articles |.com Case Studies

Visit www.thermoscientific.com/samplemanager10 or Contact us: [email protected]

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