3 navsection: installguide
4 title: Set up a compute node with Singularity
7 Copyright (C) The Arvados Authors. All rights reserved.
9 SPDX-License-Identifier: CC-BY-SA-3.0
12 {% include 'notebox_begin_warning' %}
13 This page describes the requirements for a compute node in a Slurm or LSF cluster that will run containers dispatched by @crunch-dispatch-slurm@ or @arvados-dispatch-lsf@. If you are installing a cloud cluster, refer to "Build a cloud compute node image":{{ site.baseurl }}/install/crunch2-cloud/install-compute-node.html.
14 {% include 'notebox_end' %}
16 {% include 'notebox_begin_warning' %}
17 These instructions apply when Containers.RuntimeEngine is set to @singularity@, refer to "Set up a compute node with Docker":install-compute-node-docker.html when running @docker@.
18 {% include 'notebox_end' %}
20 # "Introduction":#introduction
21 # "Install python-arvados-fuse and crunch-run and squashfs-tools":#install-packages
22 # "Set up Singularity":#singularity
23 # "Singularity mksquashfs configuration":#singularity_mksquashfs_configuration
25 h2(#introduction). Introduction
27 Please refer to the "Singularity":{{site.baseurl}}/architecture/singularity.html documentation in the Architecture section.
29 This page describes how to configure a compute node so that it can be used to run containers dispatched by Arvados on a static cluster. These steps must be performed on every compute node.
31 {% assign arvados_component = 'python-arvados-fuse crunch-run squashfs-tools' %}
33 {% include 'install_packages' %}
35 {% include 'install_cuda' %}
37 h2(#singularity). Set up Singularity
39 Follow the "Singularity installation instructions":https://sylabs.io/guides/3.7/user-guide/quick_start.html. Make sure @singularity@ and @mksquashfs@ are working:
42 <pre><code>$ <span class="userinput">singularity version</span>
44 $ <span class="userinput">mksquashfs -version</span>
45 mksquashfs version 4.3-git (2014/06/09)
50 Then update @Containers.RuntimeEngine@ in your cluster configuration:
53 <pre><code> # Container runtime: "docker" (default) or "singularity"
54 RuntimeEngine: singularity
58 {% include 'singularity_mksquashfs_configuration' %}
60 h2(#singularity_loop_device_errors). Singularity loop device errors
62 With singularity v3.9.1 and earlier, containers may fail intermittently at startup with an error message similar to the following in the container log's @stderr.txt@ (line breaks added):
65 <pre><code>FATAL: container creation failed:
66 mount /proc/self/fd/3->/usr/local/var/singularity/mnt/session/rootfs error:
67 while mounting image /proc/self/fd/3:
68 failed to find loop device:
69 could not attach image file to loop device:
70 failed to set loop flags on loop device:
71 resource temporarily unavailable
75 This problem is addressed in singularity v3.9.2. For details, please see "Arvados issue #18489":https://dev.arvados.org/issues/18489 and "singularity PR #458":https://github.com/sylabs/singularity/pull/458.