March 2017 - Allocations-admins - mailman3.cels.anl.gov

[LCRC Accounts] Project Request: Organics_DMFT
by accounts＠lcrc.anl.gov 31 Mar '17

31 Mar '17

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: Hyowon Park Applicant's institution: ANL Applicant's division: MSD Project Name: Organics_DMFT Project title: DFT and DMFT studies of strongly correlated organics Associated funding: Other Systems: Science: We will study the electronic structure and electron-phonon coupling of strongly correlated organic materials. Organic materials have very small bandwidth, therefore similar as oxides, some of organic materials such as k-organic salts show strongly correlated electronic behavior including Mott transitions, superconductivity, and charge ordering. The project will study the electronic properties of these materials using DFT+DMFT as functions of pressure and also molecular conformations. We will also compute the strength of electron-phonon couplings and study the effect of different phonon modes on the correlated electronic structure. Project description: For the calculation of correlated electronic properties of organic materials, we will use the DFT+DMFT method based on the plane-wave VASP code and DMFT code using continuous-time quantum Monte Carlo (CTQMC). Both VASP and CTQMC codes are parallelized, and scales linearly with the number of cpus. These codes are already complied in LCRC Blues machines and the PI has been using it for dmft_for_oxides project. For the electron-phonon coupling calculation, we will use the EPW code (http://epw.org.uk/) based on quantum-espresso code. Both EPW and quantum-espresso codes are freely available, therefore the PI will compile it or use it if they are already installed. The expected number of project member is only one PI. Industry partnership: Project URL: Requested allocation: 300000 Q1: 0 Q2: 100000 Q3: 100000 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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Re: [allocations-admins] SHARP-ARC - Project Allocation Request
by Bair, Raymond A. 30 Mar '17

30 Mar '17

Yiqi, When Bebop comes on line, likely in early June, we will invite PIs to revise their project requests. A lot more time will be available then. Would that help? Regards, Ray ----------------------------------------- Ray Bair Argonne National Laboratory On 3/30/17, 10:14 AM, "Yu, Yiqi" <yyu(a)anl.gov> wrote: Dear Ray, We are facing some unexpected model developing issues so that we able not able to touch these 150,000 more hours. But based on our estimation, we will be short of allocation even we get some new after April. 150,000 core hours can really be used in less than a week. Is that possible that we can save that 150,000 more hours for next quarter? Thank you Yiqi -----Original Message----- From: Bair, Raymond A. Sent: Thursday, February 23, 2017 11:11 AM To: Aithal, Shashikant M.; Yu, Yiqi Subject: Re: SHARP-ARC - Project Allocation Request Dear Yiqi, Note that your new second-half allocation will start April 1, providing more time for your project. Could you make do with 150,000 more hours now, to bridge the gap until April 1? Regards, Ray ----------------------------------------- Ray Bair Argonne National Laboratory On 2/23/17, 10:45 AM, "Aithal, Shashikant M." <aithal(a)cels.anl.gov> wrote: Thanks, Yiqi. We will try to make a decision soon. Shashi ________________________________________ From: Yu, Yiqi Sent: Thursday, February 23, 2017 10:42 AM To: Aithal, Shashikant M. Cc: Bair, Raymond A. Subject: RE: SHARP-ARC - Project Allocation Request Sure, As you know 1M elements for nek5000 case is common. So we assume we need to run the case with 1M element. It normal takes 100K core hours to converge. We need to run at least 5 of these case. We still need some time for debugging and for another code. So that's how 1M comes from. Of course, If the resource don't permit, we can try to simplify the case and use URANS instead of LES to save some time. Let me know if you need any other information. -----Original Message----- From: Aithal, Shashikant M. Sent: Thursday, February 23, 2017 10:34 AM To: Yu, Yiqi Cc: Bair, Raymond A. Subject: RE: SHARP-ARC - Project Allocation Request Thanks, Yiqi. It will be helpful if you could let us know the typical time it takes for a run and how many runs you need to finish - say if a run converges in 10 hours on 256 cores, that would be 2560 core-hours. If you have to run 10 such cases, you would need some 25-30K core-hours (assuming some runs take longer or diverge). We (the LCRC-core) can get an idea of how the allotted time is going to be used and approximately how much work can get done. Please provide us with this information (based on the runs you have already done) and we can make a quick decision as to how much time we can grant your project. Thanks, Shashi ________________________________________ From: Yu, Yiqi Sent: Thursday, February 23, 2017 10:21 AM To: Aithal, Shashikant M. Cc: Bair, Raymond A. Subject: RE: SHARP-ARC - Project Allocation Request Shashi, We are going to run some multi-physics simulation(Nek5000 and some neutronic code coupled ) with SAHRP. As you may know, we don't have choice to run these calculation on Mira and Cetus since we are not able to compile the SHARP package on these cluster (very complicated situation). The time for this project is negative now. We need to run some calculations till we can get the next round time till April 1st. Please grant us as much as you can and we will appreciate it very much. Best Yiqi -----Original Message----- From: Aithal, Shashikant M. Sent: Thursday, February 23, 2017 10:14 AM To: Yu, Yiqi Cc: Bair, Raymond A. Subject: SHARP-ARC - Project Allocation Request Yiqi: Can you give us some more information about the jobs you plan to run between now and end of March and how you computed the 1M core-hour request? As you know, our old 2500 core machine Fusion, has been "retired" to make room for the new machine. So there is almost a 30% extra load on Blues. Hence we (LCRC and the allocation committee) are unable to grant large core-hour requests at this time. We might be able to grant you about 80-100K core-hours from now to March end. You might also want to consider running some of the simulations on Mira or Theta since these machines are better suited for jobs requiring large core-hours. Please let me know if you have any other questions or concerns. Thanks, Shashi ________________________________________ From: allocations-admins-bounces(a)lcrc.anl.gov [allocations-admins-bounces(a)lcrc.anl.gov] on behalf of accounts(a)lcrc.anl.gov [accounts(a)lcrc.anl.gov] Sent: Wednesday, February 22, 2017 1:56 PM To: allocations-admins(a)lcrc.anl.gov Subject: [allocations-admins] [LCRC Accounts] Project Allocation Request Hello, A change in allocation has been requested: Requester: yyu (Yiqi Yu) Project: SHARP_ARC Title: Multi-physics Simulation of SFR Core Radial Expansion with SHARP Description: As the SHARP modeling and simulation toolkit is maturing, the focus is on customer-oriented applications and further validation exercises. This allocation will help with those applications, for performing small to moderate scale simulations and for scaling up to ALCF. The SHARP toolkit is regularly compiled on Blues using Intel or GNU compilers. The components of SHARP—the Nek5000 computational fluid dynamics code and the PROTEUS neutron transport code—have already been demonstrated to scale well not only on Blues but on Blue Gene/P. This project will be used by 4-5 analysts in the NE and MCS Divisions. Current: undetermined amount Justification: FY17 efforts for SHARP are highly focused on solving challenge problems for customers and code validation. FY16 efforts were focused on code development, as there was a major release, and so computational requirements were lower than usual. If the project is successful, we anticipate that FY17 and beyond will be highly resource intensive. The components of SHARP—the Nek5000 computational fluid dynamics code and the PROTEUS neutron transport code—have already been demonstrated to scale well not only on Fusion but on Blue Gene/P. Nek5000 has demonstrated > 80% parallel efficiency on BG/P (strong scaling) out to P=131,072 processors, using only 7300 points/processor at the largest scale. PROTEUS has demonstrated greater than 90% strong space-angle scaling at the 100,000 processer level and was nominated for the Gordon Bell Prize for its parallel performance. Requested: 1000000 A specific reason has been given: Used up all the time for now. have urgent job to finish before March 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: xtal
by Roberts, John E. 23 Mar '17

23 Mar '17

Time granted, just need to create the file set this week still. -- John Roberts Argonne National Laboratory CELS Systems jeroberts(a)anl.gov On 3/22/17, 1:08 PM, "allocations-admins-bounces(a)lcrc.anl.gov on behalf of Bair, Raymond A." <allocations-admins-bounces(a)lcrc.anl.gov on behalf of rbair(a)anl.gov> wrote: Thank you. The request is small, so I suggest that we approve it. Ray ----------------------------------------- Ray Bair Argonne National Laboratory and the University of Chicago On 3/22/17, 12:59 PM, "allocations-admins-bounces(a)lcrc.anl.gov on behalf of Low, John J." <allocations-admins-bounces(a)lcrc.anl.gov on behalf of jlow(a)mcs.anl.gov> wrote: Ray, It looks he is working in the “Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne National Laboratory, Argonne, Illinois 60439, United States” according to this journal article. http://pubs.acs.org/doi/abs/10.1021/acs.jmedchem.5b01128 John J. Low Principal Computational Science Specialist Computing, Environment and Life Sciences Building 240, 2143 9700 South Cass Avenue Argonne National Laboratory Argonne, IL 60439. 630-252-0045 www.linkedin.com/pub/john-low/15/8b0/5aa/ -----Original Message----- From: <allocations-admins-bounces(a)lcrc.anl.gov> on behalf of "Raymond A. Bair" <rbair(a)anl.gov> Reply-To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> Date: Wednesday, March 22, 2017 at 12:52 PM To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> Subject: Re: [allocations-admins] [LCRC Accounts] Project Request: xtal LCRC, I do not see Zhipu Luo in the Argonne directory. Does anyone know what his/her association is with Argonne? They could be an APS user, perhaps collaborating with someone here (though that would not be required). Ray ----------------------------------------- Ray Bair Argonne National Laboratory and the University of Chicago On 3/22/17, 12:09 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: Zhipu _______________________________________________ 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 _______________________________________________ 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 Request: PACC
by Roberts, John E. 23 Mar '17

23 Mar '17

Time granted, just need to create the file set this week still. -- John Roberts Argonne National Laboratory CELS Systems jeroberts(a)anl.gov On 3/21/17, 12:40 PM, "allocations-admins-bounces(a)lcrc.anl.gov on behalf of Bair, Raymond A." <allocations-admins-bounces(a)lcrc.anl.gov on behalf of rbair(a)anl.gov> wrote: What we could do here is to scale the 250K request (99%?), and enable use of the time between now and 6/30. Regards, Ray ----------------------------------------- Ray Bair Argonne National Laboratory and the University of Chicago On 3/20/17, 4:24 PM, "sjk" <sjk(a)anl.gov> wrote: You are correct. I didn’t realize that Q2 ends in 10 days. Lets just shift it to 250 K in Q3 and 250 K in Q4 and nothing in Q2. Thank you for pointing this out. On Mar 20, 2017, at 4:10 PM, Bair, Raymond A. <rbair(a)anl.gov> wrote: > Stephen, > > I want to make sure I understand your request. > > Q2 is Jan-Mar, Q3 is Apr-Jun, etc. > > You requested 99K to use in the next 10 days. Is that what is intended? > > Regards, > > Ray > > ----------------------------------------- > Ray Bair > Argonne National Laboratory > and the University of Chicago > > > On 3/20/17, 1:39 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 new project on the LCRC cluster has been requested. Please forward > the information on to the LCRC Allocation sub-committee. > > Applicant's name: Stephen Klippenstein > Applicant's institution: ANL > Applicant's division: CSE > Project Name: PACC > Project title: Predictive Automated Combustion Chemistry > Associated funding: DOE-ASCR > Other Systems: group owned linus cluster (48 nodes) > group owned nodes on blues (30 nodes) > I have access to about 1/5 of the CPU on these nodes > Science: To automatically generate high fidelity combustion mechanisms very high-level ab initio theoretical chemical kinetics. > Project description: The recent, largely DOE-supported, rise of theoretical gas phase chemical kinetics to a predictive science allows us to move beyond the empiricism (and concomitant limitations) of all prior mechanism development efforts. We are developing a fuel chemistry code that automatically generates high fidelity combustion mechanisms for user-selected fuels via large-scale, high-level, a priori theoretical chemical kinetics predictions. This code will exploit massively parallel computer architectures to simultaneously examine the hundreds or thousands of relevant chemical reactions, ushering in the wholistic development of mechanisms. Currently, mechanisms are generally validated against experimental data that often falls outside the range of end-use conditions and are developed sequentially one reaction at a time. The enhanced fidelity of a high level theory-derived mechanism, coupled with uncertainty driven improvement schemes, can directly access arbitrary > conditions with dramatically improved and rapidly constructed mechanisms for the end-use conditions. > > The procedure we are developing will involve the iterative application of mechanism generator routines (Reaction Mechanism Generator, RMG), an a priori theoretical kinetics routine (EStokTP), mechanism reduction routines (DRGASA) and chemical system solvers, and uncertainty quantification/global sensitivity analysis (UQ/GSA) software (Dakota). The initial step involves the generation of a reference set of reactions for the mechanism through an automated mechanism generator code (RMG). Currently in RMG, many, if not most, of the rates in this reference mechanism would be generated from crude rules based on analogies from limited data. We will replace these rough estimates with a priori theoretical kinetics predictions (EStokTP) employing a modest level of theoretical kinetics readily implemented for large numbers (1000s) of reactions. The EStokTP code will call various electronic structure codes such as GAUSSIAN, MOLPRO, and/or NWCHEM. With improved rates, RMG will be rerun to > generate a more reliable mechanism and associated theory-based estimates of the uncertainties in the predicted kinetics. The next iterations will selectively refine the mechanism by using GSA techniques under Dakota direction to shrink the uncertainties in mechanistic predictions (through further higher level theoretical evaluations) of key quantities (e.g., ignition delay, flame speeds, and speciation profiles) under arbitrary conditions. The Swift workflow software will be used to control all these codes. > > We with to use blues as the testbed for the initial stages of development of this code. We do not have information on the performance of the code as it is still being developed. However, most of the CPU will be spent on electronic structure calculations that use codes which are commonly used on blues already. Some parts of the code will be single core calculations, but that will likely be only on the order of a few% of the effort. There will be on the order of 10-20 project members. Mostly we will be running jobs that use ~10 to 20 nodes for a few hours at a time. > > > > Industry partnership: > Project URL: > Requested allocation: 499000 > Q1: 0 > Q2: 99000 > Q3: 200000 > Q4: 200000 > 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 > > _______________________________________________ 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 - HybridPerov
by Roberts, John E. 23 Mar '17

23 Mar '17

Time granted from today extending through Q3. -- John Roberts Argonne National Laboratory CELS Systems jeroberts(a)anl.gov From: <allocations-admins-bounces(a)lcrc.anl.gov> on behalf of "Bair, Raymond A." <rbair(a)anl.gov> Reply-To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> Date: Tuesday, March 21, 2017 at 1:32 PM To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation Request - HybridPerov Based on email below, the aim is to add 120K (less scaling) usable in Q2 and Q3. This seems reasonable. Ray ----------------------------------------- Ray Bair Argonne National Laboratory and the University of Chicago From: Ji-Sang Park <jspark(a)anl.gov> Date: Tuesday, March 21, 2017 at 1:16 PM To: Raymond Bair <rbair(a)anl.gov> Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation Request - HybridPerov Yes please. Thanks! Ji-Sang On Tue, Mar 21, 2017 at 12:51 PM Bair, Raymond A. <rbair(a)anl.gov<mailto:[email protected]>> wrote: Dear Ji-Sang Park, There are 10 days left in FY2017 Q2 (January-March). So, we want to focus on Q3. We could make your Q3 allocation usable immediately. OK? P.S. In August/September you will need to put in a new request for time in FY2018. Regards, Ray ----------------------------------------- Ray Bair LCRC Argonne National Laboratory and the University of Chicago On 3/21/17, 9:49 AM, "allocations-admins-bounces(a)lcrc.anl.gov<mailto:[email protected]> on behalf of accounts(a)lcrc.anl.gov<mailto:[email protected]>" <allocations-admins-bounces(a)lcrc.anl.gov<mailto:[email protected]> on behalf of accounts(a)lcrc.anl.gov<mailto:[email protected]>> wrote: Hello, A change in allocation has been requested: Requester: jipark (Ji-Sang Park) Project: HybridPerov Title: Computational investigation of optoelectronic properties of hybrid inorganic-organic perovskites Description: A detailed description of the project and its goals. Our aim is to understand the fundamental material properties and to develop a general method to enhance the solar conversion efficiency. Several physical properties need to be investigated. One of the most important properties is the band gap, according to Shockley and Queisser. Shockley and Queisser assumed that lights above the band gap energy are fully absorbed, however, thatâ€™s not the case in the reality: In this context, the absorption coefficient is a necessary fundamental property. To contribute to the solar cell research community, we will attempt to find a strategy to enhance the absorption coefficient of the materials. Computational methods. First-principles calculation based on density functional theory (DFT) is a computational modeling method used to investigate the electronic structure of many-body systems. Performing the DFT calculations, we are planning to investigate the fundamental physical properties of the hybrid perovskites including ferroelectricity, the electronic band gap, and the absorption coefficient. The absorption coefficient will be calculated by using the dielectric function as input. Software requirements. The VASP code is already installed on LCRC clusters, and we have license to run the code. Typical calculation size. 16 cores/node * 8 nodes * 24 hours of run time. Planned Calculations: 1) Investigation of 3d metal alloyed hybrid perovskites: Stability of metal impurities, optolectronic properties, 2) Basic physical properties of mixed anion like CH3NH3PbBrxCl3-x or CH3NH3PbIxCl3-x: the lattice constant and the electronic band gap 3) Effect of molecular orientation on the electronic properties and ferroelectricity Issue on number of k-points. We want to point out that finder k-points grids are needed to obtain smooth dielectric function as compared to total energy calculation. The calculation cost increases with second or third power of the number of k-points, thus more computational cost is required. Expected number of project members: Ji-Sang Park and Maria Chan. Current: undetermined amount Justification: N/A Requested: 120000 A specific reason has been given: Dear person in charge, I've used the computer time for Q1. Can I get another 120,000 hours? Note: Project name : HybridPerov Expected number of project members: Ji-Sang Park and Maria Chan. Requested allocation: 480000 for Q1: 120000 for Q2: 120000 for Q3: 120000 for Q4: 120000 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: xtal
by Bair, Raymond A. 22 Mar '17

22 Mar '17

Thank you. The request is small, so I suggest that we approve it. Ray ----------------------------------------- Ray Bair Argonne National Laboratory and the University of Chicago On 3/22/17, 12:59 PM, "allocations-admins-bounces(a)lcrc.anl.gov on behalf of Low, John J." <allocations-admins-bounces(a)lcrc.anl.gov on behalf of jlow(a)mcs.anl.gov> wrote: Ray, It looks he is working in the “Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne National Laboratory, Argonne, Illinois 60439, United States” according to this journal article. http://pubs.acs.org/doi/abs/10.1021/acs.jmedchem.5b01128 John J. Low Principal Computational Science Specialist Computing, Environment and Life Sciences Building 240, 2143 9700 South Cass Avenue Argonne National Laboratory Argonne, IL 60439. 630-252-0045 www.linkedin.com/pub/john-low/15/8b0/5aa/ -----Original Message----- From: <allocations-admins-bounces(a)lcrc.anl.gov> on behalf of "Raymond A. Bair" <rbair(a)anl.gov> Reply-To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> Date: Wednesday, March 22, 2017 at 12:52 PM To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> Subject: Re: [allocations-admins] [LCRC Accounts] Project Request: xtal LCRC, I do not see Zhipu Luo in the Argonne directory. Does anyone know what his/her association is with Argonne? They could be an APS user, perhaps collaborating with someone here (though that would not be required). Ray ----------------------------------------- Ray Bair Argonne National Laboratory and the University of Chicago On 3/22/17, 12:09 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: Zhipu _______________________________________________ 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 Request: xtal
by Low, John J. 22 Mar '17

22 Mar '17

I found him by searching for him on inside.anl.gov.<https://apps.inside.anl.gov/directory/results.php?q=luo&search_by=any%20fie…> I have attached a snapshot. John J. Low Principal Computational Science Specialist Computing, Environment and Life Sciences Building 240, 2143 9700 South Cass Avenue Argonne National Laboratory Argonne, IL 60439. 630-252-0045 www.linkedin.com/pub/john-low/15/8b0/5aa/ -----Original Message----- From: <allocations-admins-bounces(a)lcrc.anl.gov> on behalf of "Raymond A. Bair" <rbair(a)anl.gov> Reply-To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> Date: Wednesday, March 22, 2017 at 12:52 PM To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> Subject: Re: [allocations-admins] [LCRC Accounts] Project Request: xtal LCRC, I do not see Zhipu Luo in the Argonne directory. Does anyone know what his/her association is with Argonne? They could be an APS user, perhaps collaborating with someone here (though that would not be required). Ray ----------------------------------------- Ray Bair Argonne National Laboratory and the University of Chicago On 3/22/17, 12:09 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: Zhipu _______________________________________________ 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 Request: xtal
by Low, John J. 22 Mar '17

22 Mar '17

Ray, It looks he is working in the “Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne National Laboratory, Argonne, Illinois 60439, United States” according to this journal article. http://pubs.acs.org/doi/abs/10.1021/acs.jmedchem.5b01128 John J. Low Principal Computational Science Specialist Computing, Environment and Life Sciences Building 240, 2143 9700 South Cass Avenue Argonne National Laboratory Argonne, IL 60439. 630-252-0045 www.linkedin.com/pub/john-low/15/8b0/5aa/ -----Original Message----- From: <allocations-admins-bounces(a)lcrc.anl.gov> on behalf of "Raymond A. Bair" <rbair(a)anl.gov> Reply-To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> Date: Wednesday, March 22, 2017 at 12:52 PM To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> Subject: Re: [allocations-admins] [LCRC Accounts] Project Request: xtal LCRC, I do not see Zhipu Luo in the Argonne directory. Does anyone know what his/her association is with Argonne? They could be an APS user, perhaps collaborating with someone here (though that would not be required). Ray ----------------------------------------- Ray Bair Argonne National Laboratory and the University of Chicago On 3/22/17, 12:09 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: Zhipu _______________________________________________ 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 Request: xtal
by Bair, Raymond A. 22 Mar '17

22 Mar '17

LCRC, I do not see Zhipu Luo in the Argonne directory. Does anyone know what his/her association is with Argonne? They could be an APS user, perhaps collaborating with someone here (though that would not be required). Ray ----------------------------------------- Ray Bair Argonne National Laboratory and the University of Chicago On 3/22/17, 12:09 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: Zhipu

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[LCRC Accounts] Project Request: xtal
by accounts＠lcrc.anl.gov 22 Mar '17

22 Mar '17

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: Zhipu Luo Applicant's institution: ANL Applicant's division: ANL-NCI Project Name: xtal Project title: Weak SAD Data Phasing and Model Building Associated funding: Intramural Research Program of the National Cancer Institute Other Systems: NA Science: Because of the availability of large number of structures of macromolecules stored in the Protein Data Bank(PDB), the majority of X-ray crystal structures of proteins and nucleic acids are nowadays solved by the Molecular Replacement technique. However, the crystal structures containing molecules for which there is no sufciently similar atomic model available, have to be solved by the Single-wavelength Anomalous Diﬀraction (SAD) method. To solve the crystal structure of novel proteins with weak SAD signal and low resolution data, huge amount trails are need to be setup in order to find the correct solution. Then iterative model building will take several days to generate the primary reasonable 3D model on high configuration desktop. Using LCRC cluster will significantly reduce the time from getting diffraction data to solving the crystal structures. Project description: This project will use LCRC cluster to solve the crystal structures of several important disease related proteins with weak SAD signal and low resolution diffraction data collected at APS. Phenix and SHELX are the main softwares for phasing SAD data. Phenix, Arp/wARP, and Buccaneer will be used for model building. Phenix and CCP4 will be used for structure refinement. Coot and Pymol wil be used for visualizing the models and electron density map. For model building in Phenix, 100 jobs for 100 processors in each run and total 10 runs will yield a reasonable initial model. Industry partnership: NA Project URL: Requested allocation: 35200 Q1: 0 Q2: 3200 Q3: 16000 Q4: 16000 Justification: Storage requirements: 1TB 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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