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153 lines
8.1 KiB
Markdown
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Building a Linux-based HPC system on the Raspberry Pi with Ansible
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============================================================
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### Create a high-performance computing cluster with low-cost hardware and open source software.
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Image by : opensource.com
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In my [previous article for Opensource.com][14], I introduced the [OpenHPC][15] project, which aims to accelerate innovation in high-performance computing (HPC). This article goes a step further by using OpenHPC's capabilities to build a small HPC system. To call it an _HPC system_ might sound bigger than it is, so maybe it is better to say this is a system based on the [Cluster Building Recipes][16] published by the OpenHPC project.
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The resulting cluster consists of two Raspberry Pi 3 systems acting as compute nodes and one virtual machine acting as the master node:
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My master node is running CentOS on x86_64 and my compute nodes are running a slightly modified CentOS on aarch64.
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This is what the setup looks in real life:
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To set up my system like an HPC system, I followed some of the steps from OpenHPC's Cluster Building Recipes [install guide for CentOS 7.4/aarch64 + Warewulf + Slurm][17] (PDF). This recipe includes provisioning instructions using [Warewulf][18]; because I manually installed my three systems, I skipped the Warewulf parts and created an [Ansible playbook][19] for the steps I took.
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Once my cluster was set up by the [Ansible][26] playbooks, I could start to submit jobs to my resource manager. The resource manager, [Slurm][27] in my case, is the instance in the cluster that decides where and when my jobs are executed. One possibility to start a simple job on the cluster is:
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```
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[ohpc@centos01 ~]$ srun hostname
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calvin
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```
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If I need more resources, I can tell Slurm that I want to run my command on eight CPUs:
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```
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[ohpc@centos01 ~]$ srun -n 8 hostname
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hobbes
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hobbes
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hobbes
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hobbes
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calvin
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calvin
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calvin
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calvin
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```
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In the first example, Slurm ran the specified command (`hostname`) on a single CPU, and in the second example Slurm ran the command on eight CPUs. One of my compute nodes is named `calvin` and the other is named `hobbes`; that can be seen in the output of the above commands. Each of the compute nodes is a Raspberry Pi 3 with four CPU cores.
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Another way to submit jobs to my cluster is the command `sbatch`, which can be used to execute scripts with the output written to a file instead of my terminal.
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```
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[ohpc@centos01 ~]$ cat script1.sh
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#!/bin/sh
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date
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hostname
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sleep 10
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date
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[ohpc@centos01 ~]$ sbatch script1.sh
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Submitted batch job 101
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```
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This will create an output file called `slurm-101.out` with the following content:
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```
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Mon 11 Dec 16:42:31 UTC 2017
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calvin
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Mon 11 Dec 16:42:41 UTC 2017
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```
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To demonstrate the basic functionality of the resource manager, simple and serial command line tools are suitable—but a bit boring after doing all the work to set up an HPC-like system.
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A more interesting application is running an [Open MPI][20] parallelized job on all available CPUs on the cluster. I'm using an application based on [Game of Life][21], which was used in a [video][22] called "Running Game of Life across multiple architectures with Red Hat Enterprise Linux." In addition to the previously used MPI-based Game of Life implementation, the version now running on my cluster colors the cells for each involved host differently. The following script starts the application interactively with a graphical output:
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```
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$ cat life.mpi
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#!/bin/bash
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module load gnu6 openmpi3
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if [[ "$SLURM_PROCID" != "0" ]]; then
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exit
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fi
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mpirun ./mpi_life -a -p -b
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```
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I start the job with the following command, which tells Slurm to allocate eight CPUs for the job:
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```
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$ srun -n 8 --x11 life.mpi
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```
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For demonstration purposes, the job has a graphical interface that shows the current result of the calculation:
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The position of the red cells is calculated on one of the compute nodes, and the green cells are calculated on the other compute node. I can also tell the Game of Life program to color the cell for each used CPU (there are four per compute node) differently, which leads to the following output:
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Thanks to the installation recipes and the software packages provided by OpenHPC, I was able to set up two compute nodes and a master node in an HPC-type configuration. I can submit jobs to my resource manager, and I can use the software provided by OpenHPC to start MPI applications utilizing all my Raspberry Pis' CPUs.
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* * *
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_To learn more about using OpenHPC to build a Raspberry Pi cluster, please attend Adrian Reber's talks at [DevConf.cz 2018][10], January 26-28, in Brno, Czech Republic, and at the [CentOS Dojo 2018][11], on February 2, in Brussels._
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### About the author
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[][23] Adrian Reber - Adrian is a Senior Software Engineer at Red Hat and is migrating processes at least since 2010\. He started to migrate processes in a high performance computing environment and at some point he migrated so many processes that he got a PhD for that and since he joined Red Hat he started to migrate containers. Occasionally he still migrates single processes and is still interested in high performance computing topics.[More about me][12]
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--------------------------------------------------------------------------------
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via: https://opensource.com/article/18/1/how-build-hpc-system-raspberry-pi-and-openhpc
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作者：[Adrian Reber ][a]
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译者：[译者ID](https://github.com/译者ID)
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校对：[校对者ID](https://github.com/校对者ID)
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本文由 [LCTT](https://github.com/LCTT/TranslateProject) 原创编译，[Linux中国](https://linux.cn/) 荣誉推出
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[a]:https://opensource.com/users/adrianreber
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[1]:https://opensource.com/resources/what-are-linux-containers?utm_campaign=containers&intcmp=70160000000h1s6AAA
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[2]:https://opensource.com/resources/what-docker?utm_campaign=containers&intcmp=70160000000h1s6AAA
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[3]:https://opensource.com/resources/what-is-kubernetes?utm_campaign=containers&intcmp=70160000000h1s6AAA
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[4]:https://developers.redhat.com/blog/2016/01/13/a-practical-introduction-to-docker-container-terminology/?utm_campaign=containers&intcmp=70160000000h1s6AAA
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[5]:https://opensource.com/file/384031
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[6]:https://opensource.com/file/384016
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[7]:https://opensource.com/file/384021
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[8]:https://opensource.com/file/384026
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[9]:https://opensource.com/article/18/1/how-build-hpc-system-raspberry-pi-and-openhpc?rate=l9n6B6qRcR20LJyXEoUoWEZ4mb2nDc9sFZ1YSPc60vE
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[10]:https://devconfcz2018.sched.com/event/DJYi/openhpc-introduction
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[11]:https://wiki.centos.org/Events/Dojo/Brussels2018
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[12]:https://opensource.com/users/adrianreber
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[13]:https://opensource.com/user/188446/feed
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[14]:https://opensource.com/article/17/11/openhpc
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[15]:https://openhpc.community/
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[16]:https://openhpc.community/downloads/
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[17]:https://github.com/openhpc/ohpc/releases/download/v1.3.3.GA/Install_guide-CentOS7-Warewulf-SLURM-1.3.3-aarch64.pdf
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[18]:https://en.wikipedia.org/wiki/Warewulf
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[19]:http://people.redhat.com/areber/openhpc/ansible/
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[20]:https://www.open-mpi.org/
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[21]:https://en.wikipedia.org/wiki/Conway%27s_Game_of_Life
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[22]:https://www.youtube.com/watch?v=n8DvxMcOMXk
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[23]:https://opensource.com/users/adrianreber
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[24]:https://opensource.com/users/adrianreber
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[25]:https://opensource.com/users/adrianreber
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[26]:https://www.ansible.com/
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[27]:https://slurm.schedmd.com/
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[28]:https://opensource.com/tags/raspberry-pi
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[29]:https://opensource.com/tags/programming
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[30]:https://opensource.com/tags/linux
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[31]:https://opensource.com/tags/ansible
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