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

[LCRC Accounts] Project Request: WRF-NRCM
by accounts＠lcrc.anl.gov 25 Feb '10

25 Feb '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: Ramesh Balakrishnan Applicant's institution: ANL Applicant's division: LCF Project Name: WRF-NRCM Project title: WRF-Nested Regional Climate Model Simulation of a Hurricane Associated funding: internal Other Systems: Blue Gene/P Science: Climate Modeling Project description: Ramesh Balakrishnan (PI) is requesting an allocation to do nested regional climate modeling (NRCM) with the WRF code from NCAR. The NRCM combines the strengths of NCAR's WRF model and NCAR's Community Climate System Model into an instrument that will allow for fundamental progress on the understanding and prediction of regional climate variability and change. In particular, embedding WRF within CCSM will allow scientists to resolve processes that occur at the regional scale, as well as the influence of those processes on the large-scale climate, thereby improving the fidelity of climate change simulations and their utility for local and regional planning. The PI requests that John Michalakes (NCAR), who has an MCS account, be added to this project (after its approved, of course). Project URL: http://www.vets.ucar.edu/vg/WRF-NRCM/index.html Requested allocation: 299999 Justification: We have asked for an allocation that is just shy of 300,000 core hours. At this time, the PI is unable to provide a justification for a larger allocation. However, there is every expectation that the allocation required to complete this study will be a couple of multiples of the 300,000 hour limit. We will request an increase in our allocation after we have ported and benchmarked the WRF-NRCM code on Fusion. The requester has used 18 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: cfd_enginemodeling
by accounts＠lcrc.anl.gov 19 Feb '10

19 Feb '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: Sibendu Som Applicant's institution: ANL Applicant's division: Energy Systems Project Name: cfd_enginemodeling Project title: Computation Fluid Dynamics Modeling of Petrodiesel and Biodiesel Associated funding: LDRD Project Other Systems: Science: This project will use an Eulerian-Lagrangian Computation Fluid Dynamics (CFD) software called CONVERGE to model various diesel engine processes like internal nozzle flow, spray behavior, combustion and emission processes. The goal is to capture the differences between diesel and biodiesel fuels from a CFD standpoint since computer based modeling is more cost effective than performing full scale laboratory experiments. Project description: The project is dived in two parts: In the first part, engine processes will be modeled using petrodiesel. The spray data obtained from Advanced Photo Source at Argonne and single-cylinder engine performance and emission data from CAT cell will be used to further develop and validate spray and combustion models in CONVERGE and perform parametric studies. The major motivation is to develop more predictive and robust sub-models for capturing diesel engine processes. In the second part, fundamental studies will be performed to establish flame stabilization and lift-off characteristics of biodiesel using CONVERGE. A new surrogate (methyl decanoate) fuel will be used for modeling the combustion characteristics of biodiesel. Comparison will be performed between inner nozzle flow, nonevaporating and evaporating spray, combustion characteristics, engine performance and emission characteristics of biodiesel and petrodiesel. Project URL: http://www.transportation.anl.gov/ Requested allocation: 50000 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

1 0

[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 19 Feb '10

19 Feb '10

Hello, A change in allocation has been requested: Requester: borland (Michael Borland) Project: ApsRenewalLattice Title: Development of accelerator lattices for the APS Renewal Description: Our method of nonlinear optimization, which has been quite successful in optimizing the APS and other rings, is a direct one. That is, it relies on particle tracking to directly determine the dynamic and momentum apertures. This concept was developed first at APS, and is getting significant attention from other facilities. The software uses a genetic optimization script developed at APS, in either a single-objective or multi-objective mode. The script submits a series (usually 40 to 120) of single-core jobs and waits for jobs to complete. Since the execution time is nondeterministic, jobs complete asynchronously. The genetic optimizer makes use of information from the best completed jobs to "breed" new trial solutions. In this way, the number of cores in use is kept nearly constant. Performance is of course very good as the jobs are completely asynchronous and independent. Loading of the filesystem is also modest. The method relies on having sufficient computing resources to evaluate on several thousand configurations, where each configuration takes typically four hours on a single core. We have typically used 40 to 80 cores for each optimization, giving a turn-around time of about a week. When resources are available, we may run 120 cores per optimization. More recently, we have parallelized the evaluation of dynamic and momentum aperture, which opens up the possibility to run each job on up to 30 cores, limited by the nature of the dynamic aperture evaluation. This would require some development and testing to integrate with the optimizer, but should not be difficult. Also, some preliminary steps (linear optics tuning) are inherently serial and would not scale. We anticipate a parallel efficiency of about 75% for these jobs, but more testing is needed to confirm this. Once an optimization is completed, it must be evaluated using about 50 random error ensembles to ensure robustness. This takes about 2500 core hours. We are requesting an initial allocation that should be adequate to perform 10 typical optimizations and evaluations. It will also allow us to implement and test the optimization using multiple cores per configuration. The simulation software, ELEGANT, is written in C and has run on Jazz and BlueGene. The genetic optimizer and other scripts are written in Tcl/Tk. There are three expected project members, including myself. The others are software developers. Current: undetermined amount Justification: APS upgrade lattice work is urgent. I need about 40khours to do a single optimization, and I have many to perform. I've applied for time through ALCC but don't know when/if I'll receive any. The software is very efficient since it consists of many independent serial jobs running simultaneously to evaluate different possible configurations. I have run up to 1280 cores on fusion simultaneously without issues. Requested: 500000 A specific reason has been given: APS upgrade lattice work is urgent. I need about 40khours to do a single optimization, and I have many to perform. I've applied for time through ALCC but don't know when/if I'll receive any. 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] Yearly Allocation Request from kv
by John Valdes 17 Feb '10

17 Feb '10

FYI, this was me, (re)submitting the kv renewal using the renewal form (so that it appears properly in the reports and database). No action is required on our part for this. John On Wed, Feb 17, 2010 at 05:04:14PM -0600, accounts(a)lcrc.anl.gov wrote: > Hello, > > A yearly allocation for the LCRC cluster has been requested with the > following updated information: > > Submitter/PI: Benoit Roux > Project Name: kv > Division: BIO > Project title: Studies of voltage-vgated potassium channel > Associated funding: NIH/NIGMS, R01-GM062342 "Computational studies of ion channels" > > INCITE from Office of Science > > Other Systems: BG/P, NCSA, PSC, KBT > Science: Molecular dynamics of membrane proteins that are affected by the transmembrane voltage > Project description: Voltage-gated potassium (Kv) channels are membrane proteins that respond to changes in the transmembrane potential by altering their conformation to allow the passive conduction of K+ ions across the cell membrane. These channels are tetrameric proteins, in which each subunit comprises six transmembrane (TM) helical segments (S1-S6). The ion conduction pore is located at the center of the tetrameric structure and is formed by the S5 and S6 helices from the four subunits. The first four segments (S1-S4) in each subunit form a voltage-sensing domain (VSD) that is located in the lipid membrane at the periphery of the central pore domain (PD). Upon depolarization of the membrane, the VSD in each subunit undergoes a voltage-dependent transition from a resting to an active conformation, which then leads the opening of the intracellular gate of the ion conduction pore. > > The conformational changes associated with the activation of Kv channels result in the transfer of an electric charge Delta-Q across the membrane, that can be measured experimentally as a small transient capacitive current. In the Shaker K+ channel, the "gating charge" corresponds to the transfer of 12-14 elementary charge (e) along the transmembrane electric field. Correspondingly, a change V in the membrane potential shifts the relative free energy of the closed and open conformations by V*Delta-Q. The gating charge DeltaQ is, thus, a key concept to explain how channel activation is coupled to the membrane potential. Initially postulated by Hodgkin and Huxley in 1952, it was first detected and measured more than 20 years later by Armstrong and Bezanilla. > > Ultimately, explaining the voltage-gating mechanism of Kv channels in molecular terms requires gaining knowledge of the active and resting conformations, and then showing how those conformations are able to account for the experimentally observed gating charge Delta-Q. Our strategy is to first carefully construct atomic models of the active and resting states of Kv channels that are consistent with all available experimental information using protein structure prediction algorithms. We also have a novel method to compute the gating charge using all-atom MD. > > Recently, Pathak et al. have generated detailed atomic models of Kv1.2 in the open/active and closed/resting states using the Rosetta-Membrane structure prediction program. The model of the open/active state complements the information missing from the X-ray structure of the Kv1.2 channel used as a template, while the S1-S2, S2-S3, and S3-S4 loops in the voltage sensing domain were modeled de novo. These results offer a promising starting point to expand our understanding of voltage gating in Kv channels. > Some critical issues must be addressed. In particular, the stability of those structural models in the complex dynamical environment of the lipid bilayer has not be ascertained. Furthermore, the gating charge associated with the models was only evaluated within a continuum approximation where the water and membrane were treated as featureless dielectric media. > > Recently, we have developed the string method with swarms of trajectories that is able to determine dynamically relevant transition pathways in complex macromolecular systems. The method, which was directly inspired from the work of Maragliano et al. (2006), aims to discover the optimal minimum free energy path between the two end-states represented as a "chain of state" by an ordered sequence of M discrete "images"", {z1,z2 ..., zM}. Briefly, the algorithm consists in evolving the chain of state towards optimal paths by making small adjustments Delta-z to the images. In the strategy developed by us, the Delta-z is calculated as the average drift for an ensemble (swarms) of unbiased short trajectories of length tau initiated from each of the images. The algorithm refine each of the M images until the "dynamical propagation" is such that each image evolves only along the path on average. The string method with swarms-of-trajectories is based on the reasonable assumption th > at, on the timescale tau, the set of collective variables evolved as an overdamped Browninan dynamics guided by a free energy landscape. Nevertheless, we emphasize that the true dynamical evolution of the atomistic degrees of freedom of the real system undelies the method. > > Our goal is to refine the atomic models of the closed/resting and open/activated states and test their ability to account for the experimentally observed gating charge using all-atom MD and explicit lipid membrane environment. > > > REFERENCES > > M. M. Pathak, V. Yarov-Yarovoy, G. Agarwal, B. Roux, P. Barth, S. Kohout, F. Tombola, and E. Y. Isacoff. (2007). "Closing in on the Resting State of the Shaker K+ Channel." Neuron 56, 124-140. > > F. V. Campos, B. Chanda, B. Roux, and F. Bezanilla. (2007). "Two Atomic Constraints Unambiguously Position the S4 Segment Relative to S1 and S2 Segments in the Closed State of Shaker K Channel." Proceedings of the National Academy of Sciences of the United States of America 104, 7904-7909. > > > A. C. Pan, D. Sezer, and B. Roux. (2008). "Finding Transition Pathways Using the String Method with Swarms of Trajectories." J Phys Chem B 112, 3432-3440. > > B. Roux. (2008). "The Membrane Potential and Its Representation by a Constant Electric Field in Computer Simulations." Biophys J 95, 4205-4216. > > Project URL: http://thallium.bsd.uchicago.edu/RouxLab/ > Current FY Hours Used: undetermined amount > > New FY Requested allocation: 250000 > Justification: For the resources, we expect to be using MPI runs of 16-32 CPU over the next year. This easily amounts to: > > 32 CPU times 24 hours * 325 days = 250,000 > > Fusion will be an excellent platform to establish and execute the string method algorithm. > > 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] Yearly Allocation Request from kv
by accounts＠lcrc.anl.gov 17 Feb '10

17 Feb '10

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Benoit Roux Project Name: kv Division: BIO Project title: Studies of voltage-vgated potassium channel Associated funding: NIH/NIGMS, R01-GM062342 "Computational studies of ion channels" INCITE from Office of Science Other Systems: BG/P, NCSA, PSC, KBT Science: Molecular dynamics of membrane proteins that are affected by the transmembrane voltage Project description: Voltage-gated potassium (Kv) channels are membrane proteins that respond to changes in the transmembrane potential by altering their conformation to allow the passive conduction of K+ ions across the cell membrane. These channels are tetrameric proteins, in which each subunit comprises six transmembrane (TM) helical segments (S1-S6). The ion conduction pore is located at the center of the tetrameric structure and is formed by the S5 and S6 helices from the four subunits. The first four segments (S1-S4) in each subunit form a voltage-sensing domain (VSD) that is located in the lipid membrane at the periphery of the central pore domain (PD). Upon depolarization of the membrane, the VSD in each subunit undergoes a voltage-dependent transition from a resting to an active conformation, which then leads the opening of the intracellular gate of the ion conduction pore. The conformational changes associated with the activation of Kv channels result in the transfer of an electric charge Delta-Q across the membrane, that can be measured experimentally as a small transient capacitive current. In the Shaker K+ channel, the "gating charge" corresponds to the transfer of 12-14 elementary charge (e) along the transmembrane electric field. Correspondingly, a change V in the membrane potential shifts the relative free energy of the closed and open conformations by V*Delta-Q. The gating charge DeltaQ is, thus, a key concept to explain how channel activation is coupled to the membrane potential. Initially postulated by Hodgkin and Huxley in 1952, it was first detected and measured more than 20 years later by Armstrong and Bezanilla. Ultimately, explaining the voltage-gating mechanism of Kv channels in molecular terms requires gaining knowledge of the active and resting conformations, and then showing how those conformations are able to account for the experimentally observed gating charge Delta-Q. Our strategy is to first carefully construct atomic models of the active and resting states of Kv channels that are consistent with all available experimental information using protein structure prediction algorithms. We also have a novel method to compute the gating charge using all-atom MD. Recently, Pathak et al. have generated detailed atomic models of Kv1.2 in the open/active and closed/resting states using the Rosetta-Membrane structure prediction program. The model of the open/active state complements the information missing from the X-ray structure of the Kv1.2 channel used as a template, while the S1-S2, S2-S3, and S3-S4 loops in the voltage sensing domain were modeled de novo. These results offer a promising starting point to expand our understanding of voltage gating in Kv channels. Some critical issues must be addressed. In particular, the stability of those structural models in the complex dynamical environment of the lipid bilayer has not be ascertained. Furthermore, the gating charge associated with the models was only evaluated within a continuum approximation where the water and membrane were treated as featureless dielectric media. Recently, we have developed the string method with swarms of trajectories that is able to determine dynamically relevant transition pathways in complex macromolecular systems. The method, which was directly inspired from the work of Maragliano et al. (2006), aims to discover the optimal minimum free energy path between the two end-states represented as a "chain of state" by an ordered sequence of M discrete "images"", {z1,z2 ..., zM}. Briefly, the algorithm consists in evolving the chain of state towards optimal paths by making small adjustments Delta-z to the images. In the strategy developed by us, the Delta-z is calculated as the average drift for an ensemble (swarms) of unbiased short trajectories of length tau initiated from each of the images. The algorithm refine each of the M images until the "dynamical propagation" is such that each image evolves only along the path on average. The string method with swarms-of-trajectories is based on the reasonable assumption th at, on the timescale tau, the set of collective variables evolved as an overdamped Browninan dynamics guided by a free energy landscape. Nevertheless, we emphasize that the true dynamical evolution of the atomistic degrees of freedom of the real system undelies the method. Our goal is to refine the atomic models of the closed/resting and open/activated states and test their ability to account for the experimentally observed gating charge using all-atom MD and explicit lipid membrane environment. REFERENCES M. M. Pathak, V. Yarov-Yarovoy, G. Agarwal, B. Roux, P. Barth, S. Kohout, F. Tombola, and E. Y. Isacoff. (2007). "Closing in on the Resting State of the Shaker K+ Channel." Neuron 56, 124-140. F. V. Campos, B. Chanda, B. Roux, and F. Bezanilla. (2007). "Two Atomic Constraints Unambiguously Position the S4 Segment Relative to S1 and S2 Segments in the Closed State of Shaker K Channel." Proceedings of the National Academy of Sciences of the United States of America 104, 7904-7909. A. C. Pan, D. Sezer, and B. Roux. (2008). "Finding Transition Pathways Using the String Method with Swarms of Trajectories." J Phys Chem B 112, 3432-3440. B. Roux. (2008). "The Membrane Potential and Its Representation by a Constant Electric Field in Computer Simulations." Biophys J 95, 4205-4216. Project URL: http://thallium.bsd.uchicago.edu/RouxLab/ Current FY Hours Used: undetermined amount New FY Requested allocation: 250000 Justification: For the resources, we expect to be using MPI runs of 16-32 CPU over the next year. This easily amounts to: 32 CPU times 24 hours * 325 days = 250,000 Fusion will be an excellent platform to establish and execute the string method algorithm. Thank You, The LCRC Accounts System

1 0

[LCRC Accounts] Project Request: Aurora
by accounts＠lcrc.anl.gov 15 Feb '10

15 Feb '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: Ramesh Balakrishnan Applicant's institution: ANL Applicant's division: LCF Project Name: Aurora Project title: Assessing the performance of CFD codes on multicore computing platforms Associated funding: Other Systems: Blue Gene/P (at ALCF) Science: Direct Numerical Simulation (DNS), Large Eddy Simulation (LES), Reynolds Averaged Navier-Stokes (RANS), Detached Eddy Simulation (DES), and Improved Delayed Detached Eddy Simulation (IDDES) of Turbulence Phenomena Project description: Our goal is to compute high Reynolds number compressible flow in the framework of Improved Delayed Detached Eddy Simulation (IDDES) code. The code we are using for our simulations accepts overlapping multi-block structured grids of Chimera type. Our aim is to study the performance of the code with pure MPI and MPI+OpenMP parallelizations and perform a baseline run on a relatively coarse grid. Project URL: Requested allocation: 250000 Justification: The requester has used 6 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