THGY - The Hitchhiker's Guide to YULAB

Principles

• You are not working for Prof. Yu. Prof. Yu is working with you on your projects.
• Asking for what you need rather than hoping that Prof. Yu will know what to provide
• Don't expect to figure everything out by yourself. When you have a question, ask search engine first then your fellow students and Prof. Yu
• Thinking from the end. When start a project, start with a vision of what the “perfect paper” would look like. What will be novel? What will be the conceptual advance? And how will we validate it? After establishing the big goal, we then work backward to establish the work plan on how to proceed.

Survival skills

• Good programming skill (talk is cheap, show me the code)
• Git and github (harddisk breakdown randomly)
• Docker (Make sure your results can be repeated!)
• Good English reading skill (how many papers you read per day?)

IT resources

Network structure and access

Set a Static IP on Ubuntu

This tutorial explains how to set a static IP on an Ubuntu system from the command line.

Step 1: Configure the network interface

In this step, you will manually configure your network interface by editing the following files using your preferred text editor(nano gedit vi). For the purpose of this example, I'm using the "nano" editor. You can edit the appropriate file by entering the following command into the terminal:

sudo nano /etc/network/interfaces

A configuration where the IP address get's assigned automatically by DHCP will look like this:

# This file describes the network interfaces available on your system
# and how to activate them. For more information, see interfaces(5).

source /etc/network/interfaces.d/*

# The loopback network interface
auto lo
iface lo inet loopback

# The primary network interface
auto ens21f0 (or ens21f1)
iface ens21f0 inet dhcp

Statically configured network cards like this:

auto ens21f0
iface ens21f0 inet static
        address xxx.xxx.xxx.xxx(enter your ip here)
        netmask xxx.xxx.xxx.xxx
        gateway xxx.xxx.xxx.xxx(enter gateway ip here,usually the address of the router)

And here an example for Ubuntu 16.04 and newer:

# This file describes the network interfaces available on your system
# and how to activate them. For more information, see interfaces(5).

source /etc/network/interfaces.d/*

# The loopback network interface
auto lo
iface lo inet loopback

# test

# The primary network interface
auto ens21f1
iface ens21f1 inet static
 address 192.168.3.11
 netmask 255.255.255.128
 gateway 192.168.3.1

And here the complete network configuration file from an Ubuntu 16.04 system.

Step 2: Restart networking

Manually restart your network interface with the new settings.

sudo /etc/init.d/networking restart

At this point you can check if the settings are correct:

ifconfig

Then send ICMP request to a remote host to check the connectivity. For example: send to the gateway

ping 192.168.3.1

If every step goes well，you have completed the configuration of the static IP.

Computing nodes

IP	CPU	RAM	Harddisk	Current user
10.24.80.101	32 cores Intel(R) Xeon(R) [email protected]	256G+44G(Swap)	/mnt/md0(11T)+/home(49G)	liuyu/qy/ryu/xiaoxu/zoelin
10.24.80.102	64 cores Intel(R) Xeon(R) [email protected]	256G+15G(Swap)	tmpfs(330G)+/home(184G)	lhj/liuyu/lmy/ryu/xmulsm/zoelin
10.24.80.103	40 cores Intel(R) Xeon(R) [email protected]	64G+128G(Swap)	/(760G)	gmx/gmx2/jupyter/liuyu/lyc/R/txw/xiaoxu/xmulsm/yulab3/zoelin
10.24.80.105	64 cores Intel(R) Xeon(R) [email protected]	256G+15G(Swap)	/(59G)+/mnt/md0(7.3T)+/home(147G)	gmx2/hjl/lcx/liuyu/lmy/lyc/myl/qy/syw/tlx/xwt/ytl/yu
10.24.80.106	32 cores Intel(R) Xeon(R) [email protected]	64G+15G(Swap)	/mnt/md0(55T)+/mnt/md1(49T)	cx/fzy/lihaojun/liuyu/myl/qiaoying/ryu/sy01/sy02/zoelin

At present, accessing computing nodes needs public-key authentication, rather than userID+password. SSH keys, including a public key id_isa.pub and a private one id_isa, can be generated using following methods:

on Linux or Mac, using following command:

ssh-keygen -t rsa

on Windows, such key pairs can be generated using SSH tools such as XManager, PowerShell etc.

Anyone who need accession will firstly submit SSH public-key id_isa.pub to Wang Shun. And the private key id_isa shuold be saved carefully! DO NOT SHARE YOUR PRIVATE KEY WITH NOBODY!!!

Using following methods to access computing nodes throuth SSH-key authentication:

command line (Linux, Mac or build-in Linux Core on Windows):

ssh -i your_id_isa [email protected]

You can log in computing nodes without password by adding your ssh keys to your SSH tools.

Storage server

Our lab has a storage server located at 10.24.80.106. To start with, ask the system admin (currently Wang Shun is kindly to help creating user account for this server) to obtain a user name and a password. Once you have the user name and password, you can use the storage folder on Linux machiine.

On every computing node, public storage can be entered throuth /mnt/public. Only subfolder owned by yourself can be written.

If you are curious on how to setup a storage server, here is a good tutorial guide on DigitalOcean Tutorial on storage server setup.

Git & github

Yulab on github: https://github.com/xmuyulab

Using git:

• 廖雪峰Git教程
• 菜鸟教程Git

Tip: Gitee can be helpful when cloning big repo on github too slow.

Docker

• 菜鸟教程Docker
• Docker官方说明

Tip: Aliyun is very usful for docker users within China.