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

Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by Bair, Raymond A. 13 Dec '13

13 Dec '13

SepCFD was a project in FY12 but not in FY13, so we do not require a FY13 report. The request is small, so we should approve it. Ray ----------------------------------------- Ray Bair Computing, Environment, and Life Sciences Argonne National Laboratory and the University of Chicago TCS Building 240, Room 4122 9700 South Cass Avenue Argonne, IL 60439 email: rbair(at)anl.gov Phone: (630)252-5751 On 12/13/13 3:27 PM, "accounts(a)lcrc.anl.gov" <accounts(a)lcrc.anl.gov> wrote: >Hello, > >A change in allocation has been requested: > > Requester: wardle (Kent E. Wardle) > Project: SepCFD > Title: CFD Simulation of Separations Processes > Description: This project seeks to apply the open-source CFD package >OpenFOAM to simulation of the complex, multiphase flow in liquid-liquid >separations devices used for processing nuclear fuel via solvent >extraction with a particular focus on simulations of the flow in the >annular centrifugal contactor >(https://sites.google.com/site/kwardleweb/research/computational/cfd) >For such processes, complex physical phenomena including free surface >flow and liquid-liquid droplet breakup and coalescence must be >incorporated. Accurate simulation of such physics requires fine meshes >to resolve phase boundaries as well as efficient computational >performance to enable transient simulations spanning several seconds of >flow time despite the very small time steps that are required (~10-6 s). >The specific simulation techniques to be used for the OpenFOAM >simulations are based on the Volume of Fluid (VOF) method with Large Eddy >Simulation (LES) of turbulence. Recently, a hybrid multiphas > e CFD method which couples multifluid (per-phase momentum equations) >with VOF interface sharpening for selected phase interfaces was >developed. With this new solver, a three phase system can be modeled >enforcing a sharp interface for liquidair interfaces and at the same >time allow interphase dispersion and mixing for the liquidliquid flow. >Local mean droplet size can be predicted using a reduced population >balance method and interface sharpening can be switched locally according >to comparison of the local drop size and local mesh size. The current >focus is on validation of the multiphase solver for a variety of relevant >flows. > >The code package OpenFOAM uses a C++ object-oriented framework with >dynamically linked libraries and high-level solvers to enable the user to >write custom solvers and combine various physics models and equations >enabling the evaluation of unique combinations of models such as are >required for the development of advanced liquid-liquid mixing simulation >capability as targeted in this work. > >This allocation supports nuclear fuel cycle simulations efforts under >DOE-NE as well as potential collaborations with DOE-EM sites such as >Savannah River where centrifugal contactors and other multiphase >separators are in use. > Current: undetermined amount >Justification: > > Requested: 130000 > >A specific reason has been given: >No FY14 allocation was previously requested. >Q1: 10K >Q2: 40K >Q3: 40K >Q4: 40K > >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 13 Dec '13

13 Dec '13

Hello, A change in allocation has been requested: Requester: wardle (Kent E. Wardle) Project: SepCFD Title: CFD Simulation of Separations Processes Description: This project seeks to apply the open-source CFD package OpenFOAM to simulation of the complex, multiphase flow in liquid-liquid separations devices used for processing nuclear fuel via solvent extraction with a particular focus on simulations of the flow in the annular centrifugal contactor (https://sites.google.com/site/kwardleweb/research/computational/cfd) For such processes, complex physical phenomena including free surface flow and liquid-liquid droplet breakup and coalescence must be incorporated. Accurate simulation of such physics requires fine meshes to resolve phase boundaries as well as efficient computational performance to enable transient simulations spanning several seconds of flow time despite the very small time steps that are required (~10-6 s). The specific simulation techniques to be used for the OpenFOAM simulations are based on the Volume of Fluid (VOF) method with Large Eddy Simulation (LES) of turbulence. Recently, a hybrid multiphas e CFD method which couples multifluid (per-phase momentum equations) with VOF interface sharpening for selected phase interfaces was developed. With this new solver, a three phase system can be modeled enforcing a sharp interface for liquid–air interfaces and at the same time allow interphase dispersion and mixing for the liquid–liquid flow. Local mean droplet size can be predicted using a reduced population balance method and interface sharpening can be switched locally according to comparison of the local drop size and local mesh size. The current focus is on validation of the multiphase solver for a variety of relevant flows. The code package OpenFOAM uses a C++ object-oriented framework with dynamically linked libraries and high-level solvers to enable the user to write custom solvers and combine various physics models and equations enabling the evaluation of unique combinations of models such as are required for the development of advanced liquid-liquid mixing simulation capability as targeted in this work. This allocation supports nuclear fuel cycle simulations efforts under DOE-NE as well as potential collaborations with DOE-EM sites such as Savannah River where centrifugal contactors and other multiphase separators are in use. Current: undetermined amount Justification: Requested: 130000 A specific reason has been given: No FY14 allocation was previously requested. Q1: 10K Q2: 40K Q3: 40K Q4: 40K 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 10 Dec '13

10 Dec '13

Hello, A change in allocation has been requested: Requester: iddir (hakim iddir) Project: MBM Title: Modeling Battery Materials (MBM) Description: As indicated in our LCRC Fusion annual report (2013) for the MBM project, extensive Density Functional Theory (DFT) and Ab-Initio Molecular Dynamics (AIMD) calculations on both metallic and semiconducting SWCNTs have been performed. We investigated the binding of CO, OH to Pt(100) strained oxide nanofacets. We initiated studies of Mn and Mn2+ diffusion through di-vacancies (DV) in graphene as well as in crystalline Li2CO3 to determine the migration path and the overall potential energy profile. Li and Li+ diffusion through defects sites in graphene, work already in progress, which requires further investigation in relation to system size, and comparison to Mn/Mn2+ diffusion studies. We have also started a new project within the MBM on layered-layered composites cathode materials, where the end goal is to understand and perhaps design new materials that would suppress the voltage fade problem encountered with the utilization of the current composites in Li-ion batteries. In this project we will investigate the stability of several hexavalent dopant candidates and their migration in both Li2MnO3 and LiMO2 phases of the composite, in the presence of Li and O vacancies. The preliminary diffusion studies of Co and Mn show that the Nudged Elastic Band (NEB) method does not always capture the physics behind the migration, such as the disproportionation observed with Co vacancy migration. Constrained migration calculations will be necessary to capture the disproportionation effect during the migration of the transition metal. A total of about 600000 core hours would be needed to complete this project. Current: undetermined amount Justification: Mn and Mn2+ diffusion in Li2CO3 and DV in graphene will require about 200000 hours. We will use both the NEB and the constrained methods to determine the migration barriers. Several calculations will be required to investigate the effect of charge and spin during the migration. Supercells with 192 atoms (1 Li layer, 1 TM layer and 2 O layers) will be used for the doping studies, and migration studies of M and Li within the layers of Li2MnO3-LiMO2 composites. Larger supercells (doubled in the c direction, i.e. double the number of layers in the cell) with 384 atoms will be required for the migration studies between the layers, that will involve more (Li, O) vacancy configurations and the Li-M dumbbell configuration. As mentioned above, both NEB and the constrained techniques will be used in this study. NEB calculations are lengthy and expensive; particularly when DFT+U spin polarized calculations are needed. 400000 hours will be ne necessary to run these calculations. Requested: 200000 A specific reason has been given: The diffusion studies of Mn turned out to be more expensive than expected, because of the magnetization instabilities we encountered with system. We are investigating higher magnetization values on Mn as well as on the matrix with different techniques as proposed by VASP. Density of states analysis of cathode materials might require the inclusion of spin-orbit coupling in the calculations to get reliable results. These new extensive and necessary investigations will require additional computer time. This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by Bair, Raymond A. 09 Dec '13

09 Dec '13

I wrote to Paul Fischer on 11/13 -- no reply. So I later asked Shashi to talk to Paul Fischer directly. Ray ----------------------------------------- Ray Bair Computing, Environment, and Life Sciences Argonne National Laboratory and the University of Chicago TCS Building 240, Room 4122 9700 South Cass Avenue Argonne, IL 60439 email: rbair(at)anl.gov Phone: (630)252-5751 On 12/9/13 6:34 PM, "John Valdes" <valdes(a)anl.gov> wrote: >What was the decision for this request from Chaos? Recall that >Shashi's concern was that there is no one from Argonne actively >working on this project, only folks from Virginia Tech (Mark Paul, >Chistopher Mehrvarzi and Mu Xu). > >John > >On Wed, Nov 13, 2013 at 06:31:13AM -0600, Shashi Aithal wrote: >> Ray >> I think we need to discuss this case some more before making any extra >>allocation. >> >> Shashi >> >> ----- Original Message ----- >> From: "Raymond A. Bair" <rbair(a)anl.gov> >> To: "LCRC Allocations Admins" <allocations-admins(a)lists.lcrc.anl.gov>, >>allocations-admins(a)lcrc.anl.gov >> Sent: Tuesday, November 12, 2013 3:14:09 PM >> Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation >>Request >> >> It seems to make sense for us to add 125K and then take up the other >>125K >> at the next allocations meeting. >> >> Comments? >> >> Ray >> >> >> >> >> On 11/12/13 12:17 PM, "accounts(a)lcrc.anl.gov" <accounts(a)lcrc.anl.gov> >> wrote: >> >> >Hello, >> > >> >A change in allocation has been requested: >> > >> > Requester: paul (Mark Paul) >> > Project: Chaos >> > Title: Spatiotemporal chaos and turbulence in fluids >> > Description: This is a continuing project with this year's allocation >> >request building upon last year's progress. All of our calculations >>use >> >spectral element methods to explore the spatiotemporal chaos and >> >turbulence of fluid systems. The code nek5000 has previously >>demonstrated >> >scalability and efficiency for the specific problems that we are >> >interested in. >> > >> >We continue to make significant progress on the numerical simulation of >> >Rayleigh-Benard convection for experimentally realistic conditions. >> >Rayleigh-Benard convection is the buoyancy induced convection that >>occurs >> >when a fluid layer is heated uniformly from below. We are most >> >interested in cases where the fluid dynamics of the convection layer is >> >chaotic or turbulent. Specifically, the code integrates the >> >three-dimensional time-dependent Boussinesq equations, any associated >> >reaction-diffusion-advection equations for the transport of scalar >> >quantities of interest, and the linearized tangent-space equations for >> >computing Lyapunov diagnostics. The code is geometrically flexible and >> >can handle a number of experimentally appropriate boundary conditions. >> >The Lyapunov diagnostics we can compute include the spectrum of >>Lyapunov >> >exponents and vectors that can be used to provide fundamental insights >> >into the complex dynamics that include the fractal dimension and the >> >location of fast >> > growing perturbations. >> > >> >In this allocation we propose to continue exploring the following >> >problems. >> > >> >1) Transport in chaotic flow fields >> > >> >In this project we are interested in exploring the transport dynamics >>of >> >a scalar species when the underlying fluid dynamics are >>spatiotemporally >> >chaotic. During the previous year's allocation we successfully >>validated >> >our numerical approach through a careful series of numerical tests. >> >During this year's allocation we will continue with production level >> >simulations for very large spatial domains that include a range of >> >transport dynamics to study. We are most interested in the parameter >> >regime where the time scales of the chaotic convective fluid motion, >>the >> >reaction of the scalar species, and the diffusion of the scalar species >> >are comparable. We have already successfully performed preliminary >> >calculations on blues. We would like to compute the transport in a >> >cylindrical domain of aspect ratio of 40 over a range of Lewis, >> >Damkohler, and Rayleigh numbers. There are may open challenges and >>open >> >questions regarding the active transport of a scalar species in a >>chaotic >> >flow >> > field. Nearly all current work to date in the literature has focussed >> >upon the case of simple periodic flow fields. With our work we proposed >> >to explore well into the chaotic regime and to quantify the dynamics of >> >transport. >> > >> >2) Quantifying spatiotemporal chaos >> > >> >In this effort we will perform large scale numerical simulations of >> >chaotic fluid convection for the precise conditions of experiment. We >> >will explore large cylindrical domains with aspect ratios of 30 and >> >larger for very long times (several horizontal diffusion times). We are >> >particularly interested in using and developing diagnostics that shed >> >physical insight upon fundamental features of the underlying >> >high-dimensional chaos. We will use our current capability to compute >>the >> >Lyapunov exponents, Lyapunov vectors, and the fractal dimension for a >> >range of conditions of current experimental interest in the convection >> >community. One aspect we will focus upon is using the temporal and >> >spatial averages of the leading order Lyapunov vector to quantify >>regions >> >and dynamics of interest. We are interested in searching for a >> >connection between these Lyapunov based diagnostics, which can only be >> >computed and are not accessible to experiment, with quantities and >> >diagnostics that can be >> > measured in experiment. We are in direct communication with >> >experimentalists interested in comparing the results of our simulations >> >with experimental measurements. We have identified several important >>test >> >problems to explore that we will focus upon during this allocation. We >> >have already performed test runs of blues and the runs requested for >>this >> >allocation do not require significant code development. >> > >> >We have developed the ability to compute the covariant Lyapunov vectors >> >to quantify the spatial disorder in the patterns. The covariant >>Lyapunov >> >vectors are much more difficult to calculate than the Gram-Schmidt >>based >> >Lyapunov vectors but have the benefit of providing all of the >>directions >> >of perturbation growth in the high dimensional phase space (called >> >Oseledec's splitting). The covariant Lyapunov vectors have not been >> >calculated for an experimentally accessible fluid system and have the >> >potential to provide new and important insights into the regions and >> >directions that contribute most to the chaos. In order to connect with >> >experiment we are also going to explore the use of realistic boundary >> >conditions such as walls of finite thermal conductivity and varying >>fluid >> >properties. Our current code is a serial implementation of the >> >algorithm. We intend to parallelize the code in order to explore much >> >larger systems. >> > >> >3) Turbulent thermal convection. >> > >> >We would like to continue our three-dimensional numerical simulations >>of >> >fully turbulent Rayleigh-Benard convection cells for lower Prandtl >>number >> >(0.021). By going to very low Prandtl number, we will explore a region >>of >> >parameter space that has not been well-studied, either experimentally >>or >> >numerically. Low Prandtl number has direct application to convection in >> >liquid metals, and can also shed light on the convection in the >>earthâ€™s >> >liquid metal core and in the sun and other stars which can have even >> >lower Prandtl numbers. >> > >> >We would also like to perform simulations of turbulent RBC at moderate >> >Prandtl number (0.7) and Rayleigh number (10^7-10^{10}). Many >>experiments >> >are currently being performed in this moderate Prandtl number regime >>(and >> >for even higher Rayleigh numbers), but this system is not well >>understood >> >theoretically. Thermal plumes are present in turbulent convection as a >> >means of heat transport. In addition, a large-scale circulation (LSC) >>has >> >been found, which sweeps the thermal plumes along like leaves in a >>wind. >> >This LSC is not steady and also undergoes chaotic, abrupt reversals. >> >Visualizations are extremely difficult in experiments, so numerical >> >simulations are essential for bridging the gap between experiment and >> >theory. Heat transport measurements can also be determined from these >> >simulations and compared to experiments and theoretical predictions. >>Thin >> >thermal and viscous boundary layers are present, and we can perform a >> >detailed analysis of these boundary layers, which are key >> > to understanding the nature of turbulence in these cells. Finally >> >Lyapunov exponents can be computed for these systems and a correlation >>is >> >expected between the time dependence of the LSC and the time dependence >> >of one of the Lyapunov exponents. Turbulent Rayleigh-Benard systems >>have >> >application to such diverse phenomena as weather forecasting and the >> >reversal of the earth's magnetic field. >> > Current: undetermined amount >> >Justification: Not required for our request. >> > >> > Requested: 250000 >> > >> >A specific reason has been given: >> >We have nearly exhausted our current allocation on blues for the chaos >> >project and would like to request an additional 250,000 hours for the >> >first >> >6 months of the fiscal year. We used up our initial 6-month allocation >> >in >> >the first month. This is partly due to a graduate student who is >>running >> >production level simulations for their thesis. We have several >>projects >> >moving forward that are making good progress on blues that would >>benefit >> >significantly from the additional hours. >> > >> >Please let me know if there is more information I can provide. >> > >> >Mark Paul >> > >> >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 >> _______________________________________________ >> allocations-admins mailing list >> allocations-admins(a)lists.lcrc.anl.gov >> https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >_______________________________________________ >allocations-admins mailing list >allocations-admins(a)lists.lcrc.anl.gov >https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by John Valdes 09 Dec '13

09 Dec '13

What was the decision for this request from Chaos? Recall that Shashi's concern was that there is no one from Argonne actively working on this project, only folks from Virginia Tech (Mark Paul, Chistopher Mehrvarzi and Mu Xu). John On Wed, Nov 13, 2013 at 06:31:13AM -0600, Shashi Aithal wrote: > Ray > I think we need to discuss this case some more before making any extra allocation. > > Shashi > > ----- Original Message ----- > From: "Raymond A. Bair" <rbair(a)anl.gov> > To: "LCRC Allocations Admins" <allocations-admins(a)lists.lcrc.anl.gov>, allocations-admins(a)lcrc.anl.gov > Sent: Tuesday, November 12, 2013 3:14:09 PM > Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation Request > > It seems to make sense for us to add 125K and then take up the other 125K > at the next allocations meeting. > > Comments? > > Ray > > > > > On 11/12/13 12:17 PM, "accounts(a)lcrc.anl.gov" <accounts(a)lcrc.anl.gov> > wrote: > > >Hello, > > > >A change in allocation has been requested: > > > > Requester: paul (Mark Paul) > > Project: Chaos > > Title: Spatiotemporal chaos and turbulence in fluids > > Description: This is a continuing project with this year's allocation > >request building upon last year's progress. All of our calculations use > >spectral element methods to explore the spatiotemporal chaos and > >turbulence of fluid systems. The code nek5000 has previously demonstrated > >scalability and efficiency for the specific problems that we are > >interested in. > > > >We continue to make significant progress on the numerical simulation of > >Rayleigh-Benard convection for experimentally realistic conditions. > >Rayleigh-Benard convection is the buoyancy induced convection that occurs > >when a fluid layer is heated uniformly from below. We are most > >interested in cases where the fluid dynamics of the convection layer is > >chaotic or turbulent. Specifically, the code integrates the > >three-dimensional time-dependent Boussinesq equations, any associated > >reaction-diffusion-advection equations for the transport of scalar > >quantities of interest, and the linearized tangent-space equations for > >computing Lyapunov diagnostics. The code is geometrically flexible and > >can handle a number of experimentally appropriate boundary conditions. > >The Lyapunov diagnostics we can compute include the spectrum of Lyapunov > >exponents and vectors that can be used to provide fundamental insights > >into the complex dynamics that include the fractal dimension and the > >location of fast > > growing perturbations. > > > >In this allocation we propose to continue exploring the following > >problems. > > > >1) Transport in chaotic flow fields > > > >In this project we are interested in exploring the transport dynamics of > >a scalar species when the underlying fluid dynamics are spatiotemporally > >chaotic. During the previous year's allocation we successfully validated > >our numerical approach through a careful series of numerical tests. > >During this year's allocation we will continue with production level > >simulations for very large spatial domains that include a range of > >transport dynamics to study. We are most interested in the parameter > >regime where the time scales of the chaotic convective fluid motion, the > >reaction of the scalar species, and the diffusion of the scalar species > >are comparable. We have already successfully performed preliminary > >calculations on blues. We would like to compute the transport in a > >cylindrical domain of aspect ratio of 40 over a range of Lewis, > >Damkohler, and Rayleigh numbers. There are may open challenges and open > >questions regarding the active transport of a scalar species in a chaotic > >flow > > field. Nearly all current work to date in the literature has focussed > >upon the case of simple periodic flow fields. With our work we proposed > >to explore well into the chaotic regime and to quantify the dynamics of > >transport. > > > >2) Quantifying spatiotemporal chaos > > > >In this effort we will perform large scale numerical simulations of > >chaotic fluid convection for the precise conditions of experiment. We > >will explore large cylindrical domains with aspect ratios of 30 and > >larger for very long times (several horizontal diffusion times). We are > >particularly interested in using and developing diagnostics that shed > >physical insight upon fundamental features of the underlying > >high-dimensional chaos. We will use our current capability to compute the > >Lyapunov exponents, Lyapunov vectors, and the fractal dimension for a > >range of conditions of current experimental interest in the convection > >community. One aspect we will focus upon is using the temporal and > >spatial averages of the leading order Lyapunov vector to quantify regions > >and dynamics of interest. We are interested in searching for a > >connection between these Lyapunov based diagnostics, which can only be > >computed and are not accessible to experiment, with quantities and > >diagnostics that can be > > measured in experiment. We are in direct communication with > >experimentalists interested in comparing the results of our simulations > >with experimental measurements. We have identified several important test > >problems to explore that we will focus upon during this allocation. We > >have already performed test runs of blues and the runs requested for this > >allocation do not require significant code development. > > > >We have developed the ability to compute the covariant Lyapunov vectors > >to quantify the spatial disorder in the patterns. The covariant Lyapunov > >vectors are much more difficult to calculate than the Gram-Schmidt based > >Lyapunov vectors but have the benefit of providing all of the directions > >of perturbation growth in the high dimensional phase space (called > >Oseledec's splitting). The covariant Lyapunov vectors have not been > >calculated for an experimentally accessible fluid system and have the > >potential to provide new and important insights into the regions and > >directions that contribute most to the chaos. In order to connect with > >experiment we are also going to explore the use of realistic boundary > >conditions such as walls of finite thermal conductivity and varying fluid > >properties. Our current code is a serial implementation of the > >algorithm. We intend to parallelize the code in order to explore much > >larger systems. > > > >3) Turbulent thermal convection. > > > >We would like to continue our three-dimensional numerical simulations of > >fully turbulent Rayleigh-Benard convection cells for lower Prandtl number > >(0.021). By going to very low Prandtl number, we will explore a region of > >parameter space that has not been well-studied, either experimentally or > >numerically. Low Prandtl number has direct application to convection in > >liquid metals, and can also shed light on the convection in the earthâ€™s > >liquid metal core and in the sun and other stars which can have even > >lower Prandtl numbers. > > > >We would also like to perform simulations of turbulent RBC at moderate > >Prandtl number (0.7) and Rayleigh number (10^7-10^{10}). Many experiments > >are currently being performed in this moderate Prandtl number regime (and > >for even higher Rayleigh numbers), but this system is not well understood > >theoretically. Thermal plumes are present in turbulent convection as a > >means of heat transport. In addition, a large-scale circulation (LSC) has > >been found, which sweeps the thermal plumes along like leaves in a wind. > >This LSC is not steady and also undergoes chaotic, abrupt reversals. > >Visualizations are extremely difficult in experiments, so numerical > >simulations are essential for bridging the gap between experiment and > >theory. Heat transport measurements can also be determined from these > >simulations and compared to experiments and theoretical predictions. Thin > >thermal and viscous boundary layers are present, and we can perform a > >detailed analysis of these boundary layers, which are key > > to understanding the nature of turbulence in these cells. Finally > >Lyapunov exponents can be computed for these systems and a correlation is > >expected between the time dependence of the LSC and the time dependence > >of one of the Lyapunov exponents. Turbulent Rayleigh-Benard systems have > >application to such diverse phenomena as weather forecasting and the > >reversal of the earth's magnetic field. > > Current: undetermined amount > >Justification: Not required for our request. > > > > Requested: 250000 > > > >A specific reason has been given: > >We have nearly exhausted our current allocation on blues for the chaos > >project and would like to request an additional 250,000 hours for the > >first > >6 months of the fiscal year. We used up our initial 6-month allocation > >in > >the first month. This is partly due to a graduate student who is running > >production level simulations for their thesis. We have several projects > >moving forward that are making good progress on blues that would benefit > >significantly from the additional hours. > > > >Please let me know if there is more information I can provide. > > > >Mark Paul > > > >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 > _______________________________________________ > 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 06 Dec '13

06 Dec '13

Hello, A change in allocation has been requested: Requester: balaji (Pavan Balaji) Project: radix Title: Scalable Parallel System Software 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. Current: undetermined amount Justification: Requested: 300000 A specific reason has been given: We are running a bunch of experiments for our upcoming ICS and HPDC papers. We'll also be requesting for a reservation next month. This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

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Re: [allocations-admins] [LCRC Accounts] Yearly Allocation Request from lith_ox_md
by Bair, Raymond A. 04 Dec '13

04 Dec '13

Lets approve this request, and make the time good through the end of Q2. Ray On 9/4/13 4:01 PM, "accounts(a)lcrc.anl.gov" <accounts(a)lcrc.anl.gov> wrote: >Hello, > >A yearly allocation for the LCRC cluster has been requested with the >following updated information: > >Submitter/PI: John Russell >Project Name: lith_ox_md >Division: MSD >Project title: Molecular Dynamics Calculations of Lithium Oxides >Associated funding: Strategic LDRD project entitled Multiscale Modeling >of Advanced Electrical Energy Storage Systems >Other Systems: Carbon, CNM >Science: We will perform molecular dynamics (MD) simulations on >nanocrystalline lithium-oxide compounds (including Li2O and Li2O2) of >relevance to lithium-air batteries. These simulations include >determination of the structures, energies and some properties (such as >the diffusivities) of the free surfaces and grain boundaries in these >microstructures. A key feature of the simulation approach involves the >use of a method to evaluate the Coulomb energy, forces and stresses by >direct 1/r summation with spherical truncation (Wolf et al. 1999). This >order-N method, which has recently been incorporated into the LAMMPS code >that will be used for this work, is computationally superior to both the >widely used Ewald method and fast-multipole methods while at the same >time producing numerically identical and physically more transparent >results. Using this approach, we are able to consider ionic systems >consisting of a very large number of ions, thus enabling elucidation of >microstructu > ral phenomena and physical behavior that can subsequently be used as >input to parameterize a physically realistic mesoscale battery model of >microstructure evolution during the charge/discharge cycle. >Project description: The goal of this project is calculate structural >and thermodynamic properties of lithium-oxide materials and to develop >parameters for collaborators studying mesoscale models where experimental >values may be unavailable. Our initial approach will be to use a >Buckingham potential to model covalent interactions and a Wolf summation >potential for elecrostatic interactions in a fixed charge Li2O model as >implemented in the LAMMPS molecular dynamics package. Our model systems >will include free particles, surfaces and nanocrystalline materials. This >modeling approach is well suited for large systems due to the favorable >scaling of the potentials and software. LAMMPS is massively parallel with >nearly linear scaling with system size which can allow for 100k+ atom >models for tens of nanoseconds. > >We are also developing a variable charge lithium-oxide molecular dynamics >potential suitable for modeling lithium superoxide, lithium peroxide, and >Li2O. The computational cost of this method is estimated as 25x as >expensive as a Buckingham pair potential, but with much greater >flexibility to model different lithium-oxide stoichiometries. >Project URL: >Current FY Hours Used: undetermined amount > >New FY Requested allocation: 500000 > Q1: 125000 > Q2: 125000 > Q3: 125000 > Q4: 125000 > >Justification: LAMMPS is a linear scaling molecular dynamics code. We >will be using the Wolf summation potential to model electrostatics, which >is very important due to the fact that FFT methods for electrostatics >such as PPPM and PME are NlogN scaling. > >The Wolf summation is directly incoporated into our variable charge >model. The variable charge itself has costs due to charge equilibration, >which should put it on par with MEAM and AIREBO. In LAMMPS these methods >are compared to a Lennard-Jones (LJ) potential as a benchmark reference >(LJ = 1.0, Buckingham ~ 1.0). MEAM is rated at 16.5x and AIREBO at 40.6x. >This is primarily due to loops over second nearest neighbors. Therefore, >we expect the potential to be in the range of 25x scaling. > >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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