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  1. Book ; Online ; Thesis: Inhomogeneous colloidal mixtures: segregation by charge or shape

    Esztermann, Ansgar

    2005  

    Author's details vorgelegt von Ansgar Esztermann
    Keywords Monte-Carlo-Simulation ; Dichtefunktionalformalismus ; Kolloid ; Geladenes Teilchen
    Language English
    Size Online-Ressource
    Document type Book ; Online ; Thesis
    Thesis / German Habilitation thesis Univ., Diss--Düsseldorf, 2005
    Database Former special subject collection: coastal and deep sea fishing

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  2. Article ; Online: More bang for your buck: Improved use of GPU nodes for GROMACS 2018.

    Kutzner, Carsten / Páll, Szilárd / Fechner, Martin / Esztermann, Ansgar / de Groot, Bert L / Grubmüller, Helmut

    Journal of computational chemistry

    2019  Volume 40, Issue 27, Page(s) 2418–2431

    Abstract: We identify hardware that is optimal to produce molecular dynamics (MD) trajectories on Linux compute clusters with the GROMACS 2018 simulation package. Therefore, we benchmark the GROMACS performance on a diverse set of compute nodes and relate it to ... ...

    Abstract We identify hardware that is optimal to produce molecular dynamics (MD) trajectories on Linux compute clusters with the GROMACS 2018 simulation package. Therefore, we benchmark the GROMACS performance on a diverse set of compute nodes and relate it to the costs of the nodes, which may include their lifetime costs for energy and cooling. In agreement with our earlier investigation using GROMACS 4.6 on hardware of 2014, the performance to price ratio of consumer GPU nodes is considerably higher than that of CPU nodes. However, with GROMACS 2018, the optimal CPU to GPU processing power balance has shifted even more toward the GPU. Hence, nodes optimized for GROMACS 2018 and later versions enable a significantly higher performance to price ratio than nodes optimized for older GROMACS versions. Moreover, the shift toward GPU processing allows to cheaply upgrade old nodes with recent GPUs, yielding essentially the same performance as comparable brand-new hardware. © 2019 Wiley Periodicals, Inc.
    Language English
    Publishing date 2019-07-01
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1479181-X
    ISSN 1096-987X ; 0192-8651
    ISSN (online) 1096-987X
    ISSN 0192-8651
    DOI 10.1002/jcc.26011
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

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  3. Book ; Online: More Bang for Your Buck

    Kutzner, Carsten / Páll, Szilárd / Fechner, Martin / Esztermann, Ansgar / de Groot, Bert L. / Grubmüller, Helmut

    Improved use of GPU Nodes for GROMACS 2018

    2019  

    Abstract: We identify hardware that is optimal to produce molecular dynamics trajectories on Linux compute clusters with the GROMACS 2018 simulation package. Therefore, we benchmark the GROMACS performance on a diverse set of compute nodes and relate it to the ... ...

    Abstract We identify hardware that is optimal to produce molecular dynamics trajectories on Linux compute clusters with the GROMACS 2018 simulation package. Therefore, we benchmark the GROMACS performance on a diverse set of compute nodes and relate it to the costs of the nodes, which may include their lifetime costs for energy and cooling. In agreement with our earlier investigation using GROMACS 4.6 on hardware of 2014, the performance to price ratio of consumer GPU nodes is considerably higher than that of CPU nodes. However, with GROMACS 2018, the optimal CPU to GPU processing power balance has shifted even more towards the GPU. Hence, nodes optimized for GROMACS 2018 and later versions enable a significantly higher performance to price ratio than nodes optimized for older GROMACS versions. Moreover, the shift towards GPU processing allows to cheaply upgrade old nodes with recent GPUs, yielding essentially the same performance as comparable brand-new hardware.

    Comment: 41 pages, 13 figures, 4 tables. This updated version includes the following improvements: - most notably, added benchmarks for two coarse grain MARTINI systems VES and BIG, resulting in a new Figure 13 - fixed typos - made text clearer in some places - added two more benchmarks for MEM and RIB systems (E3-1240v6 + RTX 2080 / 2080Ti)
    Keywords Computer Science - Distributed ; Parallel ; and Cluster Computing ; Computer Science - Performance ; Physics - Biological Physics ; Physics - Computational Physics ; Quantitative Biology - Biomolecules
    Subject code 000
    Publishing date 2019-03-14
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Best bang for your buck: GPU nodes for GROMACS biomolecular simulations.

    Kutzner, Carsten / Páll, Szilárd / Fechner, Martin / Esztermann, Ansgar / de Groot, Bert L / Grubmüller, Helmut

    Journal of computational chemistry

    2015  Volume 36, Issue 26, Page(s) 1990–2008

    Abstract: The molecular dynamics simulation package GROMACS runs efficiently on a wide variety of hardware from commodity workstations to high performance computing clusters. Hardware features are well-exploited with a combination of single instruction multiple ... ...

    Abstract The molecular dynamics simulation package GROMACS runs efficiently on a wide variety of hardware from commodity workstations to high performance computing clusters. Hardware features are well-exploited with a combination of single instruction multiple data, multithreading, and message passing interface (MPI)-based single program multiple data/multiple program multiple data parallelism while graphics processing units (GPUs) can be used as accelerators to compute interactions off-loaded from the CPU. Here, we evaluate which hardware produces trajectories with GROMACS 4.6 or 5.0 in the most economical way. We have assembled and benchmarked compute nodes with various CPU/GPU combinations to identify optimal compositions in terms of raw trajectory production rate, performance-to-price ratio, energy efficiency, and several other criteria. Although hardware prices are naturally subject to trends and fluctuations, general tendencies are clearly visible. Adding any type of GPU significantly boosts a node's simulation performance. For inexpensive consumer-class GPUs this improvement equally reflects in the performance-to-price ratio. Although memory issues in consumer-class GPUs could pass unnoticed as these cards do not support error checking and correction memory, unreliable GPUs can be sorted out with memory checking tools. Apart from the obvious determinants for cost-efficiency like hardware expenses and raw performance, the energy consumption of a node is a major cost factor. Over the typical hardware lifetime until replacement of a few years, the costs for electrical power and cooling can become larger than the costs of the hardware itself. Taking that into account, nodes with a well-balanced ratio of CPU and consumer-class GPU resources produce the maximum amount of GROMACS trajectory over their lifetime.
    MeSH term(s) Benchmarking ; Computer Simulation ; Molecular Dynamics Simulation ; Software
    Language English
    Publishing date 2015-08-04
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1479181-X
    ISSN 1096-987X ; 0192-8651
    ISSN (online) 1096-987X
    ISSN 0192-8651
    DOI 10.1002/jcc.24030
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Density functional theory for sphere-needle mixtures: toward finite rod thickness.

    Esztermann, Ansgar / Schmidt, Matthias

    Physical review. E, Statistical, nonlinear, and soft matter physics

    2004  Volume 70, Issue 2 Pt 1, Page(s) 22501

    Abstract: For mixtures of hard spheres and hard spherocylinders of large aspect ratio a recently proposed density functional theory is extended to incorporate effects due to nonvanishing rod thickness. This is accomplished by introducing several new geometric ... ...

    Abstract For mixtures of hard spheres and hard spherocylinders of large aspect ratio a recently proposed density functional theory is extended to incorporate effects due to nonvanishing rod thickness. This is accomplished by introducing several new geometric weight functions into the framework. We demonstrate explicitly how these weight functions recover the sphere-rod Mayer bond.
    Language English
    Publishing date 2004-08
    Publishing country United States
    Document type Journal Article
    ISSN 1539-3755
    ISSN 1539-3755
    DOI 10.1103/PhysRevE.70.022501
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Density functional theory for colloidal mixtures of hard platelets, rods, and spheres.

    Esztermann, Ansgar / Reich, Hendrik / Schmidt, Matthias

    Physical review. E, Statistical, nonlinear, and soft matter physics

    2006  Volume 73, Issue 1 Pt 1, Page(s) 11409

    Abstract: A geometry-based density-functional theory is presented for mixtures of hard spheres, hard needles, and hard platelets; both the needles and platelets are taken to be of vanishing thickness. Geometrical weight functions that are characteristic for each ... ...

    Abstract A geometry-based density-functional theory is presented for mixtures of hard spheres, hard needles, and hard platelets; both the needles and platelets are taken to be of vanishing thickness. Geometrical weight functions that are characteristic for each species are given, and it is shown how convolutions of pairs of weight functions recover each Mayer bond of the ternary mixture and hence ensure the correct second virial expansion of the excess free-energy functional. The case of sphere-platelet overlap relies on the same approximation as does Rosenfeld's functional for strictly two-dimensional hard disks. We explicitly control contributions to the excess free energy that are of third order in density. Analytic expressions relevant for the application of the theory to states with planar translational and cylindrical rotational symmetry--e.g., to describe behavior at planar smooth walls--are given. For binary sphere-platelet mixtures, in the appropriate limit of small platelet densities, the theory differs from that used in a recent treatment [L. Harnau and S. Dietrich, Phys. Rev. E 71, 011504 (2004)]. As a test case of our approach we consider the isotropic-nematic bulk transition of pure hard platelets, which we find to be weakly first order, with values for the coexistence densities and the nematic order parameter that compare well with simulation results.
    Language English
    Publishing date 2006-01
    Publishing country United States
    Document type Journal Article
    ISSN 1539-3755
    ISSN 1539-3755
    DOI 10.1103/PhysRevE.73.011409
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Order via subito

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    Inter-library loan at ZB MED

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  7. Book ; Online: Best bang for your buck

    Kutzner, Carsten / Páll, Szilárd / Fechner, Martin / Esztermann, Ansgar / de Groot, Bert L. / Grubmüller, Helmut

    GPU nodes for GROMACS biomolecular simulations

    2015  

    Abstract: The molecular dynamics simulation package GROMACS runs efficiently on a wide variety of hardware from commodity workstations to high performance computing clusters. Hardware features are well exploited with a combination of SIMD, multi-threading, and MPI- ...

    Abstract The molecular dynamics simulation package GROMACS runs efficiently on a wide variety of hardware from commodity workstations to high performance computing clusters. Hardware features are well exploited with a combination of SIMD, multi-threading, and MPI-based SPMD/MPMD parallelism, while GPUs can be used as accelerators to compute interactions offloaded from the CPU. Here we evaluate which hardware produces trajectories with GROMACS 4.6 or 5.0 in the most economical way. We have assembled and benchmarked compute nodes with various CPU/GPU combinations to identify optimal compositions in terms of raw trajectory production rate, performance-to-price ratio, energy efficiency, and several other criteria. Though hardware prices are naturally subject to trends and fluctuations, general tendencies are clearly visible. Adding any type of GPU significantly boosts a node's simulation performance. For inexpensive consumer-class GPUs this improvement equally reflects in the performance-to-price ratio. Although memory issues in consumer-class GPUs could pass unnoticed since these cards do not support ECC memory, unreliable GPUs can be sorted out with memory checking tools. Apart from the obvious determinants for cost-efficiency like hardware expenses and raw performance, the energy consumption of a node is a major cost factor. Over the typical hardware lifetime until replacement of a few years, the costs for electrical power and cooling can become larger than the costs of the hardware itself. Taking that into account, nodes with a well-balanced ratio of CPU and consumer-class GPU resources produce the maximum amount of GROMACS trajectory over their lifetime.
    Keywords Computer Science - Distributed ; Parallel ; and Cluster Computing ; Computer Science - Performance ; Physics - Biological Physics ; Physics - Computational Physics ; Quantitative Biology - Biomolecules
    Subject code 000
    Publishing date 2015-07-03
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article: Colloidal rod-sphere mixtures: fluid-fluid interfaces and the Onsager limit.

    Brader, Joseph M / Esztermann, Ansgar / Schmidt, Matthias

    Physical review. E, Statistical, nonlinear, and soft matter physics

    2002  Volume 66, Issue 3 Pt 1, Page(s) 31401

    Abstract: Using a geometry-based density functional theory we investigate the free interface between demixed bulk fluid phases of a colloidal mixture of hard spheres and vanishingly thin needles. Results are presented for the spatial and orientational density ... ...

    Abstract Using a geometry-based density functional theory we investigate the free interface between demixed bulk fluid phases of a colloidal mixture of hard spheres and vanishingly thin needles. Results are presented for the spatial and orientational density distributions of the particles, as well as for the interface tension. Density profiles display oscillations on the sphere-rich side of the interface provided the sphere liquid phase is on the oscillatory side of the Fisher-Widom line in the bulk phase diagram. Needles tend to align parallel (perpendicular) to the interface on the needle-rich (sphere-rich) side displaying biaxial (uniaxial) order. Furthermore, we generalize the theory to the Onsager limit for interacting rods, and give explicit expressions for the functional in simple geometries.
    Language English
    Publishing date 2002-09
    Publishing country United States
    Document type Journal Article
    ISSN 1539-3755
    ISSN 1539-3755
    DOI 10.1103/PhysRevE.66.031401
    Database MEDical Literature Analysis and Retrieval System OnLINE

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