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Guidelines for a Good Hyak User Experience

  • Become familiar with Unix systems generally. We provide links to some good resources. Many scientific and engineering applications are distributed as source code which must be built to match the specifics of the system where they are run. Doing this requires a good working knowledge of Unix, including an understanding of the shell, variables, paths, libraries, etc., and how these things relate to each other.
  • Peruse the entire Wiki. Some of it won't make sense right away, but by looking through the whole thing you'll be better able to put things in context. You should come away from the experience with an understanding of Hyak’s filesystems, software, scheduler operations, and more. It will take time, but it’s worth it.
  • Use the environment we provide. Your new account will be configured with the bash shell and a set of minimal environment files (.bashrc, etc.). Combined with modules we provide, you have all the tools you need to set up a working software environment. There is no reason to hard code paths for any software, libraries, etc. from our supported list into your shell environment, and doing so will only cause problems for you and for our staff when you request assistance. Difficulties will arise if your shell and the shell you use to execute your job scripts differ. Unless you are an experienced shell programmer, you are strongly encouraged to use bash since, for interactive use, bash and tcsh offer the same set of features. Users are free to change their accounts to use the C shell, but support for C shell users is limited.
  • Start small. Practice by starting an [ interactive session|Hyak Job Scheduler#Interactive Sessions] and looking around at the filesystems, etc. Then use the scheduler to run some simple shell scripts. Use the development environment (compilers, etc.) to follow some of the examples (Hyak Compiling HDF5 Serial, Hyak Compiling HDF5 Parallel, Hyak MPICH2-MX, Hyak Open MPI) on the Wiki. Once you are comfortable following the instructions to reproduce the results in the examples, move on to more complex tasks.
  • Work with other experienced users. If any of your peers are experienced supercomputer users, talk to them. They might not have experience using Hyak, but the way we run things here is very similar to what you'll find at supercomputer centers worldwide. A word of caution: Do not take shell environment files (.bashrc, etc.), qsub scripts, etc. from others and expect things to work for you. While the general principles are similar across supercomputers, the details differ and that matters. To have a good experience using Hyak, or any other supercomputer, it is important that you take the time to understand the specifics of the software environment and set things up for yourself.
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