October 2015 - Allocations-admins - mailman3.cels.anl.gov

Re: [allocations-admins] [LCRC Accounts] Yearly Allocation Request for Metadynamics_LC
by Bair, Raymond A. 01 Oct '15

01 Oct '15

This seems reasonable. Lets approve. Note that this is a strategic LDRD project, now prio 2. Ray On 10/1/15, 1:44 PM, "allocations-admins-bounces(a)lcrc.anl.gov on behalf of accounts(a)lcrc.anl.gov" <allocations-admins-bounces(a)lcrc.anl.gov on behalf of accounts(a)lcrc.anl.gov> wrote: >Hello, > >A yearly allocation for the LCRC cluster has been requested with the >following updated information: > >Submitter/PI: Carolyn Phillips >Project Name: Metadynamics_LC >Division: MCS >Project title: Using Parameter Free Metadynamics to calculate LC elastic >constants >Associated funding: Internal ANL LDRD 2015-172-N0 >Other Systems: >Science: We will be exploring and expanding the state-of-the-art >metadynamics methods in the context of measuring the mechanical >properties of materials, and specifically initially, the elastic >properties of liquid crystals >Project description: We will be using a parameter-free metadynamics >method for an atomistic model of a liquid crystal >4-n-pentyl-4â€™-cyanobiphenyl (5CB), as well as the homologous series >(6CB,7CB,8CB). > >Each nCB molecule will be simulated via a coarse-grained united-atom >approximation in a classical N-body Molecular Dynamics code. We will be >using NAMD + PLUMED2. Simulations will be used to measure the elastic >constants of each liquid crystal system using metadynamics. > >NAMD is a well-parallelized stable MD code with a history of use by other >users on Blues. Equilibrium simulations of the correct scale of the >model described above parallelized across on 4x16-core nodes required >~300 MB of memory and ~36 hours to implement 10 million time steps. >However most simulations will also be paired with PLUMED2, a parallelized >version of PLUMED1.3 that can be used to implement metadynamics. >Metadynamics is not known to perform well in parallel, due to a >relatively high frequency of communication across all nodes, so I do not >expect to use more than 1-4 nodes for individual "walkers" (simulation >implementations). Instead production run simulations will likely use >multiple (~20) "walkers" each deployed on 1-4 nodes, thus requiring ~80 >nodes at a time. We will be evaluating trade-offs in length of >simulation, number of nodes per implementation, and number of walkers to >achieve convergence. Thus a better approximation of the allocation >required to > complete this project will result from the initial scoping stage of >this project. > >Previous MD + metadynamics simulations have been performed on a >different model of the system using a different MD code on Midway at >UChicago. Small runs using NAMD on Blues and Fusion have already been >issued to gain familiarity. > >Expected number of Project Members: 2 >Industry partnership: >Project URL: >Current FY Hours Used: undetermined amount > >New FY Requested allocation: 150000 > Q1: 25000 > Q2: 25000 > Q3: 50000 > Q4: 50000 > >Justification: >Storage requirements: > >Thank You, > >The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request for Metadynamics_LC
by accounts＠lcrc.anl.gov 01 Oct '15

01 Oct '15

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Carolyn Phillips Project Name: Metadynamics_LC Division: MCS Project title: Using Parameter Free Metadynamics to calculate LC elastic constants Associated funding: Internal ANL LDRD 2015-172-N0 Other Systems: Science: We will be exploring and expanding the state-of-the-art metadynamics methods in the context of measuring the mechanical properties of materials, and specifically initially, the elastic properties of liquid crystals Project description: We will be using a parameter-free metadynamics method for an atomistic model of a liquid crystal 4-n-pentyl-4’-cyanobiphenyl (5CB), as well as the homologous series (6CB,7CB,8CB). Each nCB molecule will be simulated via a coarse-grained united-atom approximation in a classical N-body Molecular Dynamics code. We will be using NAMD + PLUMED2. Simulations will be used to measure the elastic constants of each liquid crystal system using metadynamics. NAMD is a well-parallelized stable MD code with a history of use by other users on Blues. Equilibrium simulations of the correct scale of the model described above parallelized across on 4x16-core nodes required ~300 MB of memory and ~36 hours to implement 10 million time steps. However most simulations will also be paired with PLUMED2, a parallelized version of PLUMED1.3 that can be used to implement metadynamics. Metadynamics is not known to perform well in parallel, due to a relatively high frequency of communication across all nodes, so I do not expect to use more than 1-4 nodes for individual "walkers" (simulation implementations). Instead production run simulations will likely use multiple (~20) "walkers" each deployed on 1-4 nodes, thus requiring ~80 nodes at a time. We will be evaluating trade-offs in length of simulation, number of nodes per implementation, and number of walkers to achieve convergence. Thus a better approximation of the allocation required to complete this project will result from the initial scoping stage of this project. Previous MD + metadynamics simulations have been performed on a different model of the system using a different MD code on Midway at UChicago. Small runs using NAMD on Blues and Fusion have already been issued to gain familiarity. Expected number of Project Members: 2 Industry partnership: Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 150000 Q1: 25000 Q2: 25000 Q3: 50000 Q4: 50000 Justification: Storage requirements: Thank You, The LCRC Accounts System

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New LCRC report submitted for Metadynamics_LC
by support＠lcrc.anl.gov 01 Oct '15

01 Oct '15

Full project report at https://accounts.lcrc.anl.gov/reporting/project/2015/?project=Metadynamics_…

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New LCRC report submitted for CFD-TPM
by support＠lcrc.anl.gov 01 Oct '15

01 Oct '15

Full project report at https://accounts.lcrc.anl.gov/reporting/project/2015/?project=CFD-TPM

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New LCRC report submitted for CFD-TPM
by support＠lcrc.anl.gov 01 Oct '15

01 Oct '15

Full project report at https://accounts.lcrc.anl.gov/reporting/project/2015/?project=CFD-TPM

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