hpc4you_toolkit v3.0

Manual for hpc4you_toolkit.

hpc4you_toolkit v3.0

It is the v2.0 + the Web Interfaces. The Web Interface are for:

In a word, v3.0 features parallel computing cluster with web front-end.

Click for DemoπŸ”—.

hpc4you_toolkit v2.0

The hpc4you_toolkit is a simple but robust toolkit written by a computational chemist to set up a parallel computing cluster for scientific research.

No computer skills or Linux knowledge are needed. Only copy and paste the cmd from the screen then press the Enter key.

If you have some knowledge of how parallel computing clusters work, and how to administrate Linux in the cmd line and configure Linux networking, then you can try out the OpenHPC solution.

Currently, the hpc4you_toolkit supports:

  1. RHEL7, RHEL8, RHEL9 and their compatible operating systems, such as CentOS 7.x, 8.x, RockyLinux 8.x, AlmaLinux 8.x, AlmaLinux 9.x, CentOS Stream 9.
  2. Ubuntu 20.04/22.04 and their compatible operating systems.
  3. The maximum number of computing nodes depends on the capacity of your switch.

Quick Start

  1. Get the package.
  2. Edit /etc/hosts file.
  3. Upload the package hpc4you_toolkit-XXX.zip.
  4. Unzip, then run source code.

All subsequent 5 commands will be automatically displayed in green.

All you need to do is to copy and paste the green text according to the on-screen instructions.

demo

Prerequisites

  1. All servers running the same version of Linux.
  2. All servers are interconnected through a LAN, 1000 Mbps, or 10 Gbps ethernet, or may be InfiniBand.
  3. The yum/dnf/apt is working on all servers.
  4. All servers have a unique hostname.
  5. All servers share the same root password.
  6. The hostname of login node should only be master or the alias must be master if you have set the hostname to something else.
  7. The hostname of all computing nodes should only be nodeXX or the alias must be nodeXX if you have set the hostname to something else.

Get hpc4you_toolkit

Choose one machine as the management/master/login node, and run the following code,

curl https://raw.githubusercontent.com/hpc4you/hpc/main/getInfo.sh | bash

Follow the on-screen prompts carefully.

Remeber to copy and paste the blue lines into the body of your Email, please also attach the XXX.dat file with the Email.

Cluster Architectures

High-Performance Cluster

High-Performance Cluster

Intra-node Local-I/O Cluster

Intra-node Local-I/O Cluster

mini-HPC

mini-HPC

Declare Servers

On the login node, edit file /etc/hosts.

Scenario A

If you have configured the hostname for master/login node to master, and configured the hostname of computing/slave nodes to nodeXX, the content of the file /etc/hosts should be similar to the following.

### the IP and the corresponding real hostname 
192.168.1.100 master
192.168.1.101 node1
192.168.1.102 node2
192.168.1.112 node12

Scenario B

If the hostname of the login/master node is not master, and/or the hostname of any computing/slave node is not nodeXX, the content of the file /etc/hosts should be similar to the following.

# the IP and real hostname
192.168.1.100 server0
192.168.1.101 server1
192.168.1.102 server2
192.168.1.112 server12

### the IP and the corresponding alias hostname 
192.168.1.100 master
192.168.1.101 node1
192.168.1.102 node2
192.168.1.112 node12

In this example,

  1. server0 is the output of hostname on the login node.
  2. server12, is the output of hostname on the computing node which can be accessed via IP 192.168.1.112.
  3. The hostname of all compute nodes must be prefixed with node, and the the suffix numbers (β€˜0’, β€˜1’, β€˜2’, and β€˜12’ in current case) do not have to be consecutive.
  4. You can use nmtui to set hostname and configure the IP address.

Run hpc4you_toolkit

Upload the package hpc4you_toolkit-XXX.zip to the login node.

Unzip the package, then open terminal, run:

source code

Follow the on-screen prompts carefully.

You will be asked to copy and paste ./step1.sh into the current terminal. Please just do it.

Please wait a while (The waiting time depends on the network bandwidth), you would read on the screen,

Default root password for all slave nodes

Please type the root password, then press the Enter key.

Nothing to do but wait …

Copy and paste the green line, then press the Enter key, and wait …

All servers will automatically reboot at least twice, and then the slurm scheduling cluster is ready for you.

In particular, the restart operation of all compute nodes will be 1 minute lag behind the master node.

Nothing else to do, just wait.

By default, the /opt and /home from the master/login node are shared among all slave nodes. It is possible to add new share path by,

  1. Edit /etc/exports file on master/login node,
  2. Use β€˜setup_hpc –sync_do’ to update the /etc/fstab file on all slave nodes.

User Management

Add user

On login node, run

useradd_hpc tom

this will add user tom to the default group users.

useradd_hpc chem tom

this will add user tom to the group chem.

Caution:

  1. You will be prompted to set a password for the new user. You will need to enter the password twice. But the screen does not show any asterisks.
  2. Be sure to copy the private key if you have enabled enhance_security.sh module.
  3. If you have slurm accounting enabled, you should also run, 
    sacctmgr add user tom Account=hpc4you

    in which, you will give user tom the default account hpc4you. Refer slurm manual for more details.

Delete user

On the login/master node, run,

userdel_hpc tom

in this case, user tom is to be deleted.

Cluster Management

Power on

Power on the master node and all switches first, and then power on all computing nodes.

Power off

On the login/master node, run, poweroff_hpc.

Reboot

On the login/master node, run, reboot_hpc.

Add new node

  1. Clone the OS disk of any compute node. Use this hardware tool, Offline Cloning Tool.
  2. Boot the new server with the cloned disk, modify hostname and configure network with command nmtui.
  3. Add the IP and hostname of the new server to /etc/hosts on the master/login node.
  4. On the master/login node, run setup_hpc ‐‐sync_file /etc/hosts.
  5. On the new server, run slurmd ‐C | head -n 1, please copy the output.
  6. On the master/login node, paste the coppied contents into last line of file /etc/slurm/slurm.conf.
  7. On the master/login node, run setup_hpc ‐‐sync_do 'systemctl restart slurmd'; systemctl restart slurmctld.
  8. Done.

Better Security

  1. Disable internet connection on all slave/computing nodes.
  2. On login/master node, run passwd to change the root password, then run setup_hpc --sync_user.
  3. Disable password login for root user, only key authentication is allowed.
  4. Or use ssh ProxyJump server or even hardware firewall.
  5. Or run enhance_security.sh to apply awesome security hardening configurations automatically.

Usage of setup_hpc

sync file

On the login/master node, run

setup_hpc --sync_file /full/path/to/file

For example, setup_hpc --sync_file /etc/hosts will sync the hosts file on master node to all slave nodes.

run cmd

On the login/master node, run

setup_hpc --sync_do cmd

For example,

setup_hpc --sync_do uptime

will print the uptime info for all slave nodes.

setup_hpc --sync_do 'systemctl restart slurmd; utpdate -u 3.cn.pool.ntp.org'

will restart slurm client and sync time on all slave nodes.

hpc4you_toolkit solo

hpc4you_toolkit solo, is also available, which can deploy slurm to workstations by only run source code.

Pricing

hpc4you_toolkit features

FEATURES Basic Adv Pro
CPU Scheduling βœ… βœ… βœ…
GPU Scheduling1 βœ… βœ… βœ…
Job Log ❌ βœ… βœ…
User Control2 ❌ ❌ βœ…
Monitoring Historical ❌ ❌ βœ…
Monitoring Realtime ❌ ❌ βœ…
Security & OS Optimize3 ❌ ❌ βœ…
Pricing 399 USD Email ask@hpc4you.top Email ask@hpc4you.top

hpc4you_toolkit solo features

FEATURES Basic Adv
CPU Scheduling βœ… βœ…
GPU Scheduling βœ… βœ…
Job Log ❌ βœ…
Pricing 99 USD 149 USD

Discount

  1. A huge discount of up to 75% OFF is available if you choose the self-service mode.
  2. The self-service mode refers to β€˜Read the manual, watch the video tutorials, and do it all by yourself. No support is available’.
  3. δΈ­ζ–‡η”¨ζˆ·πŸ”—η‚Ήε‡»θΏ™ι‡Œ.

Demo

Live Demo

Real-time demo on how to set up HPC for scientific research with hpc4you_toolkit. Only copy and paste. No computer skills and Linux knowledge are required.

  1. All modules, πŸ”—live-demo with Ubuntu Jammy
  2. All modules, πŸ”—live-demo with Ubuntu Focal
  3. All modules, πŸ”—live-demo with CentOS 7.9
  4. All modules, πŸ”—live-demo with RockyLinux 8

Short Videos

To those who have no patience to watch real-time videos,

  1. copy+paste+Enter -> cluster ready, demonstration of hpc4you_toolkit πŸ”—BV1GY411w7ZV πŸ”—YouTube Link
  2. Deploy SLURM by only run source code, demonstration of hpc4you_toolkit solo πŸ”—BV1Gg411R7tt

Play with Linux

  1. How to add new IP and hostname informations into file /etc/hosts? πŸ”—bv19A4y1U7uX
  2. How to upload file(s) to remote Linux server? πŸ”—BV1fJ411n7uV
  3. Change hostname πŸ”—BV1yP4y1M77H
  4. Configure network πŸ”—BV1gP4y1u7Aw

Terminology

In the field of parallel computing clusters, we refer to a server as a node.

Usually, in small-scale clusters, the login server, storage node, and the contollor server can be merged into a single server, which is called as the login/master node. Accordingly, we refer to all compute nodes, as the slave nodes.

  1. SLURM natively supports GPU scheduling. However, the auto-detection mode often fails and needs to be configured manually once. If you can’t do it, I can be a helping hand, but please pay the fee.Β ↩

  2. To prevent users from sshing into nodes that they do not have a running job on, and to track the ssh connection and any other spawned processes for accounting and to ensure complete job cleanup when the job is completed. More infoΒ ↩

  3. Reference, https://github.com/decalage2/awesome-security-hardeningΒ ↩