Building and Running Application Codes on the ARL Linux Networx Cluster (JVN)

Abstract

Porting, building and running application codes in the high-performance Linux cluster environment are different than the traditional high-performance computing environment with which many users are familiar. There are multiple compiling environments to choose from, along with their associated MPICH environments and optimized scientific libraries. Determining which of these environments is best suited to a user's application is not always apparent, as is defining the user's environment to properly access the chosen compiler and libraries during the build process. After successfully building an application, creating LSF batch run scripts that will successfully and efficiently run these newly built applications to solve user-defined problems has its own unique requirements inherent to the Linux environment. The objective of this paper is to provide the information necessary for new users to the Linux cluster to determine the most appropriate compiling environment for their application, as well as the means to access the compiler and associated libraries to successfully build and, if necessary, debug the desired application. Usage of the LSF batch system to submit batch jobs that will successfully and efficiently run on Linux cluster compute nodes will also be addressed. A discussion of each compiler's characteristics will provide a basis for users to determine which compiling system is most appropriate for their application. An introduction to the use of software "modules" will provide a way for users to easily tailor their environment to use the desired compiling environment for code development/building. Finally, LSF batch script examples will be used to demonstrate correct script usage. By better understanding the ARL Linux Networx cluster environment, new users will be able to become effective and productive users of the system more quickly. By minimizing the time required by users to port their codes onto a new platform and begin production jobs, the overall efficacy of the cluster's capability as a research tool is enhanced thereby increasing its overall value to the program