July 2014 - Core-sysadmins - mailman3.cels.anl.gov

Seminar Announcement: The Assembly and Management of Scalable Computational Experiments
by Ninfa Mayorga 02 Oct '14

02 Oct '14

Computation Institute Presentation Speaker: Justin Wozniak, Mathematics and Computer Science Division, Argonne National Laboratory Host: Ian Foster Date: July 31, 2014 Time: 12:30 PM - 1:30 PM Location: Argonne National Lab, TCS Building 240, Room 5172, broadcast via Adobe Connect (see below) The Assembly and Management of Scalable Computational Experiments A large-scale, collaborative computational experiment involves more than the tuning of individual code fragments- typically, codes must be assembled, integrated in one or more programming models and languages, experimental runs must be managed and data collected. In this talk, I will present my work using the Swift programming language to assemble and run many different scientific applications on wide range of computer systems. In high-performance computing, I will present the Swift/T system for high performance dataflow applications that run on extremely large systems such as the IBM Blue Gene/P and the Cray Blue Waters system. The techniques presented will cover runtime and compiler development in the Swift context, management of big data for large scale computational experiments, and a variety of application case studies. Information: Lunch will be provided This talk will be broadcast to the University of Chicago, Searle 240A, 5735 S. Ellis Ave. You may join the broadcast from your location by using Adobe Connect. To join the meeting: http://anl.adobeconnect.com/tcs-ci -Enter as a guest If you have never attended an Adobe Connect meeting before: Test your connection: http://anl.adobeconnect.com/common/help/en/support/meeting_test.htm Get a quick overview:http://www.adobe.com/go/connectpro_overview

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LANS Informal Seminar - SASSy (Part 2)
by Ghosh, Debojyoti 04 Aug '14

04 Aug '14

LANS Informal Seminar Series What: Summer Argonne Students Symposium (SASSy) - Part 2 Informal Talks by the LANS summer students When: Tuesday, August 5th, 2014 at 1:00 PM — 4:15 PM Where: Building 240, Room 1404-1405 Goodies: Coffee and goodies will be served Speaker, Titles and Abstracts: + 13:00 - 13:15: Matt Otten (Supervisor: Misun Min) Title: Scalable Density Matrix Calculations of Coupled Quantum Systems Abstract: We study the time dynamics of a system consisting of quantum dots coupled to a single plasmon mode. The size of the density matrix grows quickly; a physically reasonable system of 16 quantum dots requires a matrix dimension of 50*2^16. At this size, extreme scale computing must be utilized. Aside from the novel physics applications, we are currently studying how best to treat this system, through different time stepping schemes (RK and exponential time integrator) and different parallelization algorithms. + 13:15 - 13:30: Harikrishnan Sreekumaran (Supervisor: Sven Leyffer) Title: On Bilevel Mixed-Integer Nonlinear Programming Problems Abstract: Bilevel programming provides a natural framework for modelling hierarchical decision making, with applications in varied fields such as market design, network planning and vulnerability analysis, and engineering design among others. In this talk, we review bilevel mixed integer nonlinear programming problems (BLMINLPs) and describe the significant challenges in the analysis and algorithm design for such problems. We present relaxation formulations for certain classes of BLMINLPs and introduce algorithms for solving such problems using these relaxations. Finally we present a few application examples and some preliminary numerical results. + 13:30 - 13:45: Paul Tranquilli (Supervisor: Cosmin Petra) Title: Building an adjoint based dynamics constrained optimization of electrical power systems Abstract: We present a mathematical framework for the solution of optimal power flow, including dynamic security constraints, using adjoint based sensitivities. We briefly discuss some implementation details of using PETSc to perform both the forward and backward time integrations. + 13:45 - 14:00: Bethany Nicholson (Supervisor: Victor Zavala) Title: Automatic Discretization of ODE and PDE Systems Using Pyomo Abstract: Dynamic optimization problems that include ordinary/partial differential equations as constraints are typically solved by discretizing the model and then solving the resulting nonlinear problem. This talk introduces a way to do model discretization automatically using the open-source modeling language Pyomo. We will discuss the straight-forward syntax behind this new functionality as well as the flexible discretization options that are available. Finally, we will look at a couple sample problems that show the wide range of dynamic optimzation problems that can now be represented and solved using Pyomo. + 14:00 - 14:15: Ahmed Attia (Supervisor: Mihai Anitescu) Title: Derivative-based solution of the constrained optimization problem(s) in DeMarco's model Abstract: Predicting cascading network failure is a vital problem for the ever increasing scale of engineered systems as electric power grids, communication networks, and internet. To predict cascading failures, for one or more branches, the bottleneck is a constrained optimization step. Without derivative information, this optimization step takes a very long time even for the simplest settings, and may even fail to converge for large simulation times. We considered a simple, but general, model developed by DeMarco to understand how small-scale failures of individual elements may propagate to produce global failures. My main task was to derive and implement the adjoint of the quadratic constraint(s). The derivative information of the cost functional and constraints, made the optimization very fast (roughly 100-150 times faster). The results are being extended now to large-scale settings. + 14:15 - 14:30: Francisco Trespalacios-Sagues (Supervisor: Victor Zavala) Title: Bound contraction algorithm for global optimization of natural gas networks Abstract: The natural gas transportation network problem has received increased attention in recent years. In this work, we first derive a convex NLP for this problem, based on a well-known non-convex NLP and two operating assumptions. We then present a non-convex model that includes the cost of both: purchasing natural gas from suppliers, and operating compressors in the network. Finally, we develop a bound contraction algorithm to solve this non-convex model. The algorithm is tested in a simplified real network, and compared against state of the art global solvers. -- 14:30 - 14:45: Break -- + 14:45 - 15:00: Matt Menickelly (Supervisor: Stefan Wild) Title: Handling Nonsmoothness in Derivative-Free Optimization Abstract: Derivative-free optimization is a branch of optimization theory concerned with optimizing functions for which derivatives are either unavailable (e.g. the objective is a black box) or are unreliable due to noise. A popular class of algorithms for derivative-free optimization is that of trust-region methods, wherein at each iteration, the objective is modeled locally using an interpolating function with respect to a choice of basis - in the scope of this research, and as is a common choice, a basis of quadratic polynomials. However, as one might expect, if there is nonsmoothness inherent in the objective, the failure of this basis to produce accurate local models of "kinks" or "corners" will cause a trust-region algorithm to stall. In this research, we explore the idea of approximate gradient sampling and the notion of convergence to Clarke stationarity to develop a mechanism to save trust-region methods from stalling as a result of nonsmoothness. + 15:00 - 15:15: Cullen Tanoue (Supervisor: Sven Leyffer) Title: Approximation and Multilevel Algorithms for Phase Retrieval Abstract: Phase retrieval poses an important optimization problem that arises in diffraction imaging, where the original structure of an object needs to be reconstructed from its diffraction data with loss of information concerning the phase of the object. Multilevel algorithms can be used to compute solutions to the standard phase retrieval optimization problem by constructing a hierarchy of problems using a series of restriction and prolongation operations. The coarser problems have a quarter of the variables as the finer problems, and hence, there are much less linear algebra requirements for solving the coarser problems. Further, the prolongation of the solutions computed for the coarser problems yield good starting points for the finer problems. We can also use an approach that alternates between solving the coarse and fine problem. Parameters for these methods include the number of levels, prolongation and restriction operations, and the number of iterations to perform at each level. We study the solutions to the standard phase retrieval optimization problem that result from exploring these parameters. + 15:15 - 15:30: Matthew Michelotti (Supervisor: Barry Smith) Title: Finding Particles in Halos: Resolving Local Effects when Simulating DNA Molecules. Abstract: Understanding how DNA molecules behave in a liquid is important for improving DNA sequencers. We can model DNA molecules as strings of charged particles. Using the GGEM method, each particle needs to receive information from other nearby particles in its "halo" to resolve local effects. We have added functionality to the libMesh library for having particles in a mesh and for finding particles in halos efficiently, in serial or parallel, for use with GGEM and similar methods. + 15:30 - 15:45: Paul Eller (Supervisor: Barry Smith) Title: Development of a User Controlled Threading Model for PETSc Abstract: In recent years multicore processors have become more common and hybrid programming models have been used to produce better performance than pure MPI in some situations. Therefore we have been working to develop a hybrid programming model for PETSc that allows users to take advantage of both MPI and threads. Multiple threaded programming models are being implemented in PETSc including models that give users more direct control of the threads. A threaded programming model introduces thread safety issues to PETSc which require non-trivial changes to routines throughout PETSc to ensure that the code produces accurate solutions without reducing performance. + 15:45 - 16:00: Wanting Xu (Supervisor: Mihai Anitescu) Title: Improving low memory state estimation of weakly constrained 4D-Var with gradient evaluation Abstract: Data assimilation is the process of estimating the states of a dynamical system with observation data. The underlying states and observables form a hidden Markov model, and the best states can be obtained by minimizing a corresponding likelihood function. We developed a recursive scheme for evaluating the gradient of the object function in a low memory fashion, and use that information in optimization. We demonstrate the improvement of our method over the existing low memory approach by simulation with Burgers' Equation and a linear PDE. + 16:00 - 16:15: Surtai Han (Supervisor: Barry Smith) Title: Web Interface for Parallel Linear Solver Selection Abstract: PETSc (Portable Extensible Toolkit for Scientific Computation) has a large selection of linear solvers to provide users with tools for a wide range of applications on parallel computers. However, it can be difficult for users to select the optimal solvers for their specific application. We built a webpage to assist users in viewing, customizing, and assembling the linear solvers by providing a GUI consisting of a hierarchy of drop-down menus and a tree diagram. Afterwards, the webpage generates the appropriate command-line options for the solvers that the user selected. A separate webpage allows users to interact with the SAWs (Scientific Applications Web Server) so that users can adjust the solver options during runtime. -- SASSy Part 3 - August 19th 1:00 - 4:00 PM (http://www.mcs.anl.gov/research/LANS/events/listn/detail.php?id=2351) -- LANS Informal Seminars Calendar: https://www.google.com/calendar/embed?src=e8r9gll7mc180cf279n49ancio%40grou… LANS Informal Semnars Listing: http://www.mcs.anl.gov/research/LANS/events/listn/ -- Debojyoti Ghosh ghosh(a)mcs.anl.gov<mailto:[email protected]>

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Cron <root@newnewman-1> /root/bin/create-mailbox-list.sh force
by root＠mcs.anl.gov 31 Jul '14

31 Jul '14

Automatically installing changes noted below. +manyu(a)mcs.anl.gov OK

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shadowserver at it again.
by rackow＠anl.gov 31 Jul '14

31 Jul '14

Shadow server apears to have been poking around again. This time for UDP port 623. In other works IPMI, asf-rmcp 623/udp ASF Remote Management and Control Protocol My guess is with the recent announcements of IPMI vulns, they are poking to see what may be a problem. Start End Sif SrcIPaddress SrcP DIf DstIPaddress DstP P Fl Pkts Octets 0728.02:02:57.480 0728.02:02:57.480 6 71.6.216.49 49092 3 192.5.186.76 623 17 0 2 102 0728.02:02:57.473 0728.02:02:57.473 6 192.5.186.76 623 3 71.6.216.49 49092 17 0 2 116 0728.15:00:29.468 0728.15:00:29.468 6 71.6.216.49 40825 3 192.5.186.80 623 17 0 2 58 0728.22:42:40.702 0728.22:42:40.702 5 184.105.247.238 41619 3 192.5.186.79 623 17 0 2 102 0728.22:42:40.747 0728.22:42:40.747 6 192.5.186.79 623 3 184.105.247.238 41619 17 0 2 116 0729.23:17:43.465 0729.23:17:43.465 5 184.105.247.250 51163 3 192.5.186.80 623 17 0 2 102 0729.23:17:43.502 0729.23:17:43.502 6 192.5.186.80 623 3 184.105.247.250 51163 17 0 2 116 0730.00:58:44.240 0730.00:58:44.240 5 184.105.247.242 48596 3 192.5.186.79 623 17 0 2 102 0730.00:58:44.290 0730.00:58:44.290 6 192.5.186.79 623 3 184.105.247.242 48596 17 0 2 116 0730.22:38:02.559 0730.22:38:02.559 5 184.105.247.250 47805 3 192.5.186.80 623 17 0 2 102 0730.22:38:02.568 0730.22:38:02.568 6 192.5.186.80 623 3 184.105.247.250 47805 17 0 2 116 0730.23:03:50.334 0730.23:03:50.334 5 184.105.247.250 34362 3 192.5.186.82 623 17 0 2 102 0730.23:03:50.364 0730.23:03:50.364 6 192.5.186.82 623 3 184.105.247.250 34362 17 0 2 116 0730.23:16:26.735 0730.23:16:26.735 5 184.105.247.250 37066 3 192.5.186.79 623 17 0 2 102 0730.23:16:26.785 0730.23:16:26.785 6 192.5.186.79 623 3 184.105.247.250 37066 17 0 2 116 0730.23:33:49.004 0730.23:33:49.004 5 184.105.247.198 36485 3 192.5.186.76 623 17 0 2 102 0730.23:33:50.076 0730.23:33:50.076 6 192.5.186.76 623 3 184.105.247.198 36485 17 0 2 116 The probe from 71.6.216.49 is a "rapid7.com" scanner. A competitor to nessus in may ways. Claims from shadowserver reports are "timestamp","ip","port","hostname","tag","ipmi_version","asn","geo","region","city","none_auth","md2_auth","md5_auth","passkey_auth","oem_auth","defaultkg","permessage_auth","userlevel_auth","usernames","nulluser","anon_login","error","deviceid","devicerev","firmwarerev","version","manufacturerid","manufacturername","productid","productname" "2014-07-28 02:35:00","192.5.186.79",623,"node0.i2u2.org","ipmi","1.5",683,"US","ILLINOIS","LEMONT","no","no","no","no","yes","-","disabled","disabled","yes","no","no",,,,,,,,, "2014-07-29 03:42:41","192.5.186.79",623,"node0.i2u2.org","ipmi","1.5",683,"US","ILLINOIS","LEMONT","no","no","no","no","yes","-","disabled","disabled","yes","no","no",,,,,,,,, "2014-07-30 04:17:43","192.5.186.80",623,"node1.i2u2.org","ipmi","1.5",683,"US","ILLINOIS","LEMONT","no","no","no","no","yes","-","disabled","disabled","yes","no","no",,,,,,,,, "2014-07-30 05:58:43","192.5.186.79",623,"node0.i2u2.org","ipmi","1.5",683,"US","ILLINOIS","LEMONT","no","no","no","no","yes","-","disabled","disabled","yes","no","no",,,,,,,,, --gene

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Seminar: Prof. François-Xavier Demoulin - Modelling of Turbulent Liquid-Gas Flows from Dense to Dilute Regime
by Werner, Janet M. 31 Jul '14

31 Jul '14

From: "Smagacz, Julie A." <smagacz(a)anl.gov<mailto:[email protected]>> Subject: Seminar: Prof. Fran�ois-Xavier Demoulin - Modelling of Turbulent Liquid-Gas Flows from Dense to Dilute Regime Date: July 31, 2014 10:14:05 AM CDT To: "mcsleadership(a)mcs.anl.gov<mailto:[email protected]>" <mcsleadership(a)mcs.anl.gov<mailto:[email protected]>>, "lcf-staff(a)alcf.anl.gov<mailto:[email protected]>" <lcf-staff(a)alcf.anl.gov<mailto:[email protected]>> Cc: "Smagacz, Julie A." <smagacz(a)anl.gov<mailto:[email protected]>>, "Bair, Raymond A." <rbair(a)anl.gov<mailto:[email protected]>>, "Som, Sibendu" <ssom(a)anl.gov<mailto:[email protected]>> Title: Modelling of Turbulent Liquid-Gas Flows from Dense to Dilute Regime Presenter: Prof. Fran�ois-Xavier Demoulin Date: August 5th, 2014 Time: 11am � 12 pm Room: Building 362, Rm. H220 Host: Dr. Sibendu Som ABSTRACT - Turbulent liquid gas flows remain an active field of research in fluid mechanics despite several decades of research and numerous applications. In particular numerical simulation is very attractive to explore such flows. Indeed, experiment can be very difficult, very often high velocity of the liquid may damage any physical probe, optical diagnostics suffer from the diffraction of the light at the liquid-gas interface. However, new diagnostic techniques such X-ray measurement (in particular at Argonne) has emerged to provide new insight in such flows. From the numerical point of view, two limit cases are addressed. In the first case, wrinkles of the interface can be resolved directly because of relatively large time scale and length scale compare to available mesh resolution. In this case interface capturing method (ICM) have reached a high degree of precision in particular during the last decade using for instance VOF, Level Set, Ghost Fluids method on parallel computer. In the other limit, one of the phases is very simplified to be represented as a set of discrete particles (DPMethod) with appropriate simplified behavior laws. In this presentation the case of atomization is considered. ICM can be used initially to determine first instabilities of the cylindrical liquid jet. Eventually, a spray is formed that can be described with DPM. However, the process of atomization is exactly the description of the destabilization of the jet that occurs continuously from ICM to DPM approaches. A large consensus have emerged to conclude that due to the large range of scales implied in this process, it is unaffordable to use ICM all the way from the initial liquid jet to the final droplet. To keep a continuous numerical approach it is necessary to deal with poorly resolved interface that cannot be described with ICM but with a very complex surface geometry to apply DPM. The pioneering work of Vallet and Borghi (Vallet and Borghi 1999; Vallet, Burluka et al. 2001) draws the bases of an appropriate model base on surface density equation, the so-called ELSA model. This presentation will present some works on this approach and some achievements that shows the possibility to use the ELSA model as a bridge between ICM and DPM to describe turbulent liquid-gas flow for any regime from the dense to dilute regime. Vallet, A. and R. Borghi. "Mod�lisation Eulerienne de L�atomisation d�un Jet Liquide." C. R. Acad. Sci., Paris, S�r. II b 327: 1015�1020, 1999. Vallet, A., A. A. Burluka and R. Borghi. "Development of a Eulerian model for the "Atomization" of a liquid jet." Atomization and Sprays 11(6): 619-642, 2001. SHORT BIOGRAPHY - Dr. Fran�ois-Xavier Demoulin is an Associate Professor at the University of Rouen in France since 2001. He is also the head of Master Energy Fluid and Environment program at the University. Prior to this, he was a postdoctoral fellow at SNECMA rocket engine division, in France. Dr. Demoulin obtained his Ph.D. from the Mechanical Engineering school at Marseille in France. Dr. Demoulin has published more than 30 journal and 50 conference papers. He is widely acclaimed for developing the ELSA two-phase flow model which is part of many commercial codes.

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half-day on Friday
by Henderson, Martino S. 31 Jul '14

31 Jul '14

My son is having a ceremony at his summer camp for the last day. I'll need to leave by noon in order to attend and pick him up. - Martino Henderson Help Desk / System Support Office: +1(630) 252-1692 Argonne National Laboratory Computer, Environment, & Life Sciences 9700 South Cass Avenue Building 240 - 3.E.18 Argonne, Illinois 60439 United States [ANL_Logo]

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LANS Informal Seminar - SASSy (Part 2)
by Ghosh, Debojyoti 31 Jul '14

31 Jul '14

LANS Informal Seminar Series What: Summer Argonne Students Symposium (SASSy) - Part 2 Informal Talks by the LANS summer students When: Tuesday, August 5th, 2014 at 1:00 PM — 4:15 PM Where: Building 240, Room 1404-1405 Goodies: Coffee and goodies will be served Speaker, Titles and Abstracts: + 13:00 - 13:15: Matt Otten (Supervisor: Misun Min) Title: Scalable Density Matrix Calculations of Coupled Quantum Systems Abstract: We study the time dynamics of a system consisting of quantum dots coupled to a single plasmon mode. The size of the density matrix grows quickly; a physically reasonable system of 16 quantum dots requires a matrix dimension of 50*2^16. At this size, extreme scale computing must be utilized. Aside from the novel physics applications, we are currently studying how best to treat this system, through different time stepping schemes (RK and exponential time integrator) and different parallelization algorithms. + 13:15 - 13:30: Harikrishnan Sreekumaran (Supervisor: Sven Leyffer) Title: On Bilevel Mixed-Integer Nonlinear Programming Problems Abstract: Bilevel programming provides a natural framework for modelling hierarchical decision making, with applications in varied fields such as market design, network planning and vulnerability analysis, and engineering design among others. In this talk, we review bilevel mixed integer nonlinear programming problems (BLMINLPs) and describe the significant challenges in the analysis and algorithm design for such problems. We present relaxation formulations for certain classes of BLMINLPs and introduce algorithms for solving such problems using these relaxations. Finally we present a few application examples and some preliminary numerical results. + 13:30 - 13:45: Paul Tranquilli (Supervisor: Cosmin Petra) Title: Building an adjoint based dynamics constrained optimization of electrical power systems Abstract: We present a mathematical framework for the solution of optimal power flow, including dynamic security constraints, using adjoint based sensitivities. We briefly discuss some implementation details of using PETSc to perform both the forward and backward time integrations. + 13:45 - 14:00: Bethany Nicholson (Supervisor: Victor Zavala) Title: Automatic Discretization of ODE and PDE Systems Using Pyomo Abstract: Dynamic optimization problems that include ordinary/partial differential equations as constraints are typically solved by discretizing the model and then solving the resulting nonlinear problem. This talk introduces a way to do model discretization automatically using the open-source modeling language Pyomo. We will discuss the straight-forward syntax behind this new functionality as well as the flexible discretization options that are available. Finally, we will look at a couple sample problems that show the wide range of dynamic optimzation problems that can now be represented and solved using Pyomo. + 14:00 - 14:15: Ahmed Attia (Supervisor: Mihai Anitescu) Title: Derivative-based solution of the constrained optimization problem(s) in DeMarco's model Abstract: Predicting cascading network failure is a vital problem for the ever increasing scale of engineered systems as electric power grids, communication networks, and internet. To predict cascading failures, for one or more branches, the bottleneck is a constrained optimization step. Without derivative information, this optimization step takes a very long time even for the simplest settings, and may even fail to converge for large simulation times. We considered a simple, but general, model developed by DeMarco to understand how small-scale failures of individual elements may propagate to produce global failures. My main task was to derive and implement the adjoint of the quadratic constraint(s). The derivative information of the cost functional and constraints, made the optimization very fast (roughly 100-150 times faster). The results are being extended now to large-scale settings. + 14:15 - 14:30: Francisco Trespalacios-Sagues (Supervisor: Victor Zavala) Title: Bound contraction algorithm for global optimization of natural gas networks Abstract: The natural gas transportation network problem has received increased attention in recent years. In this work, we first derive a convex NLP for this problem, based on a well-known non-convex NLP and two operating assumptions. We then present a non-convex model that includes the cost of both: purchasing natural gas from suppliers, and operating compressors in the network. Finally, we develop a bound contraction algorithm to solve this non-convex model. The algorithm is tested in a simplified real network, and compared against state of the art global solvers. -- 14:30 - 14:45: Break -- + 14:45 - 15:00: Matt Menickelly (Supervisor: Stefan Wild) Title: Handling Nonsmoothness in Derivative-Free Optimization Abstract: Derivative-free optimization is a branch of optimization theory concerned with optimizing functions for which derivatives are either unavailable (e.g. the objective is a black box) or are unreliable due to noise. A popular class of algorithms for derivative-free optimization is that of trust-region methods, wherein at each iteration, the objective is modeled locally using an interpolating function with respect to a choice of basis - in the scope of this research, and as is a common choice, a basis of quadratic polynomials. However, as one might expect, if there is nonsmoothness inherent in the objective, the failure of this basis to produce accurate local models of "kinks" or "corners" will cause a trust-region algorithm to stall. In this research, we explore the idea of approximate gradient sampling and the notion of convergence to Clarke stationarity to develop a mechanism to save trust-region methods from stalling as a result of nonsmoothness. + 15:00 - 15:15: Cullen Tanoue (Supervisor: Sven Leyffer) Title: Approximation and Multilevel Algorithms for Phase Retrieval Abstract: Phase retrieval poses an important optimization problem that arises in diffraction imaging, where the original structure of an object needs to be reconstructed from its diffraction data with loss of information concerning the phase of the object. Multilevel algorithms can be used to compute solutions to the standard phase retrieval optimization problem by constructing a hierarchy of problems using a series of restriction and prolongation operations. The coarser problems have a quarter of the variables as the finer problems, and hence, there are much less linear algebra requirements for solving the coarser problems. Further, the prolongation of the solutions computed for the coarser problems yield good starting points for the finer problems. We can also use an approach that alternates between solving the coarse and fine problem. Parameters for these methods include the number of levels, prolongation and restriction operations, and the number of iterations to perform at each level. We study the solutions to the standard phase retrieval optimization problem that result from exploring these parameters. + 15:15 - 15:30: Matthew Michelotti (Supervisor: Barry Smith) Title: Finding Particles in Halos: Resolving Local Effects when Simulating DNA Molecules. Abstract: Understanding how DNA molecules behave in a liquid is important for improving DNA sequencers. We can model DNA molecules as strings of charged particles. Using the GGEM method, each particle needs to receive information from other nearby particles in its "halo" to resolve local effects. We have added functionality to the libMesh library for having particles in a mesh and for finding particles in halos efficiently, in serial or parallel, for use with GGEM and similar methods. + 15:30 - 15:45: Paul Eller (Supervisor: Barry Smith) Title: Development of a User Controlled Threading Model for PETSc Abstract: In recent years multicore processors have become more common and hybrid programming models have been used to produce better performance than pure MPI in some situations. Therefore we have been working to develop a hybrid programming model for PETSc that allows users to take advantage of both MPI and threads. Multiple threaded programming models are being implemented in PETSc including models that give users more direct control of the threads. A threaded programming model introduces thread safety issues to PETSc which require non-trivial changes to routines throughout PETSc to ensure that the code produces accurate solutions without reducing performance. + 15:45 - 16:00: Wanting Xu (Supervisor: Mihai Anitescu) Title: Improving low memory state estimation of weakly constrained 4D-Var with gradient evaluation Abstract: Data assimilation is the process of estimating the states of a dynamical system with observation data. The underlying states and observables form a hidden Markov model, and the best states can be obtained by minimizing a corresponding likelihood function. We developed a recursive scheme for evaluating the gradient of the object function in a low memory fashion, and use that information in optimization. We demonstrate the improvement of our method over the existing low memory approach by simulation with Burgers' Equation and a linear PDE. + 16:00 - 16:15: Surtai Han (Supervisor: Barry Smith) Title: Web Interface for Parallel Linear Solver Selection Abstract: PETSc (Portable Extensible Toolkit for Scientific Computation) has a large selection of linear solvers to provide users with tools for a wide range of applications on parallel computers. However, it can be difficult for users to select the optimal solvers for their specific application. We built a webpage to assist users in viewing, customizing, and assembling the linear solvers by providing a GUI consisting of a hierarchy of drop-down menus and a tree diagram. Afterwards, the webpage generates the appropriate command-line options for the solvers that the user selected. A separate webpage allows users to interact with the SAWs (Scientific Applications Web Server) so that users can adjust the solver options during runtime. -- SASSy Part 3 - August 19th 1:00 - 4:00 PM (http://www.mcs.anl.gov/research/LANS/events/listn/detail.php?id=2351) -- LANS Informal Seminars Calendar: https://www.google.com/calendar/embed?src=e8r9gll7mc180cf279n49ancio%40grou… LANS Informal Semnars Listing: http://www.mcs.anl.gov/research/LANS/events/listn/ -- Debojyoti Ghosh ghosh(a)mcs.anl.gov

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Logwatch for berlin.mcs.anl.gov (Linux)
by logwatch＠mcs.anl.gov 31 Jul '14

31 Jul '14

################### Logwatch 7.3 (03/24/06) #################### Processing Initiated: Thu Jul 31 04:02:01 2014 Date Range Processed: yesterday ( 2014-Jul-30 ) Period is day. Detail Level of Output: 0 Type of Output: unformatted Logfiles for Host: berlin.mcs.anl.gov ################################################################## --------------------- pam_unix Begin ------------------------ sudo: Authentication Failures: dsouza(0) -> dsouza: 1 Time(s) ---------------------- pam_unix End ------------------------- --------------------- postfix Begin ------------------------ 2385 bytes transferred 1 messages sent 1 messages removed from queue ---------------------- postfix End ------------------------- --------------------- SSHD Begin ------------------------ Users logging in through sshd: dsouza: 140.221.10.82 (dsouza.mcs.anl.gov) 1 time ---------------------- SSHD End ------------------------- --------------------- Sudo (secure-log) Begin ------------------------ ============================================================================== dsouza => root ------------------------------------------------------------------------------ /bin/bash ---------------------- Sudo (secure-log) End ------------------------- --------------------- Disk Space Begin ------------------------ Filesystem Size Used Avail Use% Mounted on /dev/mapper/Vol0-LV00 15G 12G 2.1G 85% / /dev/md0 99M 39M 55M 42% /boot /dev/mapper/Vol0-local 1.8T 141G 1.7T 8% /local ---------------------- Disk Space End ------------------------- ###################### Logwatch End #########################

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[mrepo] changes to warehouse13.mcs.anl.gov (new: 43, removed: 39)
by mrepo＠warehouse13.mcs.anl.gov 31 Jul '14

31 Jul '14

The following changes to mrepo's repositories on warehouse13.mcs.anl.gov have been made: Dist: CentOS 5.10 (i386) (centos-5.10-i386) Repo: epel + bitlbee-3.2.2-1.el5.i386.rpm (371 kiB) + bitlbee-devel-3.2.2-1.el5.i386.rpm (39 kiB) + bitlbee-otr-3.2.2-1.el5.i386.rpm (26 kiB) + ovirt-guest-agent-1.0.10-1.el5.noarch.rpm (43 kiB) + polarssl-1.3.2-2.el5.i386.rpm (235 kiB) + polarssl-devel-1.3.2-2.el5.i386.rpm (1574 kiB) + polarssl-utils-1.3.2-2.el5.i386.rpm (98 kiB) - bitlbee-3.2.1-4.el5.i386.rpm (359 kiB) - bitlbee-devel-3.2.1-4.el5.i386.rpm (38 kiB) - bitlbee-otr-3.2.1-4.el5.i386.rpm (25 kiB) - ovirt-guest-agent-1.0.9-1.el5.noarch.rpm (36 kiB) - polarssl-1.3.2-1.el5.i386.rpm (235 kiB) - polarssl-devel-1.3.2-1.el5.i386.rpm (1574 kiB) - polarssl-utils-1.3.2-1.el5.i386.rpm (98 kiB) Dist: CentOS 5.10 (x86_64) (centos-5.10-x86_64) Repo: epel + bitlbee-3.2.2-1.el5.x86_64.rpm (369 kiB) + bitlbee-devel-3.2.2-1.el5.i386.rpm (39 kiB) + bitlbee-devel-3.2.2-1.el5.x86_64.rpm (39 kiB) + bitlbee-otr-3.2.2-1.el5.x86_64.rpm (26 kiB) + ovirt-guest-agent-1.0.10-1.el5.noarch.rpm (43 kiB) + polarssl-1.3.2-2.el5.i386.rpm (235 kiB) + polarssl-1.3.2-2.el5.x86_64.rpm (223 kiB) + polarssl-devel-1.3.2-2.el5.i386.rpm (1574 kiB) + polarssl-devel-1.3.2-2.el5.x86_64.rpm (1574 kiB) + polarssl-utils-1.3.2-2.el5.x86_64.rpm (103 kiB) - bitlbee-3.2.1-4.el5.x86_64.rpm (356 kiB) - bitlbee-devel-3.2.1-4.el5.i386.rpm (38 kiB) - bitlbee-devel-3.2.1-4.el5.x86_64.rpm (38 kiB) - bitlbee-otr-3.2.1-4.el5.x86_64.rpm (26 kiB) - ovirt-guest-agent-1.0.9-1.el5.noarch.rpm (36 kiB) - polarssl-1.3.2-1.el5.i386.rpm (235 kiB) - polarssl-1.3.2-1.el5.x86_64.rpm (223 kiB) - polarssl-devel-1.3.2-1.el5.i386.rpm (1574 kiB) - polarssl-devel-1.3.2-1.el5.x86_64.rpm (1574 kiB) - polarssl-utils-1.3.2-1.el5.x86_64.rpm (103 kiB) Dist: CentOS 6.5 (x86_64) (centos-6.5-x86_64) Repo: epel + armadillo-4.320.0-1.el6.i686.rpm (22 kiB) + armadillo-4.320.0-1.el6.x86_64.rpm (20 kiB) + armadillo-devel-4.320.0-1.el6.i686.rpm (865 kiB) + armadillo-devel-4.320.0-1.el6.x86_64.rpm (865 kiB) + bitlbee-3.2.2-1.el6.i686.rpm (335 kiB) + bitlbee-3.2.2-1.el6.x86_64.rpm (328 kiB) + bitlbee-devel-3.2.2-1.el6.i686.rpm (39 kiB) + bitlbee-devel-3.2.2-1.el6.x86_64.rpm (39 kiB) + bitlbee-otr-3.2.2-1.el6.x86_64.rpm (25 kiB) + fts-rest-3.2.7-1.el6.noarch.rpm (79 kiB) + fts-rest-cli-3.2.7-1.el6.noarch.rpm (9 kiB) + fts-rest-selinux-3.2.7-1.el6.noarch.rpm (3 kiB) + ovirt-guest-agent-1.0.10-1.el6.noarch.rpm (46 kiB) + packagedb-cli-2.4-1.el6.noarch.rpm (40 kiB) + polarssl-1.3.2-2.el6.i686.rpm (216 kiB) + polarssl-1.3.2-2.el6.x86_64.rpm (211 kiB) + polarssl-devel-1.3.2-2.el6.i686.rpm (11212 kiB) + polarssl-devel-1.3.2-2.el6.x86_64.rpm (11211 kiB) + polarssl-utils-1.3.2-2.el6.x86_64.rpm (82 kiB) + python-fts-3.2.7-1.el6.noarch.rpm (53 kiB) + python-ipython-0.13.2-5.el6.noarch.rpm (10 kiB) + python-ipython-console-0.13.2-5.el6.noarch.rpm (1283 kiB) + python-ipython-doc-0.13.2-5.el6.noarch.rpm (636 kiB) + python-ipython-gui-0.13.2-5.el6.noarch.rpm (164 kiB) + python-ipython-notebook-0.13.2-5.el6.noarch.rpm (318 kiB) + python-ipython-tests-0.13.2-5.el6.noarch.rpm (277 kiB) - armadillo-3.800.2-1.el6.i686.rpm (17 kiB) - armadillo-3.800.2-1.el6.x86_64.rpm (16 kiB) - armadillo-devel-3.800.2-1.el6.i686.rpm (688 kiB) - armadillo-devel-3.800.2-1.el6.x86_64.rpm (688 kiB) - bitlbee-3.2.1-4.el6.i686.rpm (324 kiB) - bitlbee-3.2.1-4.el6.x86_64.rpm (317 kiB) - bitlbee-devel-3.2.1-4.el6.i686.rpm (39 kiB) - bitlbee-devel-3.2.1-4.el6.x86_64.rpm (39 kiB) - bitlbee-otr-3.2.1-4.el6.x86_64.rpm (25 kiB) - ovirt-guest-agent-1.0.9-1.el6.noarch.rpm (42 kiB) - packagedb-cli-2.3.1-2.el6.noarch.rpm (39 kiB) - polarssl-1.3.2-1.el6.i686.rpm (216 kiB) - polarssl-1.3.2-1.el6.x86_64.rpm (211 kiB) - polarssl-devel-1.3.2-1.el6.i686.rpm (11212 kiB) - polarssl-devel-1.3.2-1.el6.x86_64.rpm (11211 kiB) - polarssl-utils-1.3.2-1.el6.x86_64.rpm (82 kiB) - python-ipython-0.13.2-4.el6.noarch.rpm (10 kiB) - python-ipython-console-0.13.2-4.el6.noarch.rpm (1283 kiB) - python-ipython-doc-0.13.2-4.el6.noarch.rpm (636 kiB) - python-ipython-gui-0.13.2-4.el6.noarch.rpm (164 kiB) - python-ipython-notebook-0.13.2-4.el6.noarch.rpm (318 kiB) - python-ipython-tests-0.13.2-4.el6.noarch.rpm (277 kiB)

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Where's JohnR?
by John Roberts 31 Jul '14

31 Jul '14

I'm heading to a car dealer in the morning and expect to be in around noonish. I'll be available by phone if needed. Sent from my T-Mobile 4G LTE Device

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