Configuration & Tools

Modified

November 14, 2023

Abstract

This section of the appendix introduces multiple tools commonly used for scientific computing. Furthermore, it addresses common issues and how to overcome these by configuring the user environment.

Terminal Multiplexer

A terminal multiplexer (Tmux) 1 is used to multiplex several separate shells inside a single terminal window. It is particularly useful to use with a single SSH login session for remote access to the HPC infrastructure. The terminal multiplexer Tmux 2 supports:

  • Multiplex several shells with a single terminal session
  • Organises shells with split panes and tabs
  • Persistence keeps terminal sessions during logout until reconnect
Keys Description
C-b ? Show key binding
C-b d Detach from running sessions 
# start tmux
tmux

# at some point use `C-b d` to detach
# close your SSH session, and eventully login again later
# list all sessions managed by the server
tmux list-sessions

# attach to most recently used session
tmux attach-session

We recommend to read the book The Tao of tmux 3, which gives an excellent introduction to get started with Tmux.

Git Protocol Proxy

Git uses several protocols for client-server communication:

Protocol Example Connection Address
https https://example.com/repository.git
ssh git@example.com/repository.git
git git://example.com/repository.git

In case you want to learn more about the different protocols used to connect with a Git server read Git on the Server - The Protocols 4. The https protocol is recommended, since it uses the existing configuration for HTTP proxies on the Virgo cluster:

# print the pre-configured HTTP proxies
» env | grep HTTP
HTTPS_PROXY=http://proxy-ib2.gsi.de:3128/
HTTP_PROXY=http://proxy-ib2.gsi.de:3128/

Proxy a connection over SSH using the environment variable GIT_SSH_COMMAND. Modify the ssh command executed by Git to include an option for a to configure login nodes as jump host:

GIT_SSH_COMMAND="ssh -J lxpool.gsi.de " git ...

However if access to a repository is required over the git protocol it is necessary to configure a Git proxy command. Use the login nodes as network proxy to bypass the firewall for an outgoing connection:

# create a helper script with the proxy command
cat > gitproxy <<'EOF'
#!/bin/bash
exec ssh lxpool.gsi.de nc "$@"
EOF
# make sure that is is executable
chmod +x gitproxy
# set an environment variable to use a proxy command
export GIT_PROXY_COMMAND=$PWD/gitproxy

Connection with a Git server using the Git protocol:

# the connection uses git:// as protocol prefix
git clone git://...