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The GROMACS and NAMD Software Packages Comparison

Communications in Computational Physics 2006年第4期1卷 736-743页

作者： armen H.poghosyan Grigor A.Yeghiazaryan Hrant H.Gharabekyan Aram A.Shahinyan The International Scientific-Educational Center of the National Academy of Sciences of armenia Marshall Baghramian Ave.24d375019 YerevanRepublic of Armenia

The comparable feature analysis of NAMD and GROMACS molecular dy-namics packages has been *** benchmarks of 72 and 128 Dipalmitoylphos-phatidylcholine(DPPC)/water have been constructed using a cluster(3GHz-Xeon proces-sors and Myrinet network)and the comparison has been performed using GROMOS87 and CHARMM27 force fields modified for lipids with GROMACS and NAMD software packages,*** GROMACS has been displayed as faster than NAMD,likely due to united-atom character of GROMACS and good implementation *** GROMACS reaches saturation and goes to the worst results,the reason of which is that the program spends more time on communications between processors.

关键词： NAMD GROMACS molecular dynamics phospholipid bilayers

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NAMD Package Benchmarking on the Base of armenian Grid Infrastructure

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Communications and Network 2012年第1期4卷 34-40页

作者： armen poghosyan Levon Arsenyan Hrachya Astsatryan Mikayel Gyurjyan Hovsep Keropyan Aram Shahinyan Institute for Informatics and Automation Problems National Academy of Sciences of the Republic of Armenia Yerevan Armenia Institute of Applied Problems of Physics National Academy of Sciences of the Republic of Armenia Yerevan Armenia International Scientific Educational Center National Academy of Sciences of the Republic of Armenia Yerevan Armenia

The parallel scaling (parallel performance up to 48 cores) of NAMD package has been investigated by estimation of the sensitivity of interconnection on speedup and benchmark results—testing the parallel performance of Myrinet, Infiniband and Gigabit Ethernet networks. The system of ApoA1 of 92 K atoms, as well as 1000 K, 330 K, 210 K, 110 K, 54 K, 27 K and 16 K has been used as testing systems. The armenian grid infrastructure (ArmGrid) has been used as a main platform for series of benchmarks. According to the results, due to the high performance of Myrinet and Infiniband networks, the ArmCluster system and the cluster located in the Yerevan State University show reasonable values, meanwhile the scaling of clusters with various types of Gigabit Ethernet interconnections breaks down when interconnection is activated. However, the clusters equipped by Gigabit Ethernet network are sensitive to change of system, particularly for 1000 K systems no breakdown in scaling is observed. The infiniband supports in comparison with Myrinet, make it possible to receive almost ideally results regardless of system size. In addition, a benchmarking formula is suggested, which provides the computational throughput depending on the number of processors. These results should be important, for instance, to choose most appropriate amount of processors for studied system.

关键词： Parallel Molecular Dynamics NAMD Benchmarking Grid

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NAMD Package Benchmarking on the Base of armenian Grid Infrastructure

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Communications and Network（通讯与网络） 2012年第1期

作者： armen poghosyan Levon Arsenyan Hrachya Astsatryan Mikayel Gyurjyan Hovsep Keropyan Aram Shahinyan

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