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

[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 17 Mar '15

17 Mar '15

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 have used coarse-grained simulations utilizing the MARTINI force field to create a unilamellar lipid vesicle, 30nm in diameter, solvated in water consisting of 1M particles. This vesicle size is similar to those used in neutron scattering experiments to which we want to compare the simulations results. In our previous project we calculated the free energy profile of a single lipid (DPPC) across a flat bilayer as well as a vesicle (curved membrane) using the umbrella sampling technique. Our preliminary results show an increase in the energy barrier of lipid flip-flop across the membrane in the curved case compared to the flat bilayer which indicate slower flip-flop rates. We now plan to add cholesterol to the system at extremely low and high concentrations, which will eventually partition into the lipid (DPPC) vesicle. We will then calculate the free energy profile for cholesterol across the bilayer at each concentration and also comparing to the case of a flat membrane. In the Umbrella sampling 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. The umbrella sampling technique allows us to run many short simulations in parallel which are then combined through post-processing. 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. Our previous simulations on the Fusion cluster has shown a benchmark of 7ms/timestep on 512 cores. Using a time step of 10fs, we estimate that the proposed calculations require approximately 5 microseconds of simulation requiring a total of 495,000 core-hours. Current: undetermined amount Justification: Requested: 40000 A specific reason has been given: We are in the process of simulating lipid vesicles to compare the energetics of cholesterol movement in vesicles with 2 distinct lipid composition (POPC vs POPS). Small angle scattering experiments suggest that the energetics of the movement of cholesterol in POPS membranes has two regimes: one, nearly frozen, at low temperature and another at high temperature. In POPC, the energetics of the movement of cholesterol has an Arrhenius-type behavior and thus unvarying with temperature. We will be submitting soon after we obtain these results. 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 John Valdes 13 Mar '15

13 Mar '15

Thanks. Granted. John On Fri, Mar 13, 2015 at 04:44:13PM +0000, Bair, Raymond A. wrote: > This look OK to me, and the new 100K should run until Sept. 30. > > Ray > > On 3/12/15, 3:01 PM, "John Valdes" <valdes(a)anl.gov> wrote: > > >Atmos_Chem has used up all their time for the FY. This 100K would be > >for the remainder of the FY. Any objections? > > > >On Thu, Mar 12, 2015 at 09:31:01AM -0500, accounts(a)lcrc.anl.gov wrote: > >> > >> A change in allocation has been requested: > >> > >> Requester: raok (Rao Kotamarthi) > >> Project: Atmos_Chem > >[...] > >> Requested: 100000 > >> > >> A specific reason has been given: > >> We have just received funding to support the DOE EERE for a modeling > >>project that uses high resolution models at wind farm scale. We plan to > >>test WRF-MPS and WRF-LES for this project and port these models to Mira > >>/NERSC in the near future > >> > >> This needs to be approved and the final allocation amount decided upon. > >_______________________________________________ > >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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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by Bair, Raymond A. 13 Mar '15

13 Mar '15

This look OK to me, and the new 100K should run until Sept. 30. Ray On 3/12/15, 3:01 PM, "John Valdes" <valdes(a)anl.gov> wrote: >Atmos_Chem has used up all their time for the FY. This 100K would be >for the remainder of the FY. Any objections? > >On Thu, Mar 12, 2015 at 09:31:01AM -0500, accounts(a)lcrc.anl.gov wrote: >> >> A change in allocation has been requested: >> >> Requester: raok (Rao Kotamarthi) >> Project: Atmos_Chem >[...] >> Requested: 100000 >> >> A specific reason has been given: >> We have just received funding to support the DOE EERE for a modeling >>project that uses high resolution models at wind farm scale. We plan to >>test WRF-MPS and WRF-LES for this project and port these models to Mira >>/NERSC in the near future >> >> This needs to be approved and the final allocation amount decided upon. >_______________________________________________ >allocations-admins mailing list >allocations-admins(a)lcrc.anl.gov >https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by John Valdes 12 Mar '15

12 Mar '15

Allocation granted. John On Thu, Mar 12, 2015 at 08:12:13PM +0000, Aithal, Shashikant M. wrote: > This should be approved. > ________________________________________ > From: allocations-admins-bounces(a)lcrc.anl.gov [allocations-admins-bounces(a)lcrc.anl.gov] on behalf of John Valdes [valdes(a)anl.gov] > Sent: Thursday, March 12, 2015 2:53 PM > To: LCRC Allocations Admins > Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation Request > > Any objections to granting 100K for the remainder of the quarter? > > John > > On Mon, Mar 09, 2015 at 11:14:16AM -0500, accounts(a)lcrc.anl.gov wrote: > > > > A change in allocation has been requested: > > > > Requester: svegendla (Prasad Vegendla) > > Project: CFD-TPM > [...] > > Requested: 100000 > > > > A specific reason has been given: > > Nek5000 simulations for multiphase boiling flows in Boiling water Reactors (BWR) reactors.Need to be run couple of cases (~20) for Nek-2P validation. > > > > This needs to be approved and the final allocation amount decided upon.

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by John Valdes 12 Mar '15

12 Mar '15

Allocation granted. John On Thu, Mar 12, 2015 at 08:11:58PM +0000, Aithal, Shashikant M. wrote: > This can be approved (there were 2 requests for NE_RANS) only one needs to be approved. > ________________________________________ > From: allocations-admins-bounces(a)lcrc.anl.gov [allocations-admins-bounces(a)lcrc.anl.gov] on behalf of John Valdes [valdes(a)anl.gov] > Sent: Thursday, March 12, 2015 2:55 PM > To: LCRC Allocations Admins > Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation Request > > Here's the correct request, I assume. Any objections to another 100K > for the remainder of the quarter? > > John > > On Mon, Mar 09, 2015 at 11:15:13AM -0500, accounts(a)lcrc.anl.gov wrote: > > > > A change in allocation has been requested: > > > > Requester: svegendla (Prasad Vegendla) > > Project: NE_RANS > [...] > > Requested: 100000 > > > > A specific reason has been given: > > StarCCM+ simulations for Vehicle optimization program.Need to be run 10 cases, each case will take around 10000 cpu hours. > > > > This needs to be approved and the final allocation amount decided upon.

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by Aithal, Shashikant M. 12 Mar '15

12 Mar '15

Yes, this should be 100K (10 runs x 10K each). ________________________________________ From: allocations-admins-bounces(a)lcrc.anl.gov [allocations-admins-bounces(a)lcrc.anl.gov] on behalf of John Valdes [valdes(a)anl.gov] Sent: Thursday, March 12, 2015 2:51 PM To: LCRC Allocations Admins Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation Request I assume this request for 10K was a mistake since another followed for 100K which matches the math given in the reason. John On Mon, Mar 09, 2015 at 11:10:27AM -0500, accounts(a)lcrc.anl.gov wrote: > Hello, > > A change in allocation has been requested: > > Requester: svegendla (Prasad Vegendla) > Project: NE_RANS [...] > Requested: 10000 > > A specific reason has been given: > StarCCM+ simulations for Vehicle optimization program.Need to be run 10 cases, each case will take around 10000 cpu hours. > > This needs to be approved and the final allocation amount decided upon. > _______________________________________________ allocations-admins mailing list allocations-admins(a)lcrc.anl.gov https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by Aithal, Shashikant M. 12 Mar '15

12 Mar '15

This should be approved. ________________________________________ From: allocations-admins-bounces(a)lcrc.anl.gov [allocations-admins-bounces(a)lcrc.anl.gov] on behalf of John Valdes [valdes(a)anl.gov] Sent: Thursday, March 12, 2015 2:53 PM To: LCRC Allocations Admins Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation Request Any objections to granting 100K for the remainder of the quarter? John On Mon, Mar 09, 2015 at 11:14:16AM -0500, accounts(a)lcrc.anl.gov wrote: > > A change in allocation has been requested: > > Requester: svegendla (Prasad Vegendla) > Project: CFD-TPM [...] > Requested: 100000 > > A specific reason has been given: > Nek5000 simulations for multiphase boiling flows in Boiling water Reactors (BWR) reactors.Need to be run couple of cases (~20) for Nek-2P validation. > > This needs to be approved and the final allocation amount decided upon. _______________________________________________ allocations-admins mailing list allocations-admins(a)lcrc.anl.gov https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by Aithal, Shashikant M. 12 Mar '15

12 Mar '15

This can be approved (there were 2 requests for NE_RANS) only one needs to be approved. ________________________________________ From: allocations-admins-bounces(a)lcrc.anl.gov [allocations-admins-bounces(a)lcrc.anl.gov] on behalf of John Valdes [valdes(a)anl.gov] Sent: Thursday, March 12, 2015 2:55 PM To: LCRC Allocations Admins Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation Request Here's the correct request, I assume. Any objections to another 100K for the remainder of the quarter? John On Mon, Mar 09, 2015 at 11:15:13AM -0500, accounts(a)lcrc.anl.gov wrote: > > A change in allocation has been requested: > > Requester: svegendla (Prasad Vegendla) > Project: NE_RANS [...] > Requested: 100000 > > A specific reason has been given: > StarCCM+ simulations for Vehicle optimization program.Need to be run 10 cases, each case will take around 10000 cpu hours. > > This needs to be approved and the final allocation amount decided upon. _______________________________________________ allocations-admins mailing list allocations-admins(a)lcrc.anl.gov https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by John Valdes 12 Mar '15

12 Mar '15

Atmos_Chem has used up all their time for the FY. This 100K would be for the remainder of the FY. Any objections? On Thu, Mar 12, 2015 at 09:31:01AM -0500, accounts(a)lcrc.anl.gov wrote: > > A change in allocation has been requested: > > Requester: raok (Rao Kotamarthi) > Project: Atmos_Chem [...] > Requested: 100000 > > A specific reason has been given: > We have just received funding to support the DOE EERE for a modeling project that uses high resolution models at wind farm scale. We plan to test WRF-MPS and WRF-LES for this project and port these models to Mira /NERSC in the near future > > This needs to be approved and the final allocation amount decided upon.

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by John Valdes 12 Mar '15

12 Mar '15

Here's the correct request, I assume. Any objections to another 100K for the remainder of the quarter? John On Mon, Mar 09, 2015 at 11:15:13AM -0500, accounts(a)lcrc.anl.gov wrote: > > A change in allocation has been requested: > > Requester: svegendla (Prasad Vegendla) > Project: NE_RANS [...] > Requested: 100000 > > A specific reason has been given: > StarCCM+ simulations for Vehicle optimization program.Need to be run 10 cases, each case will take around 10000 cpu hours. > > This needs to be approved and the final allocation amount decided upon.

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