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

Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by Bair, Raymond A. 08 Jun '15

08 Jun '15

A small request, so lets approve it. Ray On 6/5/15, 9:10 PM, "accounts(a)lcrc.anl.gov" <accounts(a)lcrc.anl.gov> wrote: >Hello, > >A change in allocation has been requested: > > Requester: sunhwan (Sunhwan Jo) > Project: entropy > Title: Quantifying protein-protein binding with greatly scalable >multiple copy algorithms of NAMD > Description: In PMF-based framework, a set of geometric and >conformational restraints is applied to the proteins to reduce sampling >noise and accelerate the convergence of the resulting free energy >profile. These biases are rigorously accounted for to produce the >absolute binding free energy. To enhance the PMF convergence, we will >combine the umbrella sampling with Hamiltonian and temperature (ℋ and T) >replica-exchange molecular dynamics (REM) algorithm. In the US/(ℋ,T)-REMD >simulation approach, multiple copies of the molecular  systems are >simulated concurrently, but  all with different  conditions, e.g., >umbrella potential (Hamiltonians) or temperature. Attempts are >periodically made to exchange configurations between different systems >using a Metropolis-type Monte Carlo acceptance criterion, insuring >Boltzmann-weighted statistics. Such REMD  methodology is extremely >scalable, yet also very effective to sample a rugged free energy surface. > >We anticipate the simulation systems will be comprised of ~50,000 atoms >and using at least 255 replicas concurrently. Because of its large size, >we plan to use primarily Mira for production and Fusion will be used for >initial system preparation and development of enhanced methodology in >PMF-based framework. All planned simulations will be carried out by the >open-source NAMD molecular dynamics software. The software engine used >for the planned simulations is NAMD 2.10 with Charm++ 6.4.0. We have >tested t he performance on BG/Q Mira. The scaling of parallel performance >was linear up to 512 cores for our test system comprised of 100,000 atoms >without using restraint potential and achieved the speed of about 0.025 >s/step. Using restraint potential reduces the parallel performance >significantly (~0.2 s/step). > >The expected number of project member is 3. I, Sunhwan Jo, recently >joined LCF as a postdoctoral appointee and will be the main person >performing code improvement and algorithm development under the >supervision of Wei Jiang (LCF) and Benoit Roux (UChicago). > > > Current: undetermined amount >Justification: > > Requested: 100000 > >A specific reason has been given: >A paper is published from this calculation >(http://pubs.acs.org/doi/abs/10.1021/ct501034w) and we are extending the >project to perform more sophisticated calculation. We have completed ~50% >of the calculation needed but need more time to finish the calculations. > >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 Allocation Request
by Bair, Raymond A. 08 Jun '15

08 Jun '15

A small request, so lets approve it. Ray On 6/5/15, 2:52 PM, "accounts(a)lcrc.anl.gov" <accounts(a)lcrc.anl.gov> wrote: >Hello, > >A change in allocation has been requested: > > Requester: raok (Rao Kotamarthi) > Project: Atmos_Chem > Title: Process Scale Modeling of Atmospheric Chemistry and >Transport > Description: We continue to investigate the regional scale climate >modeling and data assimilation of aerosols in chemical transport models. >The models employed for these studies include (a) WRF-CHEM (b) NRCM and >(3) GEOS-CHEM. Each of these models has been ported to the fusion luster >and uses to perform calculations by our group. All the codes use a mix of >MPI and OpenMP programming models and can scale for as few as 4 nodes to >several hundred. The GEOS-CHEM model doesn't scale beyond 32 nodes due >to gridding constraints. The NRCM (Nested Regional Scale Climate Model) >and the WRF-CHEM models are highly scalable and limited by job turnover >times and queue limitations. > >The project will have approximately 4 members. > Current: undetermined amount >Justification: > > Requested: 50000 > >A specific reason has been given: >We have doing pre-processing of regional climate model simulations using >Blues allocation. This has increased the usage of this account by our >group > >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)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 05 Jun '15

05 Jun '15

Hello, A change in allocation has been requested: Requester: sunhwan (Sunhwan Jo) Project: entropy Title: Quantifying protein-protein binding with greatly scalable multiple copy algorithms of NAMD Description: In PMF-based framework, a set of geometric and conformational restraints is applied to the proteins to reduce sampling noise and accelerate the convergence of the resulting free energy profile. These biases are rigorously accounted for to produce the absolute binding free energy. To enhance the PMF convergence, we will combine the umbrella sampling with Hamiltonian and temperature (ℋ and T) replica-exchange molecular dynamics (REM) algorithm. In the US/(ℋ,T)-REMD simulation approach, multiple copies of the molecular  systems are simulated concurrently, but  all with different  conditions, e.g., umbrella potential (Hamiltonians) or temperature. Attempts are periodically made to exchange configurations between different systems using a Metropolis-type Monte Carlo acceptance criterion, insuring Boltzmann-weighted statistics. Such REMD  methodology is extremely scalable, yet also very effective to sample a rugged free energy surface. We anticipate the simulation systems will be comprised of ~50,000 atoms and using at least 255 replicas concurrently. Because of its large size, we plan to use primarily Mira for production and Fusion will be used for initial system preparation and development of enhanced methodology in PMF-based framework. All planned simulations will be carried out by the open-source NAMD molecular dynamics software. The software engine used for the planned simulations is NAMD 2.10 with Charm++ 6.4.0. We have tested t he performance on BG/Q Mira. The scaling of parallel performance was linear up to 512 cores for our test system comprised of 100,000 atoms without using restraint potential and achieved the speed of about 0.025 s/step. Using restraint potential reduces the parallel performance significantly (~0.2 s/step). The expected number of project member is 3. I, Sunhwan Jo, recently joined LCF as a postdoctoral appointee and will be the main person performing code improvement and algorithm development under the supervision of Wei Jiang (LCF) and Benoit Roux (UChicago). Current: undetermined amount Justification: Requested: 100000 A specific reason has been given: A paper is published from this calculation (http://pubs.acs.org/doi/abs/10.1021/ct501034w) and we are extending the project to perform more sophisticated calculation. We have completed ~50% of the calculation needed but need more time to finish the calculations. 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 05 Jun '15

05 Jun '15

Hello, A change in allocation has been requested: Requester: raok (Rao Kotamarthi) Project: Atmos_Chem Title: Process Scale Modeling of Atmospheric Chemistry and Transport Description: We continue to investigate the regional scale climate modeling and data assimilation of aerosols in chemical transport models. The models employed for these studies include (a) WRF-CHEM (b) NRCM and (3) GEOS-CHEM. Each of these models has been ported to the fusion luster and uses to perform calculations by our group. All the codes use a mix of MPI and OpenMP programming models and can scale for as few as 4 nodes to several hundred. The GEOS-CHEM model doesn't scale beyond 32 nodes due to gridding constraints. The NRCM (Nested Regional Scale Climate Model) and the WRF-CHEM models are highly scalable and limited by job turnover times and queue limitations. The project will have approximately 4 members. Current: undetermined amount Justification: Requested: 50000 A specific reason has been given: We have doing pre-processing of regional climate model simulations using Blues allocation. This has increased the usage of this account by our group 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: Irridates
by John Blaas 04 Jun '15

04 Jun '15

Project created - JB

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[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 04 Jun '15

04 Jun '15

Hello, A change in allocation has been requested: Requester: zapol (Peter Zapol) Project: AlN Title: A DFT study of reaction pathways of NH3 decomposition on AlN (0001) surface Description: Structure optimizations of the adsorbate-free (0001) surface of AlN were already investigated using (2 × 2) surface unit cells. We will perform density functional theory (DFT) calculations to determine structure, bonding, and reaction energies of the adsorbed species. Periodic boundary condition (PBC) will be imposed in order to maintain periodicity of the solid support. Gradient corrected PBE density functional will be used for these calculations. The Climbing Nudged Elastic Band (cNEB) method of Henkelman and coworkers will be used to calculate transition states and activation barriers for formation of different surface species. Each structure in the supported (0001) surface of AlN typically involves ~100 atoms. To obtain accurate reaction energies and barriers, rigorous density functional theory (DFT) calculations are needed. We intend to carry out the DFT calculations using the VASP package. VASP is currently available on Blues cluster and scaling with number of processors is well established. For the MPI version of VASP with the system size of ~100 atoms, a good performance was observed up to 32 processors. Energy optimization in VASP takes approximately 750 CPU hours and we plan approximately 100 of such calculations for different adsorbate geometries. The Climbing Nudged Elastic Band (cNEB) calculation (with 5 to 7 images) takes approximately 1600 CPU hours and we plan to run 60 of these calculations to find reaction pathways. So our total request is 750*150 + 60*1600 = 208,500 core hours Current: undetermined amount Justification: Requested: 50000 A specific reason has been given: we have received considerably smaller amount than requested and as a result we have a negative balance. Please add time or at least advance the remaining balance in order to continue the project. 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 04 Jun '15

04 Jun '15

Hello, A change in allocation has been requested: Requester: zapol (Peter Zapol) Project: AlN Title: A DFT study of reaction pathways of NH3 decomposition on AlN (0001) surface Description: Structure optimizations of the adsorbate-free (0001) surface of AlN were already investigated using (2 × 2) surface unit cells. We will perform density functional theory (DFT) calculations to determine structure, bonding, and reaction energies of the adsorbed species. Periodic boundary condition (PBC) will be imposed in order to maintain periodicity of the solid support. Gradient corrected PBE density functional will be used for these calculations. The Climbing Nudged Elastic Band (cNEB) method of Henkelman and coworkers will be used to calculate transition states and activation barriers for formation of different surface species. Each structure in the supported (0001) surface of AlN typically involves ~100 atoms. To obtain accurate reaction energies and barriers, rigorous density functional theory (DFT) calculations are needed. We intend to carry out the DFT calculations using the VASP package. VASP is currently available on Blues cluster and scaling with number of processors is well established. For the MPI version of VASP with the system size of ~100 atoms, a good performance was observed up to 32 processors. Energy optimization in VASP takes approximately 750 CPU hours and we plan approximately 100 of such calculations for different adsorbate geometries. The Climbing Nudged Elastic Band (cNEB) calculation (with 5 to 7 images) takes approximately 1600 CPU hours and we plan to run 60 of these calculations to find reaction pathways. So our total request is 750*150 + 60*1600 = 208,500 core hours Current: undetermined amount Justification: Requested: 50000 A specific reason has been given: we have received considerably smaller amount than requested and as a result we have a negative balance. Please add time or at least advance the remaining balance in order to continue the project. 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 04 Jun '15

04 Jun '15

Hello, A change in allocation has been requested: Requester: zapol (Peter Zapol) Project: AlN Title: A DFT study of reaction pathways of NH3 decomposition on AlN (0001) surface Description: Structure optimizations of the adsorbate-free (0001) surface of AlN were already investigated using (2 × 2) surface unit cells. We will perform density functional theory (DFT) calculations to determine structure, bonding, and reaction energies of the adsorbed species. Periodic boundary condition (PBC) will be imposed in order to maintain periodicity of the solid support. Gradient corrected PBE density functional will be used for these calculations. The Climbing Nudged Elastic Band (cNEB) method of Henkelman and coworkers will be used to calculate transition states and activation barriers for formation of different surface species. Each structure in the supported (0001) surface of AlN typically involves ~100 atoms. To obtain accurate reaction energies and barriers, rigorous density functional theory (DFT) calculations are needed. We intend to carry out the DFT calculations using the VASP package. VASP is currently available on Blues cluster and scaling with number of processors is well established. For the MPI version of VASP with the system size of ~100 atoms, a good performance was observed up to 32 processors. Energy optimization in VASP takes approximately 750 CPU hours and we plan approximately 100 of such calculations for different adsorbate geometries. The Climbing Nudged Elastic Band (cNEB) calculation (with 5 to 7 images) takes approximately 1600 CPU hours and we plan to run 60 of these calculations to find reaction pathways. So our total request is 750*150 + 60*1600 = 208,500 core hours Current: undetermined amount Justification: Requested: 50000 A specific reason has been given: we have received considerably smaller amount than requested and as a result we have a negative balance. Please add time or at least advance the remaining balance in order to continue the project. 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 04 Jun '15

04 Jun '15

Hello, A change in allocation has been requested: Requester: zapol (Peter Zapol) Project: AlN Title: A DFT study of reaction pathways of NH3 decomposition on AlN (0001) surface Description: Structure optimizations of the adsorbate-free (0001) surface of AlN were already investigated using (2 × 2) surface unit cells. We will perform density functional theory (DFT) calculations to determine structure, bonding, and reaction energies of the adsorbed species. Periodic boundary condition (PBC) will be imposed in order to maintain periodicity of the solid support. Gradient corrected PBE density functional will be used for these calculations. The Climbing Nudged Elastic Band (cNEB) method of Henkelman and coworkers will be used to calculate transition states and activation barriers for formation of different surface species. Each structure in the supported (0001) surface of AlN typically involves ~100 atoms. To obtain accurate reaction energies and barriers, rigorous density functional theory (DFT) calculations are needed. We intend to carry out the DFT calculations using the VASP package. VASP is currently available on Blues cluster and scaling with number of processors is well established. For the MPI version of VASP with the system size of ~100 atoms, a good performance was observed up to 32 processors. Energy optimization in VASP takes approximately 750 CPU hours and we plan approximately 100 of such calculations for different adsorbate geometries. The Climbing Nudged Elastic Band (cNEB) calculation (with 5 to 7 images) takes approximately 1600 CPU hours and we plan to run 60 of these calculations to find reaction pathways. So our total request is 750*150 + 60*1600 = 208,500 core hours Current: undetermined amount Justification: Requested: 50000 A specific reason has been given: we have received considerably smaller amount than requested and as a result we have a negative balance. Please add time or at least advance the remaining balance in order to continue 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: Irridates
by Bair, Raymond A. 04 Jun '15

04 Jun '15

Approved. On 5/28/15, 4:35 PM, "Bair, Raymond A." <rbair(a)anl.gov> wrote: >After further thought, I propose that we grant this request as it stands. >I will then let Peter know that Fusion might be more available than Blues. > It is not a large enough project to make much of a point about shifting >off Blues. > >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 5/26/15, 4:25 PM, "accounts(a)lcrc.anl.gov" <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: Peter Littlewood >>Applicant's institution: ANL >> Applicant's division: PSE >> Project Name: Irridates >> Project title: Metal-insulator phase transitions in irridates >> Associated funding: DoE >> Other Systems: >> Science: Our goal is to investigate the role of the rare >>earth elements (R) in metal-insulator transitions >>of pyrochlore irridate compounds. Contrary to what >>expected, the R-dependence in a single-site DMFT >>calculation with local Coulomb interaction is >>very weak. We want to perform cluster DMFT calculations for three >>irridate compounds (Lu, Y, and Eu) with configuration-interaction-based >>exact diagonalization solvers. >> Project description: We will use MPI Fortran codes developed at >>Coulumbia University at NYC. Based on previous >>cluster DMFT calculations for a model tight >>binding Hamiltonian we estimate the CPU hours for >>a submitted job as 10k: 12 nodes * 16 cores per >>node (Blues) running for 48 hours. >>The work will be divided in multiple sets >>containing external parameters. Considering the >>limited resources, we will target parameters to >>solve instead of surveying entire phase diagram. >>Previous tests using thousands of cores >>simultaneously indicate that a better performance >>is achieved running jobs on hundreds of cores. >>The project is expected to have three members at >>most. >> Industry partnership: >> Project URL: >> Requested allocation: 350000 >> Q1: 0 >> Q2: 0 >> Q3: 0 >> Q4: 350000 >> Justification: >> Storage requirements: less that 1 TB >> >> >>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)lcrc.anl.gov >>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins > >_______________________________________________ >allocations-admins mailing list >allocations-admins(a)lcrc.anl.gov >https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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