Stickfish Supplies Scientific Grid for Wood Science Institute at Mendel University of Agriculture and Forestry in Brno

14. 6. 2010 | Reklama | Tiskové zprávy | 9357×

Mendel University of Agriculture and Forestry in Brno can pride itself on the longest history of agriculture and forestry studies in the Czech lands. It was established in 1919 as the University of Agriculture in Brno and it kept this name till 1994. Its constitution completed a longterm effort to institute an agricultural university in Moravia, which has, from of old, held an important place among countries with the most developed agricultures in Central Europe.

Mendel University of Agriculture and Forestry in Brno (MUAF in Brno) is divided into four faculties. Faculty of Agronomy, Faculty of Forestry and Wood Technology, Faculty of Business and Economics, and Institute of Lifelong Learning are all located in Brno. Faculty of Horticulture is located in Lednice. The total number of students enrolled at all four faculties was almost 8 000 in 2004.

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The research goal of the Wood Science Institute is concerned with a mathematical-physical model of electromagnetic field distribution in samples of wood upon application of electromagnetic energy in ultra-high frequencies and mathematical-physical model of distribution of heat gradients in samples of wood at a time of simultaneous infrared and microwave heating. This project is associated with a number of related professional activities at the Faculty of Forestry which can be, with a bit of immodesty, labeled as the vehicle of progress in the area of demanding computations, modern computer technologies, and computer infrastructure at the Mendel University of Agriculture and Forestry in Brno. Main topics of interest are elementary models of solid mechanics, liquids, and thermodynamics. As it belongs to the Faculty of Forestry and Wood Technology, a special emphasis is placed on the area of tree and vegetation biomechanics, wood drying, acoustics, and industrial design.

Academic need

• Compatibility of computer nodes and Sun Ray controllers with Red Hat and Scientific Linux systems.
• Extendability of the nodes and simple scalability of the number of nodes.
• Central data storage for tasks and batches of data input.
• Utilisation of the university rectorate's central LDAP data storage.

Proposed solution

• Ultra-powerful dual-core Sun Fire X4600 servers with a capacity of up to 32 cores per server.
• Data storage: SAS 15 000 RPM Sun STK 2540 HW RAID with FC access.
• Virtual clients Sun Ray 270 and Sun Ray 2 for task operators and research workers.
• High availability Sun Ray controller with failover to Sun Fire X2200 servers.
• Certified Red Hat Enterprise Linux EDU for scientific applications.
• Use of a Sun Microsystems grant for academic and education in the EU.

Solution benefits

• Better economy of computationally intensive operations.
• Very high performance in the area of mathematical models.
• Cost savings from expenditures on user and research worker workstations.
• Readiness for expansion of performance and used applications.
• Providing other university institutions with excess computing power.
• Energy saving per computing power and end-user workstations.

Starting Position

The Wood Science Institute used separate and not very powerful computing resources located in several places such as the Brno METACentrum, server room of the rectorate of the Mendel University of Agriculture and Forestry in Brno, and servers or workstations within the Faculty of Forestry. Computing elements were composed of discrete servers or built from independent components. Research workers' and computing tasks operators' workstations were based on regular PC's. With growing demand for scientific computations and specific tasks of applied research, it became apparent that the existing solution was insufficient and a modernised system was necessary for a more effective processing of computation tasks. Faculty members' PC's and workstations also did not allow for a centralised management of users and identities.

Solution

The entire computing node is now ready to take over existing insufficient computing power for scientific computations on distributed computing nodes. The number of nodes will be gradually increased by adding entire servers or cores and CPU's along with RAM to individual computing nodes. According to InfoWorld, the supplied Sun Fire X4600 server is the best High-Performance server of 2007. Brutal computing power of two 4-socket servers has been fitted in a 4U size with an extremely low consumption of energy. Up to 32 cores and 128 GB of RAM predestined the Sun Fire X4600 not only for deployment at the Tokyo Institute of Technology to become one of the TOP10 of the most powerful supercomputers in the world, but for the demanding scientific tasks at the Faculty of Forestry as well. The computing grid runs applications like CFX, Fluent, Comsol, ANSYS, and Matlab for distributed scientific computations, modeling of physical effects in microwave dehumidification, or nanotechnologies based on wooden composites.

On the side of end-users the cost savings were related not only to energy but mainly to centralised administration. Disparate workstations and high cost of maintaining individual PC's have been replaced by Sun Ray virtual display terminals. The advantage of terminals, or virtual display units, lies in the fact that they are a fully remotely-administered solution without RAM, CPU, or HD. All system resource requirements are limited to fail-over controlling servers that service the Sun Ray 270 and Sun Ray 2 clients with built-in LCD's. As opposed to Citrix-based terminals or HP and IBM solutions that function rather like diskless computers, adding applications in user profiles will not increase RAM and CPU requirements. Even after a few years it will be possible to run much more demanding applications on the same virtual desktop units. Both scientific applications running on Linux or Solaris and a regular MS Windows environment have been made available to users at the Faculty of Forestry and faculty service staff respectively. Access to either complete MS Windows desktops or only selected applications on the Sun Ray terminals is provided through the RDP protocol. The Sun Ray SW Server has recently been certified by Microsoft for its native RDP protocol version 5.

High availability for faculty members, research workers, and students as well was the main criteria from the beginning of the infrastructure design. Thanks to the Sun Ray Server SW and a built-in fail-over on the application level of terminal maintenance, the administration of virtual desktops is easy to realise without a need for a cluster. When the controlling servers are switched on, the Sun Ray Server Software is automatically started and with its help, the servers form a so-called fail-over group (on application software level). There are two key components in the Sun Ray Server Software: Authentication Manager (thereinafter AM) and Session Manager (thereinafter SM). During the start of the servers, a data warehouse service (OpenLDAP) and a DHCP server are started. OpenLDAP runs on both servers in realtime application mode (ldapsync). When the Sun Ray terminals are switched on, they send DHCPDISCOVER broadcast requests that are processed by the DHCP server running on the controlling servers. The DHCP server sends a standard set of network parameters and then a set of parameters specific to Sun Ray. These parameters include fail-over group configuration and the controlling server's address. The Sun Ray thin client is configured according to this information. If there is an active session associated with this client, it is used and the monitors connected to this terminal display a so-called login screen: access to the graphical user interface.

Client's Evaluation

Stickfish, s. r. o., provided us with exceptional services both when designing a solution and then implementing it. We would especially like to acknowledge their patience when dealing with the academic environment and its traditional vagaries which forced all participating parties to continually adapt the proposed solutions to new and new conditions of the university's unstable environment. The company's representatives greatly contributed to a revolutionary design of a hybrid terminal structure that should fulfill demanding requests of HPC on one side and regular needs of administrative workers on the other side. I would like to thank all employees of Stickfish who participated in the project's solution and took part in creating a new infrastructure at the Faculty of Forestry at the Mendel University of Agriculture and Forestry in Brno.

Ing. Petr Koňas, Ph.D.
Supercomputer centre administrator at FWF MUAF konas@mendelu.cz

Contact

Stickfish, s. r. o.
Koněvova 2660/141
130 83 Prague 3

+420 267 108 381
info@stickfish.com

About Stickfish

Stickfish is an ICT company specialising in enterprise Linux and Unix technologies. Its strategy is to supply complete solutions: from analysis of requirements and the finding of the best solution, to training and subsequent technical support or outsourcing of maintenance. Stickfish provides solutions from leading vendors such as Sun, IBM, Red Hat, Oracle, or VMware, advanced networking products from Juniper and Cisco, and also its own highly secure and fast enterprise desktop solution, Raydesk. Stickfish operates the popular electronic store 64bit.eu and the technically oriented Internet portals AbcLinuxu.cz, ITBiz.cz and Hdmag.cz.

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