March 2016 - Allocations-admins - mailman3.cels.anl.gov

[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 03 Mar '16

03 Mar '16

Hello, A change in allocation has been requested: Requester: albezanilla (Alejandro Lopez Bezanilla) Project: DopingP Title: Transport Properties Of Doped Phosphorene Nanoribbons Description: The project is progressing based on two types on calculations related to both electronic structure and transport properties of defected phosphorene structures. A large set of defected structures ranging from substitutional doping to vacancies are in progress. The code used for the first-principles calculations is SIESTA running in Blues. Multiples job running on one or two nodes for several days (non-stop) are submitted. The performance is good considering the large number of atoms in each super-cell. The transport calculations are submitted over 16 nodes in Blues for several hours each. More defects are being modelled currently and approximately 225k hours of computational time are estimated to complete the study. We expect to finish the study with the next 3 quarters. Current: undetermined amount Justification: Requested: 125000 A specific reason has been given: Numerous issues with Fusion made some long jobs to get stuck without producing any output. This consumed thousands of hours with unproductive result. If possible I would like to use additional time during the next month to complete some of the calculations already initiated, such as phonon spectra which are very time consuming. 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. 02 Mar '16

02 Mar '16

He has averaged 100K per month. Perhaps 150K is more appropriate here. Comments? Ray On 3/2/16, 5:14 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 change in allocation has been requested: > > Requester: miao (Yinbin Miao) > Project: MD_FeCr > Title: Molecular Dynamics Simulation of Radiation-induced >Microstructural Modifications in Fe-Cr Alloys > Description: In this proposed project, molecular dynamics simulation >will be used to investigate the microstructural modifications induced by >irradiation. LAMMPS code will be used to realize the MD simulation. >Multiple embedded atom method potentials will be used. The results will >be compared with the experimental post-irradiation examination (PIE) data >I or my group members collected or will collect in another DoE funded >project. LAMMPS is based on the fundamental Newton mechanics to predict >the behaviors of each atom in a system containing up to millions of >atoms. The positions and velocities of all the atoms along with their >interactions are captured by the code. A typical system contains one >million atoms and will be simulated up to 10 ns with a time step of 1 fs. >MPI was used to enhance the parallel efficiency for LAMMPS code. The same >code has been run on both LCRC clusters and the Taub cluster in >University of Illinois, for similar objectives in other classes of mate > rials. For the calculation, a typical run will need around 4 to 8 nodes >for approximately 24 hours. This project will only involve one user. > Current: undetermined amount >Justification: The code used in this project, LAMMPS, is a well-developed >and well-maintained MPI-based parallel code. The code is actively updated >and supported by Sandia National Lab. The code has been widely used by >the molecular simulation community. The efficiency has been widely tested >and accepted. Details can be found in the following link: >http://lammps.sandia.gov/bench.html. > > Requested: 200000 > >A specific reason has been given: >I only have ~40k hours left now, but my project need more time before the >end of this quarter. > >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 02 Mar '16

02 Mar '16

Hello, A change in allocation has been requested: Requester: miao (Yinbin Miao) Project: MD_FeCr Title: Molecular Dynamics Simulation of Radiation-induced Microstructural Modifications in Fe-Cr Alloys Description: In this proposed project, molecular dynamics simulation will be used to investigate the microstructural modifications induced by irradiation. LAMMPS code will be used to realize the MD simulation. Multiple embedded atom method potentials will be used. The results will be compared with the experimental post-irradiation examination (PIE) data I or my group members collected or will collect in another DoE funded project. LAMMPS is based on the fundamental Newton mechanics to predict the behaviors of each atom in a system containing up to millions of atoms. The positions and velocities of all the atoms along with their interactions are captured by the code. A typical system contains one million atoms and will be simulated up to 10 ns with a time step of 1 fs. MPI was used to enhance the parallel efficiency for LAMMPS code. The same code has been run on both LCRC clusters and the Taub cluster in University of Illinois, for similar objectives in other classes of mate rials. For the calculation, a typical run will need around 4 to 8 nodes for approximately 24 hours. This project will only involve one user. Current: undetermined amount Justification: The code used in this project, LAMMPS, is a well-developed and well-maintained MPI-based parallel code. The code is actively updated and supported by Sandia National Lab. The code has been widely used by the molecular simulation community. The efficiency has been widely tested and accepted. Details can be found in the following link: http://lammps.sandia.gov/bench.html. Requested: 200000 A specific reason has been given: I only have ~40k hours left now, but my project need more time before the end of this 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 Request: AARC1
by John Blaas 02 Mar '16

02 Mar '16

Project created and 100k granted. JB On Tue, Mar 1, 2016 at 1:28 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: hakim iddir > Applicant's institution: ANL > Applicant's division: MSD > Project Name: AARC1 > Project title: Modeling AARC 2016 > Associated funding: Work for Others > Other Systems: > Science: Materials are modeled at the atomic scale to characterize the structure of the starting material and their stability with cycling. We also identify and evaluate strategies for the design of high capacity, high energy-density cathode materials. > Project description: We perform first-principles density functional theory (DFT) at the GGA+U level. The U-ramping method as well as the more computationally expensive method based on the hybrid functional HSE06 as implemented in the VASP code, are employed. Ab-Initio Molecular Dynamics (AIMD) simulations will be performed to access activated states. Computational cells including up to four hundred atoms in the periodic unit are employed. This work is proprietary (confidential). > Industry partnership: This modeling work is performed to support a large experimental effort at the CSE within the AARC project. > > The requested allocations below are based on "Blues" performance. > The allocations should be doubled for "Fusion" > Project URL: > Requested allocation: 400000 > Q1: 0 > Q2: 100000 > Q3: 200000 > Q4: 100000 > Justification: > Storage requirements: > > > 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

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by John Blaas 02 Mar '16

02 Mar '16

2mil granted for remainder of Q2 JB On Wed, Mar 2, 2016 at 1:16 PM, accounts(a)lcrc.anl.gov <accounts(a)lcrc.anl.gov> wrote: > Hello, > > A change in allocation has been requested: > > Requester: borland (Michael Borland) > Project: ApsRenewalLattice > Title: Lattice Development and Beam Dynamics for APS Upgrade > Description: APS has developed a method of using multi-objective genetic algorithms (MOGA) for optimization of accelerator lattices. In past years, this method has been applied successfully using blues, fusion, intrepid, and a small APS > cluster to development and evaluation of lattices for the APS Upgrade. In the coming year, we will contniue working on a multi-bend achromat (MBA) lattice design that promises to push APS x-ray brightness to world-leading levels. Significant > progress has already been made developing a design that is consistent with engineering constraints. The design has been presented at external reviews related to the on-going upgrade project. > > Our approach is to create a series of lattices that gradually push performance up while simultaneously incorporating on-going constraints derived from on-going interactions with magnet and vacuum system designers. As such, the process is naturally iterative, and we have completed a series of iterations to date to conform to engineering limits. Further iterations are on-going, with interest in reducing cost also being relevant. In addition to MOGA, we must perform ensemble evaluation to assess the robustness of solutions, understand magnet quality requirements, and evaluate effects > of insertion devices on the newly-developed solutions. Finalization of the lattice design and preparation of the preliminary design report is anticipated in FY16. > > The codes being used for MOGA and ensemble evaluation have all been used in past years on fusion. These include Pelegant, a parallel accelerator simulation code used primarily for particle tracking and acceptance determination, as > well as a Tcl script used for genetic optimization. The simulations are close to embarrassingly parallel and thus scale very well. > > In addition to lattice development, we model the effects of the higher harmonic cavity (HHC), which plays a vital role in increasing the beam lifetime and reducing emittance blow-up. The simulations involve tracking beams consisting of 48 or more bunches of 100,000 or more particles each, and computing the collective electromagnetic interaction of these particles with the vacuum chamber and rf cavities. The methods are well advanced and will be employed with new lattices as they are generated. > > Beam loss analysis began in FY15 and will continue in FY16. This involves detailed and time-intensive simulation of the injection process and the Touschek scattering process. It also involves evaluation of beam loss collimation schemes, which are needed in order to protect accelerator components and reduce radiation outside the shielding wall. > > Current: undetermined amount > Justification: The primary code being used, ELEGANT, has run successfully on fusion, blues, intrepid, mira, and other systems. Most simulations are close to embarrassingly parallel, since they are of single-particle dynamics only. Simulations with collective effects show greater than 70% efficiency for 256 or more cores, depending on problem details. > > Requested: 2000000 > > A specific reason has been given: > Have used the previous allocation for high-demand APS-upgrade work. Continue to need significant resources due to schedule demands of the APS upgrade. Collective effects modeling in particular is proving very demanding. > > 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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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by John Blaas 02 Mar '16

02 Mar '16

Granted 40k JB On Wed, Mar 2, 2016 at 12:05 PM, accounts(a)lcrc.anl.gov <accounts(a)lcrc.anl.gov> wrote: > Hello, > > A change in allocation has been requested: > > Requester: poluektov (Oleg Poluektov) > Project: Solar_EPR > Title: Solar energy conversion in organic photovoltaics > Description: We are evaluating the effect of modifying the polymer portion of the BHJ solar cells to increase the delocalization of the positive polaron, which correlates with solar energy conversion efficiency. Prior work suggested delocalization ranged over multiple subunits; up to 60 Angstroms. However, due to our existing computational power we were not able to assess larger structures. Furthermore, test calculations indicated sensitivity to both conformation and external charges. The current work seeks to investigate a series of recently synthesized polymers and to include longer oligomers to test the limits of the delocalization. > > We intend to run a series of gas-phase model DFT optimizations to determine the low energy polymer conformations using standard ab initio optimization codes such as GAMESS, or NWCHEM. This will also allow us to generate a set of conformers likely to be present in the experimental samples. The resultant conformations will be used to calculate EPR parameters (g-tensors and hyperfine coupling constants) using Orca 3.0.3. Oligomers of varying length will be investigated to evaluate delocalization ranges and sensitivity of electronic structure parameters to oligomer length. The initial structure building, monomer and dimer test calculations, and analysis of spin densities will be carried out on our lab computers. > > The primary usage of fusion will be in the optimization, frequency calculation, and EPR parameter calculation steps of the work. The optimization subroutines of NWCHEM and GAMESS are highly parallelized. Orca 3.0.3 is a highly accurate program for calculating EPR parameters. It has recently been installed on fusion. Benchmarks on a small local workstation with Orca showed good scaling up to 16 processors for the EPR parameter subroutines. Test calculations performed on this small workstation for the largest oligomer we calculated so far took about 200 (small basis set) to 20,000 (large basis set) CPU hours (using PQS as the optimization engine) for optimization and frequency calculations. > > The existing allocation is being used to set-up and run optimizations using Density Functional Theory (B3LYP functional and 6-31G basis) using NWCHEM. Calculations for 3 oligomers with an average of six conformations each are in progress. Furthermore, calculations to support a paper on the role of physical deformation of the fullerenes and polymers in the thin film BHJ cells have been submitted. > > Test calculations on our local systems indicate that the amount of delocalization present is sensitive to the functional present (primarily related to the treatment of correlation effects). We thus anticipate the need to perform calculations with at least three additional functionals for the largest polymers. The EPR parameter calculation (g-tensor and hyperfine calculations) took 1200 CPU hours (using orca 3.0.3). Calculations for 8 new oligomers oligomers with an anticipated six potential conformations for each requiring 9,600 (CPU*oligomer*conformation=200*8*6) for the initial set of calculations, optimizations using alternate functionals and a medium basis set for the largest 3 oligomers will require 7200 cpu hours (400*3*6) and an additional 200,000 (20,000*10*1) CPU hours for the largest basis set calculation for the lowest energy conformation of each oligomer. The EPR parameter calculations will take 72,000 (1200*10*6) CPU hours. This totals to 288,000 CPU hours. Cons > idering that these numbers are for a system slightly smaller in size to those proposed here, 300,000 CPU hours seems to be a reasonable estimate. We did not divide the CPU hours equally as Dr. Mardis is a teaching faculty member and has less research time between October 1-December 31st than she does in the late spring and summer months. Also, the largest optimization/frequency calculations are expected to occur in the second and third quarters. > > We expect 3 project members (Mardis, Niklas, Poluektov). No non-parallel jobs will be run and all visualization and analysis will be done on local machines. > Current: undetermined amount > Justification: > > Requested: 40000 > > A specific reason has been given: > Our original allocation for the Solar_EPR project was small as we hadn't been able to show that we would effectively use the time. We now have a clearer understanding of the computational time and resources needed to succeed with our project. We are requesting additional time as we have used approximately more than half of our CPU in three months and, after a period of testing, we are now running multiple ORCA and NWCHEM calculations. Furthermore, our preliminary calculations revealed that we have a much larger number of energetically accessible conformations than we originally anticipated. Many of these calculations will require the bigmem queue on fusion in order to do the electron paramagnetic resonance (EPR) property calculations for the larger (n=3.5 and above) oligomers. Experimental data is now also available for additional oligomers that we would like to include in our study. > > > 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 02 Mar '16

02 Mar '16

Hello, A change in allocation has been requested: Requester: borland (Michael Borland) Project: ApsRenewalLattice Title: Lattice Development and Beam Dynamics for APS Upgrade Description: APS has developed a method of using multi-objective genetic algorithms (MOGA) for optimization of accelerator lattices. In past years, this method has been applied successfully using blues, fusion, intrepid, and a small APS cluster to development and evaluation of lattices for the APS Upgrade. In the coming year, we will contniue working on a multi-bend achromat (MBA) lattice design that promises to push APS x-ray brightness to world-leading levels. Significant progress has already been made developing a design that is consistent with engineering constraints. The design has been presented at external reviews related to the on-going upgrade project. Our approach is to create a series of lattices that gradually push performance up while simultaneously incorporating on-going constraints derived from on-going interactions with magnet and vacuum system designers. As such, the process is naturally iterative, and we have completed a series of iterations to date to conform to engineering limits. Further iterations are on-going, with interest in reducing cost also being relevant. In addition to MOGA, we must perform ensemble evaluation to assess the robustness of solutions, understand magnet quality requirements, and evaluate effects of insertion devices on the newly-developed solutions. Finalization of the lattice design and preparation of the preliminary design report is anticipated in FY16. The codes being used for MOGA and ensemble evaluation have all been used in past years on fusion. These include Pelegant, a parallel accelerator simulation code used primarily for particle tracking and acceptance determination, as well as a Tcl script used for genetic optimization. The simulations are close to embarrassingly parallel and thus scale very well. In addition to lattice development, we model the effects of the higher harmonic cavity (HHC), which plays a vital role in increasing the beam lifetime and reducing emittance blow-up. The simulations involve tracking beams consisting of 48 or more bunches of 100,000 or more particles each, and computing the collective electromagnetic interaction of these particles with the vacuum chamber and rf cavities. The methods are well advanced and will be employed with new lattices as they are generated. Beam loss analysis began in FY15 and will continue in FY16. This involves detailed and time-intensive simulation of the injection process and the Touschek scattering process. It also involves evaluation of beam loss collimation schemes, which are needed in order to protect accelerator components and reduce radiation outside the shielding wall. Current: undetermined amount Justification: The primary code being used, ELEGANT, has run successfully on fusion, blues, intrepid, mira, and other systems. Most simulations are close to embarrassingly parallel, since they are of single-particle dynamics only. Simulations with collective effects show greater than 70% efficiency for 256 or more cores, depending on problem details. Requested: 2000000 A specific reason has been given: Have used the previous allocation for high-demand APS-upgrade work. Continue to need significant resources due to schedule demands of the APS upgrade. Collective effects modeling in particular is proving very demanding. This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

1 0

[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 02 Mar '16

02 Mar '16

Hello, A change in allocation has been requested: Requester: poluektov (Oleg Poluektov) Project: Solar_EPR Title: Solar energy conversion in organic photovoltaics Description: We are evaluating the effect of modifying the polymer portion of the BHJ solar cells to increase the delocalization of the positive polaron, which correlates with solar energy conversion efficiency. Prior work suggested delocalization ranged over multiple subunits; up to 60 Angstroms. However, due to our existing computational power we were not able to assess larger structures. Furthermore, test calculations indicated sensitivity to both conformation and external charges. The current work seeks to investigate a series of recently synthesized polymers and to include longer oligomers to test the limits of the delocalization. We intend to run a series of gas-phase model DFT optimizations to determine the low energy polymer conformations using standard ab initio optimization codes such as GAMESS, or NWCHEM. This will also allow us to generate a set of conformers likely to be present in the experimental samples. The resultant conformations will be used to calculate EPR parameters (g-tensors and hyperfine coupling constants) using Orca 3.0.3. Oligomers of varying length will be investigated to evaluate delocalization ranges and sensitivity of electronic structure parameters to oligomer length. The initial structure building, monomer and dimer test calculations, and analysis of spin densities will be carried out on our lab computers. The primary usage of fusion will be in the optimization, frequency calculation, and EPR parameter calculation steps of the work. The optimization subroutines of NWCHEM and GAMESS are highly parallelized. Orca 3.0.3 is a highly accurate program for calculating EPR parameters. It has recently been installed on fusion. Benchmarks on a small local workstation with Orca showed good scaling up to 16 processors for the EPR parameter subroutines. Test calculations performed on this small workstation for the largest oligomer we calculated so far took about 200 (small basis set) to 20,000 (large basis set) CPU hours (using PQS as the optimization engine) for optimization and frequency calculations. The existing allocation is being used to set-up and run optimizations using Density Functional Theory (B3LYP functional and 6-31G basis) using NWCHEM. Calculations for 3 oligomers with an average of six conformations each are in progress. Furthermore, calculations to support a paper on the role of physical deformation of the fullerenes and polymers in the thin film BHJ cells have been submitted. Test calculations on our local systems indicate that the amount of delocalization present is sensitive to the functional present (primarily related to the treatment of correlation effects). We thus anticipate the need to perform calculations with at least three additional functionals for the largest polymers. The EPR parameter calculation (g-tensor and hyperfine calculations) took 1200 CPU hours (using orca 3.0.3). Calculations for 8 new oligomers oligomers with an anticipated six potential conformations for each requiring 9,600 (CPU*oligomer*conformation=200*8*6) for the initial set of calculations, optimizations using alternate functionals and a medium basis set for the largest 3 oligomers will require 7200 cpu hours (400*3*6) and an additional 200,000 (20,000*10*1) CPU hours for the largest basis set calculation for the lowest energy conformation of each oligomer. The EPR parameter calculations will take 72,000 (1200*10*6) CPU hours. This totals to 288,000 CPU hours. Cons idering that these numbers are for a system slightly smaller in size to those proposed here, 300,000 CPU hours seems to be a reasonable estimate. We did not divide the CPU hours equally as Dr. Mardis is a teaching faculty member and has less research time between October 1-December 31st than she does in the late spring and summer months. Also, the largest optimization/frequency calculations are expected to occur in the second and third quarters. We expect 3 project members (Mardis, Niklas, Poluektov). No non-parallel jobs will be run and all visualization and analysis will be done on local machines. Current: undetermined amount Justification: Requested: 40000 A specific reason has been given: Our original allocation for the Solar_EPR project was small as we hadn't been able to show that we would effectively use the time. We now have a clearer understanding of the computational time and resources needed to succeed with our project. We are requesting additional time as we have used approximately more than half of our CPU in three months and, after a period of testing, we are now running multiple ORCA and NWCHEM calculations. Furthermore, our preliminary calculations revealed that we have a much larger number of energetically accessible conformations than we originally anticipated. Many of these calculations will require the bigmem queue on fusion in order to do the electron paramagnetic resonance (EPR) property calculations for the larger (n=3.5 and above) oligomers. Experimental data is now also available for additional oligomers that we would like to include in our study. This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

1 0

[LCRC Accounts] Project Request: AARC1
by accounts＠lcrc.anl.gov 01 Mar '16

01 Mar '16

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: hakim iddir Applicant's institution: ANL Applicant's division: MSD Project Name: AARC1 Project title: Modeling AARC 2016 Associated funding: Work for Others Other Systems: Science: Materials are modeled at the atomic scale to characterize the structure of the starting material and their stability with cycling. We also identify and evaluate strategies for the design of high capacity, high energy-density cathode materials. Project description: We perform first-principles density functional theory (DFT) at the GGA+U level. The U-ramping method as well as the more computationally expensive method based on the hybrid functional HSE06 as implemented in the VASP code, are employed. Ab-Initio Molecular Dynamics (AIMD) simulations will be performed to access activated states. Computational cells including up to four hundred atoms in the periodic unit are employed. This work is proprietary (confidential). Industry partnership: This modeling work is performed to support a large experimental effort at the CSE within the AARC project. The requested allocations below are based on "Blues" performance. The allocations should be doubled for "Fusion" Project URL: Requested allocation: 400000 Q1: 0 Q2: 100000 Q3: 200000 Q4: 100000 Justification: Storage requirements: 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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