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

Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by John Valdes 28 May '10

28 May '10

FYI, this was me submitting a request on behalf of Jared/Folker. This amount was already approved at the last allocation meeting, but they never submitted a formal request (they had only emailed), so I submitted this request now so that's properly displayed on the reports. John On Fri, May 28, 2010 at 06:36:44PM -0500, accounts(a)lcrc.anl.gov wrote: > Hello, > > A change in allocation has been requested: > > Requester: jared (Jared Wilkening) > 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: 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. > > Requested: 450000 > > A specific reason has been given: > Since the beginning of the year the average weekly upload to MG-RAST has increased by a factor of 3. This has consequently increased our computational needs. At this point we estimate our weekly computational needs to be about roughly 80k cpu hours. We are achieving this via a variety of means including PADS, Fusion, Magellan, and our local cluster. Our plan to is to run 100, 200 cpu x 4hr jobs on Fusion per 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 28 May '10

28 May '10

Hello, A change in allocation has been requested: Requester: jared (Jared Wilkening) 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: 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. Requested: 450000 A specific reason has been given: Since the beginning of the year the average weekly upload to MG-RAST has increased by a factor of 3. This has consequently increased our computational needs. At this point we estimate our weekly computational needs to be about roughly 80k cpu hours. We are achieving this via a variety of means including PADS, Fusion, Magellan, and our local cluster. Our plan to is to run 100, 200 cpu x 4hr jobs on Fusion per 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 28 May '10

28 May '10

Hello, A change in allocation has been requested: Requester: jgreeley (Jeffrey Greeley) Project: DFT_corrosion Title: Electrochemical corrosion and oxidation of metal surfaces from first principles Description: We intend to use periodic DFT calculations to study corrosion (dissolution and oxidation) of transition metal surfaces. It is essential to develop an understanding of these processes in order to be able to control the long-term stability of metal electrodes in fuel cells; such electrodes are known to degrade in successive oxidation/reduction cycles over extended periods of fuel cell operation. In particular, building upon our expertise in simulations of the dissolution thermodynamics of close-packed and kinked metal surfaces1, 2, we will develop simple, electrode potential-dependent computational models of metal corrosion (including both surface oxidation and dissolution) on defect-rich single crystal surfaces and on small (d ~ 1nm) nanoparticles. The first step will be to determine the binding energies of atomic O and OH, as a function of coverage, on a single-crystal kinked Pt surfaces; Pt(763) and Pt(854) will be chosen for this purpose. Numerous configu rations will be considered for each adsorbate coverage, and the lowest-energy configurations at each coverage will be input into an atomistic thermodynamic formalism (essentially a simplified Grand Canonical Monte Carlo technique)3 to determine the O coverage as a function of electrode potential. These results will then be compared to tabulated values of the equilibrium dissolution potential of Pt as a function of the Pt2+ ion concentration in the surrounding solution; with this analysis, it will be possible to estimate the approximate coverages of surface O and OH that are present at the thermodynmically reversible potential on these surfaces, thereby providing important insights into the interplay between surface oxidation and platinum loss by dissolution. By studying how O and OH decorate the step edges at these higher potentials, it will also be possible to obtain semi-quantitative insight into passivation and place exchange mechanisms that may be operative in various potential ranges. A natural extension of this initial work will be to consider the effect of Au decoration of the kink edges on the oxidation and dissolution thermodynamics of these kinks; this type of decoration is expected to passivate the kink features. The computational procedure for the oxidation studies will be identical to that described above for the unalloyed kinked surfaces, but it is anticipated that the oxidation will be substantially suppressed by the presence of the Au atoms. Additionally, it is expected that Au will increase the reversible dissolution potential of the Pt kinks; although experimental data are not available to confirm this prediction, the DFT-based technique that we have developed to predict shifts in dissolution potentials due to alloying1 can provide semi-quantitative estimates of these changes. A final component of this study will be to contrast the corrosion properties of Pt nanoparticles of ~1 nm diameter with the corresponding properties of the kinked single crystal surfaces. As a first step, we have already identified the optimal shapes of Pt clusters with 51-55 atoms; this size range was chosen since it contains clusters with approximately the diameter mentioned above (1 nm). These shapes were identified using an EMT-based potential, combined with an extensive Monte Carlo search; the best geometries obtained with this procedure were subsequently refined with DFT calculations. The energetic differences between the various cluster sizes provide a quantative estimate of the dissolution potentials of these clusters (such data are not available experimentally). The subsequent analysis of oxidation, which will be the focus of this study, will involve optimization of the oxygen coverage of these particles as a function of potential; as with the single crystals, thi s will be accomplished using an atomistic thermodynamic technique. The final step will be to generate detailed thermodynamic phase diagrams of the dissolution and oxidation states of the clusters as a function of potential; this analysis will, in turn, permit us to obtain a thorough understanding of the interplay between oxidation and dissolution in nanoparticle corrosion processes. These computational studies will be performed in collaboration with Nenad Markovic (ANL/MSD). The computational requirements of the proposed research will be substantial. Test calculations with the Dacapo code have indicated that the relatively large kinked Pt surfaces chosen for study in this project require approximately 15 hours per total geometric optimization on 24 cores (the practical parallelization limit of Dacapo calculations) on computer clusters similar to Fusion. Considering that a large number (~1000-1500) of O, OH, and Pt configurations will need to be considered to understand the potential-dependent dissolution and oxidation of the kinked Pt surfaces and nanoparticles, we are requesting 500,000 core hours for the proposed project. Dacapo has been running successfully on Jazz for the past ~2.5 years, and we have not experienced any significant performance problems. Current: undetermined amount Justification: The computational requirements of the proposed research will be substantial. Test calculations with the Dacapo code have indicated that the relatively large kinked Pt surfaces chosen for study in this project require approximately 15 hours per total geometric optimization on 24 cores (the practical parallelization limit of Dacapo calculations) on computer clusters similar to Fusion. Considering that a large number (~1000-1500) of O, OH, and Pt configurations will need to be considered to understand the potential-dependent dissolution and oxidation of the kinked Pt surfaces and nanoparticles, we are requesting 500,000 core hours for the proposed project. Requested: 200000 A specific reason has been given: The project is producing exciting results, but we have realized that a number of additional configurations (beyond what we originally anticipated) need to be considered to completely describe the system in detail. 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: CCT1
by accounts＠lcrc.anl.gov 12 May '10

12 May '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: Jessica Swanson Applicant's institution: ANL Applicant's division: CSE Project Name: CCT1 Project title: Characterizing coupled charge transport Associated funding: DOE Other Systems: Science: Development of a new set of computational tools to characterize the coupled processes of electron transfer and proton transport in condensed phase systems. The central aim is presently to establish a protocol for treating electron transfer with a mixed ab initio/classical explicit solvent simulation. Project description: This project will involve several methods and thus, several software packages in the long run. Immediately, we will need Columbus to calculate the intersections and couplings of electronic states. These will be large memory few node jobs. We will also be running classical simulations with ideally AMBER, alternatively gromacs or NAMD. These will be smaller memory many processors jobs. With the small systems expected to be studied in the beginning it is doubtful we will go over 16 processors at a time. As we move to more complex systems this number will go up into the twenties to hundreds of processors. As we get larger than that we will consider moving to BG. We will also be using in-house developed force matching methods and coupling these with the dyanmics simulation and with optimization algorithms (simplex and genetic algorithm to start). Project URL: Requested allocation: 182800 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 Allocation Request
by accounts＠lcrc.anl.gov 09 May '10

09 May '10

Hello, A change in allocation has been requested: Requester: rajeev (Rajeev Surendran Assary) Project: Cat_Biomass Title: Computational Studies of Biomass Catalysis Description: Biomass has the potential to serve as sustainable source of energy and organic carbon for our industrialized society. The key reactions involve the process of the converting the biomass to useful chemicals are hydrolysis, dehydration, isomerization, aldol condensation, reforming, hydrogenation, and oxidation. Investigating these important reactions and modeling efficient catalysts for industrial use, by using computational chemistry methods is the aim of this project. We intent to use density functional calculations and high-level ab-initio calculations to study the thermal decomposition of glucose for the first phase in order to understand the thermodynamics and kinetics of this process. Accurate prediction of these reactions require high-level computational methods such as G4 theory, therefore we intend to analyze the accuracy of computationally less demanding major density functional methods against G4 methods and experiments. Various chemical transformations involve in the chemical transformation of glucose to different intermediates, therefore our aim is to identify the intermediates and transition states of these processes. This requires a large amount of computational resources to investigate the feasibility and governing factors of these important reactions. Modeling an effective catalyst for the processes such as, carbohydrate dehydration, rehydration of 3-hydroxy methyl furfural is the second phase of the study. This requires realistic models of catalyst and the carbohydrates. From our experience, accurate quantum mechanical calculations on these systems are computationally demanding. We indend to use Gaussian 03 and NWChem for quantum-mechanical calculations. Current: undetermined amount Justification: We indend to use Gaussian 03 and NWChem for quantum-mechanical calculations. In Gaussian 03, the DFT calculations scales well up to 8 processors, however the high-level ab-initio methods scale only up to 2 processors. Therefore these calculations do require a longer execution time Requested: 500000 A specific reason has been given: We have made significant progress in addressing the our project. Currently one paper has been accepted in J. Physical Chemistry B and another couple of papers are in the pipeline. The high-level electronic structure calculations currently performing on many molecular systems of interest do require large number of nodes (using NWChem). Therefore I request more time to enable me to continue the calculations required for the project. 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 Request: EBAC
by Bair, Raymond A. 04 May '10

04 May '10

Seems OK to me Ray ----- Original Message ----- From: allocations-admins-bounces(a)lists.lcrc.anl.gov <allocations-admins-bounces(a)lists.lcrc.anl.gov> To: allocations-admins(a)lcrc.anl.gov <allocations-admins(a)lcrc.anl.gov> Sent: Tue May 04 17:25:40 2010 Subject: Re: [allocations-admins] [LCRC Accounts] Project Request: EBAC After some back-and-forth with the PI (see ticket# 45322), he determined that he'll need 200,000 corehours for this project, not 10,000 as initially requested. OK to approve this project? Note that the limit that the Allocation Committee decided at the last meeting that we can approve is 150K, so that's the most we could give now. If OK to approve, I'll use the following, unless someone has corrections: Cat/Subcat: P/Phy POC: Steve Pieper Priority: 3 Amount: 150,000 John On Mon, Apr 26, 2010 at 02:24:00PM -0500, accounts(a)lcrc.anl.gov wrote: > 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: Tsung-Shung Lee > Applicant's institution: ANL > Applicant's division: PHY > Project Name: EBAC > Project title: Analysis of Nucleon Resonances > Associated funding: U.S. Department of Energy, Office of Nuclear Physics Division, under Contract DE-AC02-06CH11357 > Other Systems: workstation theory9 of PHY , and NERSC > Science: The objective of this project is to extract nucleon resonance information from world data of meson production reactions for advancing our understanding > of the origin of hadron matter within Quantum Chromodynamics (QCD), the fundamental theory > of strong interactions > Project description: The objectives of Analysis of Nucleon Resonances (N*) are twofold. The first is to perform dynamical coupled-channels analysis of meson production reaction data for extracting the parameters of nucleon resonances. The second objective is to develop theoretical interpretations of the determined resonance parameters in terms of hadron structure calculations such as the constituent quark model and Lattice QCD calculations. > > This project will provide information for understanding the non-perturbative aspects of QCD. > In particular, the extracted N-N* form factors will reveal the dynamical origins of quark confinement and the meson cloud associated with the spontaneously breaking of chiral symmetry. > > This project is needed to reach milestones HP3 and HP7 by 2012 set in DOE's long-range plan > of 2010. > Project URL: http://ebac-theory.jlab.org > Requested allocation: 10000 > Justification: The analysis will be carried out by solving a large set of coupled integral equation in momentum-space an performing chi-squared fits , with > about 200 parameters, to very extensive world data of pion-nucleon scattering and electromagnetic meson production reactions. > > The calculation at each energy and each set of parameters involve an inversion of an about 1000*1000 complex matrix. This has to be repeated many times in searching the best-fit parameters in > chi-squared fit to very extensive data (about 60,000 data points) using MINUIT. > > > > 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 > _______________________________________________ > 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 Request: EBAC
by John Valdes 04 May '10

04 May '10

After some back-and-forth with the PI (see ticket# 45322), he determined that he'll need 200,000 corehours for this project, not 10,000 as initially requested. OK to approve this project? Note that the limit that the Allocation Committee decided at the last meeting that we can approve is 150K, so that's the most we could give now. If OK to approve, I'll use the following, unless someone has corrections: Cat/Subcat: P/Phy POC: Steve Pieper Priority: 3 Amount: 150,000 John On Mon, Apr 26, 2010 at 02:24:00PM -0500, accounts(a)lcrc.anl.gov wrote: > 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: Tsung-Shung Lee > Applicant's institution: ANL > Applicant's division: PHY > Project Name: EBAC > Project title: Analysis of Nucleon Resonances > Associated funding: U.S. Department of Energy, Office of Nuclear Physics Division, under Contract DE-AC02-06CH11357 > Other Systems: workstation theory9 of PHY , and NERSC > Science: The objective of this project is to extract nucleon resonance information from world data of meson production reactions for advancing our understanding > of the origin of hadron matter within Quantum Chromodynamics (QCD), the fundamental theory > of strong interactions > Project description: The objectives of Analysis of Nucleon Resonances (N*) are twofold. The first is to perform dynamical coupled-channels analysis of meson production reaction data for extracting the parameters of nucleon resonances. The second objective is to develop theoretical interpretations of the determined resonance parameters in terms of hadron structure calculations such as the constituent quark model and Lattice QCD calculations. > > This project will provide information for understanding the non-perturbative aspects of QCD. > In particular, the extracted N-N* form factors will reveal the dynamical origins of quark confinement and the meson cloud associated with the spontaneously breaking of chiral symmetry. > > This project is needed to reach milestones HP3 and HP7 by 2012 set in DOE's long-range plan > of 2010. > Project URL: http://ebac-theory.jlab.org > Requested allocation: 10000 > Justification: The analysis will be carried out by solving a large set of coupled integral equation in momentum-space an performing chi-squared fits , with > about 200 parameters, to very extensive world data of pion-nucleon scattering and electromagnetic meson production reactions. > > The calculation at each energy and each set of parameters involve an inversion of an about 1000*1000 complex matrix. This has to be repeated many times in searching the best-fit parameters in > chi-squared fit to very extensive data (about 60,000 data points) using MINUIT. > > > > 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 > _______________________________________________ > 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 02 May '10

02 May '10

Hello, A change in allocation has been requested: Requester: tslee (Tsung-Shung Lee) Project: EBAC Title: Analysis of Nucleon Resonances Description: The objectives of Analysis of Nucleon Resonances (N*) are twofold. The first is to perform dynamical coupled-channels analysis of meson production reaction data for extracting the parameters of nucleon resonances. The second objective is to develop theoretical interpretations of the determined resonance parameters in terms of hadron structure calculations such as the constituent quark model and Lattice QCD calculations. This project will provide information for understanding the non-perturbative aspects of QCD. In particular, the extracted N-N* form factors will reveal the dynamical origins of quark confinement and the meson cloud associated with the spontaneously breaking of chiral symmetry. This project is needed to reach milestones HP3 and HP7 by 2012 set in DOE's long-range plan of 2010. Current: undetermined amount Justification: The analysis will be carried out by solving a large set of coupled integral equation in momentum-space an performing chi-squared fits , with about 200 parameters, to very extensive world data of pion-nucleon scattering and electromagnetic meson production reactions. The calculation at each energy and each set of parameters involve an inversion of an about 1000*1000 complex matrix. This has to be repeated many times in searching the best-fit parameters in chi-squared fit to very extensive data (about 60,000 data points) using MINUIT. Requested: 8000 A specific reason has been given: Carry out the proposed project EBAC 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 02 May '10

02 May '10

Hello, A change in allocation has been requested: Requester: tslee (Tsung-Shung Lee) Project: EBAC Title: Analysis of Nucleon Resonances Description: The objectives of Analysis of Nucleon Resonances (N*) are twofold. The first is to perform dynamical coupled-channels analysis of meson production reaction data for extracting the parameters of nucleon resonances. The second objective is to develop theoretical interpretations of the determined resonance parameters in terms of hadron structure calculations such as the constituent quark model and Lattice QCD calculations. This project will provide information for understanding the non-perturbative aspects of QCD. In particular, the extracted N-N* form factors will reveal the dynamical origins of quark confinement and the meson cloud associated with the spontaneously breaking of chiral symmetry. This project is needed to reach milestones HP3 and HP7 by 2012 set in DOE's long-range plan of 2010. Current: undetermined amount Justification: The analysis will be carried out by solving a large set of coupled integral equation in momentum-space an performing chi-squared fits , with about 200 parameters, to very extensive world data of pion-nucleon scattering and electromagnetic meson production reactions. The calculation at each energy and each set of parameters involve an inversion of an about 1000*1000 complex matrix. This has to be repeated many times in searching the best-fit parameters in chi-squared fit to very extensive data (about 60,000 data points) using MINUIT. Requested: 8000 A specific reason has been given: To carry out the proposed project EBAC 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 02 May '10

02 May '10

Hello, A change in allocation has been requested: Requester: tslee (Tsung-Shung Lee) Project: EBAC Title: Analysis of Nucleon Resonances Description: The objectives of Analysis of Nucleon Resonances (N*) are twofold. The first is to perform dynamical coupled-channels analysis of meson production reaction data for extracting the parameters of nucleon resonances. The second objective is to develop theoretical interpretations of the determined resonance parameters in terms of hadron structure calculations such as the constituent quark model and Lattice QCD calculations. This project will provide information for understanding the non-perturbative aspects of QCD. In particular, the extracted N-N* form factors will reveal the dynamical origins of quark confinement and the meson cloud associated with the spontaneously breaking of chiral symmetry. This project is needed to reach milestones HP3 and HP7 by 2012 set in DOE's long-range plan of 2010. Current: undetermined amount Justification: The analysis will be carried out by solving a large set of coupled integral equation in momentum-space an performing chi-squared fits , with about 200 parameters, to very extensive world data of pion-nucleon scattering and electromagnetic meson production reactions. The calculation at each energy and each set of parameters involve an inversion of an about 1000*1000 complex matrix. This has to be repeated many times in searching the best-fit parameters in chi-squared fit to very extensive data (about 60,000 data points) using MINUIT. Requested: 8000 A specific reason has been given: to carry out the project EBAC This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

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