Genders and PDSH

Using Genders & PDSH to manage hosts in bulk

Part of the HPC Environment Basics series

Overview

Genders provides a simple method for categorising a node inventory. To learn more about genders, read the official tutorial.

PDSH provides a CLI tool for performing commands on multiple nodes at once, utilising the data stored in genders. To learn more about using PDSH, read the manual page for the command man pdsh.

OpenFlight has it’s own build of PDSH which can be installed here and is explained further on in the documentation

Installing Genders and PDSH

The packages should be available in the package manager for your distribution. To install on CentOS/RHEL/Rocky:

dnf install pdsh genders

You will need sudo permissions to install packages, see becoming the root user for more information

Creating a Genders File

Open the genders file (/etc/genders) with your preferred text editor and add a gender in with the following format:

node01,node02,node03,node04,node05 gendername

There are alternate formats that make writing a gender easier:

node01,node02,node03,node04,node05:    node[01-05]
node3,node7,node9,node10,node11:       node[3,7,9-11]
nodei,nodej,node0,node1,node2:         nodei,nodej,node[0-2]

For example:

node[01-05] mygroup1
nodeA,nodeB,node[1,2,3,10-20],nodeC mygroup2

After adding the desired gender(s), save and close the file.

Finding the Names of Your Compute Nodes

In best practice, the hostnames of compute nodes usually follow a sequential order (e.g. node01, node02, node03… node10).

Users can find the names of their compute nodes by using the nodeattr command with a group; e.g.

Using PDSH

Users can run a command across many hosts at once using the pdsh command. This can be useful if users want to make the same change to multiple systems in the research environment - for example, installing a new software package. The pdsh command can take a number of parameters that control how commands are processed; for example: