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

Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by Low, John J. 17 Jul '14

17 Jul '14

John, I think the students will be gone by then. They seem anxious to get their work done now. John J. Low Principal Computational Science Specialist Computing, Environment and Life Sciences Building 240, 2143 9700 South Cass Avenue Argonne National Laboratory Argonne, IL 60439. 630-252-0045 www.linkedin.com/pub/john-low/15/8b0/5aa/ On Jul 17, 2014, at 4:34 PM, John Valdes <valdes(a)anl.gov> wrote: > Ray wrote: >> >> I have been interacting with Misun, and we propose adding 50K now while >> Pavan decides how to refactor the project. > > OK. I agree that the radix project needs to be reorganized into > separate projects, but for what it's worth, with only 2 months and 2 > weeks left in the current FY, I would highly recommend that they do so > for the next FY rather than doing it now. That is, keep the radix > project intact for the current FY, and when the call for new and > renewed projects is made for FY15, have them propose new projects > (plus a smaller renewal for radix) as appropriate. Just my 2¢. > > John > _______________________________________________ > allocations-admins mailing list > allocations-admins(a)lcrc.anl.gov > https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by John Valdes 17 Jul '14

17 Jul '14

Ray wrote: > > I have been interacting with Misun, and we propose adding 50K now while > Pavan decides how to refactor the project. OK. I agree that the radix project needs to be reorganized into separate projects, but for what it's worth, with only 2 months and 2 weeks left in the current FY, I would highly recommend that they do so for the next FY rather than doing it now. That is, keep the radix project intact for the current FY, and when the call for new and renewed projects is made for FY15, have them propose new projects (plus a smaller renewal for radix) as appropriate. Just my 2ï¿½. John

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by Bair, Raymond A. 17 Jul '14

17 Jul '14

I have been interacting with Misun, and we propose adding 50K now while Pavan decides how to refactor the project. Ray On 7/17/14, 2:12 PM, "accounts(a)lcrc.anl.gov" <accounts(a)lcrc.anl.gov> wrote: >Hello, > >A change in allocation has been requested: > > Requester: balaji (Pavan Balaji) > Project: radix > Title: Scalable Parallel System Software > Description: >This is a Computer Science request for 60,000 cpu-hours on Blues for >development and evaluation of a family of tools and libraries with a >direct benefit to all users of high-performance computing resources. >The Radix group in Argonnne's Mathematics and Computer Science >division conducts research and development on facilities to better >enable efficient Parallel Programming, I/O, and Scientific >Understanding. > >The Blues system represents an attractive milestone for our software >development: projects start out on our breadboard cluster and can >further explore scalability in the presence of a high speed network on >Blues before making the jump to BlueGene-scale parallelism. > >Radix experiments often are concerned with latency. The infiniband >network on Blues provides an excellent low-latency environment for >message passing and storage management research while also providing >ample bandwidth for I/O and message bandwidth testing. > >For FY2014 our Messaging middleware experiments include the usual >MPICH development. We will study the continued improvement of various MPI >features including scalability and memory usage, performance tuning, >high-level libraries on top of MPI, fault tolerance capabilities, >one-sided >communication, and collective operations. This allocation will also be >used >for studying MPI extensions including active messages, and compiler >support >for MPI refactoring. > >The NWChem library will continue to improve the performance of an >important scientific application that is widely used for science by >Argonne researchers. Specifically, we will develop inspect-executor >load-balancing techniques that will reduce network contention and >improve the overall performance and scalability of an important family >of methods (coupled-cluster methods). Furthermore, we will explore >hybrid programming models (that is, adding threading to the existing >GA/ARMCI/MPI model), particularly in the TCE module, which has been >used extensively by researchers in Argonne MSD and CSE. All the >aforementioned developments will be deployed on Blues in a production >fashion and made available to all users. This allocation will enable >Jeff Hammond to maintain the NWChem installations on Blues, as he has >done for Fusion in the past. > >We work closely with application scientists, and develop application tools >under the 'radix' allocation. For one example, the KMI project defines a >high-level standardized interface for computational biology applications >relying on distributed search and match semantics for biological reads. >We >will study efficient data management and data movement techniques to allow >scaling to large number of processes. > >The GPFS file system on Blues will allow us to experiment with I/O >strategies >on a modest scale before evaluating them at leadership scale on Mira. > >For FY 2014 our file system research extends into data storage >approaches suitable for exascale. Our research into object storage >protocols, >including high performance access and replication, fits well on Blues. >Our Exascale storage efforts will explore scalable algorithms for use in >next generation HPC storage systems. The Blues allocation will be used >to evaluate programming models, fault detection algorithms, >synchronization primitives, and fault tolerance strategies for a >prototype object storage system. > >In FY 2014 we are continuing research into new high level I/O >libraries. We anticipate Blues and Vesta will be our two main test >platforms. > >Radix projects also focus on deriving insight both about application >behavior as well as scientific insight. 16-core nodes make efforts >like in-situ visualization, where for example an application renders a >frame of a movie, ever more feasible. Even without fancy graphics >accelerators, the processing power on Blues nodes makes such analysis >and visualization feasible, especially if the visualization can take >advantage of multiple cores and multiple nodes. Naturally, the radix >visualization tools have demonstrated scalability to Blues sizes and >beyond on Blue Gene, so making full utilization of Blues should not be >a concern. > >As should be evident from the variety of planned experiments, the >Radix group plans to make full use of Blues. > >With Argonne employees and student collaborators, we expect around 20 >members in FY2014. > >We plan on about 0% of our jobs being single core jobs. It's crazy >that you even have to ask! > >While Blues may contain a modest number of compute nodes, the machine >still represents an attractive platform for testing: very fast, low >latency interconnect; 16 cores per node; The testing and experiments >the Radix group can carry out on Blues ensures the tools the group >develops today will remain relevant even as supercomputers grow. Quite >a few radix-developed projects are part of the Blues software stack: >CPU hours for this project yield improvements and benefits not just for >the radix group, but for all users of Blues and indeed users of >high-end computational resources worldwide. > > Current: undetermined amount >Justification: > > Requested: 300000 > >A specific reason has been given: >We are working on several enhancements for system software techniques, >including MPI, FT, I/O and visualization. Several of the projects took >more core hours than originally estimated, due to which we have run out >of our original allocation. > >This needs to be approved and the final allocation amount decided upon. > >Thank You, >The LCRC Accounts System >_______________________________________________ >allocations-admins mailing list >allocations-admins(a)lcrc.anl.gov >https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request for radix
by Bair, Raymond A. 17 Jul '14

17 Jul '14

Dear Pavan and Rob, Looking at the project description and FY13 project report for "radix," it appears to be a collection of different projects in the Radix group. Usually, LCRC does not approve composite projects (allocations for a combination of several distinct projects). We may make an exception for small composite projects, and radix was relatively small until mid-FY13. The initial FY14 request was 496K hours. Since then additional requests have grown the project to 1,370K hours. That puts it into the category with the largest projects in LCRC. From this point forward you should break up the radix project into its major components and submit separate project requests for them. Regards, Ray ----------------------------------------- Ray Bair Computing, Environment, and Life Sciences Argonne National Laboratory and the University of Chicago TCS Building 240, Room 4122 9700 South Cass Avenue Argonne, IL 60439 email: rbair(at)anl.gov Phone: (630)252-5751 On 7/17/14, 2:12 PM, "accounts(a)lcrc.anl.gov" <accounts(a)lcrc.anl.gov> wrote: >Hello, > >A change in allocation has been requested: > > Requester: balaji (Pavan Balaji) > Project: radix > Title: Scalable Parallel System Software > Description: >This is a Computer Science request for 60,000 cpu-hours on Blues for >development and evaluation of a family of tools and libraries with a >direct benefit to all users of high-performance computing resources. >The Radix group in Argonnne's Mathematics and Computer Science >division conducts research and development on facilities to better >enable efficient Parallel Programming, I/O, and Scientific >Understanding. > >The Blues system represents an attractive milestone for our software >development: projects start out on our breadboard cluster and can >further explore scalability in the presence of a high speed network on >Blues before making the jump to BlueGene-scale parallelism. > >Radix experiments often are concerned with latency. The infiniband >network on Blues provides an excellent low-latency environment for >message passing and storage management research while also providing >ample bandwidth for I/O and message bandwidth testing. > >For FY2014 our Messaging middleware experiments include the usual >MPICH development. We will study the continued improvement of various MPI >features including scalability and memory usage, performance tuning, >high-level libraries on top of MPI, fault tolerance capabilities, >one-sided >communication, and collective operations. This allocation will also be >used >for studying MPI extensions including active messages, and compiler >support >for MPI refactoring. > >The NWChem library will continue to improve the performance of an >important scientific application that is widely used for science by >Argonne researchers. Specifically, we will develop inspect-executor >load-balancing techniques that will reduce network contention and >improve the overall performance and scalability of an important family >of methods (coupled-cluster methods). Furthermore, we will explore >hybrid programming models (that is, adding threading to the existing >GA/ARMCI/MPI model), particularly in the TCE module, which has been >used extensively by researchers in Argonne MSD and CSE. All the >aforementioned developments will be deployed on Blues in a production >fashion and made available to all users. This allocation will enable >Jeff Hammond to maintain the NWChem installations on Blues, as he has >done for Fusion in the past. > >We work closely with application scientists, and develop application tools >under the 'radix' allocation. For one example, the KMI project defines a >high-level standardized interface for computational biology applications >relying on distributed search and match semantics for biological reads. >We >will study efficient data management and data movement techniques to allow >scaling to large number of processes. > >The GPFS file system on Blues will allow us to experiment with I/O >strategies >on a modest scale before evaluating them at leadership scale on Mira. > >For FY 2014 our file system research extends into data storage >approaches suitable for exascale. Our research into object storage >protocols, >including high performance access and replication, fits well on Blues. >Our Exascale storage efforts will explore scalable algorithms for use in >next generation HPC storage systems. The Blues allocation will be used >to evaluate programming models, fault detection algorithms, >synchronization primitives, and fault tolerance strategies for a >prototype object storage system. > >In FY 2014 we are continuing research into new high level I/O >libraries. We anticipate Blues and Vesta will be our two main test >platforms. > >Radix projects also focus on deriving insight both about application >behavior as well as scientific insight. 16-core nodes make efforts >like in-situ visualization, where for example an application renders a >frame of a movie, ever more feasible. Even without fancy graphics >accelerators, the processing power on Blues nodes makes such analysis >and visualization feasible, especially if the visualization can take >advantage of multiple cores and multiple nodes. Naturally, the radix >visualization tools have demonstrated scalability to Blues sizes and >beyond on Blue Gene, so making full utilization of Blues should not be >a concern. > >As should be evident from the variety of planned experiments, the >Radix group plans to make full use of Blues. > >With Argonne employees and student collaborators, we expect around 20 >members in FY2014. > >We plan on about 0% of our jobs being single core jobs. It's crazy >that you even have to ask! > >While Blues may contain a modest number of compute nodes, the machine >still represents an attractive platform for testing: very fast, low >latency interconnect; 16 cores per node; The testing and experiments >the Radix group can carry out on Blues ensures the tools the group >develops today will remain relevant even as supercomputers grow. Quite >a few radix-developed projects are part of the Blues software stack: >CPU hours for this project yield improvements and benefits not just for >the radix group, but for all users of Blues and indeed users of >high-end computational resources worldwide. > > Current: undetermined amount >Justification: > > Requested: 300000 > >A specific reason has been given: >We are working on several enhancements for system software techniques, >including MPI, FT, I/O and visualization. Several of the projects took >more core hours than originally estimated, due to which we have run out >of our original allocation. > >This needs to be approved and the final allocation amount decided upon. > >Thank You, >The LCRC Accounts System >_______________________________________________ >allocations-admins mailing list >allocations-admins(a)lcrc.anl.gov >https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by John Valdes 17 Jul '14

17 Jul '14

The Allocation Committee approves 2.5M. On Tue, Jul 15, 2014 at 08:17:13AM -0500, accounts(a)lcrc.anl.gov wrote: > > A change in allocation has been requested: > > Requester: borland (Michael Borland) > Project: ApsRenewalLattice > > Requested: 2500000 > > A specific reason has been given: > Incorrectly computed requirements for remainder of FY14. Should be 2.5 M core hours, not 1 M. >

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[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 17 Jul '14

17 Jul '14

Hello, A change in allocation has been requested: Requester: balaji (Pavan Balaji) Project: radix Title: Scalable Parallel System Software Description: This is a Computer Science request for 60,000 cpu-hours on Blues for development and evaluation of a family of tools and libraries with a direct benefit to all users of high-performance computing resources. The Radix group in Argonnne's Mathematics and Computer Science division conducts research and development on facilities to better enable efficient Parallel Programming, I/O, and Scientific Understanding. The Blues system represents an attractive milestone for our software development: projects start out on our breadboard cluster and can further explore scalability in the presence of a high speed network on Blues before making the jump to BlueGene-scale parallelism. Radix experiments often are concerned with latency. The infiniband network on Blues provides an excellent low-latency environment for message passing and storage management research while also providing ample bandwidth for I/O and message bandwidth testing. For FY2014 our Messaging middleware experiments include the usual MPICH development. We will study the continued improvement of various MPI features including scalability and memory usage, performance tuning, high-level libraries on top of MPI, fault tolerance capabilities, one-sided communication, and collective operations. This allocation will also be used for studying MPI extensions including active messages, and compiler support for MPI refactoring. The NWChem library will continue to improve the performance of an important scientific application that is widely used for science by Argonne researchers. Specifically, we will develop inspect-executor load-balancing techniques that will reduce network contention and improve the overall performance and scalability of an important family of methods (coupled-cluster methods). Furthermore, we will explore hybrid programming models (that is, adding threading to the existing GA/ARMCI/MPI model), particularly in the TCE module, which has been used extensively by researchers in Argonne MSD and CSE. All the aforementioned developments will be deployed on Blues in a production fashion and made available to all users. This allocation will enable Jeff Hammond to maintain the NWChem installations on Blues, as he has done for Fusion in the past. We work closely with application scientists, and develop application tools under the 'radix' allocation. For one example, the KMI project defines a high-level standardized interface for computational biology applications relying on distributed search and match semantics for biological reads. We will study efficient data management and data movement techniques to allow scaling to large number of processes. The GPFS file system on Blues will allow us to experiment with I/O strategies on a modest scale before evaluating them at leadership scale on Mira. For FY 2014 our file system research extends into data storage approaches suitable for exascale. Our research into object storage protocols, including high performance access and replication, fits well on Blues. Our Exascale storage efforts will explore scalable algorithms for use in next generation HPC storage systems. The Blues allocation will be used to evaluate programming models, fault detection algorithms, synchronization primitives, and fault tolerance strategies for a prototype object storage system. In FY 2014 we are continuing research into new high level I/O libraries. We anticipate Blues and Vesta will be our two main test platforms. Radix projects also focus on deriving insight both about application behavior as well as scientific insight. 16-core nodes make efforts like in-situ visualization, where for example an application renders a frame of a movie, ever more feasible. Even without fancy graphics accelerators, the processing power on Blues nodes makes such analysis and visualization feasible, especially if the visualization can take advantage of multiple cores and multiple nodes. Naturally, the radix visualization tools have demonstrated scalability to Blues sizes and beyond on Blue Gene, so making full utilization of Blues should not be a concern. As should be evident from the variety of planned experiments, the Radix group plans to make full use of Blues. With Argonne employees and student collaborators, we expect around 20 members in FY2014. We plan on about 0% of our jobs being single core jobs. It's crazy that you even have to ask! While Blues may contain a modest number of compute nodes, the machine still represents an attractive platform for testing: very fast, low latency interconnect; 16 cores per node; The testing and experiments the Radix group can carry out on Blues ensures the tools the group develops today will remain relevant even as supercomputers grow. Quite a few radix-developed projects are part of the Blues software stack: CPU hours for this project yield improvements and benefits not just for the radix group, but for all users of Blues and indeed users of high-end computational resources worldwide. Current: undetermined amount Justification: Requested: 300000 A specific reason has been given: We are working on several enhancements for system software techniques, including MPI, FT, I/O and visualization. Several of the projects took more core hours than originally estimated, due to which we have run out of our original allocation. 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: entropy
by John Valdes 15 Jul '14

15 Jul '14

I assume this project will only need 100K for the current quarter. Do we approve? If so, would this be a Bio project with Gyorgy as POC or other? Priority 3? John On Thu, Jul 10, 2014 at 09:46:40AM -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: Sunhwan Jo > Applicant's institution: ANL > Applicant's division: LCF > Project Name: entropy > Project title: Quantifying protein-protein binding with greatly scalable multiple copy algorithms of NAMD > Associated funding: None > Other Systems: 0 (previously had 10M core hours in BG/Q, but is expired and submitted extension) > Science: Protein-protein interactions (PPIs) represent a critical aspect of a wide range of biological processes, as most proteins need to associate to various binding partners to carry out their functions. While the basic principles of PPIs are generally understood, it is a grand challenge to accurately predict the binding affinity quantitatively for any given complex. Recently, this potential of mean force (PMF)-based methodology was extended to a much larger protein-peptide system, and we accurately determined the absolute binding free energy between the receptor protein and the ligand peptide. We plan to use our PMF-based methodology to probe effects of mutations in thermodynamics of protein-protein interaction, i.e., thermodynamic decomposition of barstar-barnase protein complex association. > Project description: In PMF-based framework, a set of geometric and conformational restraints is applied to the proteins to reduce sampling noise and accelerate the convergence of the resulting free energy profile. These biases are rigorously accounted for to produce the absolute binding free energy. To enhance the PMF convergence, we will combine the umbrella sampling with Hamiltonian and temperature (??? and T) replica-exchange molecular dynamics (REM) algorithm. In the US/(???,T)-REMD simulation approach, multiple copies of the molecular ???systems are simulated concurrently, but??? all with different??? conditions, e.g., umbrella potential (Hamiltonians) or temperature. Attempts are periodically made to exchange configurations between different systems using a Metropolis-type Monte Carlo acceptance criterion, insuring Boltzmann-weighted statistics. Such REMD??? methodology is extremely scalable, yet also very effective to sample a rugged free energy surface. > > We anticipate the simulation systems will be comprised of ~50,000 atoms and using at least 255 replicas concurrently. Because of its large size, we plan to use primarily Mira for production and Fusion will be used for initial system preparation and development of enhanced methodology in PMF-based framework. All planned simulations will be carried out by the open-source NAMD molecular dynamics software. The software engine used for the planned simulations is NAMD 2.10 with Charm++ 6.4.0. We have tested t he performance on BG/Q Mira. The scaling of parallel performance was linear up to 512 cores for our test system comprised of 100,000 atoms without using restraint potential and achieved the speed of about 0.025 s/step. Using restraint potential reduces the parallel performance significantly (~0.2 s/step). > > The expected number of project member is 3. I, Sunhwan Jo, recently joined LCF as a postdoctoral appointee and will be the main person performing code improvement and algorithm development under the supervision of Wei Jiang (LCF) and Benoit Roux (UChicago). > > > > Project URL: > Requested allocation: 400000 > Q1: 100000 > Q2: 100000 > Q3: 100000 > Q4: 100000 > Justification: > > > 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 Allocation Request
by John Valdes 15 Jul '14

15 Jul '14

I approve. :) John On Tue, Jul 15, 2014 at 06:55:25PM -0500, accounts(a)lcrc.anl.gov wrote: > Hello, > > A change in allocation has been requested: > > Requester: valdes (John Valdes) > Project: lcrc-app-engr > Title: LCRC Application Engineer support work > Description: This project will be used by the LCRC application engineers to do support work for users of the LCRC cluster. This support might be in the form of installation and debugging of both LCRC core and user applications, benchmarking and performance analysis, user startup help, etc. > > Current: undetermined amount > Justification: > > Requested: 6000 > > A specific reason has been given: > It's been a busy quarter for this project, and we've used up all our time. Requesting another quarter's worth for the remainder of the FY. > > This needs to be approved and the final allocation amount decided upon.

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by John Valdes 15 Jul '14

15 Jul '14

Granted. On Tue, Jul 15, 2014 at 04:15:32PM +0000, Bair, Raymond A. wrote: > Lets approve this request for 50K. > > Ray > > On 7/14/14, 4:41 PM, "accounts(a)lcrc.anl.gov" <accounts(a)lcrc.anl.gov> wrote: > > >Hello, > > > >A change in allocation has been requested: > > > > Requester: coliu (Cong Liu) > > Project: Hetero_Catalysis > > > > Requested: 50000 > > > >A specific reason has been given: > >More allocation is needed for the VASP calculations of the transition > >states (CI-NEB calculations) > > > >This needs to be approved and the final allocation amount decided upon.

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by John Valdes 15 Jul '14

15 Jul '14

Granted 5K. On Mon, Jul 14, 2014 at 06:07:28PM +0000, Bair, Raymond A. wrote: > > This project used up all of its 4K allocation, so lets add the 5K they > requested. > > Ray > > > On 7/14/14, 1:04 PM, "accounts(a)lcrc.anl.gov" <accounts(a)lcrc.anl.gov> wrote: > > >Hello, > > > >A change in allocation has been requested: > > > > Requester: chasman (Richard Chasman) > > Project: NuclearStructure > > > > Requested: 5000 > > > >A specific reason has been given: > >need more time > > > >This needs to be approved and the final allocation amount decided upon.

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