September 2013 - Allocations-admins - mailman3.cels.anl.gov

New LCRC report submitted for aimd_catalysis
by support＠lcrc.anl.gov 05 Sep '13

05 Sep '13

Full project report at https://accounts.lcrc.anl.gov/reporting/project/2013/?project=aimd_catalysis

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New LCRC report submitted for OSCon
by support＠lcrc.anl.gov 05 Sep '13

05 Sep '13

Full project report at https://accounts.lcrc.anl.gov/reporting/project/2013/?project=OSCon

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New LCRC report submitted for aimd_catalysis
by support＠lcrc.anl.gov 05 Sep '13

05 Sep '13

Full project report at https://accounts.lcrc.anl.gov/reporting/project/2013/?project=aimd_catalysis

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[LCRC Accounts] Yearly Allocation Request from Climate_Emulator
by accounts＠lcrc.anl.gov 04 Sep '13

04 Sep '13

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Robert Jacob Project Name: Climate_Emulator Division: MCS Project title: Building a climate emulator for use in energy policy analysis Associated funding: NSF Other Systems: Science: State-of-the-art general circulation models (GCMs) provide the best estimates of future climate change. While they are valuable tools for assessing impacts of climate change for a given scenario of future greenhouse gas emissions, they cannot be used in iterative economic models since a single multi-century simulation can take weeks to months to run and the iterative models require hundreds of thousands of iterations. For this reason, we aim to develop a statistical emulator that will accurately and efficiently reproduce GCM forecasts of regional climate change for an arbitrary trajectory of CO2 concentrations by using a library of pre-computed GCM output. Library based statistical emulation has not been possible to this date because there is no consistent and comprehensive library of climate model runs corresponding to a range of scenarios of future CO2 concentrations. Computing time on Fusion will enable us to build this unique resource by performing a series of s imulations using the Community Climate System Model (CCSM3). Since library-based statistical emulation is currently not possible, the most common approach to emulating regional climate uses linear pattern scaling, in which changes in regional temperature and precipitation are assumed to be linearly proportional to the change in global mean temperature (GMT). That is, regional climate is effectively assumed to depend solely on GMT, and not on the rate or duration of warming. Our preliminary analysis of CCSM3 output from the Climate Model Intercomparison Project (CMIP3) archive shows that this assumption is not valid for temperature projections over time scales of multiple centuries and breaks down for projections of precipitation even over decadal time scales. The CMIP3 archive, however, is not sufficient for full statistical emulation, since it is both restricted in number of runs and inconsistent in its treatment of regional climate forcing. The carefully designed library we propose here will be used to develop and test a number of alternative approaches for emulating climate model responses, including (i) nearest neighbor interpolation, (ii) a variant of pattern scaling that accounts for the rate of warming, and (iii) principal component analysis (PCA). The intended outcome of this research is a new climate emulator that will aid in the evaluation of energy policies for greenhouse gas mitigation. We anticipate that there will be a wide interest in a user-friendly, computationally tractable emulation tool from the policy, economics, and climate communities. The library itself will also be made public for further use by the community Project description: This request is for the fifth year of a continuing project on the study and emulation of transient climates – climates shortly after a change in CO2 or other radiative forcing – and of their final states after the thousands of years needed to reach a new equilibrium. The primary goal of the project has been to build tools to facilitate analysis of climate-related policies. Fusion runs enabled us to pioneer the technique of library-based climate model emulation, in which a library of pre-computed model runs is used to generate a statistical tool that reproduces the output of complex models in a fraction of the time it takes to run the full model. We used Fusion computing time from FY2010-2013 to build a climate library of runs of CCSM3 (the open-source Community Climate System Model 3 from the National Center for Atmospheric Research), to demonstrate emulation of mean climate, and to quantify and incorporate model predictions of changes in climate variability. The model runs have also facilitated much synergistic science on the physics of transient climates and their equilibrium state. We have demonstrated the causes of nonlinearities in the evolution of both precipitation and global heat uptake against global mean temperature. This work d irectly addresses major outstanding questions in climate science. In FY2013 we underspent our Fusion allocation: we were awarded 590K core-hours but used only 248K. The primary reason for the underspend was that much of our work involved comparisons with a one-column model (CliMT), which we needed to demonstrate to the climate community that our results from larger climate models run on Fusion stemmed from simple general constraints that are manifested even in simpler models. Since CliMT proved unable to compile on Fusion, we switched to the U. Chicago Research Computing Center’s Midway. We also did not begin a major planned project involving Monte Carlo sampling over model physical parameters. The project has grown in size sufficiently that it is now slated for Mira rather than Fusion / Blues. In FY2014 we have planned a number of projects that extend our studies both of climate model emulation and of climate model behavior with a total request of 360K core hours evenly spaced through all quarters. (If we drop to lower spatial resolution for some projects we would need only 284K, but we would prefer to be running at higher resolution). One series of planned projects involves continuing work with CCSM3 on several extensions of previous studies. We will conduct some branching runs to obtain higher-temporal-resolution output (a project begun in FY2013), and will existing runs by another 200 years to test obtain multiple realizations for the study of climate variability. A second series of experiments involves extending our transient climate studies to the newest version of NCAR’s climate model, now called CESM (Community Earth System Models). We completed in FY2013 a variety of test runs on Fusion using different versions of Community Earth System model (from CESM 1.0 to CESM 1.2) to help us plan for FY 2014 experiments. We will compare transient climate runs with different spatial resolutions -- the relatively low T31, i.e. 3.5ox3.5o, that we have used to date, and a more normal T85, i.e. 1.4ox1.4o – to determine if model resolution affects our previous results. Finally, we will use a slab-ocean version of CESM to study the linearity or nonlinearity of precipitation in transient climates with different levels of CO2 in the atmosphere. Slab ocean runs allow us to sample a wide range of climate conditions with far less computing time than required for fully-coupled climate models. The dominant computational requirements in CCSM3 and CESM are the models’ atmosphere and ocean components. In both cases, the atmosphere component is the Community Atmosphere Model, which currently supports four different numerical cores for solving the basic equations: a spectral transform method, a Semi-Lagrangian scheme, a finite-volume scheme, and a spectral element scheme. The ocean component is a finite-difference model called the Parallel Ocean Program, developed at Los Alamos. Both CCSM3 and CESM require Fortran90 and C compilers and the MPI and NetCDF libraries. We are storing data on the UChicago’s Reseach Computing Center (RCC), which will give us continuing sufficient disk space to store the output offsite. Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 360000 Q1: 90000 Q2: 90000 Q3: 90000 Q4: 90000 Justification: Thank You, The LCRC Accounts System

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New LCRC report submitted for Climate_Emulator
by support＠lcrc.anl.gov 04 Sep '13

04 Sep '13

Full project report at https://accounts.lcrc.anl.gov/reporting/project/2013/?project=Climate_Emula…

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[LCRC Accounts] Project Request: SRF-materials
by accounts＠lcrc.anl.gov 04 Sep '13

04 Sep '13

Hello, A new project on the LCRC cluster has been requested. Please forward the information on to the LCRC Allocation sub-committee. Applicant's name: Denise Ford Applicant's institution: ANL Applicant's division: MSD Project Name: SRF-materials Project title: Modeling of Impurity Structures in Niobium Superconducting Radio-Frequency Cavities Associated funding: DOE-HEP Other Systems: ANL CNM - Carbon, FNAL - Wilson Cluster Science: This objective of this project is to model the effects of chemical impurities on the niobium used to construct superconducting radio-frequency (SRF) cavities. Niobium SRF cavities are a key technology for high-performance linear particle accelerators, and will be used in high energy physics applications such as a proposed 8 GeV proton source at Fermilab, and potentially in accelerators for waste management from nuclear power sources, for synchrotron light sources, and for neutron sources. SRF cavity performance is characterized by the accelerating gradient and the quality factor (a measure of the stored energy versus the dissipated power), both of which are highly sensitive to the structure and composition of the top ~100 nm of a cavity’s surface. Absorption of chemical impurities during processing can affect both the maximum accelerating gradient and the quality factor. Two examples, which will be the focus of this project, are (i) the formation of a surface oxide film, approximately 20 nm thick, which is composed of layers of Nb2O5, NbO2, NbO, and a gradient of dissolved oxygen in the niobium bulk; and (ii) the formation of hydride precipitates. The niobium oxides can accommodate substantial off-stoichiometry, which results in some cases in local magnetic moments. This is detrimental for superconductivity because magnetic impurities create normal conducting states within the superconducting energy gap. Hydride precipitation is detrimental because the hydrides with an ordered structure are not superconducting above 2 K. On the other hand, the presence of interstitial oxygen, nitrogen, and carbon may be beneficial to SRF cavity performance at low concentrations. A steep drop-off of the quality factor at the onset of the RF field can be observed in cavities made from high purity niobium, but not typically in cavities from lower purity reactor grade niobium. This is because oxygen, nitrogen, and possibly carbon can trap hydrogen atoms, which prevents their diffusion and precipitate formation. The tetragonal and cubic niobium nitrides also have superconducting transition temperatures that are higher than that of pure niobium, so formation of these phases may potentially benefit niobium SRF cavities. This project will utilize VASP to model the interactions of chemical impurities in niobium and the formation of the phases described above to shed light on processes that may positively or negatively affect the performance of niobium SRF cavities. Project description: VASP will be used to perform density functional theory calculations of defective niobium and niobium oxide structures to assess the effects of impurities on the material. We will model the niobium oxides ranging from NbO - Nb2O5, including ideal structures and plausible defective structures, to determine the magnitude of magnetic impurities that the can be accommodated in the oxide surface layers. We will also model interstitial H, O, C, and N in niobium, with focus on the ability of C and N to trap H and prevent the formation of niobium hydride precipitates. We will also assess the electronic, magnetic, and structural properties of these impurities in niobium in consideration of the side-effects that they may have on SRF cavity performance. The models for these studies will involve several hundred atoms to accurately describe the structures and minimize undesired interactions between periodic images. The models for the oxide studies will require some parameter determination, such as selection of appropriate functionals, where as the models for the hydride studies have been previously established. Peter Zapol will be an additional project member. Project URL: Requested allocation: 200000 Q1: 50000 Q2: 50000 Q3: 50000 Q4: 50000 Justification: The requester has used undetermined amount hours of their initial startup project. In addition to approving an initial amount, please specify a Category and Subcategory for this project. For a list of the current selection of approved categories, please see: https://wiki.lcrc.anl.gov/wiki/Processes/Categories Once the Allocation committee has approved the project, please go to the Project Management page to create it: https://accounts.lcrc.anl.gov/projects.php Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request from glassforms
by accounts＠lcrc.anl.gov 04 Sep '13

04 Sep '13

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Peter Zapol Project Name: glassforms Division: MSD Project title: First-principles Calculations of Mineral and Glass Dissolution under Various pH Conditions Associated funding: DOE-NE Other Systems: Science: The dissolution of glass forms in nuclear waste disposal determines their long term stability, which is critical for evaluating disposal scenarios. The dissolution behavior of minerals and glasses has been found to strongly depend on the pH value of the aqueous environment. The delicate balance of ions at the solid-water interface in aqueous solutions is still a big challenge both for accurate computational modeling and for unambiguous experimental measurements. This project aims to develop physical models to simulate the water-borosilicate glass forms interface at the atomic level under various pH conditions and to calculate the rates of dissolution for Si, Al and other constituting elements under acidic, neutral and basic conditions. These studies are based on first-principles calculations and kinetic Monte Carlo simulations. The calculated reaction barriers by using DFT calculations can then be used as input in kinetic Monte Carlo simulations to estimate the over all dissolution rates and compare with experimental values. These investigations will be very important to better understanding of the dissolution behavior and prediction of dissolution rates. Project description: The first task for this year is to extend our study from simple sodium borosilicate glass to a model model glass with other constituting elements. In the past year, we have calculated hydrolysis reaction barriers of the Si-O-B bridges and the B-O-B bridges at surface sites of sodium borosilicate glass as a model system in different protonation states – neutral (≡SiOH), protonated (≡SiOH2+) and deprotonated (≡SiO-) using the Nudged Elastic Band (NEB) method. As there are other constituting elements, e.g. Al, in waste glasses, we will calculate the reaction barriers of T-O-T bridges (T=Si, Al, B) at surface sites in different protonation states – neutral (≡SiOH), protonated (≡SiOH2+) and deprotonated (≡SiO-) using the Nudged Elastic Band (NEB) method by using VASP code. The second part is studies of the bulk water effect to determine the role of aqueous solution and the entropic effect of water. Both effects contribute to the free energy reaction barriers. In this year, we will perform MD simulations to study the dissolution process of glass with Si and other constituting elements under acidic, neutral and basic conditions by using VASP and CPMD codes. Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 780000 Q1: 195000 Q2: 195000 Q3: 195000 Q4: 195000 Justification: The first-principles calculations will be carried out using the electronic-structure code VASP. In the first part, NEB calculations will be performed to calculate the reaction pathways for a variety of composing elements under acidic, neutral and basic conditions. A single geometry optimization takes 48 hours on 32 processors. We are considering 30 supercell samplings of silicate glasses including multiple T sites (Si, Al, B). The calculation for possible reactants, intermediates, products will take about 140,000 core hours. It takes about 50 hours on 160 processors (5 images) to calculate a reaction barrier along the reaction pathway. The total estimated computer time for barrier calculation is 240,000 core hours. In the second part, ab initio MD simulations will be performed, where each trajectory runs for 100 ps and it takes 32 processors to run for 96-160 hours (average 2048 core hours per trajectory). We will need to run 100 trajectories for five sets of calculations. That requires 400,000 core hours. In sum, the total requested allocation for this project is 780,000 core hours. Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request from Drude
by accounts＠lcrc.anl.gov 04 Sep '13

04 Sep '13

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Benoit Roux Project Name: Drude Division: BIO Project title: Development and validation of new polarizable force field for molecular dynamics Associated funding: LDRD on force field with Subramanian Sankaranarayanan (number not out yet) NIH grant from NIGMS R01-GM072558: Polarizable Force Field For Proteins and Lipids Other Systems: BG/P, XSEDE, Anton, kbt, Beagle Science: The functional form and parameters of a new force field accounting for induced polarization in molecular dynamics simulations must be developed, optimized, and validated for various biomolecular systems. We are mainly interested in ions binding to proteins at this point. Project description: We are mainly interested in ions binding to proteins at this point. In biomolecular simulations, the challenge is to construct functional forms that are amenable to computationally efficient simulations while remaining able to accurately capture the microscopic interactions between molecules. Our efforts, done in collaboration with Alex MacKerell, have been to develop a polarizable force field for proteins, membranes, and nucleic acids based on classical Drude oscillators. The Drude polarizable force field has been implemented in the program NAMD. It runs efficiently, at a computational cost comparable to that of non-polarizable force fields (slower only by a factor of about 1.4).By now, the parameterization for water, ions, phospholipids, and proteins has been done and we are entering an exciting phase where we will start to apply the new force field to real systems and investigate a wide range of processes (ion selectivity, ligand binding, pKa, membran es, etc). As an example, we have recently started to directly tackle the conditions under which selectivity has been quantitatively measured for KcsA, namely from the Ba2+ block experiments of Piasta and Miller.66 Now we have an accurate polarizable force field, including divalent ions,67 proteins and lipids,68 and we are in a position to carry out these calculations on the KcsA channel with its activation gate open. Comparison of the Drude model with density functional theory (DFT) calculations at the B3PW91/lanl2dz level shows that one Ba2+ coordinated by two N-methylacetamides have an energy of -133.0 kcal/mol compared to -131.4 kcal/mol with the Drude model. Preliminary MD simulations of KcsA blocked by Ba2+ with the Drude force field for the protein, lipids, water, and ions show that the system remains close to the X-ray configuration. We want to optimize ion parameters for the KcsA potassium channel and then simulate the blockade by barium ions. For this we will have to run classical MD simulations (with a force field), extract snapshots of the ion with its surrounding atoms, and then use compute energies and forces from ab initio methods as target data to optimize the force field parameters. Most of the classical simulations will be executed elsewhere, but the ab initio calculations will be carried out with Gaussian on fusion. We also want to run QM/MM simulations of the same set of atoms using CPMD to compare the atomic forces from force field and QM. We expect that about 200 snapshots for each ion type should do the job. We have to consider K+, Na+ and Ba2+. There are about 250 atoms to consider in the QM region. Project URL: http://thallium.bsd.uchicago.edu/RouxLab/ Current FY Hours Used: undetermined amount New FY Requested allocation: 800000 Q1: 200000 Q2: 200000 Q3: 200000 Q4: 200000 Justification: Gaussian and CPMD are established programs that runs efficiently on fusion. These calculations are fairly standard. Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request from radix
by accounts＠lcrc.anl.gov 04 Sep '13

04 Sep '13

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Robert Latham Project Name: radix Division: MCS Project title: Scalable Parallel System Software Associated funding: DoE core, SciDAC, NSF, FASTOS Other Systems: breadboard (unlimited) ALCF Mira/Cetus/Tukey (50,000,000 cpu hours) Science: Our mission is to develop the technologies required to dramatically increase the productivity of scientists developing applications for parallel supercomputers. The focus is fourfold: integration of parallel programming tools, reuse of parallel program components, development of scientific computing toolkits and portable libraries, and exploration of requirements of future parallel computers. Project description: This is a Computer Science request for 60,000 cpu-hours on Blues for development and evaluation of a family of tools and libraries with a direct benefit to all users of high-performance computing resources. The Radix group in Argonnne's Mathematics and Computer Science division conducts research and development on facilities to better enable efficient Parallel Programming, I/O, and Scientific Understanding. The Blues system represents an attractive milestone for our software development: projects start out on our breadboard cluster and can further explore scalability in the presence of a high speed network on Blues before making the jump to BlueGene-scale parallelism. Radix experiments often are concerned with latency. The infiniband network on Blues provides an excellent low-latency environment for message passing and storage management research while also providing ample bandwidth for I/O and message bandwidth testing. For FY2014 our Messaging middleware experiments include the usual MPICH development. We will study the continued improvement of various MPI features including scalability and memory usage, performance tuning, high-level libraries on top of MPI, fault tolerance capabilities, one-sided communication, and collective operations. This allocation will also be used for studying MPI extensions including active messages, and compiler support for MPI refactoring. The NWChem library will continue to improve the performance of an important scientific application that is widely used for science by Argonne researchers. Specifically, we will develop inspect-executor load-balancing techniques that will reduce network contention and improve the overall performance and scalability of an important family of methods (coupled-cluster methods). Furthermore, we will explore hybrid programming models (that is, adding threading to the existing GA/ARMCI/MPI model), particularly in the TCE module, which has been used extensively by researchers in Argonne MSD and CSE. All the aforementioned developments will be deployed on Blues in a production fashion and made available to all users. This allocation will enable Jeff Hammond to maintain the NWChem installations on Blues, as he has done for Fusion in the past. We work closely with application scientists, and develop application tools under the 'radix' allocation. For one example, the KMI project defines a high-level standardized interface for computational biology applications relying on distributed search and match semantics for biological reads. We will study efficient data management and data movement techniques to allow scaling to large number of processes. The GPFS file system on Blues will allow us to experiment with I/O strategies on a modest scale before evaluating them at leadership scale on Mira. For FY 2014 our file system research extends into data storage approaches suitable for exascale. Our research into object storage protocols, including high performance access and replication, fits well on Blues. Our Exascale storage efforts will explore scalable algorithms for use in next generation HPC storage systems. The Blues allocation will be used to evaluate programming models, fault detection algorithms, synchronization primitives, and fault tolerance strategies for a prototype object storage system. In FY 2014 we are continuing research into new high level I/O libraries. We anticipate Blues and Vesta will be our two main test platforms. Radix projects also focus on deriving insight both about application behavior as well as scientific insight. 16-core nodes make efforts like in-situ visualization, where for example an application renders a frame of a movie, ever more feasible. Even without fancy graphics accelerators, the processing power on Blues nodes makes such analysis and visualization feasible, especially if the visualization can take advantage of multiple cores and multiple nodes. Naturally, the radix visualization tools have demonstrated scalability to Blues sizes and beyond on Blue Gene, so making full utilization of Blues should not be a concern. As should be evident from the variety of planned experiments, the Radix group plans to make full use of Blues. With Argonne employees and student collaborators, we expect around 20 members in FY2014. We plan on about 0% of our jobs being single core jobs. It's crazy that you even have to ask! While Blues may contain a modest number of compute nodes, the machine still represents an attractive platform for testing: very fast, low latency interconnect; 16 cores per node; The testing and experiments the Radix group can carry out on Blues ensures the tools the group develops today will remain relevant even as supercomputers grow. Quite a few radix-developed projects are part of the Blues software stack: CPU hours for this project yield improvements and benefits not just for the radix group, but for all users of Blues and indeed users of high-end computational resources worldwide. Project URL: http://www.mcs.anl.gov/research/group_detail.php?id=1 Current FY Hours Used: undetermined amount New FY Requested allocation: 496000 Q1: 124000 Q2: 124000 Q3: 124000 Q4: 124000 Justification: Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request from SHARP-IF
by accounts＠lcrc.anl.gov 04 Sep '13

04 Sep '13

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Rui Hu Project Name: SHARP-IF Division: NE Project title: SHARP – Intermediate Fidelity Modeling Associated funding: DOE-Nuclear Energy, DOE-NNSA Other Systems: Science: An intermediate fidelity (IF) thermal-hydraulics modeling method is being pursued under NEAMS Reactor Product Line (SHARP) for a fast-running, modest-fidelity, whole-core transient analyses capability. The approach is essential for design scoping and engineering analyses and could lead to improvements in the design of the new generations of reactors and to the reduction of uncertainties in safety analysis. The IF method relies on RANS based turbulence modeling approach and advanced system modeling methods to represent the fluid flow and heat transfer physics. Project description: The system analysis code and the RANS-based commercial CFD code STAR-CCM+ are incorporated into the SHARP framework for a multi-scale analysis of Sodium Fast Reactors. In the previous fiscal year, the feasibility of performing coupled System code and STAR-CCM+ simulations of protected loss-of-flow accident was demonstrated. In that effort, the outlet plenum was modeled by STAR-CCM+ and the rest of the primary coolant system and the secondary system were simulated by the SFR Module, and the flow and temperature conditions at the interface were exchanged between the two codes as boundary conditions. In the planned activities for FY14, this coupling exercise will be extended to model both the cold pool and the upper plenum of the SFR in the CFD model since multi-dimensional effects and the thermal stratification in the cold pool are also important to the transient behavior of the system. Accurate predictions of flow and temperature are essential to assure the reactor safety during postulated accidents. Furthermore, the CFD code STAR-CCM+ will be used for design evaluations of reactor systems and experimental facilities. Notably, an advanced sodium fast reactor design concept; and the cross-shape twisted fuel assembly design in a conversion effort from using HEU to LEU, and the natural convection shutdown test facility that is currently being built at Argonne. This type of simulations is essential to assure the safety of the proposed design. Also, the pre-test simulation results of the NSTF will be compared against to the experimental results as a validation study of the CFD code. At Argonne, the CFD code STAR-CCM+ are routinely applied to simulations that use more than 100 cores, and good parallel performance has been observed. As problem size increases, i.e. for finer meshes and for large pin bundles, larger numbers of cores would be utilized and based on data from the developers good parallel performance will continue to be expected. On the other hand, the system code, the SFR Module based on MOOSE and RELAP-7 is a new development. The parallelization will be provided by the underlying MOOSE framework which is built on PETSc. The scalability of MOOSE has been demonstrated by other MOOSE-based applications. The system code usually relies on coarse representation of the system thus does not require significant amount of computing resources. Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 340000 Q1: 60000 Q2: 60000 Q3: 100000 Q4: 120000 Justification: Thank You, The LCRC Accounts System

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