April 2010 - Allocations-admins - mailman3.cels.anl.gov

[LCRC Accounts] Project Request: EBAC
by accounts＠lcrc.anl.gov 26 Apr '10

26 Apr '10

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: Tsung-Shung Lee Applicant's institution: ANL Applicant's division: PHY Project Name: EBAC Project title: Analysis of Nucleon Resonances Associated funding: U.S. Department of Energy, Office of Nuclear Physics Division, under Contract DE-AC02-06CH11357 Other Systems: workstation theory9 of PHY , and NERSC Science: The objective of this project is to extract nucleon resonance information from world data of meson production reactions for advancing our understanding of the origin of hadron matter within Quantum Chromodynamics (QCD), the fundamental theory of strong interactions Project description: The objectives of Analysis of Nucleon Resonances (N*) are twofold. The first is to perform dynamical coupled-channels analysis of meson production reaction data for extracting the parameters of nucleon resonances. The second objective is to develop theoretical interpretations of the determined resonance parameters in terms of hadron structure calculations such as the constituent quark model and Lattice QCD calculations. This project will provide information for understanding the non-perturbative aspects of QCD. In particular, the extracted N-N* form factors will reveal the dynamical origins of quark confinement and the meson cloud associated with the spontaneously breaking of chiral symmetry. This project is needed to reach milestones HP3 and HP7 by 2012 set in DOE's long-range plan of 2010. Project URL: http://ebac-theory.jlab.org Requested allocation: 10000 Justification: The analysis will be carried out by solving a large set of coupled integral equation in momentum-space an performing chi-squared fits , with about 200 parameters, to very extensive world data of pion-nucleon scattering and electromagnetic meson production reactions. The calculation at each energy and each set of parameters involve an inversion of an about 1000*1000 complex matrix. This has to be repeated many times in searching the best-fit parameters in chi-squared fit to very extensive data (about 60,000 data points) using MINUIT. The requester has used 0 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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[LCRC Accounts] Project Request: kcsa
by accounts＠lcrc.anl.gov 24 Apr '10

24 Apr '10

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: Benoit Roux Applicant's institution: ANL Applicant's division: BSD Project Name: kcsa Project title: Computational study of ion selectivity in the KcsA channel Associated funding: NIH-GM062342 Other Systems: Science: The selective binding of small ions (e.g., Na+, K+, Ca2+, Mg2+) to protein sites plays a key functional role in many important biological processes. The selectivity for is governed by the free energy landscape encountered by the different ions when they associated with the binding site. This, in turn, reflects the balance of ion-protein and ion-solvent interactions. Project description: The binding of small ions is a fundamental to the structure and function of biological systems. Ions are involved in the folding of proteins and nucleic acids, enzyme catalysis, and in numerous cellular signaling processes. Monovalent cations such as Na+ and K+ play an important role in the homeostasis and electric activity of living cells and in modulating biomolecular stability through both specific and non-specific interactions. The importance of those small cations is most strikingly examplified by their implication in a wide variety of membrane transport proteins, e.g., ion channels, transporters, and ATP-driven pumps. Understanding quantitatively the microscopic factors controlling ion selectivity using molecular dynamics (MD) simulations remains a great challenge. In simple terms, the concept of selectivity means that the "correct" ion, is able to binding more favorably than an "incorrect" ion. At a physical level, it is to be anticipated that energetics and solvation play a key role in this process, although different aspects of energetics may be highlighted by the various experimental methods used to probe the system. Some experimental measurements are more sensitive to the relative depth of free energy wells, while others are more sensitive to the relative height of free energy barriers. In the case of ion channels, the large hydration energy of the ions contrasts with the small free energy barriers necessary for the fast conduction observed experimentally. This implies that ion-protein association is ultimately controlled by a delicate balance of very strong interactions. Frequently, permeation involves the partial dehydration of an ion, followed by the binding to a proteinaceous environment. This archetype is well illustrated by the crystal structure of the KcsA channel. The pore of the KcsA channel comprises a wide aqueous vestibular entryway, lined by non-polar residues on the intracellular side, leading up on the extracellular side to a narrow region lined by backbone carbonyl oxygens. This region of the pore, formed by the residues corresponding to the signature sequence TTVGYG common to all K+ channels, acts as a "selectivity filter" by allowing only the passage of nearly dehydrated K+ ions across the cell membrane. Such fundamental characteristi cs of ion conduction through narrow pores are also exemplified by the gramicidin A channel (gA), where tight interactions between the permeating ion and the protein are critical. In such narrow molecular pores, a permeating ion must shed most of its surrounding water molecules and the large energetic loss due to dehydration must be compensated by coordination with the backbone carbonyl oxygens. The best strategy to address such issues is to compute the multi-ion PMF corresponding to the microscopic process in question (Berneche and Roux, Nature 2001). In particular, the calculation of the PMF enables us to pin-point the location of the largest barrier opposing the passage of a single Na+ ion while there are two K+ ions elsewhere in the pore. We carry those type of calculations using umbrella sampling MD simulations. Our plan is to compute the multi-ion free energy landscape for Na+ permeation through the KcsA channel using the open state structure that was recently determined by X-ray crystallography in the Perozo laboratory. Project URL: http://thallium.bsd.uchicago.edu/RouxLab/research.html Requested allocation: 452832 Justification: The umbrella sampling calculations described here constitute a major part of the PhD thesis of David Medovoy, a graduate student in Biophysics at the University of Chicago. The goal of the umbrella sampling MD simulation is to obtain W(z1,z2,z3) the 3-ion PMF function of the coordinate of the 3 ions in the selectivity filter. To understand the effect of selectivity, two systems must be considered: with 3 K+ ions, and with 1 Na+ and 2 K+ ions. Based on our experience with similar computations, we know that a grand total of 3931 MD window simulations is needed for two systems. Each window should be simulated for 0.6 ns, the first 0.1 ns being used for equilibration and the last 0.5 ns for sampling proper, for total aggregate MD simulation time of 2.4 microseconds for each of the two systems. The unbiased 3D PMFs are then calculated using the weighted histogram method (WHAM). The simulations are generated with NAMD, which is the most efficient program for classical MD. The total requested allocation is: 452,832 SU = (3931 windows) * (0.6 ns/window) * ((8*cores)*(12 hour)/ns) The requester has used 0 hours of their initial startup project. In addition to approving an initial amount, please specify a Category and Subcategory for this project. For a list of the current selection of approved categories, please see: https://wiki.lcrc.anl.gov/wiki/Processes/Categories Once the Allocation committee has approved the project, please go to the Project Management page to create it: https://accounts.lcrc.anl.gov/projects.php Thank You, The LCRC Accounts System

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Re: [allocations-admins] [LCRC Accounts] Project Request: Bubble
by John Valdes 14 Apr '10

14 Apr '10

OK; Category sounds like P (Physical Sciences); should the subcat be Chemistry, or maybe Material Science? Priority 4 since Zeke is MCS and they may have access to BG, or 3 since it sounds like the primary users aren't MCS and so don't have access to any other MCS resources? John On Wed, Apr 14, 2010 at 05:41:31PM -0500, Bair, Raymond A. wrote: > Lets go for the 240K allocation. > > POC would be Curtiss. > > > > Ray > > > On 4/14/10 5:26 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: Zeke Insepov > > Applicant's institution: ANL > > Applicant's division: MCS > > Project Name: Bubble > > Project title: Ab-initio simulation of bubbles in dense media > > Associated funding: RERTR > > Other Systems: Blue Gene > > Science: Summary of the project: > > Fission gases form small bubbles in nuclear fuels that leads to lattice > > swelling and cracking. Our simulation will be useful for understanding this > > phenomenon. > > To date assessments of chemistry and physics of imploding vapor-gas filled > > bubbles has been conducted with continuum mechanics formulations in > > conjunction with empirically-derived equations of state. The multitude of > > condensation-evaporation phenomena at liquid-gas interface, dissociation and > > ionization phenomena which can occur during super compression and super > > heating for complex molecules has not been possible to assess on a molecular > > dynamics scale. > > In collaboration with the University of Palermo, Italy, researchers at Purdue > > University aim to conduct scoping assessments of above-mentioned phenomena - > > in cooperation with Dr. Zeke Insepov of Argonne National Laboratory. Scoping > > assessment tool targeted for use is the Siesta code package which uses a > > linear-scaling density functional approach for capturing the physics and > > chemistry on the molecular dynamics scale. > > DFT molecular dynamics simulations can be performed for a number of points of > > the phase diagram region corresponding to the transient conditions the > > liquid-bubble interface experiences during the supercompression cycles. This > > should give information about chemical reactions that can change the behavior > > of the interface itself, an issue which is not explicitly taken into > > consideration in the empirical equation of states. > > > > Project description: computational methods: Density Functional Molecular > > Dynamics simulations using the siesta method > > > > programming model: parallel > > > > experiments planned: molecular dynamics simulations > > > > software requirements: fortran compiler (e.g. openmpi) > > > > sizes of calculations run on and/or planned for LCRC or other systems: > > hundreds of picoseconds time scale MD simulations on 100-500 atoms systems > > > > expected number of project members: 5 > > > > We expect a total of 5 project members (two including a student from Purdue > > University, and three staff from the University of Palermo). > > > > Results of assessments are expected to lead to joint proposals to NSF, DoE > > (Office of Science, and NE), and DARPA. > > > > > > Project URL: > > Requested allocation: 1500000 > > Justification: Since the number of users will be at least five, we > > request a large allocation. > > > > > > The requester has used 0 hours of their initial startup project. > > > > In addition to approving an initial amount, please specify a Category > > and Subcategory for this project. For a list of the current selection > > of approved categories, please see: > > > > https://wiki.lcrc.anl.gov/wiki/Processes/Categories > > > > Once the Allocation committee has approved the project, please go to > > the Project Management page to create it: > > > > https://accounts.lcrc.anl.gov/projects.php > > > > Thank You, > > The LCRC Accounts System > > _______________________________________________ > > allocations-admins mailing list > > allocations-admins(a)lists.lcrc.anl.gov > > https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins > > > ----------------------------------------- > Ray Bair > Computing, Environment, and Life Sciences > Argonne National Laboratory > and the University of Chicago > Building 240, Room 4126 > 9700 South Cass Avenue > Argonne, IL 60439 > email: rbair(at)anl.gov > Phone: (630)252-5751 > > > _______________________________________________ > allocations-admins mailing list > allocations-admins(a)lists.lcrc.anl.gov > https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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Re: [allocations-admins] [LCRC Accounts] Project Request: Bubble
by Bair, Raymond A. 14 Apr '10

14 Apr '10

Lets go for the 240K allocation. POC would be Curtiss. Ray On 4/14/10 5:26 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: Zeke Insepov > Applicant's institution: ANL > Applicant's division: MCS > Project Name: Bubble > Project title: Ab-initio simulation of bubbles in dense media > Associated funding: RERTR > Other Systems: Blue Gene > Science: Summary of the project: > Fission gases form small bubbles in nuclear fuels that leads to lattice > swelling and cracking. Our simulation will be useful for understanding this > phenomenon. > To date assessments of chemistry and physics of imploding vapor-gas filled > bubbles has been conducted with continuum mechanics formulations in > conjunction with empirically-derived equations of state. The multitude of > condensation-evaporation phenomena at liquid-gas interface, dissociation and > ionization phenomena which can occur during super compression and super > heating for complex molecules has not been possible to assess on a molecular > dynamics scale. > In collaboration with the University of Palermo, Italy, researchers at Purdue > University aim to conduct scoping assessments of above-mentioned phenomena - > in cooperation with Dr. Zeke Insepov of Argonne National Laboratory. Scoping > assessment tool targeted for use is the Siesta code package which uses a > linear-scaling density functional approach for capturing the physics and > chemistry on the molecular dynamics scale. > DFT molecular dynamics simulations can be performed for a number of points of > the phase diagram region corresponding to the transient conditions the > liquid-bubble interface experiences during the supercompression cycles. This > should give information about chemical reactions that can change the behavior > of the interface itself, an issue which is not explicitly taken into > consideration in the empirical equation of states. > > Project description: computational methods: Density Functional Molecular > Dynamics simulations using the siesta method > > programming model: parallel > > experiments planned: molecular dynamics simulations > > software requirements: fortran compiler (e.g. openmpi) > > sizes of calculations run on and/or planned for LCRC or other systems: > hundreds of picoseconds time scale MD simulations on 100-500 atoms systems > > expected number of project members: 5 > > We expect a total of 5 project members (two including a student from Purdue > University, and three staff from the University of Palermo). > > Results of assessments are expected to lead to joint proposals to NSF, DoE > (Office of Science, and NE), and DARPA. > > > Project URL: > Requested allocation: 1500000 > Justification: Since the number of users will be at least five, we > request a large allocation. > > > The requester has used 0 hours of their initial startup project. > > In addition to approving an initial amount, please specify a Category > and Subcategory for this project. For a list of the current selection > of approved categories, please see: > > https://wiki.lcrc.anl.gov/wiki/Processes/Categories > > Once the Allocation committee has approved the project, please go to > the Project Management page to create it: > > https://accounts.lcrc.anl.gov/projects.php > > Thank You, > The LCRC Accounts System > _______________________________________________ > allocations-admins mailing list > allocations-admins(a)lists.lcrc.anl.gov > https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins ----------------------------------------- Ray Bair Computing, Environment, and Life Sciences Argonne National Laboratory and the University of Chicago Building 240, Room 4126 9700 South Cass Avenue Argonne, IL 60439 email: rbair(at)anl.gov Phone: (630)252-5751

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[LCRC Accounts] Project Request: Bubble
by accounts＠lcrc.anl.gov 14 Apr '10

14 Apr '10

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: Zeke Insepov Applicant's institution: ANL Applicant's division: MCS Project Name: Bubble Project title: Ab-initio simulation of bubbles in dense media Associated funding: RERTR Other Systems: Blue Gene Science: Summary of the project: Fission gases form small bubbles in nuclear fuels that leads to lattice swelling and cracking. Our simulation will be useful for understanding this phenomenon. To date assessments of chemistry and physics of imploding vapor-gas filled bubbles has been conducted with continuum mechanics formulations in conjunction with empirically-derived equations of state. The multitude of condensation-evaporation phenomena at liquid-gas interface, dissociation and ionization phenomena which can occur during super compression and super heating for complex molecules has not been possible to assess on a molecular dynamics scale. In collaboration with the University of Palermo, Italy, researchers at Purdue University aim to conduct scoping assessments of above-mentioned phenomena - in cooperation with Dr. Zeke Insepov of Argonne National Laboratory. Scoping assessment tool targeted for use is the Siesta code package which uses a linear-scaling density functional approach for capturing the physics and chemistry on the molecular dynamics scale. DFT molecular dynamics simulations can be performed for a number of points of the phase diagram region corresponding to the transient conditions the liquid-bubble interface experiences during the supercompression cycles. This should give information about chemical reactions that can change the behavior of the interface itself, an issue which is not explicitly taken into consideration in the empirical equation of states. Project description: computational methods: Density Functional Molecular Dynamics simulations using the siesta method programming model: parallel experiments planned: molecular dynamics simulations software requirements: fortran compiler (e.g. openmpi) sizes of calculations run on and/or planned for LCRC or other systems: hundreds of picoseconds time scale MD simulations on 100-500 atoms systems expected number of project members: 5 We expect a total of 5 project members (two including a student from Purdue University, and three staff from the University of Palermo). Results of assessments are expected to lead to joint proposals to NSF, DoE (Office of Science, and NE), and DARPA. Project URL: Requested allocation: 1500000 Justification: Since the number of users will be at least five, we request a large allocation. The requester has used 0 hours of their initial startup project. In addition to approving an initial amount, please specify a Category and Subcategory for this project. For a list of the current selection of approved categories, please see: https://wiki.lcrc.anl.gov/wiki/Processes/Categories Once the Allocation committee has approved the project, please go to the Project Management page to create it: https://accounts.lcrc.anl.gov/projects.php Thank You, The LCRC Accounts System

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Re: [allocations-admins] [LCRC Accounts] Project Request: Cosmology
by Bair, Raymond A. 12 Apr '10

12 Apr '10

Yes, Steve would be a good contact. Priority 3. Ray On 4/12/10 9:28 PM, "John Valdes" <valdes(a)mcs.anl.gov> wrote: > On Mon, Apr 12, 2010 at 09:14:14PM -0500, Bair, Raymond A. wrote: >> Yes, 150K seems right for a start. > > OK; should I put Steve as contact? Is priority 3 good? > > John > >> On 4/12/10 7:15 PM, "John Valdes" <valdes(a)mcs.anl.gov> wrote: >> >>> Any decision on this project? The request came in the day after the >>> allocation meeting. If we approve, we need to decide: >>> >>> Amount: >>> Contact: >>> Cat/Subcat: >>> Priority: >>> >>> The request sounds good to me; I would say 150K, either Ray or Steve >>> Pieper as POC, P:Phy, and 3. >>> >>> John >>> >>> On Fri, Apr 02, 2010 at 04:09:21PM -0500, 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: Joe Bernstein >>>> Applicant's institution: ANL >>>> Applicant's division: HEP >>>> Project Name: Cosmology >>>> Project title: Harnessing Computational Cosmology Simulations to >>>> Investigate Cosmic Evolution >>>> Associated funding: None external to ANL sources >>>> Other Systems: ANL Blue Gene/P (renewal in preparation for >>>> ~300000 >>>> CPU-hrs over 4 months) >>>> Science: The evidence for dark energy represents one of >>>> the >>>> greatest mysteries of modern science. The proposed research will probe the >>>> implications of >>>> dark energy via analysis of computational cosmology simulations. Several >>>> independent observational methods provide evidence pointing to the >>>> conclusion >>>> that 95% of the current energy density of the Universe exists as part of >>>> the >>>> "dark sector" that is different from normal, i.e., >>>> "baryonic," matter. In particular, the dark sector is thought to be >>>> comprised >>>> of 22% "dark matter," which interacts with baryonic matter >>>> ostensibly only through gravity, and 73% "dark energy," which experiences >>>> gravity as a repulsive force. The nature of both dark sector components are >>>> essentially complete unknowns. It is presently an exciting time to be >>>> involved in cosmology because planned astronomical surveys will effectively >>>> result in dark sector probes becoming systematics-limited, making numerical >>>> simulations crucial to placing precision constraints on the dark sector. In >>>> addition, particle physics theorists predict that the Large Hadron Collider >>>> (LHC) and direct dark matter experiments may soon discover a dark matter >>>> candidate particle. ANL HEP staff and collaborating U. Illinois faculty are >>>> members of the Dark Energy Survey, which will provide the next generation >>>> of >>>> dark energy and (indirect) dark matter data. Local scientific simulation >>>> expertise and high-performance computing further make ANL ideally-suited to >>>> pursue answers to questions about the dark sector. The focus of the >>>> proposed research is the production and interpretation of computational >>>> cosmology simulations in order to elucidate the nature of the dark sector. >>>> Project description: The "Cosmology" project on fusion.lcrc.anl.gov >>>> (hereafter, "fusion") is in support of the one of the main research efforts >>>> of the PI as an ANL Computational Postdoctoral Fellow. The number of >>>> project >>>> members will be 3-5. We will make use of the requested number of CPU-hrs >>>> (275K) in efforts to generate initial conditions and verify scaling results >>>> for cosmology simulations run on the ANL Blue Gene/P ("BG/P"). Toward this >>>> end, we will harness piecewise-parabolic method (PPM) hydrodynamics and >>>> N-body gravity solvers, MPI for inter-processor communication, and HDF5 to >>>> implement parallel I/O. We will utilize both the C and FORTRAN90 >>>> programming >>>> languages. >>>> >>>> Paul Ricker (U. Illinois) is a computational cosmology expert working with >>>> Boyana Norris (MCS) on BG/P cosmology studies. The PI of this proposal >>>> recently transitioned from a classification as an ANL Postdoctoral >>>> Appointee >>>> to an ANL Computational Postdoctoral Fellow. His >>>> new duties include collaborating on these efforts with the goal of >>>> submitting >>>> a 2011 DOE INCITE proposal. The ultimate target of the BG/P >>>> simulation effort is runs requiring PPM+N-body simulations with a 1 Gpc (1 >>>> pc >>>> = 3.09x10^16 m) box size, 2048^3 grid cells, and 10^11 dark matter >>>> particles. >>>> We anticipate employing fusion to generate initial conditions for a suite >>>> of >>>> a few dozen BG/P simulations. Generating such initial conditions is memory >>>> intensive and cannot currently be done on the BG/P. These requirements also >>>> push the limits of existing codes. Scaling the cosmology runs to the target >>>> level represents a marked increase relative to machines used to date. >>>> Verifying scaling results, on a traditional Linux cluster such as fusion, >>>> will constitute an important part of our BG/P studies. We are highly >>>> confident of fusion's suitability for the proposed simulations because such >>>> runs have been shown to scale to upwards of 4K CPUs on other Linux >>>> clusters. >>>> >>>> The scaling studies will require approximately 10 runs each for strong and >>>> weak scaling for a total of ~20 runs. Based on Prof. Ricker's experience >>>> with >>>> PPM+N-body simulations performed at Oak Ridge National Laboratory, we >>>> estimate that a run with 2048^3 grid cells will cost approximately 400 >>>> CPU-hrs per timestep and require ~30 time steps for a total of 12K CPU-hrs. >>>> Assuming reasonable scaling, this implies a total cost of approximately >>>> 240K >>>> CPU-hrs for the scaling study. Generating initial conditions will require a >>>> significantly smaller cost by comparison. Thus, an allocation of 275K >>>> CPU-hrs >>>> will enable significant research progress. >>>> Project URL: >>>> Requested allocation: 275000 >>>> Justification: >>>> >>>> >>>> The requester has used 0 hours of their initial startup project. >>>> >>>> In addition to approving an initial amount, please specify a Category >>>> and Subcategory for this project. For a list of the current selection >>>> of approved categories, please see: >>>> >>>> https://wiki.lcrc.anl.gov/wiki/Processes/Categories >>>> >>>> Once the Allocation committee has approved the project, please go to >>>> the Project Management page to create it: >>>> >>>> https://accounts.lcrc.anl.gov/projects.php >>>> >>>> Thank You, >>>> The LCRC Accounts System >>>> _______________________________________________ >>>> allocations-admins mailing list >>>> allocations-admins(a)lists.lcrc.anl.gov >>>> https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >>> _______________________________________________ >>> allocations-admins mailing list >>> allocations-admins(a)lists.lcrc.anl.gov >>> https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >> >> >> ----------------------------------------- >> Ray Bair >> Computing, Environment, and Life Sciences >> Argonne National Laboratory >> and the University of Chicago >> Building 240, Room 4126 >> 9700 South Cass Avenue >> Argonne, IL 60439 >> email: rbair(at)anl.gov >> Phone: (630)252-5751 >> >> ----------------------------------------- Ray Bair Computing, Environment, and Life Sciences Argonne National Laboratory and the University of Chicago Building 240, Room 4126 9700 South Cass Avenue Argonne, IL 60439 email: rbair(at)anl.gov Phone: (630)252-5751

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Re: [allocations-admins] [LCRC Accounts] Project Request: Cosmology
by John Valdes 12 Apr '10

12 Apr '10

On Mon, Apr 12, 2010 at 09:14:14PM -0500, Bair, Raymond A. wrote: > Yes, 150K seems right for a start. OK; should I put Steve as contact? Is priority 3 good? John > On 4/12/10 7:15 PM, "John Valdes" <valdes(a)mcs.anl.gov> wrote: > > > Any decision on this project? The request came in the day after the > > allocation meeting. If we approve, we need to decide: > > > > Amount: > > Contact: > > Cat/Subcat: > > Priority: > > > > The request sounds good to me; I would say 150K, either Ray or Steve > > Pieper as POC, P:Phy, and 3. > > > > John > > > > On Fri, Apr 02, 2010 at 04:09:21PM -0500, 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: Joe Bernstein > >> Applicant's institution: ANL > >> Applicant's division: HEP > >> Project Name: Cosmology > >> Project title: Harnessing Computational Cosmology Simulations to > >> Investigate Cosmic Evolution > >> Associated funding: None external to ANL sources > >> Other Systems: ANL Blue Gene/P (renewal in preparation for ~300000 > >> CPU-hrs over 4 months) > >> Science: The evidence for dark energy represents one of the > >> greatest mysteries of modern science. The proposed research will probe the > >> implications of > >> dark energy via analysis of computational cosmology simulations. Several > >> independent observational methods provide evidence pointing to the conclusion > >> that 95% of the current energy density of the Universe exists as part of the > >> "dark sector" that is different from normal, i.e., > >> "baryonic," matter. In particular, the dark sector is thought to be comprised > >> of 22% "dark matter," which interacts with baryonic matter > >> ostensibly only through gravity, and 73% "dark energy," which experiences > >> gravity as a repulsive force. The nature of both dark sector components are > >> essentially complete unknowns. It is presently an exciting time to be > >> involved in cosmology because planned astronomical surveys will effectively > >> result in dark sector probes becoming systematics-limited, making numerical > >> simulations crucial to placing precision constraints on the dark sector. In > >> addition, particle physics theorists predict that the Large Hadron Collider > >> (LHC) and direct dark matter experiments may soon discover a dark matter > >> candidate particle. ANL HEP staff and collaborating U. Illinois faculty are > >> members of the Dark Energy Survey, which will provide the next generation of > >> dark energy and (indirect) dark matter data. Local scientific simulation > >> expertise and high-performance computing further make ANL ideally-suited to > >> pursue answers to questions about the dark sector. The focus of the > >> proposed research is the production and interpretation of computational > >> cosmology simulations in order to elucidate the nature of the dark sector. > >> Project description: The "Cosmology" project on fusion.lcrc.anl.gov > >> (hereafter, "fusion") is in support of the one of the main research efforts > >> of the PI as an ANL Computational Postdoctoral Fellow. The number of project > >> members will be 3-5. We will make use of the requested number of CPU-hrs > >> (275K) in efforts to generate initial conditions and verify scaling results > >> for cosmology simulations run on the ANL Blue Gene/P ("BG/P"). Toward this > >> end, we will harness piecewise-parabolic method (PPM) hydrodynamics and > >> N-body gravity solvers, MPI for inter-processor communication, and HDF5 to > >> implement parallel I/O. We will utilize both the C and FORTRAN90 programming > >> languages. > >> > >> Paul Ricker (U. Illinois) is a computational cosmology expert working with > >> Boyana Norris (MCS) on BG/P cosmology studies. The PI of this proposal > >> recently transitioned from a classification as an ANL Postdoctoral Appointee > >> to an ANL Computational Postdoctoral Fellow. His > >> new duties include collaborating on these efforts with the goal of submitting > >> a 2011 DOE INCITE proposal. The ultimate target of the BG/P > >> simulation effort is runs requiring PPM+N-body simulations with a 1 Gpc (1 pc > >> = 3.09x10^16 m) box size, 2048^3 grid cells, and 10^11 dark matter particles. > >> We anticipate employing fusion to generate initial conditions for a suite of > >> a few dozen BG/P simulations. Generating such initial conditions is memory > >> intensive and cannot currently be done on the BG/P. These requirements also > >> push the limits of existing codes. Scaling the cosmology runs to the target > >> level represents a marked increase relative to machines used to date. > >> Verifying scaling results, on a traditional Linux cluster such as fusion, > >> will constitute an important part of our BG/P studies. We are highly > >> confident of fusion's suitability for the proposed simulations because such > >> runs have been shown to scale to upwards of 4K CPUs on other Linux clusters. > >> > >> The scaling studies will require approximately 10 runs each for strong and > >> weak scaling for a total of ~20 runs. Based on Prof. Ricker's experience with > >> PPM+N-body simulations performed at Oak Ridge National Laboratory, we > >> estimate that a run with 2048^3 grid cells will cost approximately 400 > >> CPU-hrs per timestep and require ~30 time steps for a total of 12K CPU-hrs. > >> Assuming reasonable scaling, this implies a total cost of approximately 240K > >> CPU-hrs for the scaling study. Generating initial conditions will require a > >> significantly smaller cost by comparison. Thus, an allocation of 275K CPU-hrs > >> will enable significant research progress. > >> Project URL: > >> Requested allocation: 275000 > >> Justification: > >> > >> > >> The requester has used 0 hours of their initial startup project. > >> > >> In addition to approving an initial amount, please specify a Category > >> and Subcategory for this project. For a list of the current selection > >> of approved categories, please see: > >> > >> https://wiki.lcrc.anl.gov/wiki/Processes/Categories > >> > >> Once the Allocation committee has approved the project, please go to > >> the Project Management page to create it: > >> > >> https://accounts.lcrc.anl.gov/projects.php > >> > >> Thank You, > >> The LCRC Accounts System > >> _______________________________________________ > >> allocations-admins mailing list > >> allocations-admins(a)lists.lcrc.anl.gov > >> https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins > > _______________________________________________ > > allocations-admins mailing list > > allocations-admins(a)lists.lcrc.anl.gov > > https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins > > > ----------------------------------------- > Ray Bair > Computing, Environment, and Life Sciences > Argonne National Laboratory > and the University of Chicago > Building 240, Room 4126 > 9700 South Cass Avenue > Argonne, IL 60439 > email: rbair(at)anl.gov > Phone: (630)252-5751 > >

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Re: [allocations-admins] [LCRC Accounts] Project Request: Cosmology
by Bair, Raymond A. 12 Apr '10

12 Apr '10

Yes, 150K seems right for a start. Ray On 4/12/10 7:15 PM, "John Valdes" <valdes(a)mcs.anl.gov> wrote: > Any decision on this project? The request came in the day after the > allocation meeting. If we approve, we need to decide: > > Amount: > Contact: > Cat/Subcat: > Priority: > > The request sounds good to me; I would say 150K, either Ray or Steve > Pieper as POC, P:Phy, and 3. > > John > > On Fri, Apr 02, 2010 at 04:09:21PM -0500, 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: Joe Bernstein >> Applicant's institution: ANL >> Applicant's division: HEP >> Project Name: Cosmology >> Project title: Harnessing Computational Cosmology Simulations to >> Investigate Cosmic Evolution >> Associated funding: None external to ANL sources >> Other Systems: ANL Blue Gene/P (renewal in preparation for ~300000 >> CPU-hrs over 4 months) >> Science: The evidence for dark energy represents one of the >> greatest mysteries of modern science. The proposed research will probe the >> implications of >> dark energy via analysis of computational cosmology simulations. Several >> independent observational methods provide evidence pointing to the conclusion >> that 95% of the current energy density of the Universe exists as part of the >> "dark sector" that is different from normal, i.e., >> "baryonic," matter. In particular, the dark sector is thought to be comprised >> of 22% "dark matter," which interacts with baryonic matter >> ostensibly only through gravity, and 73% "dark energy," which experiences >> gravity as a repulsive force. The nature of both dark sector components are >> essentially complete unknowns. It is presently an exciting time to be >> involved in cosmology because planned astronomical surveys will effectively >> result in dark sector probes becoming systematics-limited, making numerical >> simulations crucial to placing precision constraints on the dark sector. In >> addition, particle physics theorists predict that the Large Hadron Collider >> (LHC) and direct dark matter experiments may soon discover a dark matter >> candidate particle. ANL HEP staff and collaborating U. Illinois faculty are >> members of the Dark Energy Survey, which will provide the next generation of >> dark energy and (indirect) dark matter data. Local scientific simulation >> expertise and high-performance computing further make ANL ideally-suited to >> pursue answers to questions about the dark sector. The focus of the >> proposed research is the production and interpretation of computational >> cosmology simulations in order to elucidate the nature of the dark sector. >> Project description: The "Cosmology" project on fusion.lcrc.anl.gov >> (hereafter, "fusion") is in support of the one of the main research efforts >> of the PI as an ANL Computational Postdoctoral Fellow. The number of project >> members will be 3-5. We will make use of the requested number of CPU-hrs >> (275K) in efforts to generate initial conditions and verify scaling results >> for cosmology simulations run on the ANL Blue Gene/P ("BG/P"). Toward this >> end, we will harness piecewise-parabolic method (PPM) hydrodynamics and >> N-body gravity solvers, MPI for inter-processor communication, and HDF5 to >> implement parallel I/O. We will utilize both the C and FORTRAN90 programming >> languages. >> >> Paul Ricker (U. Illinois) is a computational cosmology expert working with >> Boyana Norris (MCS) on BG/P cosmology studies. The PI of this proposal >> recently transitioned from a classification as an ANL Postdoctoral Appointee >> to an ANL Computational Postdoctoral Fellow. His >> new duties include collaborating on these efforts with the goal of submitting >> a 2011 DOE INCITE proposal. The ultimate target of the BG/P >> simulation effort is runs requiring PPM+N-body simulations with a 1 Gpc (1 pc >> = 3.09x10^16 m) box size, 2048^3 grid cells, and 10^11 dark matter particles. >> We anticipate employing fusion to generate initial conditions for a suite of >> a few dozen BG/P simulations. Generating such initial conditions is memory >> intensive and cannot currently be done on the BG/P. These requirements also >> push the limits of existing codes. Scaling the cosmology runs to the target >> level represents a marked increase relative to machines used to date. >> Verifying scaling results, on a traditional Linux cluster such as fusion, >> will constitute an important part of our BG/P studies. We are highly >> confident of fusion's suitability for the proposed simulations because such >> runs have been shown to scale to upwards of 4K CPUs on other Linux clusters. >> >> The scaling studies will require approximately 10 runs each for strong and >> weak scaling for a total of ~20 runs. Based on Prof. Ricker's experience with >> PPM+N-body simulations performed at Oak Ridge National Laboratory, we >> estimate that a run with 2048^3 grid cells will cost approximately 400 >> CPU-hrs per timestep and require ~30 time steps for a total of 12K CPU-hrs. >> Assuming reasonable scaling, this implies a total cost of approximately 240K >> CPU-hrs for the scaling study. Generating initial conditions will require a >> significantly smaller cost by comparison. Thus, an allocation of 275K CPU-hrs >> will enable significant research progress. >> Project URL: >> Requested allocation: 275000 >> Justification: >> >> >> The requester has used 0 hours of their initial startup project. >> >> In addition to approving an initial amount, please specify a Category >> and Subcategory for this project. For a list of the current selection >> of approved categories, please see: >> >> https://wiki.lcrc.anl.gov/wiki/Processes/Categories >> >> Once the Allocation committee has approved the project, please go to >> the Project Management page to create it: >> >> https://accounts.lcrc.anl.gov/projects.php >> >> Thank You, >> The LCRC Accounts System >> _______________________________________________ >> allocations-admins mailing list >> allocations-admins(a)lists.lcrc.anl.gov >> https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins > _______________________________________________ > allocations-admins mailing list > allocations-admins(a)lists.lcrc.anl.gov > https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins ----------------------------------------- Ray Bair Computing, Environment, and Life Sciences Argonne National Laboratory and the University of Chicago Building 240, Room 4126 9700 South Cass Avenue Argonne, IL 60439 email: rbair(at)anl.gov Phone: (630)252-5751

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Re: [allocations-admins] [LCRC Accounts] Project Request: Cosmology
by John Valdes 12 Apr '10

12 Apr '10

Any decision on this project? The request came in the day after the allocation meeting. If we approve, we need to decide: Amount: Contact: Cat/Subcat: Priority: The request sounds good to me; I would say 150K, either Ray or Steve Pieper as POC, P:Phy, and 3. John On Fri, Apr 02, 2010 at 04:09:21PM -0500, 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: Joe Bernstein > Applicant's institution: ANL > Applicant's division: HEP > Project Name: Cosmology > Project title: Harnessing Computational Cosmology Simulations to Investigate Cosmic Evolution > Associated funding: None external to ANL sources > Other Systems: ANL Blue Gene/P (renewal in preparation for ~300000 CPU-hrs over 4 months) > Science: The evidence for dark energy represents one of the greatest mysteries of modern science. The proposed research will probe the implications of > dark energy via analysis of computational cosmology simulations. Several independent observational methods provide evidence pointing to the conclusion that 95% of the current energy density of the Universe exists as part of the "dark sector" that is different from normal, i.e., > "baryonic," matter. In particular, the dark sector is thought to be comprised of 22% "dark matter," which interacts with baryonic matter > ostensibly only through gravity, and 73% "dark energy," which experiences gravity as a repulsive force. The nature of both dark sector components are essentially complete unknowns. It is presently an exciting time to be involved in cosmology because planned astronomical surveys will effectively result in dark sector probes becoming systematics-limited, making numerical simulations crucial to placing precision constraints on the dark sector. In addition, particle physics theorists predict that the Large Hadron Collider (LHC) and direct dark matter experiments may soon discover a dark matter candidate particle. ANL HEP staff and collaborating U. Illinois faculty are members of the Dark Energy Survey, which will provide the next generation of dark energy and (indirect) dark matter data. Local scientific simulation > expertise and high-performance computing further make ANL ideally-suited to pursue answers to questions about the dark sector. The focus of the > proposed research is the production and interpretation of computational cosmology simulations in order to elucidate the nature of the dark sector. > Project description: The "Cosmology" project on fusion.lcrc.anl.gov (hereafter, "fusion") is in support of the one of the main research efforts of the PI as an ANL Computational Postdoctoral Fellow. The number of project members will be 3-5. We will make use of the requested number of CPU-hrs (275K) in efforts to generate initial conditions and verify scaling results for cosmology simulations run on the ANL Blue Gene/P ("BG/P"). Toward this end, we will harness piecewise-parabolic method (PPM) hydrodynamics and N-body gravity solvers, MPI for inter-processor communication, and HDF5 to implement parallel I/O. We will utilize both the C and FORTRAN90 programming languages. > > Paul Ricker (U. Illinois) is a computational cosmology expert working with Boyana Norris (MCS) on BG/P cosmology studies. The PI of this proposal recently transitioned from a classification as an ANL Postdoctoral Appointee to an ANL Computational Postdoctoral Fellow. His > new duties include collaborating on these efforts with the goal of submitting a 2011 DOE INCITE proposal. The ultimate target of the BG/P > simulation effort is runs requiring PPM+N-body simulations with a 1 Gpc (1 pc = 3.09x10^16 m) box size, 2048^3 grid cells, and 10^11 dark matter particles. We anticipate employing fusion to generate initial conditions for a suite of a few dozen BG/P simulations. Generating such initial conditions is memory intensive and cannot currently be done on the BG/P. These requirements also push the limits of existing codes. Scaling the cosmology runs to the target level represents a marked increase relative to machines used to date. Verifying scaling results, on a traditional Linux cluster such as fusion, will constitute an important part of our BG/P studies. We are highly confident of fusion's suitability for the proposed simulations because such runs have been shown to scale to upwards of 4K CPUs on other Linux clusters. > > The scaling studies will require approximately 10 runs each for strong and weak scaling for a total of ~20 runs. Based on Prof. Ricker's experience with PPM+N-body simulations performed at Oak Ridge National Laboratory, we estimate that a run with 2048^3 grid cells will cost approximately 400 CPU-hrs per timestep and require ~30 time steps for a total of 12K CPU-hrs. Assuming reasonable scaling, this implies a total cost of approximately 240K CPU-hrs for the scaling study. Generating initial conditions will require a significantly smaller cost by comparison. Thus, an allocation of 275K CPU-hrs will enable significant research progress. > Project URL: > Requested allocation: 275000 > Justification: > > > The requester has used 0 hours of their initial startup project. > > In addition to approving an initial amount, please specify a Category > and Subcategory for this project. For a list of the current selection > of approved categories, please see: > > https://wiki.lcrc.anl.gov/wiki/Processes/Categories > > Once the Allocation committee has approved the project, please go to > the Project Management page to create it: > > https://accounts.lcrc.anl.gov/projects.php > > Thank You, > The LCRC Accounts System > _______________________________________________ > allocations-admins mailing list > allocations-admins(a)lists.lcrc.anl.gov > https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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[LCRC Accounts] Project Request: Cosmology
by accounts＠lcrc.anl.gov 02 Apr '10

02 Apr '10

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: Joe Bernstein Applicant's institution: ANL Applicant's division: HEP Project Name: Cosmology Project title: Harnessing Computational Cosmology Simulations to Investigate Cosmic Evolution Associated funding: None external to ANL sources Other Systems: ANL Blue Gene/P (renewal in preparation for ~300000 CPU-hrs over 4 months) Science: The evidence for dark energy represents one of the greatest mysteries of modern science. The proposed research will probe the implications of dark energy via analysis of computational cosmology simulations. Several independent observational methods provide evidence pointing to the conclusion that 95% of the current energy density of the Universe exists as part of the "dark sector" that is different from normal, i.e., "baryonic," matter. In particular, the dark sector is thought to be comprised of 22% "dark matter," which interacts with baryonic matter ostensibly only through gravity, and 73% "dark energy," which experiences gravity as a repulsive force. The nature of both dark sector components are essentially complete unknowns. It is presently an exciting time to be involved in cosmology because planned astronomical surveys will effectively result in dark sector probes becoming systematics-limited, making numerical simulations crucial to placing precision constraints on the dark sector. In addition, particle physics theorists predict that the Large Hadron Collider (LHC) and direct dark matter experiments may soon discover a dark matter candidate particle. ANL HEP staff and collaborating U. Illinois faculty are members of the Dark Energy Survey, which will provide the next generation of dark energy and (indirect) dark matter data. Local scientific simulation expertise and high-performance computing further make ANL ideally-suited to pursue answers to questions about the dark sector. The focus of the proposed research is the production and interpretation of computational cosmology simulations in order to elucidate the nature of the dark sector. Project description: The "Cosmology" project on fusion.lcrc.anl.gov (hereafter, "fusion") is in support of the one of the main research efforts of the PI as an ANL Computational Postdoctoral Fellow. The number of project members will be 3-5. We will make use of the requested number of CPU-hrs (275K) in efforts to generate initial conditions and verify scaling results for cosmology simulations run on the ANL Blue Gene/P ("BG/P"). Toward this end, we will harness piecewise-parabolic method (PPM) hydrodynamics and N-body gravity solvers, MPI for inter-processor communication, and HDF5 to implement parallel I/O. We will utilize both the C and FORTRAN90 programming languages. Paul Ricker (U. Illinois) is a computational cosmology expert working with Boyana Norris (MCS) on BG/P cosmology studies. The PI of this proposal recently transitioned from a classification as an ANL Postdoctoral Appointee to an ANL Computational Postdoctoral Fellow. His new duties include collaborating on these efforts with the goal of submitting a 2011 DOE INCITE proposal. The ultimate target of the BG/P simulation effort is runs requiring PPM+N-body simulations with a 1 Gpc (1 pc = 3.09x10^16 m) box size, 2048^3 grid cells, and 10^11 dark matter particles. We anticipate employing fusion to generate initial conditions for a suite of a few dozen BG/P simulations. Generating such initial conditions is memory intensive and cannot currently be done on the BG/P. These requirements also push the limits of existing codes. Scaling the cosmology runs to the target level represents a marked increase relative to machines used to date. Verifying scaling results, on a traditional Linux cluster such as fusion, will constitute an important part of our BG/P studies. We are highly confident of fusion's suitability for the proposed simulations because such runs have been shown to scale to upwards of 4K CPUs on other Linux clusters. The scaling studies will require approximately 10 runs each for strong and weak scaling for a total of ~20 runs. Based on Prof. Ricker's experience with PPM+N-body simulations performed at Oak Ridge National Laboratory, we estimate that a run with 2048^3 grid cells will cost approximately 400 CPU-hrs per timestep and require ~30 time steps for a total of 12K CPU-hrs. Assuming reasonable scaling, this implies a total cost of approximately 240K CPU-hrs for the scaling study. Generating initial conditions will require a significantly smaller cost by comparison. Thus, an allocation of 275K CPU-hrs will enable significant research progress. Project URL: Requested allocation: 275000 Justification: The requester has used 0 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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