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1Repair Windows errors before they cause bigger problems2Scan for outdated or missing drivers - takes under a minute3Clear out junk files and repair common Windows errorsTo find which domain or hosting account is filling a Linux server, start with df -h to identify the full filesystem, then run a filesystem-bounded du scan on the hosting tree and drill into the largest account. Check inodes separately with df -i; a server can run out of inodes while free gigabytes remain. If you use Plesk or cPanel, compare the panel’s categories and refresh time with the live command-line totals before deciding what to delete.
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The method below shows how to measure web files, mail, databases, logs and backups without accidentally counting another mount or a virtual filesystem, and explains why panel figures and du often disagree.
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What “disk usage per domain” actually measures
A domain name is not a filesystem boundary. On a hosting server, one domain’s data may be spread across a document root, mailboxes, database files, logs, caches and backups. The number shown by a control panel may therefore be a subscription or account total rather than the size of the document-root directory you expect.
Before running a scan, decide which question you are answering:
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- Which filesystem is full? Use
df -hfor mounted filesystems and their capacity. - Which top-level account or directory is large? Use
duon the relevant hosting tree, such as/home. - Which domain directory is large? Descend into the largest account and run another depth-limited
dupass. - Are there too many files? Use
df -iand, when needed,du --inodes; byte capacity and inode capacity are separate limits.
Record the path, filesystem, measurement time and command options. Those details make a later comparison with Plesk or cPanel meaningful.
Step 1: Identify the full filesystem with df -h
Run:
df -hThe command reports each mounted filesystem in human-readable units. Look at the Mounted on column and note the filesystem whose Use% is highest. A domain under /home may be on a separate volume from /; scanning the wrong mount can lead you to the wrong account.
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Read the result before scanning
- Use the exact mount point that contains the hosting data, for example
/homeif it is a distinct mount. - If the reported full filesystem is a temporary, backup or database volume, do not assume the web tree is responsible.
- Keep the available-space value in mind. A scan can take time, and deleting files while it runs can change totals.
Step 2: Rank accounts or domains with a bounded du scan
For a hosting tree on one filesystem, run:
du -xhd1 PATH | sort -hrReplace PATH with the directory that contains the accounts, such as /home. The options mean:
-xstays on the same filesystem and does not count a mounted filesystem reached belowPATH.-hprints human-readable sizes.-d1limits the report to one directory level, giving a ranked view of immediate children.sort -hrsorts human-readable values from largest to smallest.
On systems where the hosting tree is not known, first inspect mounts with df -h, then choose the path that corresponds to the full mount. Running the scan at a narrow, relevant path is safer and faster than beginning at the entire root filesystem.
Scan the root filesystem only when necessary
A server-wide triage command is:
du -h --max-depth=1 / 2>/dev/null | sort -hrA root scan can traverse virtual filesystems and bind mounts that do not represent ordinary persistent domain data. Exclude virtual filesystems such as /proc and /sys, and bind mounts such as /home/virtfs, when constructing a full-root scan. Otherwise, the result can contain duplicate views, transient kernel data or a second traversal of the same storage.
The one-level root report tells you whether the largest consumer is under /home, /var, a database directory, a backup location or another top-level path. It does not attribute that total to a domain until you descend further.
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Step 3: Drill into the largest account and domain directory
After the first ranking identifies an account directory, run another depth-limited pass there:
du -xhd1 /home/ACCOUNT | sort -hrReplace ACCOUNT with the actual account name. Inspect the largest children and continue with the same pattern:
du -xhd1 /home/ACCOUNT/LARGEST-DIRECTORY | sort -hrRepeat until the output identifies a document root, uploads directory, cache, log tree, mail store or backup directory that explains the size. Keep -x on each pass if you want every level to remain on the same filesystem.
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- Web content: document roots, media uploads, generated archives and application caches.
- Logs: access and error logs that have not been rotated or compressed.
- Mail: mailbox files, indexes and retention folders. Mail may be stored outside the web root.
- Databases: database files may live in a server database directory rather than under the domain’s document root.
- Backups: local snapshots or account archives can be much larger than the live site.
- Configuration and control-panel data: hidden directories may be omitted from a casual visual inspection but still consume space.
Do not delete a large directory solely because it appears in the ranking. Confirm ownership, service role, retention policy and whether a backup or database process is still using it.
Step 4: Check inode exhaustion separately
Run:
df -iInode capacity limits how many filesystem objects can exist. A workload that creates millions of tiny cache files, mail messages or session files can exhaust inodes while df -h still shows free gigabytes. Conversely, a few large backup files can fill bytes without consuming many inodes.
To rank directories by inode count on a filesystem, GNU du supports:
du --inodes --max-depth=1 / | sort -hrUse this on the relevant mount or directory when the inode report points there. For a root-level triage, the command above provides a one-level ranking; exclude or avoid virtual filesystems and bind mounts for the same reasons as a byte scan.
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Interpreting byte and inode results
| Symptom | Likely pressure | Next check |
|---|---|---|
df -h near 100%, df -i has headroom |
Large files or allocated blocks | Rank directories with du -xhd1; inspect logs, backups, media and databases. |
df -i near 100%, bytes remain available |
Too many small files | Use du --inodes; inspect caches, sessions, mail and temporary-file trees. |
| Both are high | Many files and substantial data | Identify the largest account, then separate web, mail, database and backup ownership before cleanup. |
Using Plesk to find disk usage per domain
Plesk exposes subscription and domain statistics in its interface. The exact totals are grouped into Web, Mail, Databases and Other, so the panel can answer a broader question than the size of one document-root directory.
Use the panel’s statistics view
- Open the subscription or domain statistics area in Plesk.
- Sort the list by the displayed usage to identify the largest subscription or domain.
- Open the usage breakdown and note which category—Web, Mail, Databases or Other—is responsible.
- Compare the category with a command-line scan of the corresponding filesystem or service storage.
Plesk normally calculates statistics during daily maintenance. A panel number can therefore be older than a live du result, particularly after a large upload, log rotation or backup job.
Refresh one domain immediately
To recalculate one domain, run:
plesk sbin statistics --calculate-one --domain-name=example.comReplace example.com with the domain you need to verify. To recalculate all domains, use:
plesk sbin statistics --calculate-allThese operations update Plesk’s statistics; they do not change the files themselves. After the calculation completes, record the new timestamp before comparing it with a fresh du pass.
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How Plesk calculates categories
Plesk documents that file usage is calculated with DU, database usage comes from MySQL data, and mail usage uses mailbox index files. Its SQL method queries domains.real_size and can list subscriptions, customers, domains, subdomains and additional domains sorted by usage. Use that documented SQL approach when you need a sortable inventory across those objects rather than a single panel screen.
Because the categories come from different sources, a Plesk total is not guaranteed to equal a single directory’s apparent size. A document-root scan may cover only web files, while the panel adds mail, database and other allocations.
Using cPanel to find account and domain usage
Account overview in the interface
In cPanel, open Files > Disk Usage for an account overview. The view can include hidden directories, mailing lists and database sizes. Its displayed figures may lag behind current filesystem contents or differ from a simple file-tree calculation because it combines account categories and control-panel accounting.
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Measure an account over SSH
For a specific cPanel account, run:
du -h --max-depth=1 /home/$user/ | sort -rhReplace $user with the account’s system username if you are entering a literal path. This reports the immediate directories beneath the account home. Drill into the largest child with another du command, and use a filesystem-bounded form such as du -xhd1 when mounted data could appear below the account.
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Server-wide cPanel triage
These commands provide a starting point when you do not yet know which account is responsible:
df -hdu -h --max-depth=1 / 2>/dev/null | sort -hrdf -idu --inodes --max-depth=1 / | sort -hrFor the root scan, exclude /proc, /sys and bind mounts. A cPanel account total can include data that is not obvious in the visible website directory, so use the interface and the SSH result as complementary views rather than treating one as automatically authoritative.
Why du, Plesk and cPanel show different numbers
A disagreement is usually a difference in scope, content, freshness or enforcement—not proof that one tool is broken. Compare the measurements on these four axes.
| Axis | Command-line view | Panel view | Question to ask |
|---|---|---|---|
| Scope | A selected filesystem, account path or directory | Filesystem, account, subscription or domain object | Are both measurements looking at the same boundary? |
| Content categories | Files reachable below the scanned path | May combine web, mail, databases, logs, backups and configuration | Which categories are included in each total? |
| Freshness | Live scan at command time | Often scheduled statistics; Plesk normally runs daily maintenance | Were files created or removed since the panel last calculated? |
| Enforcement | Observed allocation and file sizes | Reported usage or a configured account/subscription limit | Is this a measured total or a hard quota? |
Domain attribution can move data between names
Plesk documents an attribution rule that explains a common surprise: web and database files may count toward a subscription’s main domain, while mail and other data are counted for individual domains. As a result, a document-root total for one domain can be lower than the domain or subscription number shown in the panel. Neither measurement is necessarily defective; they assign shared or service-specific data differently.
The same reasoning applies when a control panel reports a subscription total but you compare it with one domain directory. Confirm whether the panel object contains several domains, subdomains, additional domains or mailboxes before looking for a missing file.
Hard quota versus reported disk space
Plesk distinguishes domain disk space—which can include multiple categories—from a hard quota imposed on files owned by a subscription system account. A reported usage total can therefore differ from the amount that would trigger a particular quota rule. Check the quota or limit definition separately when the operational question is “why was this account blocked?” rather than “which files are largest?”
A repeatable investigation procedure
- Confirm the symptom. Note whether the alert concerns bytes, inodes, an account quota or a panel statistic.
- Find the affected mount. Run
df -hand record the full filesystem and mount point. - Check inode headroom. Run
df -i; do not assume free bytes rule out exhaustion. - Choose the narrowest scan path. Use
/home, a subscription tree or another path on the affected mount instead of scanning all of/unnecessarily. - Rank the first level. Run
du -xhd1 PATH | sort -hrand identify the largest account or service directory. - Descend one level at a time. Repeat
duon the largest child until you can name the responsible category and owner. - Check panel accounting. In Plesk, inspect the Web, Mail, Databases and Other breakdown and refresh statistics when necessary. In cPanel, inspect Files > Disk Usage.
- Reconcile differences. Compare scope, category inclusion, calculation time and quota rules. For Plesk, remember the documented main-domain attribution for web and database data.
- Take a reversible action first. Rotate or archive logs according to policy, remove confirmed temporary files, or move verified backups to approved storage. Do not remove active database, mail or system files solely because they rank highly.
- Verify recovery. Re-run
df -h,df -iand the focusedduscan, then refresh the panel statistic if you rely on it for monitoring.
Troubleshooting common results
The root scan is slow or produces strange paths
Stop broad scanning and target the mount identified by df -h. Exclude /proc, /sys and bind mounts such as /home/virtfs. These paths can expose virtual or duplicate views that make a root-level ranking misleading.
du is smaller than df
The two commands answer different questions. df reports blocks allocated by the filesystem; du totals files reachable under the path you scanned. First verify that you scanned the mount that df identified and that you did not omit another top-level directory on that mount. Then consider deleted-but-still-open files, reserved filesystem space, snapshots or data outside the selected path; these conditions require system-level investigation rather than assigning the difference to a domain without evidence.
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The panel is larger than the document root
Check whether mail, databases, logs, backups, hidden directories or multiple domains are included. In Plesk, web and database usage may be attributed to the subscription’s main domain, while mail and other data remain with individual domains. In cPanel, the Disk Usage view can include hidden directories, mailing lists and database sizes.
The panel is smaller or stale
Compare calculation times. Plesk statistics normally run during daily maintenance; use plesk sbin statistics --calculate-one --domain-name=example.com or --calculate-all when an immediate refresh is required. A live du result can also change while uploads, mail delivery, database writes or log rotation are in progress.
Bytes look safe but writes fail
Run df -i. If inode use is exhausted, rank inode counts with du --inodes --max-depth=1 and investigate directories containing huge numbers of small files. Deleting arbitrary files can damage an application; identify the cache, session, mail or temporary-file lifecycle and clean it according to that service’s rules.
Safe cleanup and ongoing monitoring
Measurement should precede deletion. Once a directory is identified, verify its owner, service, retention requirement and backup status. Large files may be legitimate uploads or database tables; a directory with many tiny files may be an application cache that can be regenerated, or it may contain user data that cannot be recreated.
- Prefer the application’s rotation, purge or retention mechanism for logs, mail and caches.
- Do not delete database files from the filesystem while the database service is running unless the database documentation explicitly supports that operation.
- Preserve at least one verified backup before removing account archives or snapshots.
- After cleanup, run both byte and inode checks; removing one large file may free bytes but do nothing for an inode emergency.
- Document the path, owner, action and before/after measurements so the same growth pattern can be detected early.
For recurring operations, schedule monitoring around the same scope used for alerts. A filesystem alert based on df should not be silently compared with a per-domain panel statistic without a documented mapping between the two.
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