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

Re: [allocations-admins] [LCRC Accounts] Project Request: Concerted-Flows
by Shashi Aithal 24 May '13

24 May '13

Looks OK to me as well. Shashi ----- Original Message ----- From: "John Valdes" <valdes(a)mcs.anl.gov> To: "LCRC Allocations Admins" <allocations-admins(a)lcrc.anl.gov> Sent: Friday, May 24, 2013 5:34:04 PM Subject: Re: [allocations-admins] [LCRC Accounts] Project Request: Concerted-Flows Any objections to approving the 80K hours requested by is project for Q3? Raj & Ketan want to make some runs this weekend for a paper, but they have no time (they had been using there startup allocations which are pretty much spent). We can defer the decision for the 160K for Q4 'til the next alloc meeting. John On Fri, May 24, 2013 at 04:33:28PM -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: Raj Kettimuthu > Applicant's institution: ANL > Applicant's division: MCS > Project Name: Concerted-Flows > Project title: Concerted Flows: Infrastructure for Data Intensive Science on High Speed Networks > Associated funding: DOE ASCR > Other Systems: > Science: Our objective is to use model-driven approaches to improve the performance of distributed data and compute intensive applications. There has been a significant increase in the number of scientific applications over the recent years. Meanwhile, a wide variety of computational sites have emerged with shared access to users such that a user often has accesses to multiple sites, for each site the user has a limited chunk of resource allocation. Often times, it is not possible or not optimal to execute all the component tasks of a scientific workflow on a single site. Our goal is to develop optimization heuristics to judiciously schedule individual tasks in the workflow to resources at multiple sites to balance the workload among sites and minimize the overhead in data transfer. > Project description: Our applications will be loosely coupled - parameter sweep or bag of tasks - often with multiple stages. We have an immediate requirement to evaluate our scheduling strategy for a mineral physics workflow for which we need 65 nodes for several hours to start with. We plan to do several runs of similar types of applications. Expected number of project members is 4. > Project URL: http://wiki.mcs.anl.gov/concerted-flows/index.php/Main_Page > Requested allocation: 240000 > Q1: 0 > Q2: 0 > Q3: 80000 > Q4: 160000 > Justification: > > > The requester has used undetermined amount hours of their initial startup project. > > In addition to approving an initial amount, please specify a Category > and Subcategory for this project. For a list of the current selection > of approved categories, please see: > > https://wiki.lcrc.anl.gov/wiki/Processes/Categories > > Once the Allocation committee has approved the project, please go to > the Project Management page to create it: > > https://accounts.lcrc.anl.gov/projects.php > > Thank You, > The LCRC Accounts System > _______________________________________________ > 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

1 0

Re: [allocations-admins] [LCRC Accounts] Project Request: Concerted-Flows
by Bair, Raymond A. 24 May '13

24 May '13

Looks OK to me Ray ----- Original Message ----- From: John Valdes [mailto:[email protected]] Sent: Friday, May 24, 2013 05:34 PM To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> Subject: Re: [allocations-admins] [LCRC Accounts] Project Request: Concerted-Flows Any objections to approving the 80K hours requested by is project for Q3? Raj & Ketan want to make some runs this weekend for a paper, but they have no time (they had been using there startup allocations which are pretty much spent). We can defer the decision for the 160K for Q4 'til the next alloc meeting. John On Fri, May 24, 2013 at 04:33:28PM -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: Raj Kettimuthu > Applicant's institution: ANL > Applicant's division: MCS > Project Name: Concerted-Flows > Project title: Concerted Flows: Infrastructure for Data Intensive Science on High Speed Networks > Associated funding: DOE ASCR > Other Systems: > Science: Our objective is to use model-driven approaches to improve the performance of distributed data and compute intensive applications. There has been a significant increase in the number of scientific applications over the recent years. Meanwhile, a wide variety of computational sites have emerged with shared access to users such that a user often has accesses to multiple sites, for each site the user has a limited chunk of resource allocation. Often times, it is not possible or not optimal to execute all the component tasks of a scientific workflow on a single site. Our goal is to develop optimization heuristics to judiciously schedule individual tasks in the workflow to resources at multiple sites to balance the workload among sites and minimize the overhead in data transfer. > Project description: Our applications will be loosely coupled - parameter sweep or bag of tasks - often with multiple stages. We have an immediate requirement to evaluate our scheduling strategy for a mineral physics workflow for which we need 65 nodes for several hours to start with. We plan to do several runs of similar types of applications. Expected number of project members is 4. > Project URL: http://wiki.mcs.anl.gov/concerted-flows/index.php/Main_Page > Requested allocation: 240000 > Q1: 0 > Q2: 0 > Q3: 80000 > Q4: 160000 > Justification: > > > The requester has used undetermined amount hours of their initial startup project. > > In addition to approving an initial amount, please specify a Category > and Subcategory for this project. For a list of the current selection > of approved categories, please see: > > https://wiki.lcrc.anl.gov/wiki/Processes/Categories > > Once the Allocation committee has approved the project, please go to > the Project Management page to create it: > > https://accounts.lcrc.anl.gov/projects.php > > Thank You, > The LCRC Accounts System > _______________________________________________ > 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

1 0

Re: [allocations-admins] [LCRC Accounts] Project Request: Concerted-Flows
by John Valdes 24 May '13

24 May '13

Any objections to approving the 80K hours requested by is project for Q3? Raj & Ketan want to make some runs this weekend for a paper, but they have no time (they had been using there startup allocations which are pretty much spent). We can defer the decision for the 160K for Q4 'til the next alloc meeting. John On Fri, May 24, 2013 at 04:33:28PM -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: Raj Kettimuthu > Applicant's institution: ANL > Applicant's division: MCS > Project Name: Concerted-Flows > Project title: Concerted Flows: Infrastructure for Data Intensive Science on High Speed Networks > Associated funding: DOE ASCR > Other Systems: > Science: Our objective is to use model-driven approaches to improve the performance of distributed data and compute intensive applications. There has been a significant increase in the number of scientific applications over the recent years. Meanwhile, a wide variety of computational sites have emerged with shared access to users such that a user often has accesses to multiple sites, for each site the user has a limited chunk of resource allocation. Often times, it is not possible or not optimal to execute all the component tasks of a scientific workflow on a single site. Our goal is to develop optimization heuristics to judiciously schedule individual tasks in the workflow to resources at multiple sites to balance the workload among sites and minimize the overhead in data transfer. > Project description: Our applications will be loosely coupled - parameter sweep or bag of tasks - often with multiple stages. We have an immediate requirement to evaluate our scheduling strategy for a mineral physics workflow for which we need 65 nodes for several hours to start with. We plan to do several runs of similar types of applications. Expected number of project members is 4. > Project URL: http://wiki.mcs.anl.gov/concerted-flows/index.php/Main_Page > Requested allocation: 240000 > Q1: 0 > Q2: 0 > Q3: 80000 > Q4: 160000 > Justification: > > > The requester has used undetermined amount hours of their initial startup project. > > In addition to approving an initial amount, please specify a Category > and Subcategory for this project. For a list of the current selection > of approved categories, please see: > > https://wiki.lcrc.anl.gov/wiki/Processes/Categories > > Once the Allocation committee has approved the project, please go to > the Project Management page to create it: > > https://accounts.lcrc.anl.gov/projects.php > > Thank You, > The LCRC Accounts System > _______________________________________________ > allocations-admins mailing list > allocations-admins(a)lists.lcrc.anl.gov > https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

1 0

[LCRC Accounts] Project Request: Concerted-Flows
by accounts＠lcrc.anl.gov 24 May '13

24 May '13

Hello, A new project on the LCRC cluster has been requested. Please forward the information on to the LCRC Allocation sub-committee. Applicant's name: Raj Kettimuthu Applicant's institution: ANL Applicant's division: MCS Project Name: Concerted-Flows Project title: Concerted Flows: Infrastructure for Data Intensive Science on High Speed Networks Associated funding: DOE ASCR Other Systems: Science: Our objective is to use model-driven approaches to improve the performance of distributed data and compute intensive applications. There has been a significant increase in the number of scientific applications over the recent years. Meanwhile, a wide variety of computational sites have emerged with shared access to users such that a user often has accesses to multiple sites, for each site the user has a limited chunk of resource allocation. Often times, it is not possible or not optimal to execute all the component tasks of a scientific workflow on a single site. Our goal is to develop optimization heuristics to judiciously schedule individual tasks in the workflow to resources at multiple sites to balance the workload among sites and minimize the overhead in data transfer. Project description: Our applications will be loosely coupled - parameter sweep or bag of tasks - often with multiple stages. We have an immediate requirement to evaluate our scheduling strategy for a mineral physics workflow for which we need 65 nodes for several hours to start with. We plan to do several runs of similar types of applications. Expected number of project members is 4. Project URL: http://wiki.mcs.anl.gov/concerted-flows/index.php/Main_Page Requested allocation: 240000 Q1: 0 Q2: 0 Q3: 80000 Q4: 160000 Justification: The requester has used undetermined amount hours of their initial startup project. In addition to approving an initial amount, please specify a Category and Subcategory for this project. For a list of the current selection of approved categories, please see: https://wiki.lcrc.anl.gov/wiki/Processes/Categories Once the Allocation committee has approved the project, please go to the Project Management page to create it: https://accounts.lcrc.anl.gov/projects.php Thank You, The LCRC Accounts System

1 0

[LCRC Accounts] Project Request: Theory
by accounts＠lcrc.anl.gov 22 May '13

22 May '13

Hello, A new project on the LCRC cluster has been requested. Please forward the information on to the LCRC Allocation sub-committee. Applicant's name: Cong Liu Applicant's institution: ANL Applicant's division: Materials Science Project Name: Theory Project title: Development and Application of Accurate Theoretical Models for Calculating the Thermodynamics of Chemical Bonds for Heterogeneous Catalysis Associated funding: Postdoctoral Director’s Fellowship at Argonne Other Systems: Science: The decline of fossil fuels dependency of the US on foreign sources, has led to the exploration of utilizing alternative carbon resources, such as CO2 (as a product of fossil fuel combustion and as a greenhouse gas) and lignin (as a sustainable and high-energy content biomass). Novel and efficient catalytic processes are an essential technology for realizing the chemical transformations of these feedstocks into fuels. A number of studies on homogeneous catalysis have helped to understand the chemical and mechanistic insights of the reactions. However, heterogeneous catalysis that supports the majority of industrial processes often lacks these insights; the innate complexity of heterogeneous catalysts (e.g., metal/metal oxide surfaces, metal clusters and nanoparticles, etc.) provide great challenges for not only experimentalists but also computational scientists to investigate the chemical insights behind the catalytic reactions. Developing accurate a nd time-efficient computational methods/approaches to help better understand heterogeneous catalysis can have great contribution to rational design of catalysts that can ultimately lead to novel industrial processes. Catalytic transformation of carbon feedstocks often involves a) Activation of a polar bond, e.g., C-O bond cleavage, and b) Hydrogenation, e.g., C-H or O-H bond formation. Transition metal catalysts have been most widely used in this kind of catalysis because of their efficient properties on bond activation and formation. Metal centers are the most important reaction media and the keys to unlock chemical insights of the reactions. For instance, transition metal mediated hydrogenation first goes through an H-H bond cleavage of H2 to form an M-H bond (M = transition metal). Then the M-H bond is broken to release hydrogen (H+, H−or H•), which is used for hydrogenation to form C-H or O-H bond. The stability and the thermodynamic properties of these polar bonds, especially the M-H bond, determine the reaction barriers of the hydrogenation, which ultimately reflect the catalytic properties of the catalyst. Therefore, the accurate prediction of thermodynamic properties of a chemical bond will provide important information about the catalyst candidates and help guide catalyst design. In this study, we propose a theoretical protocol for calculating heterogeneous M-H heterolytic cleavage energy in water as an example (eq. 1). Because the evaluation of ΔG in eq. 1 requires sampling of the reverse process, the protonation of the base M- surrounded by its equilibrium hydration shell (i.e., inserting a proton into a condensed MD model system) is more challenging and costly than increasing the electron count. Thus, this problem can be worked around by introducing two reaction energy terms, the formation energy of a gas phase proton, ΔfGH+(g) (eq. 2), and the solvation energy of a proton, ΔSGH+ (eq. 3), both of which have been determined experimentally. In the following we can calculate the ionization potential of the metal (ΔIPGM-(aq), eq. 4), as well as the reaction energy of hydrogen production from M-H (ΔfGH2(g), eq. 5). In eq. 4 the electron is completely eliminated from the MD model system. To balance the oxidation reaction we can consider it as placed in a vacuum reservoir (vac) where all thermodynamic energies are by definition zero. The vac state is actually the reference state used for electrons in electrochemistry. Then we have eq. (1) = (2) + (3) ̶ (4) + (5), thus the target reaction energy ΔG = ΔfGH+(g) + ΔSGH+ ̶ ΔIPGM-(aq) + ΔfGH2(g). M-H (aq) → M- (aq) + H+ (aq) ΔG (1) ½ H2 (g) → e- (vac) + H+ (g) ΔfGH+(g) (2) H+ (g) → H+ (aq) ΔSGH+ (3) M- (aq) → M (aq) + e- (vac) ΔIPGM-(aq) (4) M-H (aq) → M (aq) + ½ H2 (aq) ΔfGH2(g) (5) In practice, the lower the ΔG, the more easily the catalyst would produce H+. Also, other thermodynamic descriptors such as pKa can be calculated based on ΔG’s. Thus this approach can be used to screen different transition metal catalysts to determine the best candidate that produces H+ for hydrogenation. For instance, systematic studies can be carried out on SiO2 embedded single metal atom catalysts (currently being developed in Larry Curtiss group), to investigate the intrinsic catalytic properties of different transition metal centers. On the other hand, similar approaches can be developed on M-H bond cleavage to H- and homolytic M-H cleavage to produce H•, as well as other important chemical bonds in a catalysis process. Project description: Structure optimizations and energy calculations of selected metal and metal hydride surfaces (~45 atoms) and H2 will be carried out using density functional theory (DFT) calculations within VASP package. The metal surfaces will be periodic systems, thus plane wave basis sets will be utilized. At the same time, molecular homogeneous models will also be considered to compare with heterogeneous systems. Therefore, Gaussian 09 will be used to perform DFT and high level ab initio calculations for accurate reaction energies. Both VASP and Gaussian 09 programs are currently available on Fusion cluster and scale reasonably well on parallel processors. Project URL: Requested allocation: 480000 Q1: 120000 Q2: 120000 Q3: 120000 Q4: 120000 Justification: The requester has used undetermined amount hours of their initial startup project. In addition to approving an initial amount, please specify a Category and Subcategory for this project. For a list of the current selection of approved categories, please see: https://wiki.lcrc.anl.gov/wiki/Processes/Categories Once the Allocation committee has approved the project, please go to the Project Management page to create it: https://accounts.lcrc.anl.gov/projects.php Thank You, The LCRC Accounts System

1 0

[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 16 May '13

16 May '13

Hello, A change in allocation has been requested: Requester: macal (Charles Macal) Project: MRSA Title: Agent-based Modeling of Methicillin-Resistant Staphylococcus Aureus Epidemiology Description: This is a collaborative National Institutes of Health-funded project being jointly completed with researchers at the University of Chicago. There are two versions of the agent-based model. One version is implemented in Repast Simphony (http://repast.sourceforge.net/repast_simphony.html) The other is implemented using Repast for High Performance Computing (HPC) (http://repast.sourceforge.net/repast_hpc.html) The Repast HPC model is being run on Fusion to prepare results for publications. Current: undetermined amount Justification: Requested: 150000 A specific reason has been given: Project has run out of time, but more time is required to finish job runs for a grant renewal/review that is coming due. (Submitted by LCRC staff on behalf of PI) This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

1 0

Re: [allocations-admins] New project request
by Bair, Raymond A. 15 May '13

15 May '13

Sounds good to me. 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 5/14/13 4:33 PM, "Shashi Aithal" <aithal(a)mcs.anl.gov> wrote: > > Applicant's name: Michael Hu > Project Name: SnI4 > Applicant's division: XSD > Project title: Crystalline and amorphous structures of SnI4 > Project request date: May 14th > Category: Physical Sciences > Sub-Category: Material Science > Priority: 3 > Time Request(Q3 & Q4): 50,000 & 150,000 > POC: Larry Curtiss

1 0

Re: [allocations-admins] New project request
by John Valdes 15 May '13

15 May '13

Excellent! :) On Tue, May 14, 2013 at 04:33:03PM -0500, Shashi Aithal wrote: > > Applicant's name: Michael Hu > Project Name: SnI4 > Applicant's division: XSD > Project title: Crystalline and amorphous structures of SnI4 > Project request date: May 14th > Category: Physical Sciences > Sub-Category: Material Science > Priority: 3 > Time Request(Q3 & Q4): 50,000 & 150,000 > POC: Larry Curtiss

1 0

New project request
by Shashi Aithal 14 May '13

14 May '13

Applicant's name: Michael Hu Project Name: SnI4 Applicant's division: XSD Project title: Crystalline and amorphous structures of SnI4 Project request date: May 14th Category: Physical Sciences Sub-Category: Material Science Priority: 3 Time Request(Q3 & Q4): 50,000 & 150,000 POC: Larry Curtiss

1 0

[LCRC Accounts] Project Request: SnI4
by accounts＠lcrc.anl.gov 14 May '13

14 May '13

Hello, A new project on the LCRC cluster has been requested. Please forward the information on to the LCRC Allocation sub-committee. Applicant's name: Michael Hu Applicant's institution: ANL Applicant's division: XSD Project Name: SnI4 Project title: Crystalline and amorphous structures of SnI4 Associated funding: DOE and NSERC (Canada) Other Systems: Science: Molecular solid SnI4, when put under pressure, demonstrates rich structure transformations, and complex processes of polymerization, metallization, and amorphization. Adding to Mossbauer spectroscopic and x-ray diffraction studies, we recently conducted phonon spectrum measurements of SnI4 under pressure. In this proposal, we outline our research forward with material simulation using modern algorithms and supercomputers, which we believe is critical to interpret our experimental results and gain insights to material properties under extreme conditions. Project description: Tin iodide SnI4 is a van der Waals-bonded molecular solid with a face-center cubic structure (fcc) under ambient conditions. It is well established that under compression at room temperature to 15 GPa a reversible solid-state amorphization was found (S. Sugai, J. Phys. C 18, 799 (1985). using x-ray diffraction and Raman scattering. Later it was found that the amorphization was not originated directly from the cubic phase (phase-I) but through an intermediate crystalline metallic phase II stable above 7.2 GPa (N. Hamaya, K. Sato, K. Usui-Watanabe, K. Fuchizaki, Y. Fujii, and Y. Ohishi, Phys. Rev. Lett. 79, 4597 (1997). The precise structure of phase-II has not yet been clarified. The amorphous structure was found to crystallize to a fcc-like lattice at 61 GPa. Several theories have been proposed to account for the loss crystallinity in the diffraction pattern and, perhaps, the idea of pseudomelting (S. Sharma and S. Sikka, Prog. Mater. Sci. 40, (1996) is the most interesting. Recently, density of the vibrational states as a function of pressure were measured using nuclear inelastic x-ray scattering experiments to explore the mechanism of the amorphization. The theoretical study proposed below is aimed to elucidate all the experimental results obtained so as to uncover the mechanism for the amorphization process. We believe is critical to interpret our experimental results and gain insights to material properties under extreme conditions. The outline of the research is as follow. The stability of the lattice in the ambient structure will be examined using finite temperature self-consistent lattice dynamics and molecular dynamics calculations. The purpose is to investigate the role of (soft) phonons in the crystal -> crystal transition at ca. 7.2 GPa. Using evolution method, possible candidate structures will be predicted and their properties (i.e. structural and electrical) will be compared with experiment. Constant molecular dynamics calculations will then be performed on prospective phase II structures to examine the mechanism of amorphization. The final goal is to characterize the crystalline structure observed experimentally at 61 GPa. First-principles methods static and dynamic calculations based on density functional approximation will be performed. Specially, structural prediction using evolution algorithms (C. Glass and A. Oganov, J. Chem. Phys. 124, 244704 (2006); Y. Wang, J. Lv, L. Zhu and Y. Ma, Phys. Rev. B 82, 094116 (2010)) and constant pressure molecular dynamics calculations will be performed. The ambient fcc unit cell of SnI4 is consisted of 40 atoms. Any calculations using a supercell model will require exceeding 320 atoms. For this purpose, significant computational resource is required. The density functional codes to be used in this study are well maintained and proven highly-parallel public domain programs SIESTA and VASP. Both codes can be used for static and dynamic calculations. Structural search will be performed using our own implementation of the evolution algorithm (Y. Yao, J.S. Tse and K. Tanaka, Phys. Rev. B 77, 052103 (2008)). Structural search and molecular dynamics calculations are computationally (both on the speed of the CPU and memory capacity) very demanding. In the initial stage, an estimate of the computation requirement is about 400,000 CPU-hours on the IBM peta computer cluster. Project URL: Requested allocation: 400000 Q1: 100000 Q2: 100000 Q3: 50000 Q4: 150000 Justification: The requester has used undetermined amount hours of their initial startup project. In addition to approving an initial amount, please specify a Category and Subcategory for this project. For a list of the current selection of approved categories, please see: https://wiki.lcrc.anl.gov/wiki/Processes/Categories Once the Allocation committee has approved the project, please go to the Project Management page to create it: https://accounts.lcrc.anl.gov/projects.php Thank You, The LCRC Accounts System

1 0