Tips for using Cluster/Unix

Useful links

• • Simple awk tutorial

  • How to sort by last field in the line: http://stackoverflow.com/a/3223025

Useful Commands

• • # to display that Std output and Std error of a job as it is running:

  • bpeek <job ID> 

  • # to search module by name:

  • module avail 2>&1 | grep -i #search_name

  • # to see available hosts and resources on the cluster:

  • bhosts

Setting up your local environment on the cluster:

Within your /home/[username]/.bashrc add/edit the following as necessary:

# to add confirmation before moving anything:

alias mv='mv -i'

# to add a confirmation before removing/deleting anything:

alias rm='rm -i'

# to list files colored by file type:

alias ls='ls --color'

# shortcut to list files with more information

alias lh='ls -hog --color'

# to grep files colored by grep query

alias grep='grep --color;

# to change the directory/host colors to make them stand out:

DIR_COLOR=$YELLOW

HOST_COLOR=$DEFWHITE

# to add date/time information to command prompt:

export PS1="\[\e[${HOST_COLOR}\][\D{%h %d}|\@][${debian_chroot:+($debian_chroot)}\u@\h:\[\e[${DIR_COLOR}\]\\w\[\e[${HOST_COLOR}\]]$"

Setting up Local Modules on Cluster:

1. In your .bash_profile, add the following:

# User specific environment and startup programs

export MOD_SW=/pi/athma.pai-umw/software/local_modules_sw

module use /pi/athma.pai-umw/local_modules

2. For each new software:

a) Download the compiled software to software_downloads directory (compile code if necessary)

b) Make [softwarename]/[version] folder in local_modules_sw directory

c) Compile or move executable files to local_modules_sw/[softwarename]/[version]/bin

d) Create folders/file: local_modules/[softwarename]/[version]

e) In that file, type:

#%Module########################################################################

# 

# module

#

# [softwarename]-[version]

#

module-whatis "[softwarename]-[version]"

set    MOD_[softwarename]    $env(MOD_SW)/[softwarename]/

set    MOD_[softwarename]_VERSION    [version]

set    MOD_[softwarename]_DIR    $MOD_[softwarename]/$MOD_[softwarename]_VERSION/

prepend-path    PATH    $MOD_[softwarename]_DIR/bin/

3. This module should now be added.

a) When typing "module avail",  you should see the module in /pi/athma.pai-umw/local_modules/

b) Load the module with "module load [software]/[version]"

c) Check that the software works - how you do this will depend on what commands the particular software requires.