Accessing CVMFS

This article is a draft

This is not a complete article. Final details are still being put in place before you can access our software stack on your own computer or cluster.

Introduction

Compute Canada provides repositories of software and data via a file system called CERN Virtual Machine File System (CVMFS). On Compute Canada systems, CVMFS is already set up for you, so the repositories are automatically available for your use. For more information on using the Compute Canada software environment, please refer to available software, using modules, Python, R and Installing software in your home directory pages.

The purpose of this page is to describe how you can install and configure CVMFS on your computer or cluster, so that you can access the same repositories (and software environment) on your system that are available on Compute Canada systems.

The software environment described on this page has been presented at Practices and Experience in Advanced Research Computing 2019 (PEARC 2019).

Before you start

Important

If you are planning to use our software environment, we ask that you first contact us at rsnt-software@computecanada.ca to let us know ahead of time.

Terms of support

The CVMFS client software is provided by CERN. The Compute Canada CVMFS repositories are provided by Compute Canada without any warranty.

CVMFS requirements

• Support for Filesystem in user space (FUSE) (in order to mount CVMFS)
• A distribution of Linux that supports RPM or DEB packages (Ubuntu, Debian, CentOS, Fedora, Red Hat, openSUSE, etc.)
• A caching SQUID proxy (for clusters)

Software environment requirements

Minimal requirements

• Supported operating systems:
  • Linux: with a Kernel 2.6.32 or more recent.
  • Windows: with Windows Subsystem for Linux version 2, with a distribution of Linux that matches the requirement above
  • Mac OS: only through a virtual machine
• CPU: x86 CPU supporting at least one of SSE3, AVX, AVX2 or AVX512 instructions

Optimal requirements

• Scheduler: Slurm or Torque (for tight integration with OpenMPI applications)
• Network interconnect: Ethernet, InfiniBand or OmniPath (for parallel applications)
• GPU: NVidia GPU with CUDA drivers (7.5 or more recent) installed (for CUDA-enabled applications). See below for caveats about CUDA
• As few Linux packages installed as possible (fewer is better)

Mounting CVMFS on your computer

Pre-installation

It is recommended that the local CVMFS cache (located at /var/lib/cvmfs by default, configurable via the CVMFS_CACHE_BASE setting) be on a dedicated filesystem so that the storage usage of CVMFS is not shared with that of other applications. Accordingly, you should provision that filesystem before installing CVMFS. The cache should typically be about 50 GB in size, but more or less may be suitable in different situations. For more details see the client configuration documentation.

Installation

Follow the instructions relative to your operating system in order to install CVMFS. These instructions have been tested on the following distributions:

• CentOS 6, CentOS 7
• Fedora 29
• Debian 9
• Ubuntu 18.04

When installing packages you may be prompted to accept some GPG keys. You should ensure that their fingerprints match these expected values:

• CernVM key: 70B9 8904 8820 8E31 5ED4 5208 230D 389D 8AE4 5CE7
• Compute Canada CVMFS key one: C0C4 0F04 70A3 6AF2 7CC4 4D5A 3B9F C55A CF21 4CFC
• Compute Canada CVMFS key two: DDCD 3C84 ACDF 133F 4BEC FBFA 49DE 2015 FF55 B476

RedHat/CentOSFedoraDebian/UbuntuSLES/openSuSEWindows

• Install the CERN YUM repository and GPG key:

[name@server ~]$ sudo yum install https://ecsft.cern.ch/dist/cvmfs/cvmfs-release/cvmfs-release-latest.noarch.rpm

• Install the Compute Canada YUM repository and GPG keys:

[name@server ~]$ sudo yum install https://package.computecanada.ca/yum/cc-cvmfs-public/Packages/computecanada-release-latest.noarch.rpm

• Install the CVMFS client and configuration packages from those YUM repositories:

[name@server ~]$ sudo yum install cvmfs cvmfs-config-default cvmfs-config-computecanada cvmfs-auto-setup

• Install the default configuration package:

[name@server ~]$ sudo dnf install https://ecsft.cern.ch/dist/cvmfs/cvmfs-config/cvmfs-config-default-latest.noarch.rpm

• Download the CVMFS client RPM for your operating system from https://cernvm.cern.ch/portal/filesystem/downloads and install it with dnf (or yum).
  • Since a yum repository for CVMFS is not available for this operating system, you will need to periodically check for updates to the CVMFS client and default configuration and install them manually.
• Apply the initial client setup:

[name@server ~]$ sudo cvmfs_config setup

• Install the Compute Canada YUM repository and GPG keys:

[name@server ~]$ sudo dnf install https://package.computecanada.ca/yum/cc-cvmfs-public/Packages/computecanada-release-latest.noarch.rpm

• Install the Compute Canada CVMFS configuration from that YUM repository:

[name@server ~]$ sudo dnf install cvmfs-config-computecanada

• Follow the instructions here to add the CERN apt repository.
• Install the CVMFS client from that repository:

[name@server ~]$ sudo apt-get install cvmfs cvmfs-config-default

• Apply the initial client setup:

[name@server ~]$ sudo cvmfs_config setup

• Download and install the Compute Canada CVMFS configuration package:

[name@server ~]$ wget https://git.computecanada.ca/cc-cvmfs-public/cvmfs-config/raw/1.3.2-repackaging/OtherPackages/cvmfs-config-computecanada-1.3-2.all.deb
[name@server ~]$ sudo dpkg -i cvmfs-config-computecanada-1.3-2.all.deb

As these operating systems are RPM-based, following the same instructions as for Fedora should work.

• For Windows, you first need to have Windows Subsystem for Linux, version 2. As of this writing (July 2019), this is supported only in a developer version of Windows. The instructions for installing it are here [1].
• Once it is installed, install the Linux distribution of your choice, and follow the appropriate instructions from one of the other tabs.

Configuration

Do not create any CVMFS configuration files of the form *.conf. In order to avoid collisions with upstream configuration sources, all locally-applied configuration must be in .local files. See structure of /etc/cvmfs for more information.

In particular, create the file /etc/cvmfs/default.local, with at least the following minimal configuration:

CVMFS_REPOSITORIES="cvmfs-config.computecanada.ca,soft.computecanada.ca"
CVMFS_QUOTA_LIMIT=44500
CVMFS_HTTP_PROXY="http://yourproxy:3128;http://anotherproxy:3128"

• CVMFS_REPOSITORIES is a comma-separated list of the repositories that you are interested in.
• CVMFS_QUOTA_LIMIT is the amount of space in MB that CVMFS will use for the local cache; it should be about 15% less than the size of the local cache filesystem.
• CVMFS_HTTP_PROXY lists the proxy servers to use. First in the list, you should have at least one (preferably two) forward caching proxies (such as Squid) deployed locally at your site/cluster/campus, then potentially other nearby or regional proxies as backups. For further details on setting CVMFS_HTTP_PROXY, including the use of load-balancing groups and round-robin DNS, see the proxy lists documentation.

For more information on client configuration see the client parameters documentation.

Testing

• Validate the configuration:

[name@server ~]$ sudo cvmfs_config chksetup

• • Make sure to address any warnings or errors that are reported.
• Check that the repositories are OK:

[name@server ~]$ cvmfs_config probe

If you encounter problems, this debugging guide may help.

Enabling our environment in your session

Once you have mounted the CVMFS repository, enabling our environment in your sessions is as simple as running

[name@server ~]$ source /cvmfs/soft.computecanada.ca/config/profile/bash.sh

The above command will not run anything if your user ID is below 1000. This is a safeguard, because you should not rely on our software environment for privileged operation. If you nevertheless want it to enable our environment, you can first define the environment variable FORCE_CC_CVMFS=1, with the command

[name@server ~]$ export FORCE_CC_CVMFS=1

or you can create a file $HOME/.force_cc_cvmfs in your home folder if you want it to always be active, with

[name@server ~]$ touch $HOME/.force_cc_cvmfs

If, on the contrary, you want to avoid enabling our environment, you can define SKIP_CC_CVMFS=1 or create the file $HOME/.skip_cc_cvmfs to ensure that the environment is never enabled in a given account.

Customizing your environment

By default, enabling our environment will automatically detect a number of features of your system, and load default modules. You can control the default behaviour by defining specific environment variables prior to enabling the environment. These are described below.

While our software environment strives to be as independent from the host operating system as possible, there are a number of system paths that are taken into account by our environment to facilitate interaction with tools installed on the host operating system.

Environment variables

CC_CLUSTER

This variable is used to identify a cluster. It is used to send some information to the system logs, as well as define behaviour relative to licensed software. By default, its value is computecanada. You may want to set the value of this variable if you want to have system logs tailored to the name of your system.

RSNT_ARCH

This environment variable is used to identify the set of CPU instructions supported by the system. By default, it will be automatically detected based on /proc/cpuinfo. However if you want to force a specific one to be used, you can define it before enabling the environment. The supported instruction sets for our software environment are:

• sse3
• avx
• avx2
• avx512

RSNT_INTERCONNECT

This environment variable is used to identify the type of interconnect supported by the system. By default, it will be automatically detected based on the presence of /sys/module/opa_vnic (for Intel OmniPath) or /sys/module/ib_core (for InfiniBand). The fall-back value is ethernet. The supported values are

• omnipath
• infiniband
• ethernet

The value of this variable will trigger different options of transport protocol to be used in OpenMPI.

LMOD_SYSTEM_DEFAULT_MODULES

This environment variable defines which modules are loaded by default. If it is left undefined, our environment will define it to load the StdEnv module, which will load by default a version of the Intel compiler, and a version of OpenMPI.

MODULERCFILE

This is an environment variable used by Lmod to define the default version of modules and aliases. You can define your own modulerc file and add it to the environment variable MODULERCFILE. This will take precedence over what is defined in our environment.

System paths

/opt/software/modulefiles

If this path exists, it will automatically be added to the default MODULEPATH. This allows the use of our software environment while also maintaining locally installed modules.

$HOME/modulefiles

If this path exists, it will automatically be added to the default MODULEPATH. This allows the use of our software environment while also allowing installation of modules inside of home directories.

/opt/software/slurm/bin, /opt/software/bin, /opt/slurm/bin

These paths are all automatically added to the default PATH. This allows your own executable to be added in the search path.

Caveats

Compute Canada configuration repository

If you already have CVMFS installed and configured in order to use other repositories, and if your CVMFS client configuration relies on the use of a configuration repository, be aware that the cvmfs-config-computecanada package sets up and enables the cvmfs-config.computecanada.ca configuration repository, which may conflict with your use of any other configuration repository and potentially break your pre-existing CVMFS client configuration, since clients can only use a single configuration repository. (The Compute Canada CVMFS configuration repository is a central source of configuration that makes all other Compute Canada CVMFS repositories available. It provides all site-independent client configuration required for Compute Canada usage and allows client configuration updates to be automatically propagated. The contents can be seen in /cvmfs/cvmfs-config.computecanada.ca/etc/cvmfs/ .)

Software packages that are not available

On Compute Canada systems, a number of commercial software packages are made available to authorized users according to the terms of the license owners, but they are not available outside of Compute Canada systems, and following these instructions will not grant you access to them. This includes for example the Intel and Portland Group compilers. While the modules for the Intel and PGI compilers are available, you will only have access to the redistributable parts of these packages, usually the shared objects. These are sufficient to run software packages compiled with these compilers, but not to compile new software.

CUDA location

For CUDA-enabled software packages, our software environment relies on having driver libraries installed in the path /usr/lib64/nvidia. However on some platforms, recent NVidia drivers will install libraries in /usr/lib64 instead. Because it is not possible to add /usr/lib64 to the LD_LIBRARY_PATH without also pulling in all system libraries (which may have incompatibilities with our software environment), we recommend that you create symbolic links in /usr/lib64/nvidia pointing to the installed NVidia libraries.

LD_LIBRARY_PATH

Our software environment is designed to use RUNPATH. Defining LD_LIBRARY_PATH is not recommended and can lead to the environment not working.

Missing libraries

Because we do not define LD_LIBRARY_PATH, and because our libraries are not installed in default Linux locations, binary packages, such as Anaconda, will often not find libraries that they would usually expect. Please see our documentation on Installing binary packages.

dbus

For some applications, dbus needs to be installed. This needs to be installed locally, on the host operating system.

CernVM File System

HyperText Transfer Protocol