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

Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by Low, John J. 13 Nov '15

13 Nov '15

Ray, It is unfortunate that this project exhausted their 6 month allocation in six weeks. Are they expecting to continue at the same pace? This contributed to blues being overallocated in October and the first week of November. I agree with your suggestion on the allocation of more time. Hopefully that will be enough for his publication. 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 "Bair, Raymond A." <rbair(a)anl.gov> Reply-To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> Date: Friday, November 13, 2015 at 9:09 AM To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation Request >Looking at the history of this project it seems reasonable to provide the >200K requested. I suggest making 70K a first quarter addition and 130K a >1st half addition. > >Regards, > >Ray > >----------------------------------------- >Ray Bair >Computing, Environment, and Life Sciences >Argonne National Laboratory > and the University of Chicago >TCS Building 240, Room 4122 >9700 South Cass Avenue >Argonne, IL 60439 >email: rbair(at)anl.gov >Phone: (630)252-5751 > > > > > >On 11/12/15, 2:12 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: qiaobf (Baofu Qiao) >> Project: DMDOHEMA_1 >> Title: Metal Ion Transport through Nano-Structured Lipophilic >>Systems: Atomistic MD Simulations >> Description: In the last few months, we have performed some preliminary >>simulation runs in understanding the supra-molecular aggregate structure >>in organic phases under the project DMDOHEMA_1 on LCRC. Some findings >>have been unveiled, e.g., the presences of water, acid, Eu(NO3)3 all >>affect the supra-molecular aggregate structure of extractant (i.e., >>DMDOHEMA) in organic phased. These findings agree with the existing >>experimental data. However, due to the small size of those simulation >>systems, the aggregation behaviors are not converged well. Therefore, in >>the renewal period of project DMDOHEMA_1, we are aiming to enlarge our >>simulation boxes so that such findings can be solidified. Moreover, one >>already finished large simulation supports that larger simulation box >>decreases the calculated error bar of the aggregation number of DMDOHEMA. >>With the simulations on large enough simulation boxes, the effects of >>water, acid, Eu(NO3)3 will be distinguished, which will surely provi >> de significant insight for the rational design of higher efficient >>extractants. Our project is expected to highly spark the development of >>rare earth element related technologies. >>In this project, classical molecular dynamics (MD) simulations will be >>performed at the all-atom resolution, in addition to the concurrent >>solvent extraction experiments at ANL. All-atom MD simulations have been >>well proven in predicting supra-molecular aggregate structures. The open >>source package GROMACS will be employed for the simulations. GROMACS is >>one of the highly recommended packages for MD simulations. GROMACS has >>been reported to be able to scale well up to around 1,000 CPU processors. >>Based on our experience on LCRC, the simulations can be LINEARLY scaled >>up to 256 CPU cores, under which condition the simulation speed is around >>3 hours/ns for a system of the size of around 17 Ã‹ 17 Ã‹ 17 = 5000 nm3. >>Two users will use this allocation time, Dr. Ross J. Ellis and Dr. Baofu >>Qiao, both at the CSE division at ANL. >>In the first phase of this project, we are studying the influence of a >>variety of components, i.e., water, acid, Eu(NO3)3, on the aggregate >>structures of DMDOHEMA extractants dissolved in n-heptane organic phases. >>As aforementioned, this project is currently ongoing. With the allocation >>from LCRC, we are able to collects some conclusions in the near fure. >>In the second phase, we plan to study the effect of extractant on the >>supra-molecula aggregate structure. The extraction of DMDBTDMA, which is >>the preceding extractant of DMDOHEMA, will be simulated and compared with >>the simulation results of DMDOHEMA systems. According to the available >>experimental data, the effects of some factors will be explore, such as >>the concentration of water, the concentration of Eu(NO3)3 complexes, the >>concentration of acidic molecule of HNO3. >> >> >> >> Current: undetermined amount >>Justification: Table. Benchmark of the simulation speed on LCRC >>#CPU cores 16 32 64 256 >>Speed >>(ns/day) 0.51 1.0 2.0 7.7 >> >>Based on the benchmark simulations, we can conclude that the scaling on >>LCRC can be linearly up to at least 256 CPU cores for our simulations. >> >> >> Requested: 200000 >> >>A specific reason has been given: >>Dear Sir/Madam, >>The allocation has been used out this week. I have a couple of >>simulations to run for the present paper. Could you please provide me >>some more allocation? Thanks a lot for your kind help! >>best regards, >>Baofu >> >>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 Bair, Raymond A. 13 Nov '15

13 Nov '15

Looking at the history of this project it seems reasonable to provide the 200K requested. I suggest making 70K a first quarter addition and 130K a 1st half addition. Regards, Ray ----------------------------------------- Ray Bair Computing, Environment, and Life Sciences Argonne National Laboratory and the University of Chicago TCS Building 240, Room 4122 9700 South Cass Avenue Argonne, IL 60439 email: rbair(at)anl.gov Phone: (630)252-5751 On 11/12/15, 2:12 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: qiaobf (Baofu Qiao) > Project: DMDOHEMA_1 > Title: Metal Ion Transport through Nano-Structured Lipophilic >Systems: Atomistic MD Simulations > Description: In the last few months, we have performed some preliminary >simulation runs in understanding the supra-molecular aggregate structure >in organic phases under the project DMDOHEMA_1 on LCRC. Some findings >have been unveiled, e.g., the presences of water, acid, Eu(NO3)3 all >affect the supra-molecular aggregate structure of extractant (i.e., >DMDOHEMA) in organic phased. These findings agree with the existing >experimental data. However, due to the small size of those simulation >systems, the aggregation behaviors are not converged well. Therefore, in >the renewal period of project DMDOHEMA_1, we are aiming to enlarge our >simulation boxes so that such findings can be solidified. Moreover, one >already finished large simulation supports that larger simulation box >decreases the calculated error bar of the aggregation number of DMDOHEMA. >With the simulations on large enough simulation boxes, the effects of >water, acid, Eu(NO3)3 will be distinguished, which will surely provi > de significant insight for the rational design of higher efficient >extractants. Our project is expected to highly spark the development of >rare earth element related technologies. >In this project, classical molecular dynamics (MD) simulations will be >performed at the all-atom resolution, in addition to the concurrent >solvent extraction experiments at ANL. All-atom MD simulations have been >well proven in predicting supra-molecular aggregate structures. The open >source package GROMACS will be employed for the simulations. GROMACS is >one of the highly recommended packages for MD simulations. GROMACS has >been reported to be able to scale well up to around 1,000 CPU processors. >Based on our experience on LCRC, the simulations can be LINEARLY scaled >up to 256 CPU cores, under which condition the simulation speed is around >3 hours/ns for a system of the size of around 17 Ã‹ 17 Ã‹ 17 = 5000 nm3. >Two users will use this allocation time, Dr. Ross J. Ellis and Dr. Baofu >Qiao, both at the CSE division at ANL. >In the first phase of this project, we are studying the influence of a >variety of components, i.e., water, acid, Eu(NO3)3, on the aggregate >structures of DMDOHEMA extractants dissolved in n-heptane organic phases. >As aforementioned, this project is currently ongoing. With the allocation >from LCRC, we are able to collects some conclusions in the near fure. >In the second phase, we plan to study the effect of extractant on the >supra-molecula aggregate structure. The extraction of DMDBTDMA, which is >the preceding extractant of DMDOHEMA, will be simulated and compared with >the simulation results of DMDOHEMA systems. According to the available >experimental data, the effects of some factors will be explore, such as >the concentration of water, the concentration of Eu(NO3)3 complexes, the >concentration of acidic molecule of HNO3. > > > > Current: undetermined amount >Justification: Table. Benchmark of the simulation speed on LCRC >#CPU cores 16 32 64 256 >Speed >(ns/day) 0.51 1.0 2.0 7.7 > >Based on the benchmark simulations, we can conclude that the scaling on >LCRC can be linearly up to at least 256 CPU cores for our simulations. > > > Requested: 200000 > >A specific reason has been given: >Dear Sir/Madam, >The allocation has been used out this week. I have a couple of >simulations to run for the present paper. Could you please provide me >some more allocation? Thanks a lot for your kind help! >best regards, >Baofu > >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_on_demand and MICCOM-Data
by Bair, Raymond A. 13 Nov '15

13 Nov '15

P.S. Note the 2TB storage request for MICCoM-Data Ray On 11/10/15, 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: >Great. Lets approve 80K for the year for LCRC_on_demand, and 150K for >MICCoM-Data for the 1st half. > >Ray > >----------------------------------------- >Ray Bair >Computing, Environment, and Life Sciences >Argonne National Laboratory > and the University of Chicago >TCS Building 240, Room 4122 >9700 South Cass Avenue >Argonne, IL 60439 >email: rbair(at)anl.gov >Phone: (630)252-5751 > > > > > >On 11/9/15, 7:24 PM, "Aithal, Shashikant M." <aithal(a)cels.anl.gov> wrote: > >>Both look OK to me. >>________________________________________ >>From: allocations-admins-bounces(a)lcrc.anl.gov >>[allocations-admins-bounces(a)lcrc.anl.gov] on behalf of Bair, Raymond A. >>[rbair(a)anl.gov] >>Sent: Monday, November 09, 2015 4:44 PM >>To: LCRC Allocations Admins >>Subject: [allocations-admins] LCRC_on_demand and MICCOM-Data >> >>Does anyone have questions about these new projects? The first half >>requests are relatively small. >> >>Regards, >> >>Ray >> >>----------------------------------------- >>Ray Bair >>Computing, Environment, and Life Sciences >>Argonne National Laboratory >> and the University of Chicago >>TCS Building 240, Room 4122 >>9700 South Cass Avenue >>Argonne, IL 60439 >>email: rbair(at)anl.gov >>Phone: (630)252-5751 >> >> >> >>_______________________________________________ >>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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New LCRC report submitted for PSO
by support＠lcrc.anl.gov 12 Nov '15

12 Nov '15

Full project report at https://accounts.lcrc.anl.gov/reporting/project/2015/?project=PSO

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[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 12 Nov '15

12 Nov '15

Hello, A change in allocation has been requested: Requester: qiaobf (Baofu Qiao) Project: DMDOHEMA_1 Title: Metal Ion Transport through Nano-Structured Lipophilic Systems: Atomistic MD Simulations Description: In the last few months, we have performed some preliminary simulation runs in understanding the supra-molecular aggregate structure in organic phases under the project DMDOHEMA_1 on LCRC. Some findings have been unveiled, e.g., the presences of water, acid, Eu(NO3)3 all affect the supra-molecular aggregate structure of extractant (i.e., DMDOHEMA) in organic phased. These findings agree with the existing experimental data. However, due to the small size of those simulation systems, the aggregation behaviors are not converged well. Therefore, in the renewal period of project DMDOHEMA_1, we are aiming to enlarge our simulation boxes so that such findings can be solidified. Moreover, one already finished large simulation supports that larger simulation box decreases the calculated error bar of the aggregation number of DMDOHEMA. With the simulations on large enough simulation boxes, the effects of water, acid, Eu(NO3)3 will be distinguished, which will surely provi de significant insight for the rational design of higher efficient extractants. Our project is expected to highly spark the development of rare earth element related technologies. In this project, classical molecular dynamics (MD) simulations will be performed at the all-atom resolution, in addition to the concurrent solvent extraction experiments at ANL. All-atom MD simulations have been well proven in predicting supra-molecular aggregate structures. The open source package GROMACS will be employed for the simulations. GROMACS is one of the highly recommended packages for MD simulations. GROMACS has been reported to be able to scale well up to around 1,000 CPU processors. Based on our experience on LCRC, the simulations can be LINEARLY scaled up to 256 CPU cores, under which condition the simulation speed is around 3 hours/ns for a system of the size of around 17 × 17 × 17 = 5000 nm3. Two users will use this allocation time, Dr. Ross J. Ellis and Dr. Baofu Qiao, both at the CSE division at ANL. In the first phase of this project, we are studying the influence of a variety of components, i.e., water, acid, Eu(NO3)3, on the aggregate structures of DMDOHEMA extractants dissolved in n-heptane organic phases. As aforementioned, this project is currently ongoing. With the allocation from LCRC, we are able to collects some conclusions in the near fure. In the second phase, we plan to study the effect of extractant on the supra-molecula aggregate structure. The extraction of DMDBTDMA, which is the preceding extractant of DMDOHEMA, will be simulated and compared with the simulation results of DMDOHEMA systems. According to the available experimental data, the effects of some factors will be explore, such as the concentration of water, the concentration of Eu(NO3)3 complexes, the concentration of acidic molecule of HNO3. Current: undetermined amount Justification: Table. Benchmark of the simulation speed on LCRC #CPU cores 16 32 64 256 Speed (ns/day) 0.51 1.0 2.0 7.7 Based on the benchmark simulations, we can conclude that the scaling on LCRC can be linearly up to at least 256 CPU cores for our simulations. Requested: 200000 A specific reason has been given: Dear Sir/Madam, The allocation has been used out this week. I have a couple of simulations to run for the present paper. Could you please provide me some more allocation? Thanks a lot for your kind help! best regards, Baofu This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

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[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 11 Nov '15

11 Nov '15

Hello, A change in allocation has been requested: Requester: wilde (Michael Wilde) Project: swift Title: Support for Swift scripting on LCRC Systems Description: Swift enables users to express and execute workflows comprising external applications and library functions. It enables users to specify workflow patterns that range from a simple set of independent tasks, up to very complex task flow graphs based on data dependencies. Swift is implicitly parallel, so the user does no need to know anything about parallel programming to write Swift workflows. It automates data transfer (to multiple compute resources) and fault recovery as well. This project will be used to support feature development specific to LCRC (for example, adjustments for LCRC resource manager behavior and/or scheduling policy); to help LCRC users with code examples and problem debugging; and to perform night;y/weekly testing of Swift on Blues and Fusion. Current: undetermined amount Justification: Requested: 75000 A specific reason has been given: For testing and support of Swift parallel scripting language and user community. This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

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New LCRC report submitted for swift
by support＠lcrc.anl.gov 11 Nov '15

11 Nov '15

Full project report at https://accounts.lcrc.anl.gov/reporting/project/2015/?project=swift

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New LCRC report submitted for swift
by support＠lcrc.anl.gov 11 Nov '15

11 Nov '15

Full project report at https://accounts.lcrc.anl.gov/reporting/project/2015/?project=swift

1 0

New LCRC report submitted for swift
by support＠lcrc.anl.gov 11 Nov '15

11 Nov '15

Full project report at https://accounts.lcrc.anl.gov/reporting/project/2015/?project=swift

1 0

[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 11 Nov '15

11 Nov '15

Hello, A change in allocation has been requested: Requester: fqiu (Feng Qiu) Project: PSO Title: Power System Optimization Description: Computational methods: Mixed-integer linear programming techniques, including cutting plane algorithms, branch-and-bound scheme, and so on. CPLEX, the solver we normally use, can run in a parallel fashion. That's why each of our computation jobs uses multiple CPU cores. Programming model: optimization models and algorithms are coded with C/ C++ or AMPL language. Algorithms are implemented within MILP solver framework. Scalability issues: Most of our models are highly combinatorial, therefore, in some cases, the branch-and-bound tree in MILP solver can grow very large, consuming a significant amount of memory when data size grows. In our previous experience, A job can run for two weeks until 64GB memory is used up. Therefore, we tend to run each instance exclusively on one node with 64GB memory. We will monitor the scalability issues and adjust the way the jobs are run. Software requirements: MILP solvers such as CPLEX (we have bought the license). C/C++ complier. Performance achieved either on LCRC or other systems: Our programs run for from a couple of minutes to a couple weeks. When the program involves practical data, the computational time tends to be longer(a couple of days, up to 10 days). Sizes of calculations run on and/or planned for LCRC or other systems: The proposed allocation is calculated in the following way: according to our past experience, a project last for 3 months on average. One third of the time is spent on debugging and computation. we tend to run a batch of 10 - 30 jobs with different parameter settings. Each job takes one node (to guarantee the job has sufficient memory). Suppose we run computations intensively for 20 days. Then the total time allocation is 24*20(day)*16(core)*15(job)=115200core hours. Efficiency of the code: The major part of the computation is done by solvers, which is out of our control. Making our code faster is an important goal of our research. Investigation on faster algorithm is part of the research. Expected project members: 1-3 Current: undetermined amount Justification: Requested: 230000 A specific reason has been given: In addition to the restoration program, we will have more projects that require computational power. For example, we will have simulation-based optimization for power system cascading failure mitigation, which runs simulation and search algorithms. We will have load restoration, which solves mixed-integer programming models. This budget should be a reasonable estimate for all these computational tasks. This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

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