- Introduction
- The "module" Command
- Compilers & Libraries
- How to build and run MPI programs
- How to build and run multi-threaded programs
- Packages and Tools
- Genomics Software
1. Introduction
Hydra is a Linux cluster running CentOS 7.6, 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 | .cshrc | read & executed at startup to configure your environment |
.login | .login | .login | read & executed at startup, next, but only by a login shell |
.emacs | .emacs | .emacs | configures 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 yourPATH
(andMANPATH
andLD_LIBRARY_PATH
, etc), use the commandmodule
(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 DoeJ@si.edu > ~/.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 commandfinger
(man finger
); - feel free to put relevant/pertinent information in them
- try
% finger hpc
Last updated SGK