May 2012 - Allocations-admins - mailman3.cels.anl.gov

Re: [allocations-admins] [LCRC Accounts] Project Request: 1atomCat
by John Valdes 22 May '12

22 May '12

On Mon, May 21, 2012 at 07:39:00PM -0500, Bair, Raymond A. wrote: > 40K now and then the rest from the q4 committee meeting seems reasonable. > > John Low -- can you help with the categories, etc.? I would say P:MatSci (Physical Science:Material Science), priority 3, Larry Curtiss as Point of Contact; sound OK? John > On 5/21/12 3:59 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: Ujjal Das > > Applicant's institution: ANL > > Applicant's division: MSD > > Project Name: 1atomCat > > Project title: Supported Single-atom Catalysts for Activation of > > Small Molecules, including Alkanes > > Associated funding: BES Chemical Sciences > > Other Systems: NA > > Science: Supported single-atom catalysts show exceptionally > > high catalytic activity compared to metal surfaces and sub-nanometer metal > > clusters. This high activity is attributed to large surface area of an > > isolated atom as well as its low coordination number. Standard techniques > > have been devised to prepare thermally stable single-atom catalysts using > > atomic layer deposition (ALD). In brief, supported single-atom catalysts show > > potential to activate very difficult bonds, including the ones in alkanes, > > with very high turn-over frequency. However, very little is known about > > background working principle of such single-atom catalysts. For example, how > > the nature of bonding of the single-atom affects its catalytic activity, how > > local charge density varies for different single-atom types, the role of a > > support, and an atomic level understanding of the mechanism of activation of > > small molecules. All these information are useful to control the activity and > > selectivi > > ty of the catalyst as well as to establish a structure-function relationship > > to understand the way such catalysts work. We plan to obtain all these > > information using high-level quantum chemical calculations. > > Project description: We will perform density functional theory (DFT) > > calculations to determine structure, bonding, and reaction energies of the > > system. Periodic boundary condition (PBC) will be imposed in order to maintain > > periodicity of the solid support. B3LYP hybrid functionals will be used in > > general, however, we may also switch to gradient corrected density functionals > > (GGA), where, B3LYP is either very expensive or not applicable. The Nudged > > Elastic Band (NEB) method of Henkelman and coworkers will be used to calculate > > transition states and activation barriers. Surface phonons will be calculated > > for accurate estimation of reaction free energies. Bader charge analysis and > > NBO population analysis will be performed to obtain information about local > > charge density and orbital electron density of the single-atom catalyst. > > > > We will primarily use the DFT code implemented in Vienna Ab-initio Simulation > > Package (VASP-version 5 or later). We will also use Gaussian-09 program to run > > calculations using small clusters. The NBO program for population analysis > > comes with Gaussian by default. Bader charge analysis will be done using the > > principles of atoms-in-molecules (AIM2000). Phonon analysis will be performed > > using "PHONON" program which is free and can be installed locally. > > > > Both VASP and Gaussian run in parallel. MPI version of VASP and Linda version > > of Gaussian will be used. For VASP-MPI calculations, increased efficiency is > > observed up to 32 processors, whereas, Gaussian-Linda version scales up to 64 > > processors. Rest of the programs only run in serials. > > > > Energy optimization in VASP takes approximately 750 CPU hours and we plan > > roughly 100 of such calculations. Hessian (second order energy derivative) > > evaluation takes roughly 1500 CPU hours and we plan to run 30 of these > > calculations. Optimization and Hessian evaluation using Gaussian take > > approximately same time for model clusters. We estimate to run a total of 100 > > calculations, each taking 400 CPU hours. > > > > The resources will be used primarily by Dr. Ujjal Das and the PI of the > > project is Dr. Larry Curtiss (curtiss(a)anl.gov) We will notify if new member > > joins this project or when additional resources are required. > > > > Total Request: 160,000 core hours in the remainder of the FY (till Sept 30) > > > > Project URL: > > Requested allocation: 160000 > > Q1: 0 > > Q2: 0 > > Q3: 40000 > > Q4: 120000 > > 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

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by John Valdes 21 May '12

21 May '12

Added. On Mon, May 21, 2012 at 07:37:29PM -0500, Bair, Raymond A. wrote: > Lets add 20k since they are 5k in the hole > > Ray > > > On 5/21/12 6:07 PM, "accounts(a)lcrc.anl.gov" <accounts(a)lcrc.anl.gov> wrote: > > > Hello, > > > > A change in allocation has been requested: > > > > Requester: felker (Kyle Gerard Felker) > > Project: cspp51087 > > Title: CSPP51087- High Performance Computing Class > > Description: The hours for this project will be shared by roughly 15 > > students of Dr. Andrew Siegel's Computer Science Professional Program "High > > Performance Computing" class at the University of Chicago. These masters-track > > students will explore various MPI communication models. Bi-weekly assignments > > over a 10 week period will have the students develop small parallel codes on > > their personal machines and then deploy their projects on the Fusion cluster > > to examine the scalability from 1-500 cores. > > > > The computational models will be simple "embarrassingly parallel" problems. In > > past years, simulations performed include a 2D heat diffusion modeler, a > > domain decomposed particle tracker, a Mandelbrot set generator, and > > applications of PETSc. > > > > The disk I/O requirements of this program are minimal. The students will only > > use disk storage for their code's performance data. > > > > The students, who all have extensive coding experience, will be under the > > instruction of Prof. Siegel (MCS/NE) and the TA Kyle Gerard Felker (MCS). > > Current: undetermined amount > > Justification: > > > > Requested: 15000 > > > > A specific reason has been given: > > The CSPP51087 High Performance Computing class has one final assignment > > involving hybrid MPI-OpenMP programming. The node requirements of this final > > assignment will be minimal. The disk requirements are nonexistent, as the > > assignment will consist solely of performance testing. > > > > > > The overuse of the core hours of the previous allocation was largely due to a > > single student. He has since been informed of his error. > > > > 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)lists.lcrc.anl.gov > > https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins > > > ----------------------------------------- > Ray Bair > Computing, Environment, and Life Sciences > Argonne National Laboratory > and the University of Chicago > Building 240, Room 4126 > 9700 South Cass Avenue > Argonne, IL 60439 > email: rbair(at)anl.gov > Phone: (630)252-5751 > > > _______________________________________________ > allocations-admins mailing list > allocations-admins(a)lists.lcrc.anl.gov > https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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Re: [allocations-admins] [LCRC Accounts] Project Request: 1atomCat
by Bair, Raymond A. 21 May '12

21 May '12

40K now and then the rest from the q4 committee meeting seems reasonable. John Low -- can you help with the categories, etc.? Ray On 5/21/12 3:59 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: Ujjal Das > Applicant's institution: ANL > Applicant's division: MSD > Project Name: 1atomCat > Project title: Supported Single-atom Catalysts for Activation of > Small Molecules, including Alkanes > Associated funding: BES Chemical Sciences > Other Systems: NA > Science: Supported single-atom catalysts show exceptionally > high catalytic activity compared to metal surfaces and sub-nanometer metal > clusters. This high activity is attributed to large surface area of an > isolated atom as well as its low coordination number. Standard techniques > have been devised to prepare thermally stable single-atom catalysts using > atomic layer deposition (ALD). In brief, supported single-atom catalysts show > potential to activate very difficult bonds, including the ones in alkanes, > with very high turn-over frequency. However, very little is known about > background working principle of such single-atom catalysts. For example, how > the nature of bonding of the single-atom affects its catalytic activity, how > local charge density varies for different single-atom types, the role of a > support, and an atomic level understanding of the mechanism of activation of > small molecules. All these information are useful to control the activity and > selectivi > ty of the catalyst as well as to establish a structure-function relationship > to understand the way such catalysts work. We plan to obtain all these > information using high-level quantum chemical calculations. > Project description: We will perform density functional theory (DFT) > calculations to determine structure, bonding, and reaction energies of the > system. Periodic boundary condition (PBC) will be imposed in order to maintain > periodicity of the solid support. B3LYP hybrid functionals will be used in > general, however, we may also switch to gradient corrected density functionals > (GGA), where, B3LYP is either very expensive or not applicable. The Nudged > Elastic Band (NEB) method of Henkelman and coworkers will be used to calculate > transition states and activation barriers. Surface phonons will be calculated > for accurate estimation of reaction free energies. Bader charge analysis and > NBO population analysis will be performed to obtain information about local > charge density and orbital electron density of the single-atom catalyst. > > We will primarily use the DFT code implemented in Vienna Ab-initio Simulation > Package (VASP-version 5 or later). We will also use Gaussian-09 program to run > calculations using small clusters. The NBO program for population analysis > comes with Gaussian by default. Bader charge analysis will be done using the > principles of atoms-in-molecules (AIM2000). Phonon analysis will be performed > using "PHONON" program which is free and can be installed locally. > > Both VASP and Gaussian run in parallel. MPI version of VASP and Linda version > of Gaussian will be used. For VASP-MPI calculations, increased efficiency is > observed up to 32 processors, whereas, Gaussian-Linda version scales up to 64 > processors. Rest of the programs only run in serials. > > Energy optimization in VASP takes approximately 750 CPU hours and we plan > roughly 100 of such calculations. Hessian (second order energy derivative) > evaluation takes roughly 1500 CPU hours and we plan to run 30 of these > calculations. Optimization and Hessian evaluation using Gaussian take > approximately same time for model clusters. We estimate to run a total of 100 > calculations, each taking 400 CPU hours. > > The resources will be used primarily by Dr. Ujjal Das and the PI of the > project is Dr. Larry Curtiss (curtiss(a)anl.gov) We will notify if new member > joins this project or when additional resources are required. > > Total Request: 160,000 core hours in the remainder of the FY (till Sept 30) > > Project URL: > Requested allocation: 160000 > Q1: 0 > Q2: 0 > Q3: 40000 > Q4: 120000 > 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 > _______________________________________________ > allocations-admins mailing list > allocations-admins(a)lists.lcrc.anl.gov > https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins ----------------------------------------- Ray Bair Computing, Environment, and Life Sciences Argonne National Laboratory and the University of Chicago Building 240, Room 4126 9700 South Cass Avenue Argonne, IL 60439 email: rbair(at)anl.gov Phone: (630)252-5751

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by Bair, Raymond A. 21 May '12

21 May '12

Lets add 20k since they are 5k in the hole Ray On 5/21/12 6:07 PM, "accounts(a)lcrc.anl.gov" <accounts(a)lcrc.anl.gov> wrote: > Hello, > > A change in allocation has been requested: > > Requester: felker (Kyle Gerard Felker) > Project: cspp51087 > Title: CSPP51087- High Performance Computing Class > Description: The hours for this project will be shared by roughly 15 > students of Dr. Andrew Siegel's Computer Science Professional Program "High > Performance Computing" class at the University of Chicago. These masters-track > students will explore various MPI communication models. Bi-weekly assignments > over a 10 week period will have the students develop small parallel codes on > their personal machines and then deploy their projects on the Fusion cluster > to examine the scalability from 1-500 cores. > > The computational models will be simple "embarrassingly parallel" problems. In > past years, simulations performed include a 2D heat diffusion modeler, a > domain decomposed particle tracker, a Mandelbrot set generator, and > applications of PETSc. > > The disk I/O requirements of this program are minimal. The students will only > use disk storage for their code's performance data. > > The students, who all have extensive coding experience, will be under the > instruction of Prof. Siegel (MCS/NE) and the TA Kyle Gerard Felker (MCS). > Current: undetermined amount > Justification: > > Requested: 15000 > > A specific reason has been given: > The CSPP51087 High Performance Computing class has one final assignment > involving hybrid MPI-OpenMP programming. The node requirements of this final > assignment will be minimal. The disk requirements are nonexistent, as the > assignment will consist solely of performance testing. > > > The overuse of the core hours of the previous allocation was largely due to a > single student. He has since been informed of his error. > > 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)lists.lcrc.anl.gov > https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins ----------------------------------------- Ray Bair Computing, Environment, and Life Sciences Argonne National Laboratory and the University of Chicago Building 240, Room 4126 9700 South Cass Avenue Argonne, IL 60439 email: rbair(at)anl.gov Phone: (630)252-5751

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[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 21 May '12

21 May '12

Hello, A change in allocation has been requested: Requester: felker (Kyle Gerard Felker) Project: cspp51087 Title: CSPP51087- High Performance Computing Class Description: The hours for this project will be shared by roughly 15 students of Dr. Andrew Siegel's Computer Science Professional Program "High Performance Computing" class at the University of Chicago. These masters-track students will explore various MPI communication models. Bi-weekly assignments over a 10 week period will have the students develop small parallel codes on their personal machines and then deploy their projects on the Fusion cluster to examine the scalability from 1-500 cores. The computational models will be simple "embarrassingly parallel" problems. In past years, simulations performed include a 2D heat diffusion modeler, a domain decomposed particle tracker, a Mandelbrot set generator, and applications of PETSc. The disk I/O requirements of this program are minimal. The students will only use disk storage for their code's performance data. The students, who all have extensive coding experience, will be under the instruction of Prof. Siegel (MCS/NE) and the TA Kyle Gerard Felker (MCS). Current: undetermined amount Justification: Requested: 15000 A specific reason has been given: The CSPP51087 High Performance Computing class has one final assignment involving hybrid MPI-OpenMP programming. The node requirements of this final assignment will be minimal. The disk requirements are nonexistent, as the assignment will consist solely of performance testing. The overuse of the core hours of the previous allocation was largely due to a single student. He has since been informed of his error. 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 Request: 1atomCat
by accounts＠lcrc.anl.gov 21 May '12

21 May '12

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: Ujjal Das Applicant's institution: ANL Applicant's division: MSD Project Name: 1atomCat Project title: Supported Single-atom Catalysts for Activation of Small Molecules, including Alkanes Associated funding: BES Chemical Sciences Other Systems: NA Science: Supported single-atom catalysts show exceptionally high catalytic activity compared to metal surfaces and sub-nanometer metal clusters. This high activity is attributed to large surface area of an isolated atom as well as its low coordination number. Standard techniques have been devised to prepare thermally stable single-atom catalysts using atomic layer deposition (ALD). In brief, supported single-atom catalysts show potential to activate very difficult bonds, including the ones in alkanes, with very high turn-over frequency. However, very little is known about background working principle of such single-atom catalysts. For example, how the nature of bonding of the single-atom affects its catalytic activity, how local charge density varies for different single-atom types, the role of a support, and an atomic level understanding of the mechanism of activation of small molecules. All these information are useful to control the activity and selectivi ty of the catalyst as well as to establish a structure-function relationship to understand the way such catalysts work. We plan to obtain all these information using high-level quantum chemical calculations. Project description: We will perform density functional theory (DFT) calculations to determine structure, bonding, and reaction energies of the system. Periodic boundary condition (PBC) will be imposed in order to maintain periodicity of the solid support. B3LYP hybrid functionals will be used in general, however, we may also switch to gradient corrected density functionals (GGA), where, B3LYP is either very expensive or not applicable. The Nudged Elastic Band (NEB) method of Henkelman and coworkers will be used to calculate transition states and activation barriers. Surface phonons will be calculated for accurate estimation of reaction free energies. Bader charge analysis and NBO population analysis will be performed to obtain information about local charge density and orbital electron density of the single-atom catalyst. We will primarily use the DFT code implemented in Vienna Ab-initio Simulation Package (VASP-version 5 or later). We will also use Gaussian-09 program to run calculations using small clusters. The NBO program for population analysis comes with Gaussian by default. Bader charge analysis will be done using the principles of atoms-in-molecules (AIM2000). Phonon analysis will be performed using "PHONON" program which is free and can be installed locally. Both VASP and Gaussian run in parallel. MPI version of VASP and Linda version of Gaussian will be used. For VASP-MPI calculations, increased efficiency is observed up to 32 processors, whereas, Gaussian-Linda version scales up to 64 processors. Rest of the programs only run in serials. Energy optimization in VASP takes approximately 750 CPU hours and we plan roughly 100 of such calculations. Hessian (second order energy derivative) evaluation takes roughly 1500 CPU hours and we plan to run 30 of these calculations. Optimization and Hessian evaluation using Gaussian take approximately same time for model clusters. We estimate to run a total of 100 calculations, each taking 400 CPU hours. The resources will be used primarily by Dr. Ujjal Das and the PI of the project is Dr. Larry Curtiss (curtiss(a)anl.gov) We will notify if new member joins this project or when additional resources are required. Total Request: 160,000 core hours in the remainder of the FY (till Sept 30) Project URL: Requested allocation: 160000 Q1: 0 Q2: 0 Q3: 40000 Q4: 120000 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

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by John Valdes 03 May '12

03 May '12

OK to grant 145K for 3rd quarter (as agreed in core meeting today). On Wed, May 02, 2012 at 02:47:09PM -0500, accounts(a)lcrc.anl.gov wrote: > Hello, > > A change in allocation has been requested: > > Requester: iddir (hakim iddir) > Project: MBM > Title: Modeling Battery Materials (MBM) [...] > Requested: 145000

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[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 02 May '12

02 May '12

Hello, A change in allocation has been requested: Requester: iddir (hakim iddir) Project: MBM Title: Modeling Battery Materials (MBM) Description: We propose to investigate the above mentioned properties (SEI formation, structure, Li transport, and reactions at the interface) on model systems using density functional theory (DFT) as implemented in the Vienna Ab Initio Simulation Package (VASP) currently available on FUSION. We have successfully investigated the growth of Li2CO3 films on graphite surfaces, as well as the diffusion of Li in Li2CO3 bulk material (TIES project). We have started to investigate the interaction of solvent molecules (EC) with both edge and basal planes of graphite, as well as Cu and Au model surfaces. During this next period we would like to continue the study of the interaction of solvent molecules with different surfaces, a work that will contribute to better understand the SEI formation and properties. This specific part of the project will be conducted in close collaboration with the group from UIUC using the Sum Generation Frequency (SFG) technique. We will particularly inve stigate the difference in interaction and diffusion properties between Li/Li+ and different graphite and graphene surfaces with several defect configurations (single, double and triple-vacancies and Stone-Wales type defect) and different types of CNT’s (semiconductor and metallic). Similar studies will be performed on Al2O3/graphite interfaces. In this case, separate MD studies will provide us with the starting structures of the interfaces that will be further optimized using VASP. This part of the project, originally proposed in TIES (2010) was not accomplished and will be proposed within this program. A total amount of 800000 hours would be necessary to complete the proposed work. Current: undetermined amount Justification: The study of solvent molecules interaction with surfaces with frequency calculations will require the investigation of about 20 different configurations per solvent molecule and surface models. For each couple solvent/surface system about 50000 hours would be needed, we anticipate the investigation of at least four types of solvent molecules (EC, VC, VEC, and PC) and four different surfaces (Cu(111), Au(111) and two graphite surfaces) hence about 200000 core hours would be necessary to complete this part of the project. Li and Li+ diffusion calculations through one defect type of graphene will require about 80000 core hours. The diffusion calculations for different defects and surfaces (graphene, graphite (top and inner layers, CNT’s and Al2O3) would require about 600000 hours. A total of 800000 core hours would be needed to perform these calculations. Requested: 145000 A specific reason has been given: The studies involving Li and Li+ diffusion calculations through a di-vacancy and SW defect type on graphene, turned out to be more complicated than anticipated, as we find that the physics involved during the diffusion of Li through the defect is highly sensitive to the supercell size and configurations. I have already started to investigate the system size effect on the electronic structure of these defect structures, by increasing the cells to 162 and 240 atoms respectively. This work will require about 145000 core hours for the current quarter and 150000 for the 4th quarter. 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 02 May '12

02 May '12

On Wed, May 02, 2012 at 08:28:14AM -0500, Shashi Aithal wrote: > > It was supposed to be 200K for the 3rd and 4th quarter. So 100K for now would be fine. It would get Justin going. OK; this project has been granted 100K now. John

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by Shashi Aithal 02 May '12

02 May '12

John: It was supposed to be 200K for the 3rd and 4th quarter. So 100K for now would be fine. It would get Justin going. Thanks, Shashi ----- Original Message ----- From: "John Valdes" <valdes(a)mcs.anl.gov> To: "LCRC Allocations Admins" <allocations-admins(a)lists.lcrc.anl.gov> Sent: Tuesday, May 1, 2012 9:19:00 PM Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation Request Yea or Nay on this? Shashi, you asked for 200K; is that 100K per quarter (3rd and 4th) or some other breakdown, or 200K for just this quarter? Since our approval limit is ~150K, we could give 100K now and defer the other 100K 'til the June Alloc Meeting, depending on the breakdown desired. John On Sat, Apr 28, 2012 at 03:53:41PM -0500, accounts(a)lcrc.anl.gov wrote: > Hello, > > A change in allocation has been requested: > > Requester: aithal (Shashi Aithal) > Project: Nek5000 [...] > Requested: 200000 > > A specific reason has been given: > The extra time is required to test various mesh and parameter configurations for an LES calculation of the turbulent flow around a nuclear fuel rod at Reynolds number of 65,000. This calculation is important for the correct calculation of a problem with 37 pins in a hexagonal bundle, which will be performed on BG/P. > > The allocation request is for 200k cpu hours. Each calculation can run on as few as 64 cores, with each run lasting about 100 hours. About 30 such runs may be needed; however, fewer is definitely possible. > > > 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)lists.lcrc.anl.gov https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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