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

Re: [allocations-admins] Project Allocation Request - MHK
by Bair, Raymond A. 16 Apr '15

16 Apr '15

Update -- I sent a poll to the Allocations Committee Wednesday evening, and we are waiting for enough responses. Ray From: Shivanesh Rao <shivanesh.rao(a)gmail.com<mailto:[email protected]>> Date: Wednesday, April 15, 2015 at 8:48 PM To: Ray Bair <rbair(a)anl.gov<mailto:[email protected]>> Cc: "Grippo, Mark A." <mgrippo(a)anl.gov<mailto:[email protected]>> Subject: Re: Project Allocation Request - MHK Hi Ray, 300k per term sounds fine. I need about 200k for a calibration run and 200k for a final simulation in the near future. I can work with 300k this term by doing a shorter calibration run. On a different note, we'd like to transfer some data (from my account) to hard drives (to ship to a colleague), would it be possible for you to transfer this data if we supplied you with the drives? or maybe if you could expand the access to Mark, so he can copy the files? Thanks, Shivanesh On Thu, Apr 16, 2015 at 11:34 AM, Bair, Raymond A. <rbair(a)anl.gov<mailto:[email protected]>> wrote: Dear Shivanesh, The Allocations Committee may request that you run exclusively on Fusion because Blues is quite full. One more question… Are you requesting 300,000 more core hours for the 3rd quarter (April-June), plus 300,000 core hours for the 4th quarter (July-Sept.)? That is how we would normally grant it. Regards, Ray From: Shivanesh Rao <shivanesh.rao(a)gmail.com<mailto:[email protected]>> Date: Wednesday, April 15, 2015 at 8:26 PM To: "Grippo, Mark A." <mgrippo(a)anl.gov<mailto:[email protected]>> Cc: Ray Bair <rbair(a)anl.gov<mailto:[email protected]>> Subject: Re: Project Allocation Request - MHK Hi Mark, Either system is fine. But doesn't the allocation work on both systems? Shivanesh On Thu, Apr 16, 2015 at 6:24 AM, Grippo, Mark A. <mgrippo(a)anl.gov<mailto:[email protected]>> wrote: Ray, Shivanesh is working remotely. Shivanesh, Does it matter whether you use blues or fusion? Mark -----Original Message----- From: Bair, Raymond A. Sent: Wednesday, April 15, 2015 3:10 PM To: Grippo, Mark A. Subject: Re: Project Allocation Request - MHK Dear Mark, Could you run this work on either Blues or Fusion? We have more availability on Fusion this semester. 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<http://anl.gov> Phone: (630)252-5751 On 4/15/15, 10:29 AM, "accounts(a)lcrc.anl.gov<mailto:[email protected]>" <accounts(a)lcrc.anl.gov<mailto:[email protected]>> wrote: >Hello, > >A change in allocation has been requested: > > Requester: mgrippo (Mark Grippo) > Project: MHK > Title: Hydrodynamic model development for Cobscook Bay > Description: The behavioral model requires the collection of fish >position data and the simulation of flow during the period for which >the fish data were collected. The fish position data were collected >during two, 72 hr periods in August 2014. Our goal for FY15 is to >simulate water flow during these two periods. Based on our previous >year of simulations using the Blues cluster, we estimate that we will >need 450k core-hours for Q1 and Q2 to complete the necessary simulations. > > > > Current: undetermined amount >Justification: Additional hours are needed to complete a final set of >calibration runs for our hydrodynamic model. Based on previous runs, >it costs 200k core hours for the last 7 days of runs we need. It will >take 1 run to calibrate the run and another run to finish the >simulation with proper calibration. Therefore, at minimum we would like >to have 400K core hours, and 600k would be ideal as a precaution in >case we need an additional run. Thank you. > > > Requested: 600000 > >A specific reason has been given: >Additional hours are needed to complete a final set of calibration runs >for our hydrodynamic model. Based on previous runs, it costs 200k core >hours for the last 7 days of runs we need. It will take 1 run to >calibrate the run and another run to finish the simulation with proper >calibration. Therefore, at minimum we would like to have 400K core >hours, and 600k would be ideal as a precaution in case we need an >additional run. Thank you. > >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<mailto:[email protected]> >https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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Re: [allocations-admins] [LCRC Accounts] Project Request: UrbanCrime
by John Blaas 15 Apr '15

15 Apr '15

As per the meeting I have granted 50000 core hours to the UrbanCrime project. - JB On Mon, Apr 13, 2015 at 11:33 AM, Low, John J. <jlow(a)mcs.anl.gov> wrote: > Ray, > > They only asked for 5000 hours. Is that all they need or could it be a > mistake? > > 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: <Bair>, "Bair, Raymond A." <rbair(a)anl.gov> > Reply-To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> > Date: Monday, April 13, 2015 at 11:30 AM > To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> > Subject: Re: [allocations-admins] [LCRC Accounts] Project Request: > UrbanCrime > >>This looks fine to me. >> >>Misc category project >> >>There is not a good subcategory. Lets make it Soft for now. >> >> >>Misun Min could be the POC >> >> >>Regards, >> >>Ray >> >>On 4/10/15, 2:08 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: Charles Catlett >>>Applicant's institution: ANL >>> Applicant's division: MCS >>> Project Name: UrbanCrime >>> Project title: Urban Crime and Weather: An Empirical Study >>> Associated funding: Arnold Foundation, LDRD >>> Other Systems: None >>> Science: The project is an empirical analysis of violent >>>crime events and weather data, using clustering and machine learning >>>algorithms to test hypotheses related to the effect of changes in weather >>>on the probability of violent crime events in urban environments. >>> Project description: The project uses Chicago crime data and NOAA >>>weather data, applying various algorithms to the data to determine >>>interrelationships between violent crime events and weather changes. >>> >>>Software is primarily Python and R, and runs out of memory on a desktop >>>system. This project aims to explore how HPC resources could be used to >>>meet the demands of current studies, and to prepare for much larger data >>>sources including (a) crimes from additional cities, and (b) higher >>>resolution weather data. >>> >>>We also will explore how HPC resources can assist in more complex >>>analysis such as including additional data beyond weather (e.g. public >>>transit schedules, census data, etc.) >>> Industry partnership: >>> Project URL: >>> Requested allocation: 5000 >>> Q1: 0 >>> Q2: 0 >>> Q3: 1000 >>> Q4: 4000 >>> Justification: >>> Storage requirements: >>> >>> >>>The requester has used undetermined amount hours of their initial startup >>>project. >>> >>>In addition to approving an initial amount, please specify a Category >>>and Subcategory for this project. For a list of the current selection >>>of approved categories, please see: >>> >>> https://wiki.lcrc.anl.gov/wiki/Processes/Categories >>> >>>Once the Allocation committee has approved the project, please go to >>>the Project Management page to create it: >>> >>>https://accounts.lcrc.anl.gov/projects.php >>> >>>Thank You, >>>The LCRC Accounts System >>>_______________________________________________ >>>allocations-admins mailing list >>>allocations-admins(a)lcrc.anl.gov >>>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >> >>_______________________________________________ >>allocations-admins mailing list >>allocations-admins(a)lcrc.anl.gov >>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins > > _______________________________________________ > allocations-admins mailing list > allocations-admins(a)lcrc.anl.gov > https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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

15 Apr '15

Hello, A change in allocation has been requested: Requester: mgrippo (Mark Grippo) Project: MHK Title: Hydrodynamic model development for Cobscook Bay Description: The behavioral model requires the collection of fish position data and the simulation of flow during the period for which the fish data were collected. The fish position data were collected during two, 72 hr periods in August 2014. Our goal for FY15 is to simulate water flow during these two periods. Based on our previous year of simulations using the Blues cluster, we estimate that we will need 450k core-hours for Q1 and Q2 to complete the necessary simulations. Current: undetermined amount Justification: Additional hours are needed to complete a final set of calibration runs for our hydrodynamic model. Based on previous runs, it costs 200k core hours for the last 7 days of runs we need. It will take 1 run to calibrate the run and another run to finish the simulation with proper calibration. Therefore, at minimum we would like to have 400K core hours, and 600k would be ideal as a precaution in case we need an additional run. Thank you. Requested: 600000 A specific reason has been given: Additional hours are needed to complete a final set of calibration runs for our hydrodynamic model. Based on previous runs, it costs 200k core hours for the last 7 days of runs we need. It will take 1 run to calibrate the run and another run to finish the simulation with proper calibration. Therefore, at minimum we would like to have 400K core hours, and 600k would be ideal as a precaution in case we need an additional run. Thank you. This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

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Re: [allocations-admins] [LCRC Accounts] Project Request: UrbanCrime
by Bair, Raymond A. 15 Apr '15

15 Apr '15

FYI, Charlie is presenting to the Secretary of Energy this week, having passed all the hurdles in the selection of new "big ideas" for his consideration. Hence he is a bit distracted. Ray On 4/13/15, 11:41 AM, "Bair, Raymond A." <rbair(a)anl.gov> wrote: >I am checking with Charlie. > >----------------------------------------- >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 4/13/15, 11:33 AM, "Low, John J." <jlow(a)mcs.anl.gov> wrote: > >>Ray, >> >>They only asked for 5000 hours. Is that all they need or could it be a >>mistake? >> >>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: <Bair>, "Bair, Raymond A." <rbair(a)anl.gov> >>Reply-To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> >>Date: Monday, April 13, 2015 at 11:30 AM >>To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> >>Subject: Re: [allocations-admins] [LCRC Accounts] Project Request: >>UrbanCrime >> >>>This looks fine to me. >>> >>>Misc category project >>> >>>There is not a good subcategory. Lets make it Soft for now. >>> >>> >>>Misun Min could be the POC >>> >>> >>>Regards, >>> >>>Ray >>> >>>On 4/10/15, 2:08 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: Charles Catlett >>>>Applicant's institution: ANL >>>> Applicant's division: MCS >>>> Project Name: UrbanCrime >>>> Project title: Urban Crime and Weather: An Empirical Study >>>> Associated funding: Arnold Foundation, LDRD >>>> Other Systems: None >>>> Science: The project is an empirical analysis of >>>>violent >>>>crime events and weather data, using clustering and machine learning >>>>algorithms to test hypotheses related to the effect of changes in >>>>weather >>>>on the probability of violent crime events in urban environments. >>>> Project description: The project uses Chicago crime data and NOAA >>>>weather data, applying various algorithms to the data to determine >>>>interrelationships between violent crime events and weather changes. >>>> >>>>Software is primarily Python and R, and runs out of memory on a desktop >>>>system. This project aims to explore how HPC resources could be used >>>>to >>>>meet the demands of current studies, and to prepare for much larger >>>>data >>>>sources including (a) crimes from additional cities, and (b) higher >>>>resolution weather data. >>>> >>>>We also will explore how HPC resources can assist in more complex >>>>analysis such as including additional data beyond weather (e.g. public >>>>transit schedules, census data, etc.) >>>> Industry partnership: >>>> Project URL: >>>> Requested allocation: 5000 >>>> Q1: 0 >>>> Q2: 0 >>>> Q3: 1000 >>>> Q4: 4000 >>>> Justification: >>>> Storage requirements: >>>> >>>> >>>>The requester has used undetermined amount hours of their initial >>>>startup >>>>project. >>>> >>>>In addition to approving an initial amount, please specify a Category >>>>and Subcategory for this project. For a list of the current selection >>>>of approved categories, please see: >>>> >>>> https://wiki.lcrc.anl.gov/wiki/Processes/Categories >>>> >>>>Once the Allocation committee has approved the project, please go to >>>>the Project Management page to create it: >>>> >>>>https://accounts.lcrc.anl.gov/projects.php >>>> >>>>Thank You, >>>>The LCRC Accounts System >>>>_______________________________________________ >>>>allocations-admins mailing list >>>>allocations-admins(a)lcrc.anl.gov >>>>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >>> >>>_______________________________________________ >>>allocations-admins mailing list >>>allocations-admins(a)lcrc.anl.gov >>>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >> >>_______________________________________________ >>allocations-admins mailing list >>allocations-admins(a)lcrc.anl.gov >>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins > >_______________________________________________ >allocations-admins mailing list >allocations-admins(a)lcrc.anl.gov >https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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Re: [allocations-admins] [LCRC Accounts] Project Request: estrogen_namd
by John Blaas 14 Apr '15

14 Apr '15

The project estrogen_namd has been activated with the POC being Gyorgy Babnigg. They have been granted 45k till the end of the year. - JB On Mon, Apr 13, 2015 at 4:20 PM, Bair, Raymond A. <rbair(a)anl.gov> wrote: > This 45K project will use biggpu nodes. > > The class, subclass and POC would be the same as project Drude. Prio 3. > > Looks OK to approve. > > Ray > > > > > On 4/13/15, 11:48 AM, "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: wei jiang >>Applicant's institution: ANL >> Applicant's division: Leadership Computing Facility >> Project Name: estrogen_namd >> Project title: Long-scale conformational activation in >>estrogen receptor with NAMD on GPU/CPU heterogeneous architecture >> Associated funding: ALCF fund >>DOD grant >> Other Systems: Mira >> Science: Structure-function relation of protein; >>Developing SIMD version force kernel for namd; >>Compare simd version CPU and GPU/CPU performance. >> Project description: Wei Jiang, Sunhwan Jo, Sichun Yang >> >>Leadership Computing Facility, Argonne National Laboratory >>Case Western Reserve University, Department of Pharmacology >> >>The ligand-binding domain (LBD) of an estrogen receptor undergoes a large >>conformational switching from an inactive to active state in response to >>hormone stimuli (see figure below). Very recently, a novel D538G mutant >>has been identified to be active in advanced breast cancer tumors. >>Despite being the key target for breast cancer therapeutics, the LBD is a >>remarkable example of conformational switching, where the dynamics of a >>C-terminal α-helix H12 from an inactive to active conformation remains >>unclear. >>The inactive conformation can be stabilized by therapeutic inhibitors >>such as tamoxifen, so H12 is in a helix-bundle forming conformation >>(marked in blue in Figure) that can block the receptor from recruiting >>coactivators for transcriptional activation. Once activated by estrogen >>binding, H12 is switched to a completely different orientation covering >>the estrogen-binding pocket in the active conformation (marked in red). >>These two well-defined conformations—active and inactive—have been >>revealed extensively by crystallographic studies. >>Our recent coarse-grained molecular dynamics shows such a transition >>could take at least in the order of 100 ns (Huang et al, JCTC, 10 (8) >>2897–2900, 2014). While this information is highly informative, a key >>question remains, i.e., whether the mutation affects the active state >>only or sculpts the entire landscape, including both inactive and active >>states. To answer this question from a broad landscape perspective, the >>modeling of such a large-scale H12 transition can be quite challenging >>for atomic-level simulations using the standard CPU-based MD simulations. >>To obtain long-scale and long-time MD trajectories, we propose to use the >>GPU version (Nvidia CUDA) NAMD package on the Blues bigmem GPU/CPU nodes. >>NAMD is the only one MD code that can run at strong scaling on massively >>distributed GPU/CPU platform such as Cray XT7. In this proposal, in >>addition to the brutal-force GPU/CPU work, we also explore AVX256 >>instruction set to optimize force kernel of NAMD for state-of-th >> e-art Intel architecture. A fully vectorized force kernel with AVX256 >>also provides a better reasonable CPU performance reference for GPU. In >>this proposal we apply a total 45,000 cpu hours, including both long >>production run on GPU/CPU nodes and code development with AVX256. >> >> Industry partnership: >> Project URL: >> Requested allocation: 45000 >> Q1: 0 >> Q2: 0 >> Q3: 20000 >> Q4: 25000 >> Justification: NAMD is the only one MD code that can run at >>strong scaling on massively distributed GPU/CPU platform such as Cray >>XT7. >> Storage requirements: 1 TB >> >> >>The requester has used undetermined amount hours of their initial startup >>project. >> >>In addition to approving an initial amount, please specify a Category >>and Subcategory for this project. For a list of the current selection >>of approved categories, please see: >> >> https://wiki.lcrc.anl.gov/wiki/Processes/Categories >> >>Once the Allocation committee has approved the project, please go to >>the Project Management page to create it: >> >>https://accounts.lcrc.anl.gov/projects.php >> >>Thank You, >>The LCRC Accounts System > > _______________________________________________ > allocations-admins mailing list > allocations-admins(a)lcrc.anl.gov > https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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Re: [allocations-admins] [LCRC Accounts] Project Request: estrogen_namd
by Bair, Raymond A. 13 Apr '15

13 Apr '15

This 45K project will use biggpu nodes. The class, subclass and POC would be the same as project Drude. Prio 3. Looks OK to approve. Ray On 4/13/15, 11:48 AM, "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: wei jiang >Applicant's institution: ANL > Applicant's division: Leadership Computing Facility > Project Name: estrogen_namd > Project title: Long-scale conformational activation in >estrogen receptor with NAMD on GPU/CPU heterogeneous architecture > Associated funding: ALCF fund >DOD grant > Other Systems: Mira > Science: Structure-function relation of protein; >Developing SIMD version force kernel for namd; >Compare simd version CPU and GPU/CPU performance. > Project description: Wei Jiang, Sunhwan Jo, Sichun Yang > >Leadership Computing Facility, Argonne National Laboratory >Case Western Reserve University, Department of Pharmacology > >The ligand-binding domain (LBD) of an estrogen receptor undergoes a large >conformational switching from an inactive to active state in response to >hormone stimuli (see figure below). Very recently, a novel D538G mutant >has been identified to be active in advanced breast cancer tumors. >Despite being the key target for breast cancer therapeutics, the LBD is a >remarkable example of conformational switching, where the dynamics of a >C-terminal α-helix H12 from an inactive to active conformation remains >unclear. >The inactive conformation can be stabilized by therapeutic inhibitors >such as tamoxifen, so H12 is in a helix-bundle forming conformation >(marked in blue in Figure) that can block the receptor from recruiting >coactivators for transcriptional activation. Once activated by estrogen >binding, H12 is switched to a completely different orientation covering >the estrogen-binding pocket in the active conformation (marked in red). >These two well-defined conformations—active and inactive—have been >revealed extensively by crystallographic studies. >Our recent coarse-grained molecular dynamics shows such a transition >could take at least in the order of 100 ns (Huang et al, JCTC, 10 (8) >2897–2900, 2014). While this information is highly informative, a key >question remains, i.e., whether the mutation affects the active state >only or sculpts the entire landscape, including both inactive and active >states. To answer this question from a broad landscape perspective, the >modeling of such a large-scale H12 transition can be quite challenging >for atomic-level simulations using the standard CPU-based MD simulations. >To obtain long-scale and long-time MD trajectories, we propose to use the >GPU version (Nvidia CUDA) NAMD package on the Blues bigmem GPU/CPU nodes. >NAMD is the only one MD code that can run at strong scaling on massively >distributed GPU/CPU platform such as Cray XT7. In this proposal, in >addition to the brutal-force GPU/CPU work, we also explore AVX256 >instruction set to optimize force kernel of NAMD for state-of-th > e-art Intel architecture. A fully vectorized force kernel with AVX256 >also provides a better reasonable CPU performance reference for GPU. In >this proposal we apply a total 45,000 cpu hours, including both long >production run on GPU/CPU nodes and code development with AVX256. > > Industry partnership: > Project URL: > Requested allocation: 45000 > Q1: 0 > Q2: 0 > Q3: 20000 > Q4: 25000 > Justification: NAMD is the only one MD code that can run at >strong scaling on massively distributed GPU/CPU platform such as Cray >XT7. > Storage requirements: 1 TB > > >The requester has used undetermined amount hours of their initial startup >project. > >In addition to approving an initial amount, please specify a Category >and Subcategory for this project. For a list of the current selection >of approved categories, please see: > > https://wiki.lcrc.anl.gov/wiki/Processes/Categories > >Once the Allocation committee has approved the project, please go to >the Project Management page to create it: > >https://accounts.lcrc.anl.gov/projects.php > >Thank You, >The LCRC Accounts System

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[LCRC Accounts] Project Request: estrogen_namd
by accounts＠lcrc.anl.gov 13 Apr '15

13 Apr '15

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: wei jiang Applicant's institution: ANL Applicant's division: Leadership Computing Facility Project Name: estrogen_namd Project title: Long-scale conformational activation in estrogen receptor with NAMD on GPU/CPU heterogeneous architecture Associated funding: ALCF fund DOD grant Other Systems: Mira Science: Structure-function relation of protein; Developing SIMD version force kernel for namd; Compare simd version CPU and GPU/CPU performance. Project description: Wei Jiang, Sunhwan Jo, Sichun Yang Leadership Computing Facility, Argonne National Laboratory Case Western Reserve University, Department of Pharmacology The ligand-binding domain (LBD) of an estrogen receptor undergoes a large conformational switching from an inactive to active state in response to hormone stimuli (see figure below). Very recently, a novel D538G mutant has been identified to be active in advanced breast cancer tumors. Despite being the key target for breast cancer therapeutics, the LBD is a remarkable example of conformational switching, where the dynamics of a C-terminal α-helix H12 from an inactive to active conformation remains unclear. The inactive conformation can be stabilized by therapeutic inhibitors such as tamoxifen, so H12 is in a helix-bundle forming conformation (marked in blue in Figure) that can block the receptor from recruiting coactivators for transcriptional activation. Once activated by estrogen binding, H12 is switched to a completely different orientation covering the estrogen-binding pocket in the active conformation (marked in red). These two well-defined conformations—active and inactive—have been revealed extensively by crystallographic studies. Our recent coarse-grained molecular dynamics shows such a transition could take at least in the order of 100 ns (Huang et al, JCTC, 10 (8) 2897–2900, 2014). While this information is highly informative, a key question remains, i.e., whether the mutation affects the active state only or sculpts the entire landscape, including both inactive and active states. To answer this question from a broad landscape perspective, the modeling of such a large-scale H12 transition can be quite challenging for atomic-level simulations using the standard CPU-based MD simulations. To obtain long-scale and long-time MD trajectories, we propose to use the GPU version (Nvidia CUDA) NAMD package on the Blues bigmem GPU/CPU nodes. NAMD is the only one MD code that can run at strong scaling on massively distributed GPU/CPU platform such as Cray XT7. In this proposal, in addition to the brutal-force GPU/CPU work, we also explore AVX256 instruction set to optimize force kernel of NAMD for state-of-th e-art Intel architecture. A fully vectorized force kernel with AVX256 also provides a better reasonable CPU performance reference for GPU. In this proposal we apply a total 45,000 cpu hours, including both long production run on GPU/CPU nodes and code development with AVX256. Industry partnership: Project URL: Requested allocation: 45000 Q1: 0 Q2: 0 Q3: 20000 Q4: 25000 Justification: NAMD is the only one MD code that can run at strong scaling on massively distributed GPU/CPU platform such as Cray XT7. Storage requirements: 1 TB The requester has used undetermined amount hours of their initial startup project. In addition to approving an initial amount, please specify a Category and Subcategory for this project. For a list of the current selection of approved categories, please see: https://wiki.lcrc.anl.gov/wiki/Processes/Categories Once the Allocation committee has approved the project, please go to the Project Management page to create it: https://accounts.lcrc.anl.gov/projects.php Thank You, The LCRC Accounts System

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Re: [allocations-admins] [LCRC Accounts] Project Request: UrbanCrime
by Bair, Raymond A. 13 Apr '15

13 Apr '15

I am checking with Charlie. ----------------------------------------- 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 4/13/15, 11:33 AM, "Low, John J." <jlow(a)mcs.anl.gov> wrote: >Ray, > >They only asked for 5000 hours. Is that all they need or could it be a >mistake? > >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: <Bair>, "Bair, Raymond A." <rbair(a)anl.gov> >Reply-To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> >Date: Monday, April 13, 2015 at 11:30 AM >To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> >Subject: Re: [allocations-admins] [LCRC Accounts] Project Request: >UrbanCrime > >>This looks fine to me. >> >>Misc category project >> >>There is not a good subcategory. Lets make it Soft for now. >> >> >>Misun Min could be the POC >> >> >>Regards, >> >>Ray >> >>On 4/10/15, 2:08 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: Charles Catlett >>>Applicant's institution: ANL >>> Applicant's division: MCS >>> Project Name: UrbanCrime >>> Project title: Urban Crime and Weather: An Empirical Study >>> Associated funding: Arnold Foundation, LDRD >>> Other Systems: None >>> Science: The project is an empirical analysis of >>>violent >>>crime events and weather data, using clustering and machine learning >>>algorithms to test hypotheses related to the effect of changes in >>>weather >>>on the probability of violent crime events in urban environments. >>> Project description: The project uses Chicago crime data and NOAA >>>weather data, applying various algorithms to the data to determine >>>interrelationships between violent crime events and weather changes. >>> >>>Software is primarily Python and R, and runs out of memory on a desktop >>>system. This project aims to explore how HPC resources could be used to >>>meet the demands of current studies, and to prepare for much larger data >>>sources including (a) crimes from additional cities, and (b) higher >>>resolution weather data. >>> >>>We also will explore how HPC resources can assist in more complex >>>analysis such as including additional data beyond weather (e.g. public >>>transit schedules, census data, etc.) >>> Industry partnership: >>> Project URL: >>> Requested allocation: 5000 >>> Q1: 0 >>> Q2: 0 >>> Q3: 1000 >>> Q4: 4000 >>> Justification: >>> Storage requirements: >>> >>> >>>The requester has used undetermined amount hours of their initial >>>startup >>>project. >>> >>>In addition to approving an initial amount, please specify a Category >>>and Subcategory for this project. For a list of the current selection >>>of approved categories, please see: >>> >>> https://wiki.lcrc.anl.gov/wiki/Processes/Categories >>> >>>Once the Allocation committee has approved the project, please go to >>>the Project Management page to create it: >>> >>>https://accounts.lcrc.anl.gov/projects.php >>> >>>Thank You, >>>The LCRC Accounts System >>>_______________________________________________ >>>allocations-admins mailing list >>>allocations-admins(a)lcrc.anl.gov >>>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >> >>_______________________________________________ >>allocations-admins mailing list >>allocations-admins(a)lcrc.anl.gov >>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins > >_______________________________________________ >allocations-admins mailing list >allocations-admins(a)lcrc.anl.gov >https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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

13 Apr '15

Ray, They only asked for 5000 hours. Is that all they need or could it be a mistake? 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: <Bair>, "Bair, Raymond A." <rbair(a)anl.gov> Reply-To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> Date: Monday, April 13, 2015 at 11:30 AM To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> Subject: Re: [allocations-admins] [LCRC Accounts] Project Request: UrbanCrime >This looks fine to me. > >Misc category project > >There is not a good subcategory. Lets make it Soft for now. > > >Misun Min could be the POC > > >Regards, > >Ray > >On 4/10/15, 2:08 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: Charles Catlett >>Applicant's institution: ANL >> Applicant's division: MCS >> Project Name: UrbanCrime >> Project title: Urban Crime and Weather: An Empirical Study >> Associated funding: Arnold Foundation, LDRD >> Other Systems: None >> Science: The project is an empirical analysis of violent >>crime events and weather data, using clustering and machine learning >>algorithms to test hypotheses related to the effect of changes in weather >>on the probability of violent crime events in urban environments. >> Project description: The project uses Chicago crime data and NOAA >>weather data, applying various algorithms to the data to determine >>interrelationships between violent crime events and weather changes. >> >>Software is primarily Python and R, and runs out of memory on a desktop >>system. This project aims to explore how HPC resources could be used to >>meet the demands of current studies, and to prepare for much larger data >>sources including (a) crimes from additional cities, and (b) higher >>resolution weather data. >> >>We also will explore how HPC resources can assist in more complex >>analysis such as including additional data beyond weather (e.g. public >>transit schedules, census data, etc.) >> Industry partnership: >> Project URL: >> Requested allocation: 5000 >> Q1: 0 >> Q2: 0 >> Q3: 1000 >> Q4: 4000 >> Justification: >> Storage requirements: >> >> >>The requester has used undetermined amount hours of their initial startup >>project. >> >>In addition to approving an initial amount, please specify a Category >>and Subcategory for this project. For a list of the current selection >>of approved categories, please see: >> >> https://wiki.lcrc.anl.gov/wiki/Processes/Categories >> >>Once the Allocation committee has approved the project, please go to >>the Project Management page to create it: >> >>https://accounts.lcrc.anl.gov/projects.php >> >>Thank You, >>The LCRC Accounts System >>_______________________________________________ >>allocations-admins mailing list >>allocations-admins(a)lcrc.anl.gov >>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins > >_______________________________________________ >allocations-admins mailing list >allocations-admins(a)lcrc.anl.gov >https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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Re: [allocations-admins] [LCRC Accounts] Project Request: UrbanCrime
by Bair, Raymond A. 13 Apr '15

13 Apr '15

This looks fine to me. Misc category project There is not a good subcategory. Lets make it Soft for now. Misun Min could be the POC Regards, Ray On 4/10/15, 2:08 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: Charles Catlett >Applicant's institution: ANL > Applicant's division: MCS > Project Name: UrbanCrime > Project title: Urban Crime and Weather: An Empirical Study > Associated funding: Arnold Foundation, LDRD > Other Systems: None > Science: The project is an empirical analysis of violent >crime events and weather data, using clustering and machine learning >algorithms to test hypotheses related to the effect of changes in weather >on the probability of violent crime events in urban environments. > Project description: The project uses Chicago crime data and NOAA >weather data, applying various algorithms to the data to determine >interrelationships between violent crime events and weather changes. > >Software is primarily Python and R, and runs out of memory on a desktop >system. This project aims to explore how HPC resources could be used to >meet the demands of current studies, and to prepare for much larger data >sources including (a) crimes from additional cities, and (b) higher >resolution weather data. > >We also will explore how HPC resources can assist in more complex >analysis such as including additional data beyond weather (e.g. public >transit schedules, census data, etc.) > Industry partnership: > Project URL: > Requested allocation: 5000 > Q1: 0 > Q2: 0 > Q3: 1000 > Q4: 4000 > Justification: > Storage requirements: > > >The requester has used undetermined amount hours of their initial startup >project. > >In addition to approving an initial amount, please specify a Category >and Subcategory for this project. For a list of the current selection >of approved categories, please see: > > https://wiki.lcrc.anl.gov/wiki/Processes/Categories > >Once the Allocation committee has approved the project, please go to >the Project Management page to create it: > >https://accounts.lcrc.anl.gov/projects.php > >Thank You, >The LCRC Accounts System >_______________________________________________ >allocations-admins mailing list >allocations-admins(a)lcrc.anl.gov >https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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