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Scan for outdated or missing drivers - takes under a minuteDriver Scan →Clear out junk files and repair common Windows errorsFree Scan →On a VPS, /etc holds host configuration, /usr holds mostly shareable programs and resources, and /var holds data that changes while services run. The other directories under / support booting, users, applications, devices, processes, and temporary state. Treat / as the root of a namespace, not automatically as one disk partition: a provider may mount /var, /usr, /home, or an application volume separately.
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What the Linux filesystem hierarchy means on a VPS
The Filesystem Hierarchy Standard (FHS) is a convention for placing files so the operating system, packages, scripts, and administrators can interoperate. It defines the purpose of the root filesystem and the major /usr and /var hierarchies, while distributions and applications decide many implementation details.
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The slash at the beginning of a path is the namespace root. It does not tell you that every directory is stored on the same virtual disk. A VPS image can use separate filesystems, logical volumes, provider-attached volumes, or bind mounts beneath that tree. Before deleting a large directory, determine whether it is a mount point, a symbolic link, or an ordinary directory.
Essential startup and recovery material must remain reachable from the root filesystem. The FHS allows /usr, /opt, and /var to be separate filesystems, but the boot arrangement must still make required files available when the machine starts.
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The top-level directories at a glance
| Path | Purpose on a VPS | Operational guidance |
|---|---|---|
/ |
Root of the complete directory tree | Keep free space for boot, package, and recovery operations. |
/boot |
Static boot-loader files and kernels | Protect it from casual deletion; contents vary by distribution. |
/etc |
Host-specific, static configuration | Back up important service settings, but do not use it for changing application data. |
/bin |
Essential user command binaries in the traditional layout | Often a symbolic link into /usr/bin on modern systems. |
/sbin |
Essential system and recovery binaries | Administrative commands may also be under /usr/sbin or /usr/local/sbin. |
/lib and /lib64 |
Essential shared libraries and kernel modules | Usually managed by the distribution; may point into /usr. |
/usr |
Programs, libraries, documentation, and architecture-independent resources | Generally shareable and read-only; do not put changing service state here. |
/usr/local |
Software installed by the local administrator | Keep local additions distinct from distribution-managed files. |
/opt |
Add-on application packages | Useful for self-contained third-party or vendor installations. |
/home |
Ordinary users’ home directories | Use a deliberate service account and path for deployed applications. |
/root |
Home directory of the root account | Separate from /, despite the similar name. |
/srv |
Data for services provided by the system | Use when the distribution or application documents it as the data location. |
/var |
Variable data such as logs, queues, caches, databases, and package state | Monitor growth; a full filesystem can stop services and package operations. |
/tmp |
Short-lived temporary files | Disposable by policy; never use it for durable backups. |
/var/tmp |
Temporary files intended to survive a reboot | Still temporary and subject to cleanup. |
/run |
Volatile runtime state created during boot and service operation | Not a normal persistent-data directory. |
/dev |
Device nodes and interfaces | Managed runtime state, normally supplied by a device filesystem. |
/proc |
Kernel and process information | Generated by the kernel, not ordinary application data. |
/sys |
Kernel and hardware/device model information | Generated by the kernel and device-management layers. |
/media and /mnt |
Removable-media and temporary mount points | May be unused on a VPS; actual mounts depend on the provider and administrator. |
Configuration and software: /etc, /usr, and friends
/etc: static host configuration
The FHS states that the /etc hierarchy contains configuration files. These files describe how this particular machine and its services should operate: network settings, users and groups, service definitions, security policy, scheduled jobs, package repositories, and application configuration. A configuration file controls a program and is static rather than an executable binary.
Start service investigations in /etc, then follow the service documentation for included files and drop-in directories. A web server, database, or SSH daemon may read a main file plus fragments in a subdirectory. Back up the relevant files while preserving ownership and permissions; copying every file in /etc blindly can capture transient host details or secrets you do not intend to restore.
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/usr: distribution-managed programs and resources
The FHS describes /usr as shareable, read-only data. It commonly contains executable programs in /usr/bin, administrative programs in /usr/sbin, libraries in /usr/lib, documentation in /usr/share/doc, and architecture-independent resources in /usr/share. Package managers own most of these files, so manually removing a large-looking directory can break dependencies or leave the package database inconsistent.
/usr/local and /opt
/usr/local is for software and data installed by the local administrator rather than by the operating system’s package set. It is a sensible place for locally compiled utilities when you want them separated from vendor files. /opt is intended for add-on application packages, especially self-contained installations that do not follow the distribution’s normal package layout. Neither location is automatically the correct place for mutable databases, uploads, or logs; follow the application’s documented data path.
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/bin, /sbin, and libraries after the merged-/usr transition
Historically, /bin contained a small set of essential user commands, /sbin held essential system commands, and the corresponding /usr directories held larger collections. Current distributions commonly use a merged-/usr layout: /bin, /sbin, /lib, and sometimes /lib64 are symbolic links into /usr. systemd documents that these paths should be on the root filesystem or be symlinks to the /usr filesystem.
Consequently, seeing both /bin and /usr/bin does not prove that two copies of every command exist or that they are separate disks. Check the resolved path with readlink -f /bin and inspect the package owner with your distribution’s package manager before changing anything.
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/home and /root
/home contains ordinary users’ personal files and shell configuration. On a server, an application should normally run under a dedicated service account with a deliberate directory and restricted permissions rather than being placed casually in an administrator’s home directory. The root account’s home is /root; it is a directory in the root filesystem, not an alternate spelling for /.
/srv, application directories, and mounted volumes
/srv is designated for data served by the system. A distribution or application may document it as the location for website content, repositories, or service data, but many deployments instead use a path under /var/lib, /var/www, /opt, or a separate volume. Do not infer the location from the service name alone. Inspect the service unit, configuration, container definition, or deployment documentation.
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Provider images can attach block volumes at any path. A website’s uploads or a database may therefore live outside the original root disk even though the application reaches it through an ordinary directory. Include those mounts in capacity checks and backup plans.
Changing state: understanding /var
The FHS defines /var as the home of variable data, including spool directories and files, administrative and logging data, and transient files. Unlike /usr, its contents change as the machine runs.
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/var/log
Logs and audit-style records normally live under /var/log. Retention, compression, and rotation are distribution- and service-specific. Deleting an active log file can confuse a daemon that still has the file open; use the service’s supported rotation mechanism or the system’s log-management tools. If the filesystem is full, identify the largest service directory and check both ordinary files and deleted files still held open by processes.
/var/lib
/var/lib stores persistent state maintained by applications and system packages: database files, package metadata, service indexes, and other data whose format belongs to a particular program. Back it up when the application depends on it, and restore it using that application’s documented procedure. A raw copy made while a database is writing may not be a consistent backup.
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/var/cache and package state
/var/cache contains re-creatable caches, so it is usually a lower backup priority than /var/lib. It is not universally safe to erase: some programs use cache entries for indexes or downloads, and deleting them can cause a large rebuild or service disruption. Ask the package manager or application to clean its own cache instead of using a recursive deletion.
/tmp and /var/tmp
/tmp is for temporary files that may be removed according to local policy, including at boot. /var/tmp is also temporary but is intended to survive a reboot. Neither directory is a backup target, durable upload store, or database location. Check permissions before using either for a short-lived operation, and ensure sensitive temporary files are protected from other users.
Virtual and runtime directories
/run
/run is created and populated during boot with volatile state such as process identifiers, sockets, locks, and service metadata. It disappears across a reboot. systemd also requires /var to be writable before the local-filesystem target is reached; this is why a damaged or read-only /var can prevent normal service startup.
/dev, /proc, and /sys
/dev exposes device nodes and interfaces, normally through a managed device filesystem. /proc presents kernel and process information, while /sys presents the kernel’s hardware and device model. These trees are generated views, not ordinary directories to archive. Copying them into a backup wastes space and can produce meaningless files; exclude them unless a specialized diagnostic tool explicitly requires a live view.
How to discover where a VPS is using space
Use read-only inspection first. Run df -hT to see each filesystem’s size, usage, type, and mount point. Then run findmnt to display the mount hierarchy and identify separate volumes. To measure one filesystem without crossing into other mounts, use du -xhd1 /var; repeat for /home, /srv, or an application path as needed.
Resolve symbolic links before drawing conclusions: readlink -f /bin shows the destination of a merged-/usr link. Use mountpoint /path to test whether a directory is itself a mount point, and inspect a suspicious file with stat /path for ownership, permissions, and timestamps. If df reports a full filesystem but du cannot account for the space, look for deleted files still open by running processes and restart or signal the responsible service through its normal procedure.
What to back up
A useful backup is organized by function rather than by blindly copying every path below /.
- Configuration: preserve the service files you need from
/etc, including drop-ins, certificates, and access-control settings. Protect secrets during storage and transfer. - Persistent application state: identify the service’s documented data directory, often under
/var/lib,/srv,/home,/opt, or a dedicated mounted volume. Use an application-consistent export for databases when available. - User and site content: include home directories, uploads, repositories, and web content that the service actually serves.
- Package and runtime trees: normally reinstall
/usr,/bin,/sbin,/lib,/dev,/proc,/sys, and/runfrom the image or package manager instead of archiving them. - Caches and temporary files: exclude
/tmp,/var/tmp, and re-creatable cache data unless an application’s backup guide specifically requires an item.
Test a restore on a separate instance. A backup that contains configuration but omits a mounted database volume, or contains database files without the matching configuration and credentials, is incomplete even if the archive itself succeeds.
Cleaning without breaking the server
- Check capacity with
df -hTand locate growth withdu -xhd1. Confirm the path is not a separate mount or symlink target. - For logs, use the service’s rotation and retention controls. Do not recursively remove files from
/var/logwhile daemons are writing. - For package downloads, use the distribution’s package-manager cache-clean command rather than deleting package directories by hand. The exact command differs between distributions.
- For application caches, use the application’s maintenance command and verify that it can rebuild the cache.
- Leave
/usr,/lib,/bin, and/sbinunder package-manager control. Removing an apparently unused library can make unrelated programs unbootable. - After cleanup, rerun
df -hT, inspect service status, and review recent logs. A successful deletion is not proof that the service still has all required state.
Comparing VPS images and distributions
The FHS supplies common meanings, but an image’s implementation determines the paths you will actually administer. When comparing images, check these six points:
- Whether the image uses a merged or split
/usrlayout. - Which directories are separate mounts and which share the root filesystem.
- Where each distribution places service data, logs, and package metadata.
- Whether
/tmpis a volatile mount or an ordinary directory. - Which package manager owns system files and how it performs upgrades and cleanup.
- Which provider volumes, snapshots, or image-specific mount paths are attached.
Two servers can therefore show the same familiar names while having different disk-failure modes. A separate /var may protect the root filesystem from log growth but can itself fill and stop services. A single root volume is simpler to inspect but lets one workload consume space needed by the operating system.
Quick Recap
A practical investigation sequence
- List the top level with
ls -la /and note unusual names, symlinks, and mount-looking directories. - Map filesystems with
findmntand capacity withdf -hT. - Classify the path: configuration in
/etc, software in/usr, changing state in/var, user or service content in/homeor/srv, or live kernel/runtime state in/proc,/sys,/dev, and/run. - Read the service’s unit and configuration to find its actual data directory instead of guessing from convention.
- Measure only the relevant filesystem with
du -x, then choose a supported backup, rotation, or cleanup operation. - Record the result, including mount points, package ownership, and restore steps, so the next administrator does not have to rediscover the layout.
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