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

Re: [allocations-admins] Fwd: Re: Negative Allocation Balance
by Bair, Raymond A. 07 Feb '11

07 Feb '11

OK with me. If people do not use all the advance, do they lose it? Ray ----- Original Message ----- From: John Valdes [mailto:[email protected]] Sent: Monday, February 07, 2011 05:41 PM To: allocations-admins(a)lcrc.anl.gov <allocations-admins(a)lcrc.anl.gov> Subject: Re: [allocations-admins] Fwd: Re: Negative Allocation Balance Gary was asking to have some of his 2nd half time forwarded for project dynamics. OK to advance 100K? John On Thu, Jan 27, 2011 at 06:58:47PM -0600, John Valdes wrote: > Gary Leaf is running low on time on his project "dynamics" and asked > (in person) if we could advance 100K to his project. dynamics was > initially given 150K, most of which has been used in the past 2 > months. Gary said he has more runs to do as does a collaborator, and > between them they can probably use up the 100K by midyear. OK to > advance the 100K? > > John > > ----- Forwarded message from Gary Leaf <leaf(a)mcs.anl.gov> ----- > > Date: Thu, 27 Jan 2011 14:35:01 -0600 (CST) > From: Gary Leaf <leaf(a)mcs.anl.gov> > To: John Valdes <valdes(a)mcs.anl.gov> > cc: Gary Leaf <leaf(a)mcs.anl.gov> > Subject: Re: Negative Allocation Balance > > John : What do I need to do in order to obtain > some positive balance? > > -2414%)./start.x > Notice: Project "dynamics" has a negative allocation balance; > your job will run at the lowest priority. > 508211.fmgt2.lcrc.anl.gov > (fusion-2415%) > > GKL > > ----- End forwarded message ----- > _______________________________________________ > 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

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by John Valdes 07 Feb '11

07 Feb '11

A request for additional time. Note that this is Bob Olson's project, RAST, not Folker's project, MG-RAST. Bob initially requested 50K for FY11 which was granted in full. He's now requesting 250K more (see the reason given under the "A specific reason has been given:" heading). John On Mon, Jan 31, 2011 at 12:00:41PM -0600, accounts(a)lcrc.anl.gov wrote: > Hello, > > A change in allocation has been requested: > > Requester: olson (Robert Olson) > Project: RAST > Title: Rapid Genome Annotation Technology > Description: The RAST server is a genome annotation server developed by the bioinformatics group in MCS that was funded by the NIH Bioinformatics Resource Centers program. Throughout the history of the RAST server, we have made use only of the computational cluster that was funded by NIH for the purpose of hosting RAST. The configuration of this cluster was extensively hand-tuned for the purposes of running RAST. We believe the technology has reached a state of maturity such that we can develop the tools to enable the core computation to execute on a general-purpose scientific cluster like the LCRC. > The real test of the success of this work will be to process real genomic data at scale. To this end we will work toward the integration of the RAST server (which provides facilities for the upload of new genomic data, the monitoring of the progress of the pipeline, and tools for online browsing and analysis of the completed annotation as well as downloads of the completed annotation in one of several export formats) with the LCRC as a computational backend. Initially this integration will be manually supervised, but we plan to investigate the technology for a more automated integration. > Advances in the RAST technology have decreased the overall computational load on a per-genome basis, but the number of genomes submitted to RAST continues to rise. In 2010 we were successful at porting the core RAST computations to Fusion, but at the same time we brought the more highly optimized computation online on the core RAST server, highly reducing the requirement for the computational offload. In 2011, however, we envision the return for the need for this offload. We plan to further automate the integration of RAST and Fusion, as well as to leverage the Magellan cluster to engineer a family of computational offload facilities for RAST. > The RAST project has also made effective use of the Fusion resource for other computations related to the curation of the protein families that underpin the RAST system. We perform detailed all-to-all analyses of the genomes within families of organisms (for instance, all sequenced genomes in the Brucella family of pathogenic bacteria) to determine the precise relationship between the genes in these organisms. Fusion is an excellent platform for such analyses, and we plan to continue such analyses on the other pathogen groups. > > > Current: undetermined amount > Justification: > > Requested: 250000 > > A specific reason has been given: > We have been running a new large-scale computation to compute detailed similarities between the genomes in our database. We are using the results of this data to compute detailed correspondences between genomes in the database. This data, combined with the data we curate on the linkages between annotations and the published literature, will allow us to create highly consistent and accurate annotations across the entire genome database. > > The computation thus far has consumed around 40K core hours. It is roughly 18% through the total calculation (based on sequence counts), which gives us an estimate of about 224K core hours for the entire calculation. We are requesting an additional 250K core hours in order to complete this computation with some additional overage in the event our estimates are not completely accurate. > > This needs to be approved and the final allocation amount decided upon. > > Thank You, > The LCRC Accounts System > _______________________________________________ > allocations-admins mailing list > allocations-admins(a)lists.lcrc.anl.gov > https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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Re: [allocations-admins] Fwd: Re: Negative Allocation Balance
by John Valdes 07 Feb '11

07 Feb '11

Gary was asking to have some of his 2nd half time forwarded for project dynamics. OK to advance 100K? John On Thu, Jan 27, 2011 at 06:58:47PM -0600, John Valdes wrote: > Gary Leaf is running low on time on his project "dynamics" and asked > (in person) if we could advance 100K to his project. dynamics was > initially given 150K, most of which has been used in the past 2 > months. Gary said he has more runs to do as does a collaborator, and > between them they can probably use up the 100K by midyear. OK to > advance the 100K? > > John > > ----- Forwarded message from Gary Leaf <leaf(a)mcs.anl.gov> ----- > > Date: Thu, 27 Jan 2011 14:35:01 -0600 (CST) > From: Gary Leaf <leaf(a)mcs.anl.gov> > To: John Valdes <valdes(a)mcs.anl.gov> > cc: Gary Leaf <leaf(a)mcs.anl.gov> > Subject: Re: Negative Allocation Balance > > John : What do I need to do in order to obtain > some positive balance? > > -2414%)./start.x > Notice: Project "dynamics" has a negative allocation balance; > your job will run at the lowest priority. > 508211.fmgt2.lcrc.anl.gov > (fusion-2415%) > > GKL > > ----- End forwarded message ----- > _______________________________________________ > 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] Fwd: FW: advance on the next part of our allocation
by Bair, Raymond A. 07 Feb '11

07 Feb '11

Test to list -- ignore On 2/7/11 5:12 PM, "John Valdes" <valdes(a)mcs.anl.gov> wrote: > Forwarding to allocations-admins list so that I can find this request > more easily when preparing for the next Allocations meeting. > > ----- Forwarded message from "Bair, Raymond A." <rbair(a)anl.gov> ----- > > Date: Fri, 4 Feb 2011 16:54:11 -0600 > From: "Bair, Raymond A." <rbair(a)anl.gov> > To: "Valdes, John P." <valdes(a)mcs.anl.gov>, > "Hedden, Jason E." <jhedden(a)mcs.anl.gov>, > "Low, John J." <jlow(a)mcs.anl.gov>, > "Aithal, > Shashikant M." <aithal(a)mcs.anl.gov> > Subject: FW: advance on the next part of our allocation > > Lets grant the 150K advance to MG-RAST. He thinks that he will not need to > ask for more time in the 2nd half, because they have transferred most of the > work to Magellan. > > Ray > > ------ Forwarded Message > From: Folker Meyer <folker.meyer(a)gmail.com> > Date: Fri, 4 Feb 2011 16:43:33 -0600 > To: Raymond Bair <rbair(a)anl.gov> > Cc: Jared Wilkening <jared.wilkening(a)gmail.com> > Subject: advance on the next part of our allocation > > Ray: > > as discussed just now, can we get an advance for the 2nd half of the year ( > potentially 150k hours ) > > Best, > Folker > > > > > ------ End of Forwarded Message > > > ----- End forwarded message ----- > _______________________________________________ > 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 TCS Building 240, Room 4126 9700 South Cass Avenue Argonne, IL 60439 email: rbair(at)anl.gov Phone: (630)252-5751

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Fwd: Fw: compnano and nanocatalysis allocations
by John Valdes 07 Feb '11

07 Feb '11

Forwarding to allocations-admins list. John ----- Forwarded message from "Bair, Raymond A." <rbair(a)anl.gov> ----- Date: Fri, 4 Feb 2011 17:24:49 -0600 From: "Bair, Raymond A." <rbair(a)anl.gov> To: "Aithal, Shashikant M." <aithal(a)mcs.anl.gov>, "Low, John J." <jlow(a)mcs.anl.gov>, "Valdes, John P." <valdes(a)mcs.anl.gov>, "Hedden, Jason E." <jhedden(a)mcs.anl.gov> Subject: Fw: compnano and nanocatalysis allocations Peter is requesting a 150K advance on both compnano and nanocatalysis. Ray ----- Original Message ----- From: Zapol, Peter Sent: Friday, February 04, 2011 05:22 PM To: Bair, Raymond A. Subject: RE: compnano and nanocatalysis allocations Ray, Thank you. This will keep us going for a while. Peter -----Original Message----- From: Bair, Raymond A. Sent: Friday, February 04, 2011 5:08 PM To: Zapol, Peter Subject: Re: compnano and nanocatalysis allocations How much of an advance would you need for each? The LCRC staff can advance up to 150K hours (each). Ray On 2/4/11 5:05 PM, "Peter Zapol" <zapol(a)anl.gov> wrote: > I am requesting to advance our allocation for compnano and nanocatalysis > projects since we have run out of time. > > Thanks, > Peter > > Peter Zapol > > > > Materials Science Division > > Argonne National Laboratory > > 9700 South Cass Avenue > > Argonne, IL 60439 > > USA > > ----------------------------------------- Ray Bair Computing, Environment, and Life Sciences Argonne National Laboratory and the University of Chicago TCS Building 240, Room 4126 9700 South Cass Avenue Argonne, IL 60439 email: rbair(at)anl.gov Phone: (630)252-5751 ----- End forwarded message -----

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Fwd: FW: advance on the next part of our allocation
by John Valdes 07 Feb '11

07 Feb '11

Forwarding to allocations-admins list so that I can find this request more easily when preparing for the next Allocations meeting. ----- Forwarded message from "Bair, Raymond A." <rbair(a)anl.gov> ----- Date: Fri, 4 Feb 2011 16:54:11 -0600 From: "Bair, Raymond A." <rbair(a)anl.gov> To: "Valdes, John P." <valdes(a)mcs.anl.gov>, "Hedden, Jason E." <jhedden(a)mcs.anl.gov>, "Low, John J." <jlow(a)mcs.anl.gov>, "Aithal, Shashikant M." <aithal(a)mcs.anl.gov> Subject: FW: advance on the next part of our allocation Lets grant the 150K advance to MG-RAST. He thinks that he will not need to ask for more time in the 2nd half, because they have transferred most of the work to Magellan. Ray ------ Forwarded Message From: Folker Meyer <folker.meyer(a)gmail.com> Date: Fri, 4 Feb 2011 16:43:33 -0600 To: Raymond Bair <rbair(a)anl.gov> Cc: Jared Wilkening <jared.wilkening(a)gmail.com> Subject: advance on the next part of our allocation Ray: as discussed just now, can we get an advance for the 2nd half of the year ( potentially 150k hours ) Best, Folker ------ End of Forwarded Message ----- End forwarded message -----

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[LCRC Accounts] Project Request: Globus-Online
by accounts＠lcrc.anl.gov 07 Feb '11

07 Feb '11

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: Raj Kettimuthu Applicant's institution: ANL Applicant's division: MCS Project Name: Globus-Online Project title: Globus Online: Hosted Service for High-speed, Reliable, Secure Data Movement Associated funding: DOE Other Systems: ALCF, NERSC, PADS Science: The objective of this project is to make bulk data movement much easier for scientists. Project description: Globus Online delivers high-performance, reliable data movement services to end-users without requiring construction of custom, end-to-end systems. Implemented as an online, hosted service, Globus Online makes the same robust file transfer capabilities traditionally available only on the largest scale grid implementations, accessible to users that do not have the benefit of well-funded, technically savvy IT organizations. Software requirements: GridFTP server Expected number of project members: 5 Project URL: http://www.globusonline.org Requested allocation: 50000 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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[LCRC Accounts] Project Request: power-grid-sim
by accounts＠lcrc.anl.gov 31 Jan '11

31 Jan '11

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: Cong Liu Applicant's institution: ANL Applicant's division: DIS, MCS, ES Project Name: power-grid-sim Project title: Novel Power System Operations Methods for Wind-powered Plug-in Hybrid Electric Vehicles Associated funding: LDRD, DOE-OE Other Systems: Science: In this project, the objective is to propose a novel power system operations method, namely a new stochastic unit commitment and contingency analysis, which can address the uncertainty and variability brought by wind and electric vehicles, while maintaining the stability and reliability of the system. The proposed method will make use of a unified high-performance parallel computing framework for solving the stochastic unit commitment problem as well as implementing contingency analysis. These capabilities can be used by system operators to manage the grid. It can also be applied in planning studies to assess the impact of high penetration of wind and PHEVs on the power system. Project description: The task will be seperated into two subtasks. 1.The biggest challenge of contingency analysis for bulk power systems is the limited computational capability for power flow optimization. Due to the nature of power flow computation, a thorough contingency analysis usually has to confront a brute-force enumeration of contingency scenarios. The number of scenarios is astronomically increased if multiple contingencies are taken into account at the same time (N-k). In addition, the extremely expanded scale of power systems also raises the computational cost for each single power flow run. Last but not least, there has been a need for near-real-time contingency analysis since off-line studies cannot reflect the accurate system conditions due to the mismatch between the real operating states and presumed conditions. However, taking advantage of modern monitoring techniques such as phasor measurement units, contingency analysis tends to be implemented in real time. This kind of on-line contingency analysis calls for more advanced algorithms to achieve reasonable accuracy in a timely manner. 2. Stochastic optimization problems are suitable for high-performance parallel computing architectures since a large fraction of the variables of the problem can be decoupled between uncertainty realizations or scenarios. In the unit commitment problem, the number of coupling variables is proportional to the number of power units to be committed and the scheduling horizon. In the particular case of wind power generation, the number of units can increase dramatically. This loosely coupled structure can be decomposed at the model level (outside the optimization solver). Model-level decomposition techniques such as Lagrangean relaxation and Benders decomposition are easy to implement through a parallel computing way. Six members from different divisions at Argonne will work on this project. The project will use open-source solver such as sparse linear system sover, CBC(mixed integer programming) to solve the problems Project URL: Requested allocation: 350000 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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[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 31 Jan '11

31 Jan '11

Hello, A change in allocation has been requested: Requester: olson (Robert Olson) Project: RAST Title: Rapid Genome Annotation Technology Description: The RAST server is a genome annotation server developed by the bioinformatics group in MCS that was funded by the NIH Bioinformatics Resource Centers program. Throughout the history of the RAST server, we have made use only of the computational cluster that was funded by NIH for the purpose of hosting RAST. The configuration of this cluster was extensively hand-tuned for the purposes of running RAST. We believe the technology has reached a state of maturity such that we can develop the tools to enable the core computation to execute on a general-purpose scientific cluster like the LCRC. The real test of the success of this work will be to process real genomic data at scale. To this end we will work toward the integration of the RAST server (which provides facilities for the upload of new genomic data, the monitoring of the progress of the pipeline, and tools for online browsing and analysis of the completed annotation as well as downloads of the completed annotation in one of several export formats) with the LCRC as a computational backend. Initially this integration will be manually supervised, but we plan to investigate the technology for a more automated integration. Advances in the RAST technology have decreased the overall computational load on a per-genome basis, but the number of genomes submitted to RAST continues to rise. In 2010 we were successful at porting the core RAST computations to Fusion, but at the same time we brought the more highly optimized computation online on the core RAST server, highly reducing the requirement for the computational offload. In 2011, however, we envision the return for the need for this offload. We plan to further automate the integration of RAST and Fusion, as well as to leverage the Magellan cluster to engineer a family of computational offload facilities for RAST. The RAST project has also made effective use of the Fusion resource for other computations related to the curation of the protein families that underpin the RAST system. We perform detailed all-to-all analyses of the genomes within families of organisms (for instance, all sequenced genomes in the Brucella family of pathogenic bacteria) to determine the precise relationship between the genes in these organisms. Fusion is an excellent platform for such analyses, and we plan to continue such analyses on the other pathogen groups. Current: undetermined amount Justification: Requested: 250000 A specific reason has been given: We have been running a new large-scale computation to compute detailed similarities between the genomes in our database. We are using the results of this data to compute detailed correspondences between genomes in the database. This data, combined with the data we curate on the linkages between annotations and the published literature, will allow us to create highly consistent and accurate annotations across the entire genome database. The computation thus far has consumed around 40K core hours. It is roughly 18% through the total calculation (based on sequence counts), which gives us an estimate of about 224K core hours for the entire calculation. We are requesting an additional 250K core hours in order to complete this computation with some additional overage in the event our estimates are not completely accurate. This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

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Fwd: Re: Negative Allocation Balance
by John Valdes 27 Jan '11

27 Jan '11

Gary Leaf is running low on time on his project "dynamics" and asked (in person) if we could advance 100K to his project. dynamics was initially given 150K, most of which has been used in the past 2 months. Gary said he has more runs to do as does a collaborator, and between them they can probably use up the 100K by midyear. OK to advance the 100K? John ----- Forwarded message from Gary Leaf <leaf(a)mcs.anl.gov> ----- Date: Thu, 27 Jan 2011 14:35:01 -0600 (CST) From: Gary Leaf <leaf(a)mcs.anl.gov> To: John Valdes <valdes(a)mcs.anl.gov> cc: Gary Leaf <leaf(a)mcs.anl.gov> Subject: Re: Negative Allocation Balance John : What do I need to do in order to obtain some positive balance? -2414%)./start.x Notice: Project "dynamics" has a negative allocation balance; your job will run at the lowest priority. 508211.fmgt2.lcrc.anl.gov (fusion-2415%) GKL ----- End forwarded message -----

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