Raspberry Pi Server
DESIGN AND APPLICATION OF AN EFFECTIVE LABORATORY-BASED RASPBERRY PI BIOINFORMATICS TEST SERVER
Dominic Theis1,2, Mafer Correa1, Mark Panning1, Holly A. F. Stessman2
1Division of IT, Research and Development Lab and 2Department of Pharmacology, School of Medicine, Creighton University, Omaha, NE
ABSTRACT: High performance computing has become an essential component in bioinformatics research because of the growing size of data that needs to be processed. A test environment is useful for program troubleshooting without changing the configuration of the production server environment. In the absence of institutional test space, laboratories must develop their own virtual test environment to test new pieces of software that is inexpensive, easy to assemble, and has a small-footprint. Since its introduction in 2016, the Raspberry Pi 3 has been widely adapted to be a flexible, easily customizable option for many computing purposes. Industrial test server spaces can be very expensive and hard to maintain. The cost for an Intel server is around $1,000, and that does not include the power, networking, or the housing. According to ZDNet, in the U.S., the average cost of a server to run for a full year is $731.94. Production server space can be used as a test environment, but changing the configuration for a single program can affect how other programs run and possibly bring the server to a halt. We hypothesized that a Raspberry Pi 3 cluster could be built and implemented in a cost-effective and timely manner functioning effectively as a laboratory test environment. The core of our test server was built from four Raspberry Pi 3’s, each with a 32 GB micro SD storage card. The power was supplied by a 12A USB hub, and the Pi’s were connected through a 10/1000 Ethernet, 2.4 GHz wireless network switch which allowed access from any user over the network. The Raspbian operating system, a Linux-based environment, was downloaded on to each micro SD card. To make our server more permanent, a low-profile chassis was 3D printed with a Stratasys Dimension SST 1200 3D printer with ABS plastic filament including room for a 50 mm fan for proper ventilation. The physical server components were assembled in one hour. All components were purchased from Amazon for a cost of approximately $250. The basic installation of the Raspbian operating system was completed in less than one day using universal peripherals (i.e., a mouse, keyboard, and monitor). In preliminary testing, Our Raspberry Pi server could execute simple Python scripts in close to a quarter of the time of a single Raspberry Pi alone. We have successfully constructed a research computing cluster consisting of four nodes using Raspberry Pi 3 micro computers. We have tested our server with simple Python scripts and saw a drastic reduction in time compared to a single Raspberry Pi. The Raspberry Pi 3 cluster has proven to be a cost-effective, flexible, power-efficient option to test new lab software before uploading to a production server.
Dominic Theis1,2, Mafer Correa1, Mark Panning1, Holly A. F. Stessman2
1Division of IT, Research and Development Lab and 2Department of Pharmacology, School of Medicine, Creighton University, Omaha, NE
ABSTRACT: High performance computing has become an essential component in bioinformatics research because of the growing size of data that needs to be processed. A test environment is useful for program troubleshooting without changing the configuration of the production server environment. In the absence of institutional test space, laboratories must develop their own virtual test environment to test new pieces of software that is inexpensive, easy to assemble, and has a small-footprint. Since its introduction in 2016, the Raspberry Pi 3 has been widely adapted to be a flexible, easily customizable option for many computing purposes. Industrial test server spaces can be very expensive and hard to maintain. The cost for an Intel server is around $1,000, and that does not include the power, networking, or the housing. According to ZDNet, in the U.S., the average cost of a server to run for a full year is $731.94. Production server space can be used as a test environment, but changing the configuration for a single program can affect how other programs run and possibly bring the server to a halt. We hypothesized that a Raspberry Pi 3 cluster could be built and implemented in a cost-effective and timely manner functioning effectively as a laboratory test environment. The core of our test server was built from four Raspberry Pi 3’s, each with a 32 GB micro SD storage card. The power was supplied by a 12A USB hub, and the Pi’s were connected through a 10/1000 Ethernet, 2.4 GHz wireless network switch which allowed access from any user over the network. The Raspbian operating system, a Linux-based environment, was downloaded on to each micro SD card. To make our server more permanent, a low-profile chassis was 3D printed with a Stratasys Dimension SST 1200 3D printer with ABS plastic filament including room for a 50 mm fan for proper ventilation. The physical server components were assembled in one hour. All components were purchased from Amazon for a cost of approximately $250. The basic installation of the Raspbian operating system was completed in less than one day using universal peripherals (i.e., a mouse, keyboard, and monitor). In preliminary testing, Our Raspberry Pi server could execute simple Python scripts in close to a quarter of the time of a single Raspberry Pi alone. We have successfully constructed a research computing cluster consisting of four nodes using Raspberry Pi 3 micro computers. We have tested our server with simple Python scripts and saw a drastic reduction in time compared to a single Raspberry Pi. The Raspberry Pi 3 cluster has proven to be a cost-effective, flexible, power-efficient option to test new lab software before uploading to a production server.