Creating a Repository (Stratum 0)

CernVM-FS is a file system with a single source of (new) data. This single source, the repository Stratum 0, is maintained by a dedicated release manager machine or installation box. A read-writable copy of the repository is accessible on the release manager machine. The CernVM-FS server tool kit is used to publish the current state of the repository on the release manager machine. Publishing is an atomic operation.

All data stored in CernVM-FS have to be converted into a CernVM-FS repository during the process of publishing. The CernVM-FS repository is a form of content-addressable storage. Conversion includes creating the file catalog(s), compressing new and updated files and calculating content hashes. Storing the data in a content-addressable format results in automatic file de-duplication. It furthermore simplifies data verification and it allows for file system snapshots.

In order to provide a writable CernVM-FS repository, CernVM-FS uses a union file system that combines a read-only CernVM-FS mount point with a writable scratch area [Wright04]. This figure below outlines the process of publishing a repository.

CernVM-FS Server Quick-Start Guide

System Requirements

  • Apache HTTP server or S3 compatible storage service

  • union file system in the kernel

  • Officially supported platforms

    • Scientific Linux 5 (64 bit)

    • Scientific Linux 6 (64 bit - with custom AUFS enabled kernel - Appendix “Available RPMs”)

    • CentOS/SL >= 7.3, provided that /var/spool/cvmfs is served by an ext4 file system.

    • Fedora 22 and above (with kernel \(\ge\) 4.2.x)

    • Ubuntu 12.04 64 bit and above

      • Ubuntu < 15.10: with installed AUFS kernel module (cf. linux-image-extra package)
      • Ubuntu 15.10 and later (using upstream OverlayFS)

Installation

  1. Install cvmfs and cvmfs-server packages
  2. Ensure enough disk space in /var/spool/cvmfs (>50GiB)
  3. For local storage: Ensure enough disk space in /srv/cvmfs
  4. Create a repository with cvmfs_server mkfs (See Repository Creation)

Content Publishing

  1. cvmfs_server transaction <repository name>
  2. Install content into /cvmfs/<repository name>
  3. Create nested catalogs at proper locations
  4. cvmfs_server publish <repository name>

Backup Policy

  • Create backups of signing key files in /etc/cvmfs/keys
  • Entire repository content
    • For local storage: /srv/cvmfs
    • Stratum 1s can serve as last-ressort backup of repository content

Installing the AUFS-enabled Kernel on Scientific Linux 6

CernVM-FS uses the union file-system aufs to efficiently determine file-system tree updates while publishing repository transactions on the server (see Figure below). Note that this is only required on a CernVM-FS server and not on the client machines.

We provide customised kernel packages for Scientific Linux 6 (see Appendix “Available RPMs”) and keep them up-to-date with upstream kernel updates. The kernel RPMs are published in the cernvm-kernel yum repository.
Please follow these steps to install the provided customised kernel:
  1. Download the latest cvmfs-release package from the CernVM website

  2. Install the cvmfs-release package: yum install cvmfs-release*.rpm
    This adds the CernVM yum repositories to your machine’s configuration.
  3. Install the aufs enabled kernel from cernvm-kernel:
    yum --disablerepo=* --enablerepo=cernvm-kernel install kernel
  4. Install the aufs user utilities:
    yum --enablerepo=cernvm-kernel install aufs2-util
  5. Reboot the machine

Once a new kernel version is released yum update will not pick the upstream version but it will wait until the patched kernel with aufs support is published by the CernVM team. We always try to follow the kernel updates as quickly as possible.

Publishing a new Repository Revision

CernVM-FS server schematic update overview

Updating a mounted CernVM-FS repository by overlaying it with a copy-on-write union file system volume. Any changes will be accumulated in a writable volume (yellow) and can be synchronized into the CernVM-FS repository afterwards. The file catalog contains the directory structure as well as file metadata, symbolic links, and secure hash keys of regular files. Regular files are compressed and renamed to their cryptographic content hash before copied into the data store.

Since the repositories may contain many file system objects (i.e. ATLAS contains \(70 * 10^6\) file system objects – February 2016), we cannot afford to generate an entire repository from scratch for every update. Instead, we add a writable file system layer on top of a mounted read-only CernVM-FS repository using a union file system. This renders a read-only CernVM-FS mount point writable to the user, while all performed changes are stored in a special writable scratch area managed by the union file system. A similar approach is used by Linux Live Distributions that are shipped on read-only media, but allow virtual editing of files where changes are stored on a RAM disk.

If a file in the CernVM-FS repository gets changed, the union file system first copies it to the writable volume and applies any changes to this copy (copy-on-write semantics). Also newly created files or directories will be stored in the writable volume. Additionally the union file system creates special hidden files (called white-outs) to keep track of file deletions in the CernVM-FS repository.

Eventually, all changes applied to the repository are stored in this scratch area and can be merged into the actual CernVM-FS repository by a subsequent synchronization step. Up until the actual synchronization step takes place, no changes are applied to the CernVM-FS repository. Therefore, any unsuccessful updates to a repository can be rolled back by simply clearing the writable file system layer of the union file system.

Requirements for a new Repository

In order to create a repository, the server and client part of CernVM-FS must be installed on the release manager machine. Furthermore you will need a kernel containing a union file system implementation as well as a running Apache2 web server. Currently we support Scientific Linux 6, Ubuntu 12.04+ and Fedora 22+ distributions. Please note, that Scientific Linux 6 does not ship with an aufs enabled kernel, therefore we provide a compatible patched kernel as RPMs (see Installing the AUFS-enabled Kernel on Scientific Linux 6 for details).

Historically CernVM-FS solely used aufs as a union file system. However, the Linux kernel community favoured OverlayFS, a competing union file system implementation that was merged upstream.

Since CernVM-FS 2.2.0 we support the usage of both OverlayFS and aufs. Note however, that the first versions of OverlayFS were broken and will not work properly with CernVM-FS. At least a 4.2.x kernel is needed to use CernVM-FS with OverlayFS. (Red Hat) Enterprise Linux >= 7.3 works, too, provided that /var/spool/cvmfs is served by an ext4 file system. Furthermore note that OverlayFS cannot fully comply with POSIX semantics, in particular hard links must be broken into individual files. That is usually not a problem but should be kept in mind when installing certain software distributions into a CernVM-FS repository.

Notable CernVM-FS Server Locations and Files

There are a number of possible customisations in the CernVM-FS server installation. The following table provides an overview of important configuration files and intrinsical paths together with some customisation hints. For an exhaustive description of the CernVM-FS server infrastructure please consult Appendix “CernVM-FS Server Infrastructure”.

File Path Description
/cvmfs Repository mount points Contains read-only union file system mountpoints that become writable during repository updates. Do not symlink or manually mount anything here.
/srv/cvmfs Central repository storage location Can be mounted or symlinked to another location before creating the first repository.
/srv/cvmfs/<fqrn> Storage location of a repository Can be symlinked to another location before creating the repository <fqrn>.
/var/spool/cvmfs Internal states of repositories Can be mounted or symlinked to another location before creating the first repository. Hosts the scratch area described here, thus might consume notable disk space during repository updates.
/etc/cvmfs Configuration files and keychains Similar to the structure described in this table. Do not symlink this directory.
/etc/cvmfs/cvmfs_server_hooks.sh Customisable server behaviour See “Customizable Actions Using Server Hooks” for further details
/etc/cvmfs/repositories.d Repository configuration location Contains repository server specific configuration files.

CernVM-FS Repository Creation and Updating

The CernVM-FS server tool kit provides the cvmfs_server utility in order to perform all operations related to repository creation, updating, deletion, replication and inspection. Without any parameters it prints a short documentation of its commands.

Repository Creation

A new repository is created by cvmfs_server mkfs:

cvmfs_server mkfs my.repo.name

The utility will ask for a user that should act as the owner of the repository and afterwards create all the infrastructure for the new CernVM-FS repository. Additionally it will create a reasonable default configuration and generate a new release manager certificate and software signing key. The public key in /etc/cvmfs/keys/my.repo.name.pub needs to be distributed to all client machines.

The cvmfs_server utility will use /srv/cvmfs as storage location by default. In case a separate hard disk should be used, a partition can be mounted on /srv/cvmfs or /srv/cvmfs can be symlinked to another location (see Notable CernVM-FS Server Locations and Files). Besides local storage it is possible to use an S3 compatible storage service as data backend.

Once created, the repository is mounted under /cvmfs/my.repo.name containing only a single file called new_repository. The next steps describe how to change the repository content.

The repository name resembles a DNS scheme but it does not need to reflect any real server name. It is supposed to be a globally unique name that indicates where/who the publishing of content takes place. A repository name must only contain alphanumeric characters plus -, _, and . and it is limited to a length of 60 characters.

Repositories for Volatile Files

Repositories can be flagged as containing volatile files using the -v option:

cvmfs_server mkfs -v my.repo.name

When CernVM-FS clients perform a cache cleanup, they treat files from volatile repositories with priority. Such volatile repositories can be useful, for instance, for experiment conditions data.

Confidential Repositories

Repositories can be created with the -V options or republished with the -F option with a membership requirement. Clients that mount repositories with a membership requirement will grant or deny access to the repository based on the decision made by an authorization helper. See Section Authorization Helpers for details on authorization helpers.

For instance, a repository can be configured to grant access to a repository only to those users that have a X.509 certificate with a certain DN. Note that the corresponding client-side X.509 authorization helper is not part of CernVM-FS but is provided as a third-party plugin by the Open Science Grid.

A membership requirement makes most sense if the repository is served by an HTTPS server that requires client-side authentication. Note that such repositories cannot be replicated to Stratum 1 servers. Such repositories also cannot benefit from site proxies. Instead, such repositories are either part of a (non CernVM-FS) HTTPS content distribution network or they might be installed for a small number of users that, for example, require access to licensed software.

S3 Compatible Storage Systems

CernVM-FS can store files directly to S3 compatible storage systems, such as Amazon S3, Huawei UDS and OpenStack SWIFT. The S3 storage settings are given as parameters to cvmfs_server mkfs or cvmfs_server add-replica:

cvmfs_server mkfs -s /etc/cvmfs/.../mys3.conf \
  -w http://s3.amazonaws.com/mybucket-1-1 my.repo.name

The file “mys3.conf” contains the S3 settings (see :ref: table below <tab_s3confparameters>). The “-w” option is used define the S3 server URL, e.g. http://localhost:3128, which is used for accessing the repository’s backend storage on S3. Note that this URL can be different than the S3 server address that is used for uploads, e.g. if a proxy server is deployed in front of the server. Note that the buckets need to exist before the repository is created. In the example above, a single bucket mybucket-1-1 needs to be created beforehand.

Parameter Meaning
CVMFS_S3_ACCOUNTS Number of S3 accounts to be used, e.g. 1. With some S3 servers use of multiple accounts can increase the upload speed significantly
CVMFS_S3_ACCESS_KEY S3 account access key(s) separated with :, e.g. KEY-A:KEY-B:...
CVMFS_S3_SECRET_KEY S3 account secret key(s) separated with :, e.g. KEY-A:KEY-B:...
CVMFS_S3_BUCKETS_PER_ACCOUNT S3 buckets used per account, e.g. 1. With some S3 servers use of multiple buckets can increase the upload speed significantly
CVMFS_S3_HOST S3 server hostname, e.g. s3.amazonaws.com
CVMFS_S3_BUCKET S3 bucket base name. Account and bucket index are appended to the bucket base name. If you use just one account and one bucket, e.g. named mybucket, then you need to create only one bucket called mybucket-1-1
CVMFS_S3_MAX_NUMBER_OF_PARALLEL_CONNECTIONS Number of parallel uploads to the S3 server, e.g. 400

In addition, if the S3 backend is configured to use multiple accounts or buckets, a proxy server is needed to map HTTP requests to correct buckets. This mapping is needed because CernVM-FS does not support buckets but assumes that all files are stored in a flat namespace. The recommendation is to use a Squid proxy server (version \(\geq 3.1.10\)). The squid.conf can look like this:

http_access allow all
http_port 127.0.0.1:3128 intercept
cache_peer swift.cern.ch parent 80 0 no-query originserver
url_rewrite_program /usr/bin/s3_squid_rewrite.py
cache deny all

The bucket mapping logic is implemented in s3_squid_rewrite.py file. This script is not provided by CernVM-FS but needs to be written by the repository owner (the CernVM-FS Git repository contains an example). The script needs to read requests from stdin and write mapped URLs to stdout, for instance:

in: http://localhost:3128/data/.cvmfswhitelist
out: http://swift.cern.ch/cernbucket-9-91/data/.cvmfswhitelist

Repository Update

Typically a repository publisher does the following steps in order to create a new revision of a repository:

  1. Run cvmfs_server transaction to switch to a copy-on-write enabled CernVM-FS volume
  2. Make the necessary changes to the repository, add new directories, patch certain binaries, ...
  3. Test the software installation
  4. Do one of the following:
    • Run cvmfs_server publish to finalize the new repository revision or
    • Run cvmfs_server abort to clear all changes and start over again

CernVM-FS supports having more than one repository on a single server machine. In case of a multi-repository host, the target repository of a command needs to be given as a parameter when running the cvmfs_server utility. The cvmfs_server resign command should run every 30 days to update the signatures of the repository. Most cvmfs_server commands allow for wildcards to do manipulations on more than one repository at once, cvmfs_server migrate *.cern.ch would migrate all present repositories ending with .cern.ch.

Repository Import

The CernVM-FS server tools support the import of a CernVM-FS file storage together with its corresponding signing keychain. The import functionality is useful to bootstrap a release manager machine for a given file storage.

cvmfs_server import works similar to cvmfs_server mkfs (described in Repository Creation) except it uses the provided data storage instead of creating a fresh (and empty) storage. In case of a CernVM-FS 2.0 file storage cvmfs_server import also takes care of the file catalog migration into the latest catalog schema (see Legacy Repository Import for details).

During the import it might be necessary to resign the repository’s whitelist. Usually because the whitelist’s expiry date has exceeded. This operations requires the corresponding masterkey to be available in /etc/cvmfs/keys. Resigning is enabled by adding -r to cvmfs_server import.

An import can either use a provided repository keychain placed into /etc/cvmfs/keys or generate a fresh repository key and certificate for the imported repository. The latter case requires an update of the repository’s whitelist to incorporate the newly generated repository key. To generate a fresh repository key add -t -r to cvmfs_server import.

Refer to Section Repository Signature for a comprehensive description of the repository signature mechanics.

Legacy Repository Import

We strongly recommend to install CernVM-FS 2.1 on a fresh or at least a properly cleaned machine without any traces of the CernVM-FS 2.0 installation before installing CernVM-FS 2.1 server tools.

The command cvmfs_server import requires the full CernVM-FS 2.0 data storage which is located at /srv/cvmfs by default as well as the repository’s signing keys. Since the CernVM-FS 2.1 server backend supports multiple repositories in contrast to its 2.0 counterpart, we recommend to move the repository’s data storage to /srv/cvmfs/<FQRN> upfront to avoid later inconsistencies.

The following steps describe the transformation of a repository from CernVM-FS 2.0 into 2.1. As an example we are using a repository called legacy.cern.ch.

  1. Make sure that you have backups of both the repository’s backend storage and its signing keys

  2. Install and test the CernVM-FS 2.1 server tools on the machine that is going to be used as new Stratum 0 maintenance machine

  3. Place the repository’s backend storage data in /srv/cvmfs/legacy.cern.ch
    (default storage location)
  4. Transfer the repository’s signing keychain to the machine (f.e. to /legacy_keys/)

  5. Run cvmfs_server import like this:

    cvmfs_server import
      -o <username of repo maintainer> \
      -k ~/legacy_keys \
      -l               \ # for 2.0.x file catalog migration
      -s               \ # for further repository statistics
      legacy.cern.ch
    
  6. Check the imported repository with cvmfs_server check legacy.cern.ch for integrity (see Integrity Check)

Customizable Actions Using Server Hooks

The cvmfs_server utility allows release managers to trigger custom actions before and after crucial repository manipulation steps. This can be useful for example for logging purposes, establishing backend storage connections automatically or other workflow triggers, depending on the application.

There are six designated server hooks that are potentially invoked during the repository update procedure:

  • When running cvmfs_server transaction:
    • before the given repository is transitioned into transaction mode
    • after the transition was successful
  • When running cvmfs_server publish:
    • before the publish procedure for the given repository is started
    • after it was published and remounted successfully
  • When running cvmfs_server abort:
    • before the unpublished changes will be erased for the given repository
    • after the repository was successfully reverted to the last published state

All server hooks must be defined in a single shell script file called:

/etc/cvmfs/cvmfs_server_hooks.sh

The cvmfs_server utility will check the existence of this script and source it. To subscribe to the described hooks one needs to define one or more of the following shell script functions:

  • transaction_before_hook()
  • transaction_after_hook()
  • publish_before_hook()
  • publish_after_hook()
  • abort_before_hook()
  • abort_after_hook()

The defined functions get called at the specified positions in the repository update process and are provided with the fully qualified repository name as their only parameter ($1). Undefined functions automatically default to a NO-OP. An example script is located at cvmfs/cvmfs_server_hooks.sh.demo in the CernVM-FS sources.

Maintaining a CernVM-FS Repository

CernVM-FS is a versioning, snapshot-based file system. Similar to versioning systems, changes to /cvmfs/...are temporary until they are committed (cvmfs_server publish) or discarded (cvmfs_server abort). That allows you to test and verify changes, for instance to test a newly installed release before publishing it to clients. Whenever changes are published (committed), a new file system snapshot of the current state is created. These file system snapshots can be tagged with a name, which makes them named snapshots. A named snapshot is meant to stay in the file system. One can rollback to named snapshots and it is possible, on the client side, to mount any of the named snapshots in lieu of the newest available snapshot.

Two named snapshots are managed automatically by CernVM-FS, trunk and trunk-previous. This allows for easy unpublishing of a mistake, by rolling back to the trunk-previous tag.

Integrity Check

CernVM-FS provides an integrity checker for repositories. It is invoked by

cvmfs_server check

The integrity checker verifies the sanity of file catalogs and verifies that referenced data chunks are present. Ideally, the integrity checker is used after every publish operation. Where this is not affordable due to the size of the repositories, the integrity checker should run regularly.

The checker can also run on a nested catalog subtree. This is useful to follow up a specific issue where a check on the full tree would take a lot of time:

cvmfs_server check -s <path to nested catalog mountpoint>

Optionally cvmfs_server check can also verify the data integrity (command line flag -i) of each data object in the repository. This is a time consuming process and we recommend it only for diagnostic purposes.

Named Snapshots

Named snapshots or tags are an easy way to organise checkpoints in the file system history. CernVM-FS clients can explicitly mount a repository at a specific named snapshot to expose the file system content published with this tag. It also allows for rollbacks to previously created and tagged file system revisions. Tag names need to be unique for each repository and are not allowed to contain spaces or spacial characters. Besides the actual tag’s name they can also contain a free descriptive text and store a creation timestamp.

Named snapshots are best to use for larger modifications to the repository, for instance when a new major software release is installed. Named snapshots provide the ability to easily undo modifications and to preserve the state of the file system for the future. Nevertheless, named snapshots should not be used excessively. Less than 50 named snapshots are a good number of named snapshots in many cases.

Automatically Generated Tags

By default, new repositories will automatically create a generic tag if no explicit tag is given during publish. The automatic tagging can be turned off using the -g option during repository creation or by setting CVMFS_AUTO_TAG=false in the /etc/cvmfs/repositories.d/$repository/server.conf file.

The life time of automatic tags can be restriced by the CVMFS_AUTO_TAG_TIMESPAN parameter or by the -G option to cvmfs_server mkfs. The parameter takes a string that the date utility can parse, for instance "4 weeks ago". On every publish, automatically generated tags older than the defined threshold are removed.

Creating a Named Snapshot

Tags can be added while publishing a new file system revision. To do so, the -a and -m options for cvmfs_server publish are used. The following command publishes a CernVM-FS revision with a new revision that is tagged as “release-1.0”:

cvmfs_server transaction
# Changes
cvmfs_server publish -a release-1.0 -m "first stable release"

Managing Existing Named Snapshots

Management of existing tags is done by using the cvmfs_server tag command. Without any command line parameters, it will print all currently available named snapshots. Snapshots can be inspected (-i <tag name>), removed (-r <tag name>) or created (-a <tag name> -m <tag description> -h <catalog root hash>). Furthermore machine readable modes for both listing (-l -x) as well as inspection (-i <tag name> -x) is available.

Rollbacks

A repository can be rolled back to any of the named snapshots. Rolling back is achieved through the command cvmfs_server rollback -t release-1.0 A rollback is, like restoring from backups, not something one would do often. Use caution, a rollback is irreversible.

Managing Nested Catalogs

CernVM-FS stores meta-data (path names, file sizes, ...) in file catalogs. When a client accesses a repository, it has to download the file catalog first and then it downloads the files as they are opened. A single file catalog for an entire repository can quickly become large and impractical. Also, clients typically do not need all of the repository’s meta-data at the same time. For instance, clients using software release 1.0 do not need to know about the contents of software release 2.0.

With nested catalogs, CernVM-FS has a mechanism to partition the directory tree of a repository into many catalogs. Repository maintainers are responsible for sensible cutting of the directory trees into nested catalogs. They can do so by creating and removing magic files named .cvmfscatalog.

For example, in order to create a nested catalog for software release 1.0 in the hypothetical repository experiment.cern.ch, one would invoke

cvmfs_server transaction
touch /cvmfs/experiment.cern.ch/software/1.0/.cvmfscatalog
cvmfs_server publish

In order to merge a nested catalog with its parent catalog, the corresponding .cvmfscatalog file needs to be removed. Nested catalogs can be nested on arbitrary many levels.

Recommendations for Nested Catalogs

Nested catalogs should be created having in mind which files and directories are accessed together. This is typically the case for software releases, but can be also on the directory level that separates platforms. For instance, for a directory layout like

/cvmfs/experiment.cern.ch
  |- /software
  |    |- /i686
  |    |    |- 1.0
  |    |    |- 2.0
  |    `    |- common
  |    |- /x86_64
  |    |    |- 1.0
  |    `    |- common
  |- /grid-certificates
  |- /scripts

it makes sense to have nested catalogs at

/cvmfs/experiment.cern.ch/software/i686
/cvmfs/experiment.cern.ch/software/x86_64
/cvmfs/experiment.cern.ch/software/i686/1.0
/cvmfs/experiment.cern.ch/software/i686/2.0
/cvmfs/experiment.cern.ch/software/x86_64/1.0

A nested catalog at the top level of each software package release is generally the best approach because once package releases are installed they tend to never change, which reduces churn and garbage generated in the repository from old catalogs that have changed. In addition, each run only tends to access one version of any package so having a separate catalog per version avoids loading catalog information that will not be used. A nested catalog at the top level of each platform may make sense if there is a significant number of platform-specific files that aren’t included in other catalogs.

It could also make sense to have a nested catalog under grid-certificates, if the certificates are updated much more frequently than the other directories. It would not make sense to create a nested catalog under /cvmfs/experiment.cern.ch/software/i686/common, because this directory needs to be accessed anyway whenever its parent directory is needed. As a rule of thumb, a single file catalog should contain more than 1000 files and directories but not contain more than \(\approx\)200000 files. See Inspecting Nested Catalog Structure how to find catalogs that do not satisfy this recommendation.

Restructuring the repository’s directory tree is an expensive operation in CernVM-FS. Moreover, it can easily break client applications when they switch to a restructured file system snapshot. Therefore, the software directory tree layout should be relatively stable before filling the CernVM-FS repository.

Managing Nested Catalogs with .cvmfsdirtab

Rather than managing .cvmfscatalog files by hand, a repository administrator may create a file called .cvmfsdirtab, in the top directory of the repository, which contains a list of paths relative to the top of the repository where .cvmfscatalog files will be created. Those paths may contain shell wildcards such as asterisk (*) and question mark (?). This is useful for specifying patterns for creating nested catalogs as new files are installed. A very good use of the patterns is to identify directories where software releases will be installed.

In addition, lines in .cvmfsdirtab that begin with an exclamation point (!) are shell patterns that will be excluded from those matched by lines without an exclamation point. For example a .cvmfsdirtab might contain these lines for the repository of the previous subsection:

/software/*
/software/*/*
! */common
/grid-certificates

This will create nested catalogs at

/cvmfs/experiment.cern.ch/software/i686
/cvmfs/experiment.cern.ch/software/i686/1.0
/cvmfs/experiment.cern.ch/software/i686/2.0
/cvmfs/experiment.cern.ch/software/x86_64
/cvmfs/experiment.cern.ch/software/x86_64/1.0
/cvmfs/experiment.cern.ch/grid-certificates

Note that unlike the regular lines that add catalogs, asterisks in the exclamation point exclusion lines can span the slashes separating directory levels.

Automatic Management of Nested Catalogs

An alternative to .cvmfsdirtab is the automatic catalog generation. This feature automatically generates nested catalogs based on their weight (number of entries). It can be enabled by setting CVMFS_AUTOCATALOGS=true in the server configuration file.

Catalogs are split when their weight is greater than a specified maximum threshold, or removed if their weight is less than a minimum threshold. Automatically generated catalogs contain a .cvmfsautocatalog file (along with the .cvmfscatalog file) in its root directory. User-defined catalogs (containing only a .cvmfscatalog file) always remain untouched. Hence one can mix both manual and automatically managed directory sub-trees.

The following conditions are applied when processing a nested catalog:

  • If the weight is greater than CVMFS_AUTOCATALOGS_MAX_WEIGHT, this catalog will be split in smaller catalogs that meet the maximum and minimum thresholds.
  • If the weight is less than CVMFS_AUTOCATALOGS_MIN_WEIGHT, this catalog will be merged into its parent.

Both CVMFS_AUTOCATALOGS_MAX_WEIGHT and CVMFS_AUTOCATALOGS_MIN_WEIGHT have reasonable defaults and usually do not need to be defined by the user.

Inspecting Nested Catalog Structure

The following command visualizes the current nested file catalog layout of a repository.

cvmfs_server list-catalogs

Additionally this command allows to spot degenerated nested catalogs. As stated here the recommended maximal file entry count of a single catalog should not exceed \(\approx\)200000. One can use the switch list-catalogs -e to inspect the current nested catalog entry counts in the repository. Furthermore list-catalgos -s will print the file sizes of the catalogs in bytes.

Repository Mount Point Management

CernVM-FS server maintains two mount points for each repository (see CernVM-FS Server Infrastructure for details) and needs to keep them in sync with transactional operations on the repository.

In rare occasions (for example at reboot of a release manager machine) CernVM-FS might need to perform repair operations on those mount points. As of CernVM-FS 2.2.0 those mount points are not automatically mounted on reboot of the release manager machine anymore. Usually the mount point handling happens automatically and transparently to the user when invoking arbitrary cvmfs_server commands.

Nevertheless cvmfs_server mount <repo name> allows users to explicitly trigger this repair operation anytime for individual repositories. Mounting all hosted repositories is possible with the -a parameter but requires root privileges. If you want to have all hosted repositories mounted after reboot then put cvmfs_server mount -a in a boot script, for example in /etc/rc.local.

# properly mount a specific repository
cvmfs_server mount test.cern.ch

# properly mount all hosted repositories (as root)
sudo cvmfs_server mount -a

Syncing files into a repository with cvmfs_rsync

A common method of publishing into CernVM-FS is to first install all the files into a convenient shared filesystem, mount the shared filesystem on the publishing machine, and then sync the files into the repository during a transaction. The most common tool to do the syncing is rsync, but rsync by itself doesn’t have a convenient mechanism for avoiding generated .cvmfscatalog and .cvmfsautocatalog files in the CernVM-FS repository. Actually the --exclude option is good for avoiding the extra files, but the problem is that if a source directory tree is removed, then rsync will not remove the corresponding copy of the directory tree in the repository if it contains a catalog, because the extra file remains in the repository. For this reason, a tool called cvmfs_rsync is included in the cvmfs-server package. This is a small wrapper around rsync that adds the --exclude options and removes .cvmfscatalog and .cvmfsautocatalog files from a repository when the corresponding source directory is removed. This is the usage:

cvmfs_rsync [rsync_options] srcdir /cvmfs/reponame[/destsubdir]

This is an example use case:

$ cvmfs_rsync -av --delete /data/lhapdf /cvmfs/cms.cern.ch

Migrate File Catalogs

In rare cases the further development of CernVM-FS makes it necessary to change the internal structure of file catalogs. Updating the CernVM-FS installation on a Stratum 0 machine might require a migration of the file catalogs.

It is recommended that cvmfs_server list is issued after any CernVM-FS update to review if any of the maintained repositories need a migration. Outdated repositories will be marked as “INCOMPATIBLE” and cvmfs_server refuses all actions on these repositories until the file catalogs have been updated.

In order to run a file catalog migration use cvmfs_server migrate for each of the outdated repositories. This will essentially create a new repository revision that contains the exact same file structure as the current revision. However, all file catalogs will be recreated from scratch using the updated internal structure. Note that historic file catalogs of all previous repository revisions stay untouched and are not migrated.

After cvmfs_server migrate has successfully updated all file catalogs repository maintenance can continue as usual.

Change File Ownership on File Catalog Level

CernVM-FS tracks the UID and GID of all contained files and exposes them through the client to all using machines. Repository maintainers should keep this in mind and plan their UID and GID assignments accordingly.

Repository operation might occasionally require to bulk-change many or all UIDs/GIDs. While this is of course possible via chmod -R in a normal repository transaction, it is cumbersome for large repositories. We provide a tool to quickly do such adaption on CernVM-FS catalog level using UID and GID mapping files:

cvmfs_server catalog-chown -u <uid map> -g <gid map> <repo name>

Both the UID and GID map contain a list of rules to apply to each file meta data record in the CernVM-FS catalogs. This is an example of such a rules list:

# map root UID/GID to 1001
0 1001

# swap UID/GID 1002 and 1003
1002 1003
1003 1002

# map everything else to 1004
* 1004

Note that running cvmfs_server catalog-chown produces a new repository revision containing CernVM-FS catalogs with updated UIDs and GIDs according to the provided rules. Thus, previous revisions of the CernVM-FS repository will not be affected by this update.

Repository Garbage Collection

Since CernVM-FS is a versioning file system it is following an insert-only policy regarding its backend storage. When files are deleted from a CernVM-FS repository, they are not automatically deleted from the underlying storage. Therefore legacy revisions stay intact and usable forever (cf. Named Snapshots) at the expense of an ever-growing storage volume both on the Stratum 0 and the Stratum 1s.

For this reason, applications that frequently install files into a repository and delete older ones - for example the output from nightly software builds - might quickly fill up the repository’s backend storage. Furthermore these applications might actually never make use of the aforementioned long-term revision preservation rendering most of the stored objects “garbage”.

CernVM-FS supports garbage-collected repositories that automatically remove unreferenced data objects and free storage space. This feature needs to be enabled on the Stratum 0 and automatically scans the repository’s catalog structure for unreferenced objects both on the Stratum 0 and the Stratum 1 installations on every publish respectively snapshot operation.

Garbage Sweeping Policy

The garbage collector of CernVM-FS is using a mark-and-sweep algorithm to detect unused files in the internal catalog graph. Revisions that are referenced by named snapshots (cf. Named Snapshots) or that are recent enough are preserved while all other revisions are condemned to be removed. By default this time-based threshold is three days but can be changed using the configuration variable CVMFS_AUTO_GC_TIMESPAN both on Stratum 0 and Stratum 1. The value of this variable is expected to be parseable by the date command, for example 3 days ago or 1 week ago.

Enabling Garbage Collection

Creating a Garbage Collectable Repository

Repositories can be created as garbage-collectable from the start by adding -z to the cvmfs_server mkfs command (cf. Repository Creation). It is generally recommended to also add -g to switch off automatic tagging in a garbage collectable repository. For debugging or bookkeeping it is possible to log deleted objects into a file by setting CVMFS_GC_DELETION_LOG to a writable file path.

Enabling Garbage Collection on an Existing Repository (Stratum 0)

Existing repositories can be reconfigured to be garbage collectable by adding
CVMFS_GARBAGE_COLLECTION=true and CVMFS_AUTO_GC=true to the server.conf of the repository. Furthermore it is recommended to switch off automatic tagging by setting CVMFS_AUTO_TAG=false for a garbage collectable repository. The garbage collection will be enabled with the next published transaction.

Enabling Garbage Collection on an Existing Replication (Stratum 1)

In order to use automatic garbage collection on a stratum 1 replica CVMFS_AUTO_GC=true needs to be added in the server.conf file of the stratum 1 installation. This will only work if the upstream stratum 0 repository has garbage collection enabled.

Limitations on Repository Content

Because CernVM-FS provides what appears to be a POSIX filesystem to clients, it is easy to think that it is a general purpose filesystem and that it will work well with all kinds of files. That is not the case, however, because CernVM-FS is optimized for particular types of files and usage. This section contains guidelines for limitations on the content of repositories for best operation.

Data files

First and foremost, CernVM-FS is designed to distribute executable code that is shared between a large number of jobs that run together at grid sites, clouds, or clusters. Worker node cache sizes and web proxy bandwidth are generally engineered to accommodate that application. The total amount read per job is expected to be roughly limited by the amount of RAM per job slot. The same files are also expected to be read from the worker node cache multiple times for the same type of job, and read from a caching web proxy by multiple worker nodes.

If there are data files distributed by CernVM-FS that follow similar access patterns and size limits as executable code, it will probably work fine. In addition, if there are files that are larger but read slowly throughout long jobs, as opposed to all at once at the beginning, that can also work well if the same files are read by many jobs. That is because web proxies have to be engineered for handling bursts at the beginning of jobs and so they tend to be lightly loaded a majority of the time.

In general, a good rule of thumb is to calculate the maximum rate at which jobs typically start and limit the amount of data that might be read from a web proxy to per thousand jobs, assuming a reasonable amount of overlap of jobs onto the same worker nodes. Also, limit the amount of data that will be put into any one worker node cache to . Of course, if you have a special arrangement with particular sites to have large caches and bandwidths available, these limits can be made higher at those sites. Web proxies may also need to be engineered with faster disks if the data causes their cache hit ratios to be reduced.

Also, keep in mind that the total amount of data distributed is not unlimited. The files are stored and distributed compressed, and files with the same content stored in multiple places in the same repository are collapsed to the same file in storage, but the storage space is used not only on the original repository server, it is also replicated onto multiple Stratum 1 servers. Generally if only executable code is distributed, there is no problem with the space taken on Stratum 1s, but if many large data files are distributed they may exceed the Stratum 1 storage capacity. Data files also tend to not compress as well, and that is especially the case of course if they are already compressed before installation.

Tarballs, zip files, and other archive files

If the contents of a tarball, zip file, or some other type of archive file is desired to be distributed by CernVM-FS, it is usually better to first unpack it into its separate pieces first. This is because it allows better sharing of content between multiple releases of the file; some pieces inside the archive file might change and other pieces might not in the next release, and pieces that don’t change will be stored as the same file in the repository. CernVM-FS will compress the content of the individual pieces, so even if there’s no sharing between releases it shouldn’t take much more space.

File permissions

Care should be taken to make all the files in a repository readable by “other”. This is because permissions on files in the original repository are generally the same as those seen by end clients, except the files are owned by the “cvmfs” user and group. The write permissions are ignored by the client since it is a read-only filesystem. However, unless the client has set

CVMFS_CHECK_PERMISSIONS=no

(and most do not), unprivileged users will not be able to read files unless they are readable by “other” and all their parent directories have at least “execute” permissions. It makes little sense to publish files in CernVM-FS if they won’t be able to be read by anyone.