This tutorial will explain how to compile and link programs on HPC, how to submit the programs to the PBS queuing system and how to monitor and manage jobs that you've submitted. The default tutorial uses C and OpenMPI – see below for other languages and MPI implementations. Some of these tutorial sections will not apply to you. For example, if you will not be using C, C++ or Fortran, then you do not need to read the sections on compiling and linking those programs.

Make sure you read the Monitoring and Controlling Jobs on HPC page, especially the section on QDel.

Tutorial Sections

1. Compiling and Linking C, C++ and Fortran Programs
   1. Compiling C Programs on HPC – demonstrates the process of compiling C programs, both serial and parallel. Uses OpenMPI for parallel jobs. We have equivalent pages for other languages: Fortran 77, Fortran 90 and C++.
   2. Linking Programs on HPC – explains how to link programs, both serial and parallel.
2. General Job Submission
   1. HPC Parallel Job Submission – explains how to run parallel jobs on the cluster nodes. Parallel jobs are jobs that use multiple cluster nodes together for a single computation.
   2. HPC Serial Job Submission – explains how to run serial jobs on the cluster nodes. Serial jobs are jobs that do not require communication between cluster nodes.
3. Submitting Jobs for Interpreted Languages
   1. Running Matlab on HPC – how to run Matlab on HPC's cluster nodes
   2. Running R on HPC
   3. Running SAS on HPC
   4. Running IDL on HPC
4. Monitoring and Controlling Jobs on HPC – details the qstat and qdel commands which let you monitor and cancel jobs.

More Detailed Pages

While OpenMPI is easy to use, it is currently much slower than MVAPICH 1 & 2 on our cluster for some ranges of message sizes. After you work through the main tutorial, see the following pages to learn to use MVAPICH 1 or 2:

• Running Parallel Hello World Using MVAPICH
• Running Parallel Hello World Using MVAPICH2

If you want help choosing between OpenMPI, MVAPICH and MVAPICH2, or choosing between the PGI and GCC compiler suites, see this page: Choosing a Compiler and MPI Implementation.

For information about how to tweak your qsub scripts and how to get your job to run sooner, see this page: Using QSub. If you want more details on running jobs on HPC, see this page: Running Jobs on HPC. It is quite extensive, and assumes you have read through the tutorial already.