Matlab mcp failed to connect in terminal-in-matlab, but successfully connects outside Matlab in PowerShell or CMD

[aaortizb]

Description

I have shareMATLABSession() in startup.m. I open a terminal in matlab commnad window:

t = terminal()

In the terminal in matlab:

D:\NICETOOLS>claude mcp list

I get this:

claude.ai Google Drive: https://drivemcp.googleapis.com/mcp/v1 - ✔ Connected claude.ai Gmail: https://gmailmcp.googleapis.com/mcp/v1 - ✔ Connected claude.ai Google Calendar: https://calendarmcp.googleapis.com/mcp/v1 - ✔ Connected codebase-memory-mcp: C:/Users/Alejandro/.local/bin/codebase-memory-mcp.exe - ✔ Connected matlab: C:\Users\Alejandro\.matlab\agentic-toolkits\bin\matlab-mcp-server.exe --matlab-root=C:\Program Files\MATLAB\R2026a --initialize-matlab-on-startup=true --log-folder=C:\Users\Alejandro\matlab-mcp-server-logs - ✘ Failed to connect

Now, in a CMD terminal outside Matlab:

D:\NICETOOLS>claude mcp list

I get this:

claude.ai Google Drive: https://drivemcp.googleapis.com/mcp/v1 - √ Connected claude.ai Gmail: https://gmailmcp.googleapis.com/mcp/v1 - √ Connected claude.ai Google Calendar: https://calendarmcp.googleapis.com/mcp/v1 - √ Connected codebase-memory-mcp: C:/Users/Alejandro/.local/bin/codebase-memory-mcp.exe - √ Connected matlab: C:\Users\Alejandro\.matlab\agentic-toolkits\bin\matlab-mcp-server.exe --matlab-root=C:\Program Files\MATLAB\R2026a --initialize-matlab-on-startup=true --log-folder=C:\Users\Alejandro\matlab-mcp-server-logs - √ Connected

So, matlab mcp does not connect in the terminal inside Matlab, but successfully connects in a terminal outside Matlab. Why is this behavior?

[ybenouag]

Hello @aaortizb , thanks for raising this issue.

Is there any chance you could share the server logs of those two sessions so we can compare them and see if we can find any evidence of what failed in the terminal session ?

They should be located in the log folder you specified C:\Users\Alejandro\matlab-mcp-server-logs

Thanks a lot !
Yannis.

[aaortizb]

@ybenouag Unfortunately, I deleted the log file for those sessions while trying to fix the problem, but I created a new one. The finding is that only the logging from outside MATLAB is saved to the log file. The corresponding one to the session inside MATLAB is not saved to the log file. I attach the file.

server-2975106206.log

watchdog-2975106206.log

[ybenouag]

Could you grab the following, all from inside the MATLAB terminal?

1. The CLI error. Run claude mcp get matlab and claude --debug mcp list, and paste the output, the failing server's stderr should show up there and likely names the exact problem.

2. The environment. Compare our env vars inside vs. outside the terminal:

   • CMD: set MW_MCP_SERVER_
   • PowerShell: Get-ChildItem Env:MW_MCP_SERVER_*

3. Two quick questions:

   • Did you ever run t = terminal(Agentic=true) (the first-run wizard), or only t = terminal()?
   • Does it still fail with a fresh t = terminal() if you remove shareMATLABSession() from startup.m?

[aaortizb]

@ybenouag
Re: 1)
claude mcp get matlab:

matlab:
Scope: User config (available in all your projects)
Status: ✘ Failed to connect
Issue: -32000: MCP error -32000: Connection closed
Type: stdio
Command: C:\Users\Alejandro\.matlab\agentic-toolkits\bin\matlab-mcp-server.exe        
Args: --matlab-root=C:\Program Files\MATLAB\R2026a --initialize-matlab-on-startup=true
--log-folder=C:\Users\Alejandro\matlab-mcp-server-logs
Environment:

To remove this server, run: claude mcp remove matlab -s user

claude --debug mcp list: this actually opens a claude session, so instead of this, I had to do the following inside the claude session:

`/debug mcp list`:
 Searched for 1 pattern, ran 1 shell command 

● Found two distinct issues in the debug log:

  1. matlab MCP server failed to connect
  Error with supplied arguments: option "matlab-root" is not compatible with MATLAB session mode set to "existing".
  The server was launched with both --matlab-root and a session mode of "existing" (i.e., attach to an already-running MATLAB), which are   
  mutually exclusive. Connection closed immediately (-32000).

  2. codebase-memory skill file has broken YAML frontmatter
  Failed to parse YAML frontmatter in C:\Users\Alejandro\.claude\skills\codebase-memory\SKILL.md: YAML Parse error: Unexpected token        
  This means the skill's frontmatter is ignored — it likely still loads as a skill but without proper metadata (name/description used for   
  matching).

  Only codebase-memory-mcp connected successfully (0.9.0, stdio, 317ms) — that's why only that MCP server appears in your currently loaded  
  tools, not matlab.

  Let me check the MCP config to find the fix for the matlab server.

  Searched for 3 patterns, read 1 file, ran 2 shell commands 

● Now I see the full picture.

  Root cause of matlab MCP failing:
   
  C:\Users\Alejandro\.matlab\agentic-toolkits\config.json has "sessionMode": "auto" (line 19). In "auto" mode, the server detects an        
  already-running MATLAB instance and attaches to it (session mode resolves to "existing"). But the launch args baked into .claude.json     
  (both the global and project-scoped matlab MCP entries, lines 1102-1111 and 1223-1232) still pass --matlab-root=C:\Program 
  Files\MATLAB\R2026a. That flag is only valid when starting a new MATLAB process — it conflicts with attaching to an existing session, so  
  the server exits immediately with:
 
  Error with supplied arguments: option "matlab-root" is not compatible with MATLAB session mode set to "existing".
   
  Fix — pick one:
  1. If you want it to always attach to an already-running MATLAB, remove --matlab-root=... from the args array in both matlab MCP entries  
  in .claude.json.
  2. If you want the server to launch its own MATLAB (using that root), close any running MATLAB first, or change sessionMode in config.json
  from "auto" to "new".

  Since you have MATLAB R2026a and presumably want a specific root pinned, option 2 (set sessionMode: "new") is likely cleaner — but if you 
  routinely already have MATLAB open and want to reuse it, option 1 is simpler. Want me to apply one of these edits?

  Secondary issue (unrelated): C:\Users\Alejandro\.claude\skills\codebase-memory\SKILL.md has malformed YAML frontmatter, so its
  description/trigger metadata is being dropped — the skill loads but Claude Code can't use its frontmatter to decide when to invoke it.    
  Want me to look at that file and fix the YAML?

BOTTOM LINE: I didn't perform any of the solutions listed above yet.

Re: 2)
INSIDE: set MW_MCP_SERVER_ :

MW_MCP_SERVER_MATLAB_SESSION_CONNECTION_DETAILS={"port":31516,"apiKey":"vv7FpXXSgbRbgMgG","certificate":"C:\\Users\\Alejandro\\AppData\\Roam
ing\\MathWorks\\MATLAB\\R2026a\\thisMatlab.pem"}

OUTSIDE: set MW_MCP_SERVER_ :
Environment variable MW_MCP_SERVER_ not defined

Re: 3)

• I didn't try t = terminal(Agentic=true) because I installed the Agentic Toolkit, so I just do t = terminal().
• By removing shareMATLABSession() from the startup.m, the issue still persists.

[ybenouag]

Hello @aaortizb

Thanks a lot for trying all the steps I mentioned and running some analysis.

I can see that we got a clear error message and some proposed fixes.

Error with supplied arguments: option "matlab-root" is not compatible with MATLAB session mode set to "existing".

Fix — pick one:

1. If you want it to always attach to an already-running MATLAB, remove --matlab-root=... from the args array in both matlab MCP entries
   in .claude.json.
2. If you want the server to launch its own MATLAB (using that root), close any running MATLAB first, or change sessionMode in config.json
   from "auto" to "new".

Since you have MATLAB R2026a and presumably want a specific root pinned, option 2 (set sessionMode: "new") is likely cleaner — but if you
routinely already have MATLAB open and want to reuse it, option 1 is simpler. Want me to apply one of these edits?

Those are correct and I was wondering if you tried any of those ? That should be enough to have the MATLAB MCP Server string inside the Terminal in MATLAB.

Thanks a lot !

Yannis.