High-Performance, Low-Cost Computational Chemistry: Servers in a Stick, Box, and Cloud. Nathan Vance Polik Group Hope College February 19, 2015

Transcription

1 High-Performance, Low-Cost Computational Chemistry: Servers in a Stick, Box, and Cloud Nathan Vance Polik Group Hope College February 19, 2015

2 Outline The use and history of computing in chemistry The computing server Software Hardware

3 Computer Modeling in Chemistry Computers in chemistry are used to model molecular structure, spectra and reactivity

4 Scientific Computing Over Time Cray Y-MP Dorm Room Laptop Cloud Computing Wave of the future $20 Million $635 Pay only as needed 2.1 GigaFLOPS 43 GigaFLOPS Server is abstracted, so processing power is dynamic $9.5 Million per GigaFLOPS $15 per GigaFLOPS Costs decline as technology improves

5 Server Client Model The server is abstract; various implementations are possible Servers and clients communicate over the internet via a common protocol Clients are physical devices; they can be computers, tablets, or smart phones Server Internet Client Client Client

6 Server Side Software The computational chemistry server consists of: Operating system (Linux) Webserver (Apache) Interface (WebMO) Quantum chemistry engine (Mopac, Gamess)

7 Traditional Server Hardware MU3C Cluster: $680,000 + Installation + Maintenance Dedicated desktop server: $500 + Installation + Maintenance High performance clusters are too expensive for most organizations Desktops are not free and have installation and maintenance costs; performance is limited A solution is needed that maximizes performance and minimizes hardware, installation, and maintenance costs.

8 Server Hardware: Server on a Stick 4GB USB stick: $6 Pros: Minimizes hardware costs by using a preexisting computer to act as a computational chemistry server for a short period of time, then the computer is reverted back to its previous role Installation and maintenance is minimal Cons: A computational chemistry server installed on a bootable Linux does not contain drivers for all hardware; some individual computers may USB stick not be supported, such as macs Performance is limited by computer s processor; writing data to stick is slow Current status: In production and circulation

9 Server Hardware: Server in a Box Virtualbox: Free download A computational chemistry server installed as a virtual machine. Pros: Minimizes hardware costs by using a preexisting computer to run Server in a Box alongside its regular purpose Server is (mostly) hardware independent Cons: The virtualbox environment will need to be installed on the server computer, which is additional installation cost The real machine s firewall needs to be set up to allow traffic in and out of the virtual machine, more installation cost Performance is limited to a fraction of computer s processor Current status: Proof of concept demonstrated

10 Server Hardware: Server in the Cloud Cloud costs: variable Pros: No hardware to maintain or upgrade Can dynamically select hardware capabilities (large disk, large memory) No initial cost Cons: Pay for ongoing use A computational chemistry server hosted remotely Current status: Concept under investigation

11 Future Work Summer 2015: Evaluate cost models for cloud computing Create a cloud image for Amazon or Google Cloud Select linux distribution Migrate Stick/Box server to this distribution Automate image creation from software sources Evaluate issues associated with turning cloud servers on/off Latency time Saving of data Evaluate computing performance of cloud servers with different characteristics Future: Divide webserver from compute server Create a means to dynamically spawn compute nodes

12 Acknowledgments Dr. William Polik, Hope College Dr. JR Schmidt, University of Wisconsin - Madison WebMO, LLC Hope College Chemistry Department