Install Fathom: the complete guide

Follow this once, top to bottom. It takes about 10 minutes of your attention; the rest is waiting for downloads. Everything is free and nothing is sent to us. You choose how Fathom is installed and exactly where every part goes: it never moves or deletes anything you did not ask for.

1. Choose how to get it

Don't want to install anything? Open Fathom Online on the website: find words in files, merge and split PDFs, convert and shrink pictures, zip, checksums and more, inside your browser. Nothing is uploaded. Otherwise there are two ways to install:

• The setup wizard (Windows): download the zip, extract it, and double-click Fathom-Setup.vbs. A normal window with pages opens (Welcome, Where, Programs, Shortcuts, Summary, Installing, Finished). You choose what to install (LibreOffice, Calibre, 7-Zip, the free assistant) and which folder or drive gets the Fathom app, its data, and every program one by one. Best if you want to decide where things go. It works without the Microsoft Store, winget or Edge, so it is also the right pick for slimmed-down Windows such as Tiny10 and Tiny11.
• The direct way (every system): extract the same zip and run Fathom.bat (Windows), Fathom.command (Mac) or ./fathom.sh (Linux). Nothing is asked and nothing is moved: Fathom installs inside the folder you extracted and Windows keeps the programs in their usual places. Best if you just want it to work, or want a portable copy.

Full or Lite? The website offers fathom.zip (Full) and fathom-lite.zip (Lite). Full has everything: Word, Excel, PowerPoint and old Office files, e-books, RAR and 100+ more formats, plus the free AI assistant that runs on your own PC. It needs about 12 GB free and a long first download. Lite is the small version: search, pictures, audio, video, PDF, text and data files, all PDF tools, the editor, stamp, sign, scan, print, rename and compare. It leaves out LibreOffice, Calibre, 7-Zip and the local AI and needs roughly 2 to 3 GB (estimates; your real use depends on what you add). In the wizard you can also tick or untick every part yourself.

2. Which computers work

• Yes: Windows 10 and 11, 64-bit. macOS 11 or newer. Linux (Ubuntu, Debian, Fedora, Arch, openSUSE, Raspberry Pi OS 64-bit, Chromebook Linux, WSL).
• Should work, not tested by the author: every other Windows 10 or 11 build: LTSC, IoT and Server editions, modified or slimmed-down builds (Tiny10, Tiny11, AtlasOS, ReviOS and similar), and Windows on ARM (runs through Windows' own emulation, so slower). Chromebooks work once Linux is turned on in Settings.
• No, not natively: Windows 7, 8 and 8.1, any 32-bit system, and systems nobody has tested such as FreeBSD. The app needs 64-bit Windows 10 or newer, macOS or a mainstream Linux. These can still use Fathom Online in a browser, or open a Fathom running on another computer (section 5).
• Phones, tablets and everything else with a browser: use Fathom Online, or open a Fathom that runs on a computer you own (section 5).

You need an internet connection that stays on during setup, an account that can approve the administrator question (UAC) on Windows, and free space: Full about 12 GB, Lite about 3 GB. The wizard shows how much room each drive has and checks before it starts. Do not let the PC sleep while it installs.

3. Install on Windows

A. With the setup wizard (you choose what and where)

1. Download fathom.zip (or fathom-lite.zip) from the website. Right-click it > Extract All... > Extract. Do not run anything from inside the zip window.
2. Open the extracted fathom folder and double-click Fathom-Setup.vbs. If Windows shows a blue SmartScreen box (Fathom is not code-signed yet), click More info, then Run anyway. If nothing happens (some slimmed-down Windows builds have no script host), open the same folder, click in the address bar, type cmd, press Return, and type Fathom.bat setup: it opens the same wizard.
3. Welcome: choose Everything, Smallest (Lite) or Let me choose each part.
4. Where should Fathom go? Pick a folder for the Fathom app and a folder for its data (settings, chat history, saved results, Python packages). Any drive works; the window lists your drives and their free space. You can also keep the data in Windows' usual place.
5. Programs Fathom uses: tick the parts you want (Python is always needed). Then choose: keep them together in one folder, give each program its own folder, or let Windows put them in its usual places. The AI assistant's model, which is several GB, has its own folder too.
6. Shortcuts: a Desktop icon and a Start-menu entry, if you want them.
7. Ready to install: a summary of every choice and how much room each drive needs. Click Back to change anything, or Install.
8. Click Yes when Windows asks for permission. The Installing page shows the step it is on, a live log, and a line that says Please wait, this takes time with the time so far and an approximate time left (a rough guess that gets better as the steps finish). Fathom copies itself to the folders you chose, then installs Python, Windows parts, packages, the programs you ticked, models, a self-test and the shortcuts. Leave the PC on.
9. Fathom opens by itself when it is ready, and the wizard says Finished. Use the Fathom icon from now on.
10. Check the version: press ? (top right) and read the first line, for example Fathom 1.0.0 - running from folder ....

B. With the direct way (no questions)

1. Extract the zip as above.
2. Open the extracted fathom folder and double-click Fathom.bat (or right-click it > Run as administrator). Click Yes when Windows asks. SmartScreen: More info, Run anyway.
3. Wait with the black window open. Everything installs where you extracted it, with the programs in Windows' usual places. Fathom opens by itself when it is ready.

What is written where? With the wizard, exactly where you chose: the app in your app folder, the data in your data folder, and each program in its own folder. Windows keeps tiny folder links (a few KB) at the usual places for Python, LibreOffice, Calibre, 7-Zip and Ollama so every program still finds its files; the AI model is not linked, Ollama is told where it is with the OLLAMA_MODELS setting. Old copies are removed only after the new copy has been checked. With the direct way, everything stays in the folder you extracted plus Windows' normal program folders. Windows itself and its own installer records always stay on the drive Windows is on. To undo a choice and install right where the folder is, run Fathom.bat here. If an earlier setup had left a program in some other folder, the wizard moves it to the folder you choose now and only renames the old one to <name>.moved; delete that folder yourself when everything works.

How long does it take? Lite: roughly 10 to 25 minutes. Full: the programs take roughly 20 to 40 minutes, and the assistant's model (about 3.3 GB) is the long part: at 2.5 MB per second it is about 22 minutes, at 10 MB per second about 6 minutes. The model downloads only once and can continue if the connection drops (run Fathom.bat repair).

4. Updating Fathom

1. Let any running setup finish, or close its window.
2. Extract the new zip into a new folder. Do not extract over the old one.
3. Double-click the new Fathom-Setup.vbs (choose the same folders as before) or run the new Fathom.bat. It updates what is already installed. Your history, settings, chats and results are kept.
4. Prefer one click? Put the new zip in your Downloads folder and double-click support\4-Update-From-Zip.cmd inside your Fathom folder. It copies the new program files over the current ones and finishes the update.
5. Press ? and check the version. If it still shows the old number, you are starting an old folder: use the Desktop shortcut the setup just remade, or run the new Fathom.bat again.

5. Install on Mac, Linux, phone or tablet

• macOS: unzip, open Terminal, type bash (with a space), drag install.sh into the window, press Return. It asks whether to install LibreOffice and the free assistant and where to keep Fathom's data, then sets everything up. Next time double-click Fathom.command. If macOS says the file is from an unidentified developer: System Settings > Privacy & Security > Open Anyway. For no questions, run fathom.sh instead.
• Linux: unzip fathom.zip && cd fathom && bash install.sh (or ./fathom.sh for no questions). The installer detects apt, dnf, pacman or zypper for the optional extras and asks before using sudo. It adds a Fathom entry to your applications menu.
• Phone or tablet: Fathom runs on a computer and you open it from the phone. On the computer run Fathom.bat serve --https (Windows) or ./fathom.sh --serve --https, then open the private link it prints on the phone and choose Add to Home Screen. Anyone with that link can see the files Fathom can see, so treat it like a password.

6. Switching between Lite and Full later

• Lite to Full: run Fathom.bat full from the Fathom folder (as administrator), or run Fathom-Setup.vbs again and tick the parts you want. It installs the missing programs and the assistant.
• Full to Lite for a fresh install: use the Lite zip or untick the extras in the wizard. Programs that are already installed are left alone.
• Repair or update at any time: Fathom.bat repair (or support\8-Repair-Fathom.cmd). It never reinstalls what is already there.

7. If something goes wrong

• The window closes immediately or says it cannot find its files: you ran it from inside the zip. Extract first.
• Double-clicking Fathom-Setup.vbs does nothing: your Windows may have the script host switched off. Run Fathom.bat setup from a Command Prompt in the Fathom folder; it opens the same wizard. Or use the direct way (Fathom.bat).
• It still shows the old version: you started an old folder or an old shortcut. Run the new Fathom.bat once, then press ? to check.
• SmartScreen or antivirus complains: choose More info > Run anyway. The setup files are plain text you can read in Notepad. If your antivirus quarantines files, add the Fathom folders to its exclusions and run Fathom.bat repair.
• Not enough space on a drive you chose: the wizard warns you before it starts. Go Back and choose another drive, or untick some programs.
• A download failed or stalled: run Fathom.bat repair. Finished parts are not downloaded again.
• Windows Package Manager (winget) is missing: that is fine. Fathom downloads LibreOffice, Calibre, 7-Zip and Ollama directly from their makers and uses winget only as a second way.
• The Fathom window does not open on a slimmed-down Windows: if Windows has no web view component, Fathom opens in your normal browser instead.
• The assistant says the model was not found, or ollama list shows nothing: double-click Fix-Ollama.cmd in the Fathom folder. The usual cause is that Ollama's model folder sits behind a folder link (a Windows "junction"): Ollama 0.40 downloads the model but cannot read it through such a link, so it says "not found" or "bad manifest". Fathom's setup and Fix-Ollama.cmd detect this and point Ollama straight at the real folder with the OLLAMA_MODELS setting, which is the way Ollama documents it. No model or file of yours is deleted: only the small link itself is removed, and the models stay where they are. If Ollama still hides a model, setup tests with a tiny model, switches to another free model that works, and saves ollama-report.txt in the data folder.
• The Assistant is very slow to answer: the free assistant runs on your own graphics card. Fathom uses the fast qwen3-vl:4b-instruct model (the plain qwen3-vl:4b model is an always-thinking edition that spends minutes thinking before it answers), gives it more working memory (OLLAMA_CONTEXT_LENGTH, so Fathom's long instructions are not cut off), and loads it into the graphics card when Fathom starts. Fathom also reads its long instructions once in the background while it starts and keeps the model loaded for an hour, so the first question starts quickly; wait about three minutes after opening Fathom before your very first message. A message the first time can still take a few minutes on a modest card, and the window then says so: Please wait, this takes time with the time so far and an approximate time left. If it is still slow, update your graphics driver (Ollama's own log says when the AMD driver is too old). In Assistant > Settings the model name should read qwen3-vl:4b-instruct. A bigger graphics card or the qwen3-vl:8b-instruct model trades speed for quality; an online AI (Claude, OpenAI) is fastest of all.
• The assistant says it could not reach Ollama: Ollama is the free local AI and it must be running. Fathom takes care of it: it starts Ollama by itself when Fathom opens, hidden (no window, only its llama icon in the system tray, near the clock), and closes it again when you close Fathom. If it is ever stopped meanwhile, the assistant starts it by itself the moment you send a message. An Ollama you started yourself is left running when Fathom closes.
• The Talk button keeps saying "Understanding what you said": the first time, Fathom needs its speech model (about 480 MB). Setup now downloads it for you; if it was skipped, the first Talk downloads it once, which can take a few minutes on a slow connection. The window shows Please wait, this takes time with the time so far while it works. After that, Talk answers in a second or two.
• Anything slow says so: any action that takes more than a few seconds (conversions, searches, repairs, the assistant's first answer) shows a note at the top of the window: Please wait, this takes time, how long it has taken so far and an approximate time left. Jobs with a progress bar work the time left out from how far they are; other work uses how long the same action took before on this PC, and says "the time left is not known yet" when it cannot tell.
• Help scripts: the folder support inside the Fathom folder has double-click scripts that check Fathom, repair Ollama, scan for leftovers, download the fast model, time the AI, update Fathom from a new zip and repair the setup. README-SUPPORT.txt explains each one. Each .cmd only starts a .ps1 file you can read in Notepad. None of them deletes your files or models.
• Still stuck: run support\1-Check-Everything.cmd and send the text file it saves in Downloads. Or open the data folder (type %LOCALAPPDATA%\Fathom in the Explorer address bar) and look at setup.log and bat.log. In the app, ? > Save a problem report gathers them for you. The move to your chosen folders logs to Fathom-move.log in your Temp folder (type %TEMP% in the Explorer address bar).

8. Uninstall

1. Open the Fathom folder (the one with Fathom.bat) and double-click Uninstall-Fathom.cmd. Click Yes when Windows asks.
2. It asks two questions: delete Fathom's own data (settings, chat history, saved results, downloaded models), and also remove the programs Fathom installed (LibreOffice, Calibre, 7-Zip, Ollama and its AI model). Answer Y to both for a complete removal. Say N to the second if you use those programs for other things.
3. It closes Fathom, removes the shortcuts, the data and the programs you chose, wherever you put them (through their normal uninstallers first), and a few seconds after you close the window it deletes the Fathom folder itself. Your own files are never touched.
4. Python 3.12 is left in place because other programs may use it. Remove it in Settings > Apps if you want it gone.
5. Fathom does not add itself to Settings > Apps, so use Uninstall-Fathom.cmd (or delete the folders by hand, plus the Desktop and Start-menu shortcuts). On Mac and Linux delete the Fathom folder and the data folder (~/.fathom unless you chose another).

9. What was tested

Everything in the app was tested in a Linux test environment, including the search, converters, tools and the screens in a real browser. The setup wizard's pages, checks and the choices it writes were tested with a simulated window, and its scripts were checked for errors, but the wizard window itself, the folder moves, the Ollama install and the model download could not be run on a real Windows PC while this was written, and neither could the Mac and Linux installer scripts on a real Mac. So the first install on your PC is the real test. If a step fails, the logs above tell exactly where.

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