May 2014 - Allocations-admins - mailman3.cels.anl.gov

[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 30 May '14

30 May '14

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: 450000 A specific reason has been given: I believe I had made a request back in Jan/Feb for 725000 and am just now realizing I never heard anything. I have been pulled into experimental work until now and am getting back to the CFD work. In addition, I will have a student working with me this summer, Olabanji Shonibare, and we will need CPU-hours to support his effort as well. This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

1 0

[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 27 May '14

27 May '14

Hello, A change in allocation has been requested: Requester: perezsalas (Ursula Perez Salas) Project: lipidmovement Title: Curvature Effect on the Movement of Lipids Within and Between Membranes Description: We will use a coarse-grained description of the system using the MARTINI force field to create lipid vesicles of various diameters solvated in water. Cholesterol will be added to the system at extremely low and high concentrations, which will then partition into the lipid vesicle. A vesicle of 30 nm diameter results in a system of approximately 1M particles. The free energy profile across bilayer for a lipid is then calculated using the umbrella sampling technique. In this technique the phase space is divided into many small regions, which are sampled independently and then combined using the Weighted Histogram Analysis method to provide a single energy profile. In addition to the free energy profiles, long simulations will be run in order to directly observe the lipid movement. We will use the molecular dynamics program NAMD, which is developed at University of Illinois at Urbana-Champaign and is freely available for download (http://www.ks.uiuc.edu/Research/namd/) NAMD is highly parallel and scales efficiently with the number of particles in the system. Preliminary simulations of the system at the UIC cluster has shown a benchmark of 130ms/timestep on 64 cores. Using a time step of 20fs, we estimate that the proposed calculations require approximately 4 microseconds of simulation requiring a total of 460,000 core-hours. Current: undetermined amount Justification: Requested: 300000 A specific reason has been given: We have used the initial allocation of this project, in which we have obtained equilibrated structures of the lipid vesicle and started the umbrella sampling simulations. However, completing the project requires additional resources as was estimated in the initial proposal. So, we request another 300,000 core-hours to complete the project. This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

1 0

[LCRC Accounts] Project Request: DMDOHEMA_1
by accounts＠lcrc.anl.gov 22 May '14

22 May '14

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: Ross Ellis Applicant's institution: ANL Applicant's division: CSE Project Name: DMDOHEMA_1 Project title: Metal Ion Transport through Nano-Structured Lipophilic Systems: Atomistic MD Simulations Associated funding: DOE-BES Other Systems: There are two computer clusters available in addition to LCRC, i.e., the TARDIS at Prof. Monica Olvera de la Cruz’s group, and the QUEST, both at Northwestern University. Involved in several projects, the collaborating user Dr. Baofu Qiao has uses aroud 100,000 CPU hours on QUEST, and more than 1,000,000 CPU hours on TARDIS. Science: The interactions and transport mechanisms of metal ions through nano-structured soft matter systems is woefully lacking in fundamental understanding. Such systems are imported in a huge range of applications, such as: extractive separations; forming meso-porous catalytic supports; nano-particle synthesis; life-mimicking systems; etc. Understanding multi-scale structures and interactions is key to developing these important applications and is at the forefront of meso-science. However, soft-matter systems containing coordinating metal ions are notoriously difficult to probe structurally, with the best techniques being synchrotron SAXS and EXAFS giving information on the atomic metal-centric scale and supramolecular scale, respectively. Interpreting such experimental data from these complex systems can give a general idea of coordination environment and the morphology of the supramolecular solvent. However, in order to gain a truly multi-scale understa nding with atomic resolution, we must couple these experimental data with MD simulations, which can be done conveniently and powerfully by directly fitting SAXS and EXAFS data with the simulated systems. This methodology will provide a breakthrough in new fundamental insights into the structural complexity of metal ion – soft matter systems. Project description: In this project, we will investigate the supra-molecular aggregate structure in organic phases. In particular, we are planning to explore the role of the Eu(III) complexes on the morphology of reverse micelles, which are composed of amphiphilic extractant molecules. These studies will highly aid in our understanding of the exraction behavior of rare-earth elements from the aquuesous phase to the organic phase. With this work, we are aiming for rational design of higher efficienty extractants, which are expected to highly spark the development of rare earth element related technologies. In this project, classical molecular dynamics (MD) simulations will be performed at the all-atom resolution, in addition to the concurrent solvent extraction experiments at ANL. All-atom MD simulaitons have been well proven in predicting supra-molecular aggregate structures. The open source package GROMACS will be employed for the simulations. GROMACS is one of the highly recommended packages for MD simulations. GROMACS has been reported to be able to scale well up to around 1,000 CPU processors. In this project, system size up to 20 × 20 × 20 = 8000 nm3 will be simulated, which will include around 800,000 atoms. Similar systems have been previously performed using the TARDIS cluster, which showed calculation speed of around 1,000 CPU hours per nanosecond simulation time using a single CPU. GROMACS shows very good scalability on TARDIS, where a peak number of CPU of around 100 CPU has been used due to the limites size of the TARDIS cluster. Two users will use this allocation time, Dr. Ross J. Ellis at ANL and Dr. Baofu Qiao at Northwestern University. In the first phase of this project, we will study the aggregate structures of DMDOHEMA extractants dissolved in n-heptane organic phases at the absence of Eu(II) complexes. The initial systems will be obtained by removing the Eu(NO3)3 complexes from our previous simulations. In other words, by changing the concentrations of Eu(NO3) complexes, the role of the Eu(NO3) complexes on the supra-molecular aggregate structure will be illustrated. In the second phase, we plan to study the effect of extractant on the supra-molecula aggregate structure. The extraction of DMDBTDMA, which is the preceding extractant of DMDOHEMA, will be simulated and compared with the simulation results of DMDOHEMA systems. According to the available experimental data, the effects of some factors will be explore, such as the concentration of water, the concentration of Eu(NO3)3 complexes, the concentration of acidic molecule of HNO3. Project URL: Requested allocation: 400000 Q1: 100000 Q2: 100000 Q3: 100000 Q4: 100000 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: StochJuMP
by accounts＠lcrc.anl.gov 19 May '14

19 May '14

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: Cosmin Petra Applicant's institution: ANL Applicant's division: MCS Project Name: StochJuMP Project title: Parallel modelling of stochastic power grid in Julia Associated funding: ASCR,OE Other Systems: Mira 2.5 million Science: The objective of this project is to develop and test a parallel, memory-distributed, modeling framework for stochastic optimization problems arising in the optimization of power grid models under uncertainty. We plan to prove scalability and real-time capabilities that make the framework feasible to existing operational practices. Project description: Our previous parallel runs showed that the solver scales very well (>90% parallel efficiency on Intrepid, Mira and Fusion) but determined that the instantiation of the model is far beyond this efficiency. To remove this bottleneck we have moved from AMPL (who is an outdated modeling language for mathematical optimization with virtually no parallel capabilities) to Julia, which has been used by collaborators from MIT to develop JuMP, a modeling framework for optimization. Collaborators from MIT have build a JuMP extension for stochastic optimization problems. The parallelism in the instantiation of such problems comes from the particular structure these problem have (which has been very successfully exploited by the solver, as we mentioned above). Preliminary results on workstations shows that the efficiency of the parallel instantiation is even better than the efficiency of the solver. We expect this to scale up to the full Blues/Fusion. We expect a few full machine runs and other smaller runs that are needed to investigate scaling efficiencies. Since we want to show a full integration with the solver PIPS, we will need to solve these problems to optimality. For this we expect to use around 200 thousand core hours in the summer of 2014. I expect the project will have 4 or 5 members (collaborators + summer student(s)). Project URL: Requested allocation: 250000 Q1: 0 Q2: 0 Q3: 0 Q4: 250000 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 17 May '14

17 May '14

Hello, A change in allocation has been requested: Requester: albezanilla (Alejandro Lopez Bezanilla) Project: STOandPlus Title: Ab initio calculations for transition metal oxides Description: We will require VASP code (licence already obtained), and abinit code. We do not expect special requirements to run these codes in parallel. Current: undetermined amount Justification: Requested: 150000 A specific reason has been given: The remaining 1570 will not be enough to complete the ongoing study on transition metal oxides. We are in the writing process of a manuscript but still need some additional computational time to achieve our final results. Expensive calculation based on the VASP code using up to 18 nodes in Blues for about 5 hours each job yield 1600 hours a single simulation. We still require about 40 launches to observe the evolution of an electronic state for different unit cell size parameters. Approximately 100000 will be devoted to this part of the study. In addition, 50000 are estimated for an exploration of magnetic properties of a similar oxide compound with the same code. This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

1 0

Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by Bair, Raymond A. 16 May '14

16 May '14

Request looks OK. Ray On 5/15/14, 5:33 PM, "accounts(a)lcrc.anl.gov" <accounts(a)lcrc.anl.gov> wrote: >Hello, > >A change in allocation has been requested: > > Requester: zapol (Peter Zapol) > Project: glassforms > Title: First-principles Calculations of Mineral and Glass >Dissolution under Various pH Conditions > Description: The first task for this year is to extend our study from >simple sodium borosilicate glass to a model model glass with other >constituting elements. In the past year, we have calculated hydrolysis >reaction barriers of the Si-O-B bridges and the B-O-B bridges at surface >sites of sodium borosilicate glass as a model system in different >protonation states – neutral (≡SiOH), protonated (≡SiOH2+) and >deprotonated (≡SiO-) using the Nudged Elastic Band (NEB) method. As there >are other constituting elements, e.g. Al, in waste glasses, we will >calculate the reaction barriers of T-O-T bridges (T=Si, Al, B) at surface >sites in different protonation states – neutral (≡SiOH), protonated >(≡SiOH2+) and deprotonated (≡SiO-) using the Nudged Elastic Band (NEB) >method by using VASP code. >The second part is studies of the bulk water effect to determine the role >of aqueous solution and the entropic effect of water. Both effects >contribute to the free energy reaction barriers. In this year, we will >perform MD simulations to study the dissolution process of glass with Si >and other constituting elements under acidic, neutral and basic >conditions by using VASP and CPMD codes. > > Current: undetermined amount >Justification: The first-principles calculations will be carried out >using the electronic-structure code VASP. In the first part, NEB >calculations will be performed to calculate the reaction pathways for a >variety of composing elements under acidic, neutral and basic conditions. >A single geometry optimization takes 48 hours on 32 processors. We are >considering 30 supercell samplings of silicate glasses including multiple >T sites (Si, Al, B). The calculation for possible reactants, >intermediates, products will take about 140,000 core hours. It takes >about 50 hours on 160 processors (5 images) to calculate a reaction >barrier along the reaction pathway. The total estimated computer time for >barrier calculation is 240,000 core hours. In the second part, ab initio >MD simulations will be performed, where each trajectory runs for 100 ps >and it takes 32 processors to run for 96-160 hours (average 2048 core >hours per trajectory). We will need to run 100 trajectories for five >sets of > calculations. That requires 400,000 core hours. In sum, the total >requested allocation for this project is 780,000 core hours. > > Requested: 200000 > >A specific reason has been given: >We have used all allocated time productively and we need to run >additional calculations. > >This needs to be approved and the final allocation amount decided upon. > >Thank You, >The LCRC Accounts System

1 0

[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 15 May '14

15 May '14

Hello, A change in allocation has been requested: Requester: zapol (Peter Zapol) Project: glassforms Title: First-principles Calculations of Mineral and Glass Dissolution under Various pH Conditions Description: The first task for this year is to extend our study from simple sodium borosilicate glass to a model model glass with other constituting elements. In the past year, we have calculated hydrolysis reaction barriers of the Si-O-B bridges and the B-O-B bridges at surface sites of sodium borosilicate glass as a model system in different protonation states – neutral (≡SiOH), protonated (≡SiOH2+) and deprotonated (≡SiO-) using the Nudged Elastic Band (NEB) method. As there are other constituting elements, e.g. Al, in waste glasses, we will calculate the reaction barriers of T-O-T bridges (T=Si, Al, B) at surface sites in different protonation states – neutral (≡SiOH), protonated (≡SiOH2+) and deprotonated (≡SiO-) using the Nudged Elastic Band (NEB) method by using VASP code. The second part is studies of the bulk water effect to determine the role of aqueous solution and the entropic effect of water. Both effects contribute to the free energy reaction barriers. In this year, we will perform MD simulations to study the dissolution process of glass with Si and other constituting elements under acidic, neutral and basic conditions by using VASP and CPMD codes. Current: undetermined amount Justification: The first-principles calculations will be carried out using the electronic-structure code VASP. In the first part, NEB calculations will be performed to calculate the reaction pathways for a variety of composing elements under acidic, neutral and basic conditions. A single geometry optimization takes 48 hours on 32 processors. We are considering 30 supercell samplings of silicate glasses including multiple T sites (Si, Al, B). The calculation for possible reactants, intermediates, products will take about 140,000 core hours. It takes about 50 hours on 160 processors (5 images) to calculate a reaction barrier along the reaction pathway. The total estimated computer time for barrier calculation is 240,000 core hours. In the second part, ab initio MD simulations will be performed, where each trajectory runs for 100 ps and it takes 32 processors to run for 96-160 hours (average 2048 core hours per trajectory). We will need to run 100 trajectories for five sets of calculations. That requires 400,000 core hours. In sum, the total requested allocation for this project is 780,000 core hours. Requested: 200000 A specific reason has been given: We have used all allocated time productively and we need to run additional calculations. This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

1 0