June 2014 - Allocations-admins - mailman3.cels.anl.gov

Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by John Valdes 30 Jun '14

30 Jun '14

On Mon, Jun 30, 2014 at 09:56:31PM +0000, Low, John J. wrote: > Have you added the 500K to the metadissolve account? Not yet; I'll be adding it today though. You'll get an email once the allocation is granted. John

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by Low, John J. 30 Jun '14

30 Jun '14

Have you added the 500K to the metadissolve account? The lcrc-qbank command shows that it is still shows a negative balance to me. 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/ On 6/27/14, 5:15 PM, "John Valdes" <valdes(a)anl.gov> wrote: >500K approved by LCRC Allocations Committee. > >John > >On Thu, Jun 26, 2014 at 03:09:32PM -0500, accounts(a)lcrc.anl.gov wrote: >> >> A change in allocation has been requested: >> >> Requester: jlow (John J. Low) >> Project: metadissolve >> >> Requested: 500000 >> >> A specific reason has been given: >> A large fraction of the allocation was used in production runs for >>another project "SRF-materials". Now that cp2k has been modified to >>enable these calculations, the requested time will be used to complete >>original work. >> >_______________________________________________ >allocations-admins mailing list >allocations-admins(a)lists.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 30 Jun '14

30 Jun '14

Hello, A change in allocation has been requested: Requester: scarcell (Riccardo Scarcelli) Project: GDI_lean_burn Title: Investigation of advanced, high-efficiency, lean-burn or dilute gasoline combustion Description: Specific tasks designed to mitigate this barrier include a comprehensive understanding of intake air flow, evolution of the fuel spray, ignition, combustion and emissions formation mechanisms, and their interaction with chamber/piston geometry and fuel injection strategies over a wide operating range as well as a systematic investigation of new ignition systems. 3D-CFD simulation will provide proper insight into the experimental results and offer guidance for improvements. Following the homogeneous operation, basic stratification strategies will be proposed through CFD and evaluated experimentally. Upon completion of the baseline engine assessment the focus will be shifted towards evaluation of advanced ignition systems.Improved combustion stability as well as potential extension of lean operating limits are going to be the key criteria for the assessment of advanced ignition systems. Given the different performance variables of these advanced ignition systems (ignition energy, location of ignition, multi-pulse etc.), 3D-CFD simulation will play a key role in determining engine operating parameters to fully utilize the potential of each advanced ignition system. CFD simulations will be performed with CONVERGE Current: undetermined amount Justification: Requested: 150000 A specific reason has been given: Increased amount of simulation needs for Q4 FY2014. The plan is to run multi-cycle engine simulations to assess potential in capturing engine cyclic variability through high-resolution RANS. The results will be included in a technical paper for the next SAE World Congress (the deadline is at the end of September 2014) as well as next year's DOE Annual Merit Review. 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. 30 Jun '14

30 Jun '14

Checking with Silverio. ----------------------------------------- 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 6/30/14, 1:56 PM, "John Valdes" <valdes(a)anl.gov> wrote: >On Mon, Jun 30, 2014 at 12:55:54PM -0500, accounts(a)lcrc.anl.gov wrote: >> >> A change in allocation has been requested: >> >> Requester: svasquez (Silverio Vasquez) >> Project: ESMF >> Requested: 340000 >> >> A specific reason has been given: >> The ESMF project needs additional allocation because our tests are >>taking longer to complete than anticipated. > >That's quite a jump in requested time. They had only asked for 10K >for the whole year, and previous years' requests have also been small >(<50K for the full FY). Do we know if this request is correct? The >committee at the last meeting approved 2.5K (what they had requested >per quarter this FY) plus time to cover their negative balance. > >John >_______________________________________________ >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 Allocation Request
by John Valdes 30 Jun '14

30 Jun '14

On Mon, Jun 30, 2014 at 12:55:54PM -0500, accounts(a)lcrc.anl.gov wrote: > > A change in allocation has been requested: > > Requester: svasquez (Silverio Vasquez) > Project: ESMF > Requested: 340000 > > A specific reason has been given: > The ESMF project needs additional allocation because our tests are taking longer to complete than anticipated. That's quite a jump in requested time. They had only asked for 10K for the whole year, and previous years' requests have also been small (<50K for the full FY). Do we know if this request is correct? The committee at the last meeting approved 2.5K (what they had requested per quarter this FY) plus time to cover their negative balance. John

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[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 30 Jun '14

30 Jun '14

Hello, A change in allocation has been requested: Requester: svasquez (Silverio Vasquez) Project: ESMF Title: Earth System Modeling Framework Description: The goal of the Earth System Modeling Framework project is to build high performance, flexible software infrastructure to increase ease of use, performance portability, interoperability, and reuse in climate, numerical weather prediction, data assimilation, and other Earth science applications. The framework is intended for use by individual researchers as well as major operational and research centers. ESMF products include an API specification, a reference implementation accompanied by extensive documentation, and an exhaustive regression test suite that includes 4600+ unit tests, system tests, and examples. The ESMF software consists of a superstructure for coupling and exchanging data between models components (e.g., atmosphere, ocean) and an infrastructure consisting of 1) data structures for representing grids and fields and 2) an optimized, portable set of low-level utilities. The data constructs and low-level utilities can be used by the coupling superstructure and may also be used separately to compose scientific applications. As computing architectures evolve, optimizations of the ESMF software is ongoing. Future changes include updates for codes running on computers with general purpose GPUs or accelerators, where data movement in and out of device memory is the source of the major performance bottleneck. Accelerators provide increased computational power which can be leveraged by ESMF in the intensive portion of the code, such as the grid remapping algorithms. However, the main focus in ongoing performance optimization of ESMF is to ensure that the software scales readily and does not introduce overhead as codes start to routinely run on hundreds of thousands of processors. In addition to ESMF full Fortran 90 and partial C/C++ interfaces, ESMPy, a Python package for high-performance grid remapping using ESMF, was released during spring 2013. ESMPy improves on the previous ESMF Python interface, which was called ESMP, by making it more objected oriented. ESMPy is a Python interface that promotes fast prototyping of coupled Earth system modeling codes by providing access to a high-performance and scalable grid remapping package. The main feature is that it allows for high-performance and scalable regridding between 2D and 3D logically rectangular and unstructured grids using a variety of methods and options. At the present time, the ESMPy supports bilinear, finite element patch recovery and first-order conservative methods, for 2D and 3D logically rectangular and unstructured grids. There is also an option to ignore unmapped destination points and mask out points on either the source or destination. Regridding on the sphere takes place in 3D Cartesian space, so the pole problem is not an issue as it can be with other Earth system grid remapping software. Current users of the ESMF Python interface include individuals as well as UV-CDAT (PCMDI) - Ultrascale Visualization Climate Data Analysis Tools; PyFerret (NOAA) – a Python-based interactive visualization and analysis environment; and the Community Surface Dynamics Modeling System (CSDMS) – tools for hydrological and other surface modeling processes. Current: undetermined amount Justification: Requested: 340000 A specific reason has been given: The ESMF project needs additional allocation because our tests are taking longer to complete than anticipated. 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 27 Jun '14

27 Jun '14

500K approved by LCRC Allocations Committee. John On Thu, Jun 26, 2014 at 03:09:32PM -0500, accounts(a)lcrc.anl.gov wrote: > > A change in allocation has been requested: > > Requester: jlow (John J. Low) > Project: metadissolve > > Requested: 500000 > > A specific reason has been given: > A large fraction of the allocation was used in production runs for another project "SRF-materials". Now that cp2k has been modified to enable these calculations, the requested time will be used to complete original work. >

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Re: [allocations-admins] [LCRC alloc-com] LCRC Project Allocation Request - metadissolve
by Bair, Raymond A. 27 Jun '14

27 Jun '14

Thank you for the quick response. 5 yes, 0 no, so far. That seems sufficient. Ray On 6/27/14, 9:58 AM, "Bair, Raymond A." <rbair(a)anl.gov> wrote: >Dear LCRC allocation Committee, > >John Low is requesting 500K core-hours for his project metadissolve (see >below). He is out of time because a postdoc on the project burned it up >by charging to the wrong project (should have been SRF-materials). So >John requests more time so he can finish the science, without the >postdoc's "help". Is it OK to grant the time? Based on expected usage, >we should be OK in terms of the total time granted, and John will run on >Fusion if Blues gets backed up. > >Regards, > >Ray Bair > >-----Original Message----- >From: allocations-admins-bounces(a)lists.lcrc.anl.gov >[mailto:[email protected]] On Behalf Of >accounts(a)lcrc.anl.gov >Sent: Thursday, June 26, 2014 3:10 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: jlow (John J. Low) > Project: metadissolve > Title: Ab Initio Molecular Dynamics Simulations of Aqueous >Reactions of AluminoSilicates > Description: The project will predict the rates of aqueous >polymerization reactions of aluminosilicates with ab initio molecular >dynamics. We will generate free energy surfaces for dimerization >reactions of SiOH4 + SiOH4, Al(OH)3 + SiOH4 and B(OH3) + SiOH4 in water >and vacuum. Each of these reactions will carried in pH neutral, acidic >(1M HCl) and basic (1M NaOH) solutions to model the effect of pH on these >reactions. We will use metadynamics to define the reaction coordinate >and estimates of free energies. Umbrella sampling will be use to predict >accurate free energies and estimates of rates. > >CPMD (http://www.cpmd.org) PLUMED (http://www.plumed-code.org) and WHAM >(http://membrane.urmc.rochester.edu/content/wham) will be used in this >project. > >CPMD is a plane-wave pseudopotential code which exploits Carr-Parrinello >Molecular Dynamics. CPMD is very efficient method for ab initio molecular >dynamics. > >PLUMED is an open source plugin, which works together with CPMD, for free >energy calculations in molecular systems. Although CPMD can do >metadynamics, PLUMED implements the reaction path collective variable >(RPCV). The RPCV should increase the efficiency of metadynamics and >umbrella sampling. > >WHAM is a program which performs a weighted histogram analysis of the >trajectory from umbrella sampling to generate the free energy changes >along the reaction coordinate. > >CPMD is a highly scalable parallel code. The hybrid MPI/openMP Version of >CPMD 3.15.3 scales very well. CPMD can use 560 cores on either blues or >fusion very efficiently for these models considered in this project. >Additional scaling can be obtained with multiple walkers and task groups, >which is available in CPMD. This will enable additional levels of >parallelism could scale efficiently to thousands of cores. >PLUMED implements a reaction path collective variable will allow us to >simulate this reaction with one dimensional metadynamics. One >dimensional metadynamics is at least two to three times more efficient >than two or three dimensional sampling. PLUMED will increase the >efficiency of our metadynamics and umbrella sampling by a factor of two >to three. > >We expect that there will three members of this project. > > Current: undetermined amount >Justification: CPMD is well known as a program with efficient parallel >scaling. I have documented the scaling of CPMD in previous project >reports for aimd_catalysis. > >The table below show the scaling of CPMD for Cellobiose (C12O11H22) >dissolved in 1M HCL (6HCl + 256 H2O) for a total on 569 atoms. > >CPMD scaling on blues on cellobiose in 1M HCl. > >MPI OMP Task # of elasped time > Core cores (seconds) > >216 1 1 216 31138 >216 4 1 864 9180 >432 4 4 1728 5695 >432 8 4 3456 4290 > >The new version of CPMD (3.17.1) is claimed to scale better then 3.15.3. >Using the new version will likely increase the efficiency of the code. > >It is possible that performance profiling of the code will reveal >opportunities for vectorization. We study the CPU and communications >bottlenecks of the code to determine whether code modifications may >improve performance. > > Requested: 500000 > >A specific reason has been given: >A large fraction of the allocation was used in production runs for >another project "SRF-materials". Now that cp2k has been modified to >enable these calculations, the requested time will be used to complete >original work. > >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 >_______________________________________________ >alloc-com mailing list >alloc-com(a)lists.lcrc.anl.gov >https://lists.lcrc.anl.gov/mailman/listinfo/alloc-com

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[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 27 Jun '14

27 Jun '14

Hello, A change in allocation has been requested: Requester: ruhu (Rui Hu) Project: SHARP-IF Title: SHARP – Intermediate Fidelity Modeling Description: The system analysis code and the RANS-based commercial CFD code STAR-CCM+ are incorporated into the SHARP framework for a multi-scale analysis of Sodium Fast Reactors. In the previous fiscal year, the feasibility of performing coupled System code and STAR-CCM+ simulations of protected loss-of-flow accident was demonstrated. In that effort, the outlet plenum was modeled by STAR-CCM+ and the rest of the primary coolant system and the secondary system were simulated by the SFR Module, and the flow and temperature conditions at the interface were exchanged between the two codes as boundary conditions. In the planned activities for FY14, this coupling exercise will be extended to model both the cold pool and the upper plenum of the SFR in the CFD model since multi-dimensional effects and the thermal stratification in the cold pool are also important to the transient behavior of the system. Accurate predictions of flow and temperature are essential to assure the reactor safety during postulated accidents. Furthermore, the CFD code STAR-CCM+ will be used for design evaluations of reactor systems and experimental facilities. Notably, an advanced sodium fast reactor design concept; and the cross-shape twisted fuel assembly design in a conversion effort from using HEU to LEU, and the natural convection shutdown test facility that is currently being built at Argonne. This type of simulations is essential to assure the safety of the proposed design. Also, the pre-test simulation results of the NSTF will be compared against to the experimental results as a validation study of the CFD code. Current: undetermined amount Justification: At Argonne, the CFD code STAR-CCM+ are routinely applied to simulations that use more than 100 cores, and good parallel performance has been observed. As problem size increases, i.e. for finer meshes and for large pin bundles, larger numbers of cores would be utilized and based on data from the developers good parallel performance will continue to be expected. On the other hand, the system code, the SFR Module based on MOOSE and RELAP-7 is a new development. The parallelization will be provided by the underlying MOOSE framework which is built on PETSc. The scalability of MOOSE has been demonstrated by other MOOSE-based applications. The system code usually relies on coarse representation of the system thus does not require significant amount of computing resources. Requested: 100000 A specific reason has been given: The orginal allocated core-hours have been completed spent. Need additional allocation to perform CFD simulations for this project. 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 26 Jun '14

26 Jun '14

Hello, A change in allocation has been requested: Requester: jlow (John J. Low) Project: metadissolve Title: Ab Initio Molecular Dynamics Simulations of Aqueous Reactions of AluminoSilicates Description: The project will predict the rates of aqueous polymerization reactions of aluminosilicates with ab initio molecular dynamics. We will generate free energy surfaces for dimerization reactions of SiOH4 + SiOH4, Al(OH)3 + SiOH4 and B(OH3) + SiOH4 in water and vacuum. Each of these reactions will carried in pH neutral, acidic (1M HCl) and basic (1M NaOH) solutions to model the effect of pH on these reactions. We will use metadynamics to define the reaction coordinate and estimates of free energies. Umbrella sampling will be use to predict accurate free energies and estimates of rates. CPMD (http://www.cpmd.org) PLUMED (http://www.plumed-code.org) and WHAM (http://membrane.urmc.rochester.edu/content/wham) will be used in this project. CPMD is a plane-wave pseudopotential code which exploits Carr-Parrinello Molecular Dynamics. CPMD is very efficient method for ab initio molecular dynamics. PLUMED is an open source plugin, which works together with CPMD, for free energy calculations in molecular systems. Although CPMD can do metadynamics, PLUMED implements the reaction path collective variable (RPCV). The RPCV should increase the efficiency of metadynamics and umbrella sampling. WHAM is a program which performs a weighted histogram analysis of the trajectory from umbrella sampling to generate the free energy changes along the reaction coordinate. CPMD is a highly scalable parallel code. The hybrid MPI/openMP Version of CPMD 3.15.3 scales very well. CPMD can use 560 cores on either blues or fusion very efficiently for these models considered in this project. Additional scaling can be obtained with multiple walkers and task groups, which is available in CPMD. This will enable additional levels of parallelism could scale efficiently to thousands of cores. PLUMED implements a reaction path collective variable will allow us to simulate this reaction with one dimensional metadynamics. One dimensional metadynamics is at least two to three times more efficient than two or three dimensional sampling. PLUMED will increase the efficiency of our metadynamics and umbrella sampling by a factor of two to three. We expect that there will three members of this project. Current: undetermined amount Justification: CPMD is well known as a program with efficient parallel scaling. I have documented the scaling of CPMD in previous project reports for aimd_catalysis. The table below show the scaling of CPMD for Cellobiose (C12O11H22) dissolved in 1M HCL (6HCl + 256 H2O) for a total on 569 atoms. CPMD scaling on blues on cellobiose in 1M HCl. MPI OMP Task # of elasped time Core cores (seconds) 216 1 1 216 31138 216 4 1 864 9180 432 4 4 1728 5695 432 8 4 3456 4290 The new version of CPMD (3.17.1) is claimed to scale better then 3.15.3. Using the new version will likely increase the efficiency of the code. It is possible that performance profiling of the code will reveal opportunities for vectorization. We study the CPU and communications bottlenecks of the code to determine whether code modifications may improve performance. Requested: 500000 A specific reason has been given: A large fraction of the allocation was used in production runs for another project "SRF-materials". Now that cp2k has been modified to enable these calculations, the requested time will be used to complete original work. This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

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