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Inspur Computational Chemistry Molecule Simulation Solution

[summary]

General description: with our rich solution integration experiences, professional services and quality products, our high-performance products necessarily address the needs for large-scale scientific computations in computational chemistry. The system runs efficiently and stably and guarantees the effective utilization of client applications.

1. Demands and challenges

Molecule simulation involves the simulation of the microscopic conducts of molecular motions in theoretical method and computational technology. It is extensively applied in computational chemistry, computational biology and material science. It can be adopted as the research object for a single chemical molecule and a complicated biological system or material system alike. With the development of computer technology and the continuous progress of physical and chemical theories, high-performance computers have been extensively applied in the research on molecule nature and development of new materials. Fundamentally, molecule simulation mainly involves two parts: the quantum chemistry simulation based on the first principle, and the molecular mechanics simulation based on classical mechanics. With continuously increasing complication of the research system and people's increasing needs for accurate computational results, some cross disciplines have also emerged such as the molecular dynamics of the first principle and other new research methods that combine the advantages of quantitative simulation and molecular simulation.

Molecule simulation (material physics/computational chemistry) is a fast-developing subject in recent years. It has molecule simulation as the tool for calculation of various core chemical questions and becomes a bridge between theoretical chemistry and empirical chemistry. Its main goal is to utilize effective mathematic approximation and computer program for computation of molecule nature (e.g. total energy, dipole moment, quadrupole moment, vibrating frequency, reactive activity, etc.) and explanation of some specific chemical issues. Theoretically, any molecule can be computed in a highly accurate theoretical method. Much computational software already includes these accurate methods. As these methods’ computational load increases exponentially with the increasing number of electrons, they are only applicable for very small molecules. For larger-scale systems, some other higher-level approximation methods are normally required in order to keep balance between computational load and result.

Scope of application

Application

Quantitative computation

GaussianVASPADFMolproMolcasWien2kMaterials StudioMedeA,ATK/VNL,ADFAMBER,CHARMMPWSCF

Molecule dynamics

AmberGromHyperChemChemLab

2. Inspur high-performance computation chemical molecule solution

With the development of computer hardware, computing speed has increased significantly. Yet computation is highly complicated in the chemical sector, particularly for a large-scale system, so that high-performance computer systems become essential for theoretical chemical computations. Therefore, an excellent high-performance solution not only enables the researcher to accomplish a computation task faster, but also guides how to better fulfill it. The following molecule simulation configuration is recommended:

Type of nodes

Applications

Functional server

Cluster management, login and IO node

Dual-channel blade

Applicable for applications in molecule dynamics and large-scale parallelism; also as supercomputer center or computational node

GPU/MIC acceleration

Applicable for applications in molecule dynamics that support GPU ; or the programs independently developed by some users

Eight/four-channel 

fat nodes

  Large-scale Gaussian and VASP computation tasks

Storage system

  Gaussian imposes very high pressure on IO bandwidth

3. Advantages and value of Inspur solution

Close combination of computational system and client application

The typical applications of computational chemistry client are fully considered in the design of Inspur TS10K system and the system is tailor-made to customer applications. Fat nodes are configured in response to hidden finite element analysis and NF8460M3 four channels or TS860 eight channels of fat nodes are optional. Dual-channel mainstream computation nodes are furnished for fluid applications and the options include NF5279M2 and dual-channel flagship product NF5280M3; graphical workstations of a tower and rack type are optional for pretreatment and post-treatment; NAS storage, fiber storage and IB SAN storage solutions are available; and, Inspur Ts Exastor parallel file system may be furnished where there is a particularly high requirement on IO bandwidth.

Well-established interconnection system

Inspur TS10K system includes 4 sets of networks. The management network is a 1G network that has 10G network as the trunk network. Independent IP may be established for educational network/public networks so that WAN users can log in and use the cluster; IPMI network is a non-linear 1G switch for interconnection of all nodes and the administrator can realize the off-band administration of the cluster via an office computer. The KVM local monitoring network can realize KVM monitoring of 960 computers at the maximum in a daisy chain mode. The computation network is characterized by interconnection at fully linear speed via IB network with a bandwidth of 56Gb/s and a delay within 1 millisecond to fully guarantee data exchange during computation.

Advanced and efficient dispatching system

Inspur ClusterEngine cluster administration software is customized for Inspur TianSuo HPS cluster. It has a B/S architecture and operates via browser (IE, Firefox, etc.) for all-around cluster monitoring, administration, and alarm. The user submits its scientific computation task via the ClusterEngine graphical interface and ClusterEngine will reasonably dispatch the tasks submitted by the user according to the use of cluster resources and the operation’s demand for resources, hence increasing the utilization ratio and efficiency of resources. ClusterEngine can also summarize the resource consumption and resource use conditions and generates a statement for the cluster administrator as the criteria of system optimization.

Green and energy efficiency of cluster system

All nodes are furnished with 80PLUS highly efficient power sources to increase the efficiency of power source switching and reduce user’s operating and maintenance costs. Coupled with ClusterEngine energy-saving components, the free resources are automatically set in a standby or shutdown state, hence reducing the general energy consumption by 20%.

With our rich solution integration experiences, professional services and quality products, our high-performance products well address the needs for large-scale scientific computations in computational chemistry. The system runs efficiently, stably and guarantees the effective utilization of client applications.

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