March 2010 - Allocations-admins - mailman3.cels.anl.gov

[LCRC Accounts] Project Request: CEES-Si
by accounts＠lcrc.anl.gov 31 Mar '10

31 Mar '10

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: Maria Chan Applicant's institution: ANL Applicant's division: CNM Project Name: CEES-Si Project title: Investigations of silicon surfaces and interfaces for lithium ion batteries Associated funding: DOE Energy Frontier Research Center -- Center for Electrical Energy Storage (CEES) Other Systems: CNM Carbon Science: This project uses density functional theory (DFT) to investigate silicon as an anode material for lithium ion batteries. Silicon is attractive as an alternative to carbon-based anode materials due to enhanced safety and superior capacity. A key question that arises in the design and operation of Si-based anodes concerns the ability of these anodes to ad(b)sorb lithium ions; numerous studies suggest that the Si lithiation process involves a rich combination of adsorption and absorption phenomena, together with surface reconstructions, highly localized volumetric expansions of the Si lattice, and phase transitions between crystalline and amorphous structures. At the atomic and nanoscales, however, even the simplest details of these processes remain poorly understood. We aim to providing atomistic insights on these processes by carrying out DFT studies of the adsorption, initial stages of insertion, and diffusion of Li in the surfaces, interfaces betwee n phases, and nanowires. This will aid the design of optimal surface and interfacial structures for battery performance and stability. Project description: We will use total energy calculations with DFT to obtain the adsorption energies of Li on different sites on the surface and subsurface layers. In addition, the nudged elastic band method and ab initio molecular dynamics will be used to compute diffusion barriers and constants. The calculations will involve a large ensemble of total energies corresponding to various silicon surface terminations and lithiation states. For bulk crystalline silicon, we consider common surfaces, Si(100)-1x1, Si(100)-2x1, and unreconstructed Si(111). In addition, surfaces of amorphous silicon and interface between crystalline and amorphous silicon, as well as silicon nanowires, will be considered. Using the projector-augmented wave method, only valence electrons will be included which reduces computational costs. We will use well-established DFT codes VASP and GPAW, which use a plane wave basis set and real space grids respectively. Project URL: http://www.anl.gov/energy-storage-science/ Requested allocation: 250000 Justification: The requester has used 0 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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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by John Valdes 30 Mar '10

30 Mar '10

I haven't heard back from Folker today regarding his requests, so I just submitted a request for 55K for MG-RAST on his behalf. I'll grant this request since Ray's already approved it. John On Tue, Mar 30, 2010 at 07:09:51PM -0500, accounts(a)lcrc.anl.gov wrote: > Hello, > > A change in allocation has been requested: > > Requester: folker (Folker Meyer) > Project: MG-RAST > Title: Analysis of metagenomes using MG-RAST > Description: Goal is to provide initial analysis for the two large data sets that represent the current state of the art in soil metagenome analysis. Both projects are well aligned with Argonne's strategic plan the BESI metagenomics initiative goals. > Current: undetermined amount > Justification: > > Requested: 55000 > > A specific reason has been given: > MG-RAST is in the red, and we need about another 5000 hours per day this week. > > This needs to be approved and the final allocation amount decided upon. > > Thank You, > The LCRC Accounts System > _______________________________________________ > allocations-admins mailing list > allocations-admins(a)lists.lcrc.anl.gov > https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 30 Mar '10

30 Mar '10

Hello, A change in allocation has been requested: Requester: folker (Folker Meyer) Project: MG-RAST Title: Analysis of metagenomes using MG-RAST Description: Goal is to provide initial analysis for the two large data sets that represent the current state of the art in soil metagenome analysis. Both projects are well aligned with Argonne's strategic plan the BESI metagenomics initiative goals. Current: undetermined amount Justification: Requested: 55000 A specific reason has been given: MG-RAST is in the red, and we need about another 5000 hours per day this week. This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

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[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 27 Mar '10

27 Mar '10

Hello, A change in allocation has been requested: Requester: emconsta (Emil M Constantinescu) Project: uncertainty-climate Title: Uncertainty in weather forecasting Description: The aim is to create very accurate uncertainty estimates of the weather forecasts to be used for optimal management of energy systems such as wind- and solar-power generation or building management. The purpose of using Fusion is to execute several scenarios and obtain forecast and uncertainty information about ambient variables by running weather/climate simulation codes (such as WRF). This information is used in a stochastic optimization control loop that provides an optimal operational point for energy systems. For the practical part of the project, we will develop a framework (C or FORTRAN, MPI, XML, Python) to run WRF in a realistic fashion and illustrate theoretical findings. We consider running several WRF instances (each on one node) at the same time. Partial results are collected on a separate node and processed before they are sent back to each specific instance. The instances will continue to run and produce new results. In terms of parallelism, this application framework is embarrassingly parallel since each instance run independently. In FY10, we need to run additional uncertainty quantification experiments with higher resolution and more samples in order to achieve a better level of accuracy. The improved weather forecast accuracy simulations allow us to find a more robust operational point for the operation of energy systems (wind power for electricity generation and building heating and cooling). Current: undetermined amount Justification: Requested: 200000 A specific reason has been given: After a careful scalability and resource metering, we have discovered that additional CPU hours are needed to carry out part of our LDRD-funded project. We need to simulate weather at a resolution of 1x1 km. in order to make an impact in this project. Fusion allows us to make accurate predictions and uncertainty estimates of wind speed, solar irradiates and other atmospheric states, which are relevant for a robust management of energy systems. We therefore need extra CPU hours to provide the DOE scientists with the appropriate fine resolution data in order for them to carry out their projects. This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

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[LCRC Accounts] Project Request: gsavalid
by accounts＠lcrc.anl.gov 26 Mar '10

26 Mar '10

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: Michael Davis Applicant's institution: ANL Applicant's division: cse Project Name: gsavalid Project title: Theoretical validation of chemical kinetic mechanisms using global sensitivity analysis Associated funding: DOE-BES, Integrated Biofuel Strategic LDRD Other Systems: Mac workstations Science: Validation of chemical-kinetic mechanisms using global sensitivity analysis. Project description: Global sensitivity is used to study the importance of competing chemical reactions in a chemical-kinetic mechanism. Such analysis requires the repeated integration of large systems of differential equations over a large number of initial physical parameters, sampled via Monte-Carlo techniques. These calculations are very time-consuming for the mechanisms of biofuels. For example, the ignition of butanol, which is a well-studied biofuel, is described by over 250 differential equations involving 1440 reactions, and requires times on the order of several processor-days to obtain adequate convergence for a single set of initial physical parameters such as pressure and temperature. The Monte-Carlo calculations as well as the sampling of the physical considitions can be distributed over multiple processors in a very efficient manner. We have run the code previously in a very efficient manner on 20 and 40 processors on a linux cluster at the Universit y of Colorado, with linear speed-up. This project is a joint collaborations among CSE, the University of Colorado, Boulder, and Leeds University and includes approximately 5 total collaborators. At the present time we are using are own software. Project URL: Requested allocation: 200000 Justification: The requester has used 0 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] Project Request: MG-RAST_NEC
by accounts＠lcrc.anl.gov 25 Mar '10

25 Mar '10

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: Folker Meyer Applicant's institution: ANL Applicant's division: IGSB Project Name: MG-RAST_NEC Project title: Analysis of NEC metagenomes. Associated funding: NIH Other Systems: Science: Annotation of metagenomic data from a large scale study of NEC twins. (NEC= necrotizing entero colitis) a medical condition primarily seen in premature infants. Understanding the role of microbiota through metagenomics will provide key insights to understanding the disease. Project description: Running sequence similarity searches using a variety of algorithms including BLAST, BLAT, uclust, vmatch against a large non-redundant sequence database. Project URL: Requested allocation: 580,000 Justification: "During the last allocation we have scaled up from running single node jobs to jobs of an arbitrary size. Additionally we worked to efficiently utilize backfill time slots due to the flexible run time of our code. Over the next allocation we plan to experiment with new more efficient algorithms that will make use of the large memory nodes." The requester has used 0 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 Atmos_Chem
by accounts＠lcrc.anl.gov 23 Mar '10

23 Mar '10

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Rao Kotamarthi Project Name: Atmos_Chem Division: ER Project title: Process Scale Modeling of Atmospheric Chemistry and Transport Associated funding: DOE,BLM,NASA Other Systems: NERSC Science: The scientific aim of the proposed modeling activity is to further the understanding of the chemistry and distribution of aerosols over certain regional domains and calculate the heating rates as a result of increased aerosol loading primarily over India. This modeling effort supports the Ganges Valley Aerosol Project (GVAX) a one-year field study funded by DOE BER for the years 2011-2012. Project description: 1. What are the sources and sinks of the aerosols comprising the “Asian brown cloud,” and what effects does it have on clear-sky radiation fields, as well as on cloud micro- and macrophysical properties? What effect does the diurnal PBL cycle in the Ganges valley have on the atmospheric distribution of aerosols? Recent studies indicate that nearly 50 90% of the measured black carbon aerosols that give rise to brown clouds over the Indian Ocean are from biomass burning (residential cooking and agricultural burning), but little quantitative information is available regarding how properties of these aerosols — such as light scattering and absorption and droplet nucleating properties — evolve as a function of time near the source Ganges valley region. Very little is also known about the vertical structure of the distribution of aerosols and the fraction of the aerosols that are available for regional- and global-scale transport from the source region in the Ganges valley. The one-year long AMF deployment is uniquely positioned to make continuous, high frequency measurements through the atmospheric column of aerosol optical properties, radiative transfer and cloud properties. In addition, to bring additional focus on resolving some of the more regional and chemical composition relate d questions inherent in this objective, we propose to conduct a winter intensive field operation starting from January 15th 2012 to March 15th 2012, at a time where aerosol loading over this part of India is known to be the highest. During this intensive, the G 1 will add the additional capability of generating in situ measurements and vertical profiles within the PBL and above to generate estimates of the amounts of aerosols that are transported into the mid troposphere and to regional scales. Additional resources such as MAOS, a surface site below in the valley from the location of AMF and a number of supporting surface sites operated by ISRO/IISc will be available. A more detailed description of this intensive is provided below. 2. What effect do increasing aerosols in the Ganges Valley have on the ISM? What effect do aerosols have on shortwave radiative forcing, mid-tropospheric heating and convective activity over continental India? With the AMF, we will be in a position to make continuous, extended estimates of heating rates within cloud over continental India by measuring cloud properties, drop sizes, and LWC and making complete radiative balance measurements of clouds. The uncertainty in parameterization of deep convective activity in climate models has a profound impact on the calculated climate sensitivity to rising CO2. Deep convective activity is common during much of the summer and pre-monsoon period; the initial onset of monsoon over the southern tip of India is initiated by land-sea circulation and then enhanced and driven by deep convective activity over the northern Indian plains. Specific to this study would be an opportunity to measure the influence of aerosols on deep convection. This highly complex, little understood problem in modeling deep convection is complementary to the elevated heat pump hypothesis. Measurement of aerosols from surface supersites to identify their chemical and phys ical characteristics will provide key constraints to the estimates of radiative forcing heating rates from these aerosols in the PBL during the winter and early spring intensive as discussed above. A second intensive operating period, during the pre-monsoon, is planned for the period extending from April 15th 2011 to June 15th 2011 for the purpose of coupling the surface measurements made by the AMF with measurements of in situ cloud properties and aerosol measurements made the IISc/ISRO Beechcraft-20, as well as ongoing Indian activities (Aerosol Radiative Forcing over India; ARFI) to obtain a regional footprint. This would be the first ever such effort to synthesize the various measurements into a combined data product over this region that would be available for model validation and evaluating current cloud level aerosol heating hypotheses. We plan to use a combination of models for the project, including the CCSM4.0, GEOS-CHEM for aerosol transport and IMAGE model for aerosol cloud interactions. Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 100000 Justification: Thank You, The LCRC Accounts System

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[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 15 Mar '10

15 Mar '10

Hello, A change in allocation has been requested: Requester: robl (Robert Latham) Project: radix Title: Scalable Parallel System Software Description: This is a Computer Science request for time on Fusion 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 Fusion 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 Fusion before making the jump to BlueGene-scale parallelism. Radix experiments fall into two broad categories. Often, we are concerned with latency. The infiniband network on Fusion 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. Fusion hosts two quality parallel file systems, GPFS and PVFS. The wider HPC community often asks the Radix file system researchers to compare these file systems head-to-head. Fusion provides us the opportunity to do just that. Hosting two parallel file systems allows us to do more than just drag-race (so to speak). The two file systems have distinct characteristics, and act differently in the broader role of the I/O software stack. On Fusion, we can utilize a single software stack (application, parallel-netcdf, ROMIO), and compare the impact of a change in the underlying file system on overall application behavior. We know from other research, for example, that the two-phase optimization in ROMIO needs to adapt to the underlying file system, and that aligning variables to file system boundaries can yield performance improvements for parallel-netcdf. Fusion compute nodes actually look fairly attractive to active storage research. These nodes have enough disk space to store non-trivial datasets, and powerful enough processors to carry out complex computations without much impact on storage performance. Radix projects also focus on deriving insight both about application behavior as well as scientific insight. 8 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 Fusion 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 Fusion sizes and beyond on BlueGene, so making full utilization of Fusion should not be a concern. As should be evident from the variety of planned experiments, the Radix group plans to make full use of the new features Fusion brings to LCRC and the flexibility of a Linux-based cluster. With Argonne employees and student collaborators, we expect around 20 members in FY2010. While Fusion may contain a modest number of compute nodes, the machine still represents an attractive platform for testing: very fast, low latency interconnect; 8 cores per node; .25 TB of storage per compute node. The testing and experiments the Radix group can carry out on Fusion ensures the tools the group develops today will remain relevant even as supercomputers grow. Quite a few radix-developed projects are part of the Fusion software stack: CPU hours for this project yield improvements and benefits not just for the radix group, but for all users of Fusion and indeed users of high-end computational resources worldwide. Current: undetermined amount Justification: Requested: 200000 A specific reason has been given: We consumed a large number of hours for experiments in support of a paper. Here is the abstract for that work: In the past few years, network performance has significantly increased, especially in the domain of scientific high-end computing. High-speed networks such as InfiniBand (IB) offer end-to-end performance capabilities of up to 32 Gbps today, with a promise to deliver up to 100 Gbps by 2012. While clearly faster networks have continued to improve the performance of scientific applications, at what point do we have enough network capacity that the additional performance difference does not justify the cost associated with increase in network bandwidth? In this work, we studied the performance improvement that applications can achieve by increasing network bandwidth, using a wide class of applications from the Spec MPI 2007 benchmark suite. We used InfiniBand as an example network and measured application performance using network hardware bandwidths of 4 Gbps, 8 Gbps, 16 Gbps and 32 Gbps on a 2048-core cluster. This allows us to understand the performance improvements possible for different applications with the increasing network capability. Our studies show several interesting insights into the impact of network capability on the performance of scientific applications. This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request from ESMF
by accounts＠lcrc.anl.gov 10 Mar '10

10 Mar '10

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Silverio Vasquez Project Name: ESMF Division: MCS Project title: Earth System Modeling Framework Associated funding: DOD, NASA, NSF, NOAA Other Systems: external: NERSC, NCAR, ORNL, NCSA, NASA Science: The Earth System Modeling Framework (ESMF) enables the coupling of model components in high performance Earth system modeling codes. ESMF component interfaces have been implemented in most of the prominent climate and weather codes in the U.S.: CCSM, WRF, NASA GEOS-5, EMC GFS/NEMS, NRL COAMPS and the GFDL MOM4 ocean. In general, componentization with ESMF has been implemented at the level of major physical domains, where simulated interactions require inter-component data communications (e.g. atmosphere, ocean). This implementation is compatible with codes such as WRF that impose their own interoperability conventions at the level of individual physics parameterizations. The codes listed above, plus the full GFDL modeling system under FMS, can now operate within a component-based, hierarchical architecture in which large-scale components can be called as subroutines. This was not the case when ESMF began. The current level of ESMF adoption represents a major and necessary step towards enabling U.S. centers to exchange large-scale components, and is an excellent basis for further advances in code interoperability. The recent technical focus has been on continued development of ESMF grid classes and a regridding capability. These are built on a base of two flexible data representations that were constructed in previous years: an unstructured finite element mesh library and a general array class designed to support fields on logically rectangular grids. At this point ESMF can produce non-conservative interpolation weights, in parallel or serial, 2D or 3D, for grids that can be represented by triangles or quadrilaterals. Users can also read in external interpolation weights, from a package such as SCRIP, if they need an interpolation option ESMF does not provide. Project description: The goal of the Earth System Modeling Framework project is to build high performance, flexible software infrastructure to increase ease of use, performance portability, interoperability, and reuse in climate, numerical weather prediction, data assimilation, and other Earth science applications. The framework is intended for use by individual researchers as well as major operational and research centers. ESMF products include an API specification, a reference implementation accompanied by extensive documentation, and an exhaustive regression test suite that inncludes 3000+ unit tests, system tests, and examples. The ESMF software consists of a superstructure for coupling and exchanging data between models components (e.g., atmosphere, ocean) and an infrastructure consisting of 1) data structures for representing grids and fields and 2) an optimized, portable set of low-level utilities. The data constructs and low-level utilities can be used by the coupling superstructure and may also be used separately to compose scientific applications. ESMF uses a mixture of C++ and F90. Most of the low level classes are implemented in C++ and have Fortran bindings. We have worked out a detailed interoperability specification which allows F90/C to interact on multiple platforms. Communication is handled using a combination of pthreads and MPI which allows ESMF to support both pure-distributed, pure-shared, and hybrid parallel programming models. In FY10, we will continue to use the extensive compiler set on Fusion as a development platform and to run the ESMF regression test suite. Project URL: http://www.earthsystemmodeling.org Current FY Hours Used: undetermined amount New FY Requested allocation: 50000 Justification: Thank You, The LCRC Accounts System

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[LCRC Accounts] Project Request: NuclearBurn
by accounts＠lcrc.anl.gov 09 Mar '10

09 Mar '10

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: Ray Bair Applicant's institution: ANL Applicant's division: CLS Project Name: NuclearBurn Project title: Buoyancy-Driven Turbulent Nuclear Burning Associated funding: Astrophysics and Cosmology Strategic Initiative LDRD Other Systems: Intrepid Science: Type Ia supernovae are powerful stellar explosions with the property that a large majority of explosions of this type are remarkably homogeneous; yet the mechanism by which they explode is not well understood. A proposed mechanism is the Gravitationally Confined Detonation (GCD) model, where ash created during a deflagration (subsonic nuclear combustion) is ejected from the star, flows around the surface, and collides with itself at the opposite point of breakout, sparking a detonation. In this joint Argonne - U. Chicago LDRD project we will quantify the scale-dependence of flame surface structure induced by buoyancy-generated turbulence. The current work focuses on determining the sensitivity of the properties of SN Ia explosions to the initial conditions. These simulations also provide input data to radiation transfer calculations of the light curves and spectra of SN Ia, enabling the Flash Center to validate the four current models of SNe Ia by comparing them with high-quality observations. Project description: This project carries out high-resolution 2D studies of the how buoyancy instabilities enhance flame surface and burning rate for thermonuclear flames. These studies compliment the 3D studies being performed elsewhere. The Center for Astrophysical Thermonuclear Flashes (the "Flash Center") has developed FLASH, a highly capable, fully modular, extensible, community code that is widely used in astrophysics, cosmology, fluid dynamics, plasma physics, and other fields. FLASH has demonstrated good scaling on the largest systems. For the larger 3D simulations in this LDRD project, the FLASH computations scale to the entire Intrepid system. For the 2D simulations and test 3D problems we plan on Fusion, Project URL: Requested allocation: 300000 Justification: For example, in strong scaling runs, the execution time of FLASH benchmark runs varies less than 7% from 128 to 16384 processors. The requester has used 0 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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