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Getting Started on the UL HPC platform

 Copyright (c) 2013-2021 UL HPC Team <hpc-sysadmins@uni.lu>

This tutorial will guide you through your first steps on the UL HPC platform.

Before proceeding:

  • make sure you have an account (if not, follow this procedure), and an SSH client.
  • take a look at the quickstart guide
  • ensure you operate from a Linux / Mac environment. Most commands below assumes running in a Terminal in this context. If you're running Windows, you can use MobaXterm, Putty tools etc. as described on this page yet it's probably better that you familiarize "natively" with Linux-based environment by having a Linux Virtual Machine (consider for that VirtualBox) or Windows Subsystem for Linux.

From a general perspective, the Support page describes how to get help during your UL HPC usage.

Convention

In the below tutorial, you'll proposed terminal commands where the prompt is denoted by $>.

In general, we will prefix to precise the execution context (i.e. your laptop, a cluster frontend or a node). Remember that # character is a comment. Example:

    # This is a comment
    $> hostname

    (laptop)$> hostname         # executed from your personal laptop / workstation

    (access-iris)$> hostname    # executed from access server of the Iris cluster

Platform overview.

You can find a brief overview of the platform with key characterization numbers on this page.

The general organization of each cluster is depicted below:

UL HPC clusters general organization

Details on this organization can be found here

Discovering, visualizing and reserving UL HPC resources

In the following sections, replace <login> in the proposed commands with you login on the platform (ex: svarrette).

Step 1: the working environment

After a successful login onto one of the access node (see Cluster Access), you end into your personal homedir $HOME which is shared over GPFS between the access node and the computing nodes.

Otherwise, you have to be aware of at least two directories:

  • $HOME: your home directory under NFS.
  • $SCRATCH: a non-backed up area put if possible under Lustre for fast I/O operations

Your homedir is under a regular backup policy. Therefore you are asked to pay attention to your disk usage and the number of files you store there.

  • Estimate file space usage and summarize disk usage of each FILE, recursively for directories using the ncdu command:

    (access)$> ncdu
    
  • You can get an overview of the quotas and your current disk usage with the following command:

    (access)$> df-ulhpc
    
  • You shall also pay attention to the number of files in your home directory. You can count them as follows:

    (access)$> df-ulhpc -i
    

Step 2: web monitoring interfaces

Each cluster offers a set of web services to monitor the platform usage:

Ganglia

Ganglia is a scalable distributed monitoring system for high-performance computing systems such as clusters and Grids. Ganglia provides plots the system usage for each individual compute nodes (CPU, memory, I/O and network usage).

These information will help you identify and understand the behavior of your jobs on the cluster.

It is interesting to identify the limiting factor of your job:

  • Memory

Memory bound job on ganglia

  • CPU

CPU bound job on ganglia

  • Storage I/O

I/O bound job on ganglia

  • Network bound

Network bound job on ganglia

This is covered in the other tutorial Monitoring and profiling

SLURM Web

SLURM Web is a website that show the status of jobs and nodes with a nice graphical interface.

You can use the SLURM web interface for a visualization of the job scheduler state (list and gantt chart visualization).

Sample Usage on the UL HPC platform: Kernel compilation

We will illustrate the usage of GNU screen by performing a compilation of a recent linux kernel.

  • start a new screen session

    (access)$> screen
    
  • rename the screen window "Frontend" (using CTRL+a A)

  • create a new window and rename it "Compile"

  • within this new window, start a new interactive job over 1 node and 2 cores for 4 hours

    (access)$> si --time 2:00:0 -N 1 -c 2
    
  • detach from this screen (using CTRL+a d)

  • kill your current SSH connection and your terminal
  • re-open your terminal and connect back to the cluster frontend
  • list your running screens:

    (access)$> screen -ls
    There is a screen on:
        9143.pts-0.access   (05/04/2014 11:29:43 PM) (Detached)
    1 Socket in /var/run/screen/S-svarrette.
    
  • re-attach your previous screen session

    (access)$> screen -r      # OR screen -r 9143.pts-0.access (see above socket name)
    
  • in the "Compile" windows, go to the temporary directory and download the Linux kernel sources

    (node)$> cd /tmp/
    (node)$> curl -O https://cdn.kernel.org/pub/linux/kernel/v4.x/linux-4.19.163.tar.xz
    

IMPORTANT to avoid overloading the shared file system with the many small files involves in the kernel compilation (i.e. NFS and/or Lustre), we will perform the compilation in the local file system, i.e. either in /tmp or (probably more efficient) in /dev/shm (i.e in the RAM):

    (node)$> mkdir /dev/shm/PS1
    (node)$> cd /dev/shm/PS1
    (node)$> tar xf /tmp/linux-4.19.163.tar.xz
    (node)$> cd linux-4.19.163
    (node)$> make mrproper
    (node)$> make alldefconfig
    (node)$> make 2>&1 | tee /dev/shm/PS1/kernel_compile.log
  • You can now detach from the screen and take a coffee

The last compilation command make use of tee, a nice tool which read from standard input and write to standard output and files. This permits to save in a log file the message written in the standard output.

Question: why using the make 2>&1 sequence in the last command?

Question: why working in /dev/shm is more efficient?

  • Reattach from time to time to your screen to see the status of the compilation
  • Your compilation is successful if it ends with the sequence:

    [...]
    Kernel: arch/x86/boot/bzImage is ready  (#2)
    
  • Restart the compilation, this time using multiple cores and parallel jobs within the Makefile invocation (-j option of make)

    (node)$> make clean
    (node)$> time make -j $SLURM_CPUS_ON_NODE 2>&1 | tee /dev/shm/PS1/kernel_compile.2.log
    

The table below should convince you to always run make with the -j option whenever you can...

Context time (make) time (make -j 16)
Compilation in /tmp(HDD / chaos) 4m6.656s 0m22.981s
Compilation in /tmp(SSD / gaia) 3m52.895s 0m17.508s
Compilation in /dev/shm (RAM) 3m11.649s 0m17.990s
  • Use the Ganglia interface to monitor the impact of the compilation process on the node your job is running on.
  • Connect to your interactive job using the command sjoin <jobid>. Use the following system commands on the node during the compilation:

    • htop
    • top
    • free -m
    • uptime
    • ps aux