1. Introduction
    1. Unix Basic Configuration
    2. Module
    3. EMail forwarding
    4. The plan/project files
  2. The "module" Command
    1. Introduction
    2. Available Module Files
    3. How to Write your Own Modules Files
  3. Compilers & Libraries
    1. How to build and run MPI programs
    2. How to build and run multi-threaded programs
  4. Packages and Tools
    1. IDL & FL
    2. Java
    3. Julia
    4. Matlab
    5. Python
    6. R (old)
    7. Conda: Anaconda & Miniconda
  5. Genomics Software
    1. BLAST
    2. BLAST2GO

1. Introduction

Hydra is a Linux cluster running Rocky 8.9, while the software installation is managed using Bright Cluster management (BCM or CM).

Like any Linux machine, your Un*x environment on Hydra can be configured to your liking.

How to configure a Un*x environment is beyond the scope of this set of documentation.

Unix Basic Configuration

A set of configuration files, located in your home directory, sets up your Un*x environment - a default set of such files is provided when a new account is created:

Login shell
Bash shell (bash)Bourne shell (sh)C-shell (csh or tcsh)Action
.bash_profile.profile.cshrcread & executed at startup to configure your environment
.login.login.loginread & executed at startup, next, but only by a login shell
.emacs.emacs.emacsconfigures the emacs editor
.bash_logout.logout.logout

read & executed when logging out (login shell)

Note

qsub'ed job scripts are not started as a login shell, hence unless you fully understand the idiosyncrasies of the bash shell startup rules,

it is recommended that you use the Bourne shell (sh) or the C-shell (csh), and not the bash shell (bash) when submitting jobs.

Module

The command module is available on Hydra:

  • Instead of editing your .bash_profile file (or .profile or .cshrc) to configure your PATH (and MANPATH and LD_LIBRARY_PATH, etc), use the command module (as explained below).

EMail Forwarding

  • Email sent on the cluster is delivered to the head node (that you should not use),
  • To access these emails (like job notifications),  a ~/.forward file  was created with your "canonical/home" email address, i.e.:

      % echo [email protected] > ~/.forward

  • While you are welcome to edit this file and change the forwarding email:
    • do not delete it, and
    • use an email address you will read.
  • Note that by SD931, we must communicate with users via their work email, not their private one
  • You "on file" email (used for things like password reset and HPCC-L listserv) will remain you "canonical/home" email (the one that ends in .edu )

The plan/project files

  • the content of the files ~/.plan and ~/.project are displayed by the command pinky (man pinky);
    • feel free to put relevant/pertinent information in them.
  • The command finger is no longer available under Rocky 8:
    • the tools/local-user module offers a finger replacement.
  • Try 
      % pinky -l hpc

or

 % finger hpc

Last updated  SGK