- View All
For Reporting Year
Final Report:The Deep Carbon Observatory Instrumentation Fund—Phase II
Grant Number: 2012-3-01 1 April 2012 to 31 October 2015
New scientific instruments drive discovery by creating new pathways for cutting-edge scientific research. In 2009, the Deep Carbon Observatory (DCO) Founders Committee recommended investing in next-generation instrumentation during DCO’s early years to spur the study of deep carbon while engaging a diverse international group of scientists in the emerging program. There were three phases of DCO instrumentation support with funds from the Alfred P. Sloan Foundation totaling approximately $2.25 million. This support has leveraged tens of millions in funds from other sources to develop and promote scientific activity necessary to meet the DCO’s decadal goals. Here, we report on Grant 2012-3-01, Phase II instrumentation, which has leveraged over $10 million in additional support to date. The full magnitude of this grant’s impact and leveraging will become more evident as time passes. However, it is already clear that DCO’s efforts have facilitated both improved and novel instrumentation development, which is contributing to scientific advances beyond the scope of DCO’s original intent.
DCO launched its Phase II Instrumentation efforts in 2011 with an open call for instrumentation ideas in the DCO newsletter and on the DCO website. The DCO Executive Committee reviewed and ranked 25 concept papers and the DCO Secretariat developed a proposal based on these recommendations. The resulting award from Sloan provided $1.0 million for prototype instrument development, a dedicated DCO Computer Cluster, and two “sandpit style” workshops to identify new instrumentation strategies and solutions to address specific scientific challenges. Each workshop led to an additional instrument development project, also funded through this grant.
DCO’s instrumentation initiatives are highlighted on deepcarbon.net with dynamically-generated content, including publications, to provide up to date information and news. A faceted browser for all DCO instruments is currently in development.
Instrumentation Project Reports
Summaries of the instrumentation subawards’ progress are below.
1) Combined Instrument for Molecular Imaging in Geochemistry (CIMIG)
Principal Investigator: Andrew Steele, Carnegie Institution of Washington
Subaward Recipient and Collaborator: Tim McCoy, Smithsonian Institution
Earth’s greatest potential carbon reservoirs are the lower mantle and core, where even a few parts per million (ppm) carbon in metallic or silicate phases may represent many times the confirmed planetary carbon content. Measuring trace amounts of carbon (1 to 10 ppm) without the introduction of contamination in a variety of geologically relevant samples, including mineral phases that are nominally acarbonaceous, has been a longstanding challenge requiring new instrumentation technology. Principal Investigator (PI) Andrew Steele proposed a feasibility study to prototype a Combined Instrument for Molecular Imaging and Geochemistry (CIMIG) to address these issues. An existing $2 million Time of Flight Secondary Ion Mass Spectrometry (ToF-SIMS) instrument at the Smithsonian Institution was available to become the base platform and test the feasibility of combining several techniques in a single amalgamated instrument. The experimental regime proposed to test instrument individually while discussing combining all the instruments into a single prototype instrument. The prototype incorporated surface and depth profiling techniques, combined with an integrated sample preparation system for the detection and contamination-free 3-D mapping of inorganic and organic materials at ~100 nm spatial resolution. Nanoscale analysis of this kind was previously impossible by any other single technique. The combined instrument was intended to become an unparalleled facility to analyze C-bearing samples avoiding the surficial contamination that plagues other methodologies. The prototype was used successfully to analyze a variety of samples, many relevant to DCO—including minute fluid inclusions, cellular fossil remains, biofilms, diamonds, and Martian meteorites.
Although the CIMIG components were never fully integrated, the work proved that performing a series of techniques on a common platform was desirable and productive. A number of publications resulted from the science, but PI Steele and the Smithsonian did not obtain the additional funds needed to complete physical integration of the prototype instrument. Due to the high annual maintenance and operational costs of keeping the CIMIG prototype functioning, let alone improving and evolving, the Smithsonian is sending it to the NASA Jet Propulsion Lab for continued use during its operational lifetime. However, the DCO’s instrument development work caught the attention of Witec and TESCAN, a corporation that supplies scientific instruments globally. TESCAN—which has headquarters in the Czech Republic and divisions in the US, China, and UK—had the resources to invest in the new technology through a series of co-operative grants in Europe and used the CIMIG initiative as a proof of commercial requirements for such an instrument. As a result, an extraordinary instrument (GAIA3) based on the CIMIG concept is now commercially available.
Bryson KL, Salama F, Elsaesser A, Peeters Z, Ricco AJ, Foing BH, Goreva Y (2015) First results of the ORGANIC experiment on EXPOSE-R on the ISS. International Journal of Astrobiology 14 (1):55-66
Tang M, Arevalo Jr. R, Goreva Y, McDonough W (2015) Elemental fractionation during condensation of plasma plumes generated by laser ablation: a ToF-SIMS study of condensate blankets. Journal of Analytical Atomic Spectrometry (11):2316-2322
Simkus DN, Goreva Y, McCoy TJ, Herd CDK (2015) ToF-SIMS Analysis of Prebiotic Organic Compounds in the Murchison Meteorite. 46th Lunar and Planetary Science Conference, LPI Contribution (1832):2513
Simkus DN, Herd CDK, Goreva Y, McCoy TJ (2015) ToF-SIMS Analysis of Prebiotic Organics in Meteorites: Gaining Insight into Formation Pathways. Astrobiology Science Conference 2015
Steele A, McCubbin FM, Benning L, Siljeström S, Cody GD, Goreva Y, Hauri E, Wang J, Kilcoyne ALD, Grady M, Verchovsky AB, Sabbah H, Smith C, Freissinet C, Glavin DP, Burton AS, Fries M, Rodriguez Blanco JD, Glamoclija M, Rogers K, Mikhail S, Zare RN, Wu Q, Ismail A, Dworkin JP, Bhartia R (2014) Hydrothermal Organic Synthesis on Mars: Evidence from the Tissint Meteorite. 77th Annual Meteoritical Society Meeting 5331
Steele A, McCubbin FM, Benning L, Siljeström S, Cody GD, Goreva Y, Hauri E, Wang J, Kilcoyne ALD, Grady M, Smith C, Freissinet C, Glavin DP, Burton AS, Fries M, Rodriguez Blanco JD, Glamoclija M, Rogers K, Mikhail S, Dworkin JP (2013) Organic carbon inventory of the Tissint meteorite. 44th Lunar and Planetary Science Conference, LPI Contribution 2854
2) Novel Large-Volume Diamond Anvil Cell (LV-DAC)
Principal Investigator: Malcolm Guthrie, Carnegie Institution of Washington (during subaward), European Spallation Source, Lund, Sweden (current affiliation)
Collaborators: Reinhard Boehler, Carnegie Institution of Washington; Jamie Molaison, Spallation Neutron Source, Oak Ridge National Laboratory; Chris Tulk (Lead Instrument Scientist, SNAP) Spallation Neutron Source, Oak Ridge National Laboratory
Designing and constructing a new generation of large-volume apparatus is critical to accomplishing specific DCO decadal goals related to investigating reactions under the extreme pressure and temperature conditions of Earth’s mantle, particularly reactions involving the evolution of mantle fluid phases. The “traditional” diamond-anvil cell (DAC) has become ubiquitous for experiments at P > 10 GPa, where only a microscopic volume is required. DACs provide access to a range of pressure-temperature conditions common throughout the mantle and approaching those of Earth’s inner core, while providing optical access to an environment that is chemically inert. However, for certain critical techniques, the microscopic volumes of traditional DAC designs are insufficient. To address this need for increased volume, the science team proposed to develop a novel cell with single-crystal diamond apertures and target volumes of 0.1-1.0 mm3 capable of operating at pressures of more than 50 GPa. In addition to facilitating neutron diffraction in new regimes of pressure, this device would permit laser-heating techniques to provide access to unprecedented high temperatures (>1000°C) for the first time.
The resulting cell design is capable of supporting 10 tons—vastly more than a traditional DAC—and has been tested to 100 GPa with 1.0 mm beveled culets. In addition, a built-in membrane system permits remote operation without an external clamp. To date, the device has been used for neutron diffraction experiments on several beamlines including the Spallation Neutron and Pressure Diffractometer (SNAP) at the $1.2 billion Spallation Neutron Source (SNS) at Oak Ridge National Laboratory (ORNL), at the Advanced Photon Source (APS) at Argonne National Laboratory (ANL) for high-energy diffraction measurements, and at Penn State University for “large” volume synthesis. A variation of the design, with an increased diffracted beam aperture, was built by the University of Edinburgh to be used on at the ISIS neutron source of the Science & Technology Facilities Council (STFC) the United Kingdom.
The successful 2014 DCO LV-DAC is key to leveraging these multi-million dollar international facilities and optimizing their use on behalf of research relevant to achieving DCO’s decadal goals.
3) Quantum Cascade Laser-infrared Absorption Spectrometer for Clumped Methane Isotope Thermometry
Principal Investigator: Shuhei Ono, Massachusetts Institute of Technology
Collaborators: David Nelson, Aerodyne Research, Inc.; Mark Zahniser, Aerodyne Research, Inc.; and Barry McManus, Aerodyne Research, Inc.
A major DCO instrumentation objective is to measure ratios of methane molecules with doubly-substituted rare isotopes (e.g., 13CH3D and 12CH2D2) that might provide information on methane formation temperatures and help resolve questions related to abiotic versus microbial origins, a DCO decadal goal. By leveraging start-up funds from DCO Instrumentation Grant 2012-3-01, PI Shuhei Ono (Massachusetts Institute of Technology), in collaboration with Aerodyne Research, developed a high-risk, high-reward prototype instrument for measuring clumped isotopes based on quantum cascade laser absorption spectroscopy. This highly successful prototype also has great potential to be mobilized and miniaturized for future field applications.
The new instrument can precisely measure four methane isotopologues, 13CH4, 13CH3D, 12CH4, and 12CH3D. Initially, the funds from DCO allowed the team to purchase a critical component of the instrument—a continuous wave-quantum cascade laser from Alpes Laser that is tuned to measure absorption bands of three isotopologues of methane (13CH3D, 12CH4, and 12CH3D) at 1168 cm-1. The laser was installed in the laser spectrometer platform in December 2012, followed by installation of a second quantum cascade (QC) laser to measure 13CH4. The research team characterized the target absorption lines and tested various sample inlet systems, with the final inlet system allowing automated introduction of CH4 gas into the laser system. DCO funds also contributed to the construction of the inlet system.
Ono’s exciting results were reported at the first two DCO International Science Meetings (Washington, DC, March 2013: Munich, Germany, March 2015). Following the excellent proof of concept made possible by the DCO investment, the initial DCO/Sloan investment has been highly leveraged with support from the U.S. National Science Foundation, DOE, NASA, as well as from Shell and Exxon-Mobil via the MIT-energy initiative. DCO Grant 2010-3-01 provided additional support to Dr. Ono to construct and test a sample preparation manifold at MIT.
A method paper in Analytical Chemistry (Ono et al., 2014) was followed by a pair of papers in Science, including an initial global survey of methane isotopologues using the instrument (Wang et al., 2015). Additional manuscripts are in progress or have been submitted.
Inagaki F, Hinrichs KU, Kubo Y, Bowles M, Heuer V, Hong WL, Hoshino T, Ijiri A, Imachi H, Ito M, Kaneko M, Lever M, Lin YS, Methe BA, Morita S, Morono Y, Tanikawa W, Bihan M, Bowden SA, Elvert M, Glombitza C, Gross D, Harrington GJ, Hori T, Li K, Limmer D, Liu CH, Murayama M, Ohkouchi N, Ono S, Park YS, Phillips SC, Prieto-Mollar X, Purkey M, Riedinger N, Sanada Y, Sauvage J, Snyder GA, Susilawati R, Takano Y, Tasumi E, Terada T, Tomaru H, Trembath-Reichert E, Wang D, Yamada Y (2015) Exploring deep microbial life in coal-bearing sediment down to 2.5 km below the ocean floor. Science 349 (6246):420-424
Ono S, Wang DT, Gruen DS, Sherwood Lollar B, Zahniser MS, McManus BJ, Nelson DD (2014) Measurement of a Doubly Substituted Methane Isotopologue, 13CH3D, by Tunable Infrared Laser Direct Absorption Spectroscopy. Analytical Chemistry 86:6487-6494
Wang D, Gruen D, Sherwood Lollar B, Hinrichs KU, Stewart LC, Holden JF, Hristov AN, Pohlman JW, Morrill P, Konneke M, Delwiche KB, Reeves EP, Sutcliffe C, Ritter DJ, Seewald J, McIntosh JC, Hemond HF, Kubo M, Cardace D, Hoehler TM, Ono S (2015) Nonequilibrium clumped isotope signals in microbial methane. Science 348 (6233):428-431
5 March 2015 New Detector Sniffs out Origins of Methane
4) Development of an ultrafast laser instrument for in situ measurements of thermodynamic properties of carbon bearing fluids and crystalline materials
Principal Investigator: Alexander Goncharov, Carnegie Institution of Washington
Understanding the physics and chemistry of carbon at the conditions existing in Earth’s deep interior is an important DCO decadal goal. Scientific advance in this area requires developing comprehensive thermodynamic models of phase stability and physical properties of C-H-O fluid systems and their interactions with other deep phases—models that rely on as-yet-unknown thermodynamic properties of C-bearing materials. To fill this void, a prototype ultrafast laser instrument for in situ measurements aims to rapidly determine thermodynamic properties at submicron-length scales to enable measurements in previously unattainable pressure-temperature regimes.
With the DCO instrument grant funding, an ultrafast laser system was modified for time-resolved measurements of the optical properties and emissivity of materials at high temperatures—leading to measurements of lattice and radiative thermal conductivity of Earth materials at simultaneous conditions of high pressures and temperatures. These cutting-edge measurements led to publications in Proceedings of the National Academy of Sciences and Physics of the Earth and Planetary Interiors. The evolving instrument resides in the lab of Dr. Alex Goncharov at the Geophysical Laboratory of the Carnegie Institution of Washington (GL/CIW). It has been used in collaborative research with a number of scientists from institutions including the Deutsches Elektronen-Synchrotron research center (Germany), University of Edinburg (United Kingdom), the University of Texas at Austin (USA), and the University of Illinois (USA).
Prototype instrument development and improvement are part of an ongoing process with each achievement paving the way for new advances. In 2015, PI Goncharov started a new collaboration with scientists from the University of Pierre and Marie Curie in Paris, France, including Prof. F. Decremps, an expert in laser ultrasonics. The group has measured sound velocities of H2 and D2 up to 55 GPa in Paris. For the next step, with support from CIW, they will establish a laser ultrasonics system at GL/CIW in Washington, DC. This additional capability will allow researchers to obtain revolutionary measurements, including the reaction mechanisms and kinetics of abiotic hydrocarbon generation, determination of sound velocities, and measurement of thermal conductivity of fluids under conditions of very high P (100 GPa) and T (4000°K). The science team is finalizing the proposed system’s design, but to continue advancing the instrument’s development and further leverage the DCO investment, Goncharov is submitting instrument proposals to multiple funding sources in the United States and China.
Goncharov A, Lobanov S, Tan X, Hohensee GT, Cahill DG, Lin JF, Thomas SM, Okuchi T, Tomioka N (2015) Experimental study of thermal conductivity at high pressures: Implications for the deep Earth’s interior. Physics of the Earth and Planetary Interiors 247:11-16
McWilliams RS, Dalton DA, Konôpková Z, Mahmood MF, Goncharov A (2015) Opacity and conductivity measurements in noble gases at conditions of planetary and stellar interiors. Proceedings of the National Academy of Sciences 112 (26):7925-7930
McWilliams RS, Konôpková Z, Goncharov A (2015) A flash heating method for measuring thermal conductivity at high pressure and temperature: Application to Pt. Physics of the Earth and Planetary Interiors 247:17-26
Goncharov A, Gauthier M, Ayrinhac V, Antonangeli D, Freiman YA, Grechnev A, Tretyak SM (2015) Elasticity of Hydrogen at High Pressures. AGU 2015 Fall Meeting, Abstract MR13C-2726
Lobanov S, Holtgrewe N, Goncharov A, Lin JF (2015) Probing iron spin state by optical absorption in laser-heated diamond anvil cell, AGU 2015 Fall Meeting, Abstract MR11A-1
Instrumentation Development “Sandpit” Workshops
“Sandpit” workshops provide a unique approach for promoting high-risk instrument innovation. The concept involves identifying a research need with no clear solution, gathering expert researchers with varied backgrounds and perspectives, and requesting participants to self-organize and identify novel solutions. Guaranteed funding reserved for an award ensures an outcome and a product. Sloan initially awarded funds for three such sandpit workshops. Two workshops were held leading to the DCO instrument development described below. The funds for the third workshop were reprogrammed to purchase computational nodes.
5a) Gas Instrumentation Sandpit Workshop
Workshop Organizer: Adrian Jones, University College London
A DCO decadal goal is to improve global monitoring of volcanic gas emissions in order to improve our understanding of Earth’s deep carbon cycle. The paucity of volcanic gas monitoring is due to both insufficient resources and inadequate instrumentation. This grant supported a gas analysis and remote sensing workshop that assembled leaders in the field to discuss the most promising opportunities for instrument development. The workshop was held 2-5 September 2013 near Mount Etna, Sicily, Italy.
Mount Etna is a well-supported European “laboratory volcano,” and the workshop brought together research and development representatives from both academic technical and industrial sectors to address the needs of international field volcanologists. Workshop participants evaluated and discussed new designs, as well as new technology prototypes. In this instance, the needs were clear, but the prioritized instruments had to evolve quickly towards practical engineering solutions: high-risk, but high-reward. The primary requirements for monitoring volcano degassing include greater proliferation of ground and airborne instruments as well as long-term planning for integration with Earth observational satellite systems.
5b) Laser Isotope Ratio-meter (LIR) for real time in-situ measurement of 12CO2/13CO2
Principal Investigator: Damien Weidmann, Rutherford Appleton Laboratory, UK
Volcanic degassing is the primary pathway for carbon release from the Earth’s interior to the atmosphere. To constrain and better understand Earth’s deep carbon cycle, scientists must quantify the relative contributions from various gas sources of volcanic origin. Quantitative knowledge of the isotopic composition of outgassed CO2—specifically 13CO2/12CO2 ratio—helps identify carbon sources and can validate degassing models. Understanding carbon fluxes is critical to the overarching goals of DCO’s Reservoirs & Fluxes Community, which include identifying Earth’s principal deep carbon reservoirs, determining the mechanisms and rates by which carbon moves among these reservoirs, and assessing the total carbon budget of Earth.
Due to the number of Earth’s active volcanoes, achieving these scientific goals requires developing technologies and instrumentation that deliver data affordably at relevant temporal and spatial scales. As an outcome of the Gas Instrumentation Sandpit Workshop, PI Damien Weidmann (Rutherford Appleton Laboratory, Science & Technology Facilities Council, United Kingdom) and colleagues received DCO Instrumentation grant funding to develop a novel concept for real-time monitoring of carbon isotope ratios that enabled compact, rugged and portable deployment. High-resolution middle infrared (2-20 µm) laser spectroscopy is used to precisely fingerprint isotopologues that, owing to their slight mass difference, vibrate with different frequencies that can be resolved by lasers. The advantages of this approach include precision, non-contact measurements, large immunity to interferences, limited sample preparation, real time measurements in a compact format, and the possibility for absolute concentration measurements.
Weidmann’s project required modifying a laboratory prototype into a field deployable instrument and conducting volcanic field testing. The DCO instrumentation subaward supported modifications to the existing prototype that included making the instrument more compact and rugged, without loss of sensitivity; designing and adding dedicated field electronics so it could operate using portable power sources; and designing and implementing a specific gas handling system to sustain the chemical mixture collected.
In summer 2015, a modified Laser Isotope Ratio-meter (LIR) was deployed for one week to La Solfatara, Campi Fleigrei, Italy in collaboration with Stefano Caliro (Istituto Nazionale di Geofisica e Vulcanologia, Naples). During the one-week campaign all aspects of the system were tested in field conditions. The LIR operated smoothly and made a series of isotopic measurements using different sampling approaches. Caliro simultaneously collected samples for standard isotope mass spectrometry lab analysis, which subsequently corroborated the LIR field data. At the end of the DCO support, future plans were for the instrument to be further improved based on its first field test then to be deployed on additional field campaigns. In the long term, the system will be ultra-miniaturized, using integrated optics technologies, in order to develop an autonomous, miniature LIR that produces real-time streaming data on the isotopic composition of CO2. The ultimate objective is to have several field sites instrumented with such a system.
In January 2016, Weidmann announced the launch of MIRICO Ltd., the Mid Infra-Red Instrumentation Company, with the LIR as the cornerstone product. This UK-based laser spectroscopy instrumentation company formed in late 2015 as a spin-out from the United Kingdom’s Science and Technology Facilities Council, of which Rutherford Appleton Laboratory (RAL) is part. RAL’s Space Laser Spectroscopy Team, led by Weidmann, developed the technology underpinning the new company. Additional information about the formation of MIRICO Ltd. and development of the LIR can be found in this deepcarbon.net news article.
6a) Experimental High-P and T Bioreactor Workshop
Workshop Organizer: Isabelle Daniel, Université Claude Bernard Lyon1, France
On 25-29 August 2013, twenty industry and academic scientists from six countries gathered on the shores of Lake Annecy in Veyrier-du-Lac, France, to identify specifications for instrumentation to facilitate high-pressure biological and geochemical investigations. Such research is necessary to address DCO decadal goals to better understand the nature and extent of deep microbial life. Bioreactors—vessels supporting biologically active environments—are essential instruments in these efforts. Existing bioreactor chambers are customized to meet the needs of individual research labs and are often incompatible, making global collaboration difficult.
This sandpit-style workshop gathered participants from a diverse range of disciplines to discuss the issues in a creative, open, and collaborative environment. Experts in deep life research, industry, and instrument design immersed themselves in intense discussion, with the ultimate goal of distributing $100,000 in instrument development funding. Workshop participants first focused on the universal need for portable sample containers that allow researchers to share and transport high-pressure samples—challenges amplified by international and airline travel regulations. Vessels exist for collecting deep-sea or deep-continental samples under pressure for in situ analysis, but they are not engineered to sustain samples at high pressure throughout the entire sequence of collection, transportation, and multiple analyses.
Workshop attendees also discussed specifications for a prototype bioreactor capable of hosting a range of cutting-edge experiments conducted at conditions matching Earth’s most extreme biological environments. However, it soon became apparent that funds far exceeding those available from the DCO instrumentation grant would be required to develop the envisioned bioreactor. Workshop attendees generated a range of ideas for the collaboration and fundraising necessary to make a community bioreactor feasible.
6b) 50mL Pressurized Underwater Sample Handler (PUSH50)
Principal Investigators: Isabelle Daniel, Université Claude Bernard Lyon1,
Karyn Rogers, Rensselaer Polytechnic Institute
The most important outcome of the Experimental High-Pressure and Temperature Bioreactor Sandpit Workshop was the group’s decision to recommend that the available DCO funding support a new generation of high-pressure and high-temperature vessels to sample and transport subsurface fluids. The purpose of the vessels is to encourage high-pressure biological and geochemical research and to facilitate collaboration among researchers. The specifications identified during the workshop were modified with feedback from the broader community to develop a request for proposals to which 15 vendors were invited to respond.
Ultimately, Top Industrie was chosen for the custom construction of ten 50 mL Pressurized Underwater Sample Handler (PUSH50) which were delivered to PIs Isabelle Daniel (Université Claude Bernard Lyon 1) and Karyn Rogers (Rensselaer Polytechnic Institute) in September 2015. The PUSH50 is able to both sample and transport biological samples under constant pressure and is certified for airline transport. These sampler handlers are equipped with a 50mL reservoir and can maintain samples at up to100 MPa and 160 °C.
Two high-pressure facilities are being established with this DCO-supported sample and transport equipment that will be available for use by all members of the DCO Community. Each facility will include five PUSH50s as well as a skid, pump, compensator, and pressure sensor. The new facilities are being set up in 2016 in the laboratories of Drs. Daniel and Rogers where the PUSH50s and their accompanying equipment continued to be tested before the protocol for community use is finalized and implemented. As constructed, the PUSH50 is compatible for use on a SeaBird carousel deployed from ships and plans also are underway to adapt it for use with submersibles and other deep-sea sampling equipment. More detailed information about the PUSH50 and the vision for the new high-pressure facilities are available in the deepcarbon.net news article.
16 December 2015 PUSH50: New Instrumentation for Microbial Exploration
7) DCO Computer Cluster
Principal Investigator: Peter Fox, Rensselaer Polytechnic Institute
High-end computation is essential to addressing DCO’s decadal goals. Early in the program’s history, the DCO Executive Committee recognized the need to invest in a major DCO computational effort. The Committee agreed upon securing a dedicated DCO computer cluster in a computation center without the long waiting times involved at national facilities. Identifying the ideal location and administrative facility for such a cluster was challenging. Complications included obtaining the necessary space as well as arranging for long-term maintenance and oversight of user access. Once Dr. Peter Fox (Rensselaer Polytechnic Institute) agreed to host the DCO Computer Cluster, ordering and setting up the cluster proceeded quickly.
In late 2013, a Linux cluster (purchase value $268,995) and a back-up system (value approximately $49,000) were installed in the Research Computing Facility in the Center for Industrial Innovation on RPI’s Troy NY campus. The DCO Computer Cluster comprises a PSSC Labs PowerWulf MMx Cluster with 640 Intel® Xeon® 2.4 GHz Compute Processor Cores and 544GB System Memory - 1GB Memory Per Compute Processor Core. The cluster has 154TB of System Storage, a high-speed internal InfiniBand network, and a fast backup system. The estimated power and cooling costs are $10,133 and $2,265 per year, respectively. Since the cluster is hosted free of operating expenses, this amounts to ~$31,000 cost savings to the DCO community to date.
The cluster provides all DCO Communities with state-of-the-art computer power for performing a wide range of calculations—from modeling chemical and physical processes in deep Earth to other data analyses. Its initial purpose as a resource for the Extreme Physics and Chemistry Community (i.e., software for simulations and electronic structure calculations) was quickly broadened to include projects involving the Deep Energy and Reservoirs & Fluxes Communities. The majority of the software is open-source and has been downloaded from the web or developed by DCO-related research groups. Licensed parallel compiler suite Intel XE Composer 2013 and 2016 versions are also installed with relevant libraries and utilities (annual direct cost to DCO, via a DCO Secretariat award, $3,360).
A team of DCO Community representatives with relevant computational expertise manages the cluster. At present, the team consists of ex officio members Craig Manning (EPC chair) and Wendy Mao (EPC co-chair), as well as the institutional host, Peter Fox. The management team receives requests, reviews applications, and assigns time to projects based on science needs and specific resource requests. All DCO researchers may apply to use the computer cluster. Questions about the DCO Computer Cluster should be directed to firstname.lastname@example.org.
At the end of Grant 2012-3-01, there were approximately 21 registered accounts with 15 approved projects for use on the cluster. The first year, following its late 2013 installation, three users dominated the queues and the average utilization was estimated at 85%. During the second year, utilization dropped to ~75% due to increased competition for nodes and jobs waiting for available resources. To date, usage of the cluster has been self-enforcing through the cluster queuing system. Due to reduced utilization, and after user requests, the cluster management team worked with the community to develop terms in May 2015 that led to improved utilization. Details of cluster use, a project application form, a list of relevant publications, and summaries of projects and key findings are available upon request. Several DCO researchers have stated that their research would not have been possible without access to the DCO Computer Cluster and a few groundbreaking publications have resulted.
Boulard E, Pan D, Galli G, Liu Z, Mao W (2015) Tetrahedrally coordinated carbonates in Earth’s lower mantle. Nature Communications 6 (6311)
Pan D, Wan Q, Galli G (2014) The refractive index and electronic gap of water and ice increase with increasing pressure. Nature Communications 5 (3919)
Gautam S, Liu T, Rother G, Jalarvo N, Mamontov E, Welch S, Cole D (2014) Effect of temperature and pressure on the dynamics of nanoconfined propane. AIP Conference Proceedings 1591:1353-1355
18 February 2015 Novel Carbon Bonding at High Pressure
26 November 2013 DCO Computer Cluster Comes Online
The Sloan Foundation funds provided through Grant 2012-3-01 supported the development and construction of six prototype instruments, a powerful DCO computing resource, and two workshops that identified the best ways to address several DCO instrumentation challenges. This investment has leveraged complementary support and catalyzed new funding from numerous other sources. In addition, there is a tremendous leveraging factor when new instruments are brought on line through the support of users, related infrastructure, resultant publications, etc. This cumulative progress makes critical experiments and research possible in order to address DCO’s decadal goals.