Claude Code failed to connect Serena in Idea CE 2025.2 but works in VS Code

[holywen]

I've checked another issue and tried with
MCP_TIMEOUT=60000 but it's not working, the MCP server is not started at all (no browser window open)

Steps to reproduce:

1. Idea CE 2025.2, installed claude extention
2. claude mcp add serena -- uvx --from git+https://github.com/oraios/serena serena start-mcp-server --context ide-assistant --project $(pwd)
3. in Idea, click the Claude icon, and /mcp to check the status, and it says failed. no further log can be found. (where can I find the startup logs for a mcp server in claude? I was not able to find this information)

But I tried to open the same project in VS Code and it works (VS Code 1.104.1 + claude plugin), the MCP server was started successfully, and browser was activated and logs shown.
OS: Ubuntu 24.04

[MischaPanch]

Can you try starting with claude --debug from your Terminal within intellij instead? It's the same functionality as using the button, but gives better logs

[holywen]

holywen@dellxps15:~/IdeaProjects/acm-express$ claude --debug
[DEBUG] Watching for changes in setting files /home/holywen/IdeaProjects/acm-express/.claude/settings.local.json...
[DEBUG] Writing to temp file: /home/holywen/.claude.json.tmp.19248.1758515689918
[DEBUG] Preserving file permissions: 100664
[DEBUG] Temp file written successfully, size: 53886 bytes
[DEBUG] Applied original permissions to temp file
[DEBUG] Renaming /home/holywen/.claude.json.tmp.19248.1758515689918 to /home/holywen/.claude.json
[DEBUG] File /home/holywen/.claude.json written atomically
[DEBUG] Applying permission update: Adding 56 allow rule(s) to destination 'localSettings': ["Bash(mkdir:)","Bash(sudo apt:)","Bash(sudo apt install:)","Bash(php:)","Bash(curl:)","Read(//tmp/**)","Bash(composer install:)","Bash(sudo systemctl start:)","Bash(sudo systemctl status:)","Bash(redis-cli:)","Bash(time curl:)","Bash(/dev/null)","Bash(xargs:)","Bash(while read key)","Bash(done)","Bash(sudo systemctl enable:)","Bash(sudo:)","Read(//etc/php/8.3/mods-available/**)","Bash(cat:)","Read(//usr/lib/php/20230831/)","Bash(psql:)","Bash(lsof:)","Read(//var/log/)","Bash(scp:)","Bash(ssh:)","Bash(git add:)","Bash(ping:)","Bash(chmod:)","Bash(./deploy-to-server.sh:)","Read(//home/holywen/Pictures/Screenshots/**)","Bash(git commit:)","Bash(git push:)","mcp__playwright__browser_fill_form","mcp__playwright__browser_click","mcp__playwright__browser_snapshot","mcp__playwright__browser_select_option","mcp__playwright__browser_close","mcp__playwright__browser_navigate","mcp__playwright__browser_type","mcp__playwright__browser_wait_for","mcp__playwright__browser_evaluate","mcp__playwright__browser_take_screenshot","mcp__playwright__browser_console_messages","mcp__playwright__browser_handle_dialog","Bash(pkill:*)","Bash(export PGPASSWORD=acm_pass)","Bash(export PGPASSWORD=postgres)","mcp__sequential-thinking__sequentialthinking","mcp__serena__find_symbol","mcp__serena__find_referencing_symbols","mcp__serena__search_for_pattern","mcp__serena__activate_project","mcp__serena__list_dir","mcp__serena__find_file","mcp__serena__read_file","mcp__serena__get_symbols_overview"]
[DEBUG] Creating shell snapshot for bash (/bin/bash)
[DEBUG] Creating snapshot at: /home/holywen/.claude/shell-snapshots/snapshot-bash-1758515690042-idrt5l.sh
[DEBUG] Writing to temp file: /home/holywen/.claude/todos/fbf704f4-2668-4204-bd13-aace782ccbbf-agent-fbf704f4-2668-4204-bd13-aace782ccbbf.json.tmp.19248.1758515690049
[DEBUG] Temp file written successfully, size: 2 bytes
[DEBUG] Renaming /home/holywen/.claude/todos/fbf704f4-2668-4204-bd13-aace782ccbbf-agent-fbf704f4-2668-4204-bd13-aace782ccbbf.json.tmp.19248.1758515690049 to /home/holywen/.claude/todos/fbf704f4-2668-4204-bd13-aace782ccbbf-agent-fbf704f4-2668-4204-bd13-aace782ccbbf.json
[DEBUG] File /home/holywen/.claude/todos/fbf704f4-2668-4204-bd13-aace782ccbbf-agent-fbf704f4-2668-4204-bd13-aace782ccbbf.json written atomically
[DEBUG] Writing to temp file: /home/holywen/.claude.json.tmp.19248.1758515690060
[DEBUG] Preserving file permissions: 100664
[DEBUG] Temp file written successfully, size: 53478 bytes
[DEBUG] Applied original permissions to temp file
[DEBUG] Renaming /home/holywen/.claude.json.tmp.19248.1758515690060 to /home/holywen/.claude.json
[DEBUG] File /home/holywen/.claude.json written atomically
[DEBUG] Found 0 plugins (0 enabled, 0 disabled) from 0 repositories and 0 npm packages
[DEBUG] Registered 0 hooks from 0 plugins
[DEBUG] Ripgrep first use test: PASSED (mode=builtin, path=/usr/lib/node_modules/@anthropic-ai/claude-code/vendor/ripgrep/x64-linux/rg)
[DEBUG] Total plugin commands loaded: 0
[DEBUG] Shell snapshot created successfully (1814 bytes)

[DEBUG] MCP server "sequential-thinking": Starting connection with timeout of 60000ms
[DEBUG] MCP server "context7": Starting connection with timeout of 60000ms
[DEBUG] MCP server "magic": Starting connection with timeout of 60000ms
[DEBUG] Writing to temp file: /home/holywen/.claude.json.tmp.19248.1758515690298
[DEBUG] Preserving file permissions: 100664
[DEBUG] Temp file written successfully, size: 53478 bytes
[DEBUG] Applied original permissions to temp file
[DEBUG] Renaming /home/holywen/.claude.json.tmp.19248.1758515690298 to /home/holywen/.claude.json
[DEBUG] File /home/holywen/.claude.json written atomically
[DEBUG] Executing hooks for SessionStart:startup
[DEBUG] Getting matching hook commands for SessionStart with query: startup
[DEBUG] Found 0 hook matchers in settings
[DEBUG] Matched 0 unique hooks for query "startup" (0 before deduplication)
[DEBUG] Found 0 hook commands to execute

[DEBUG] AutoUpdaterWrapper: Installation type: unknown, using native: false
[DEBUG] Writing to temp file: /home/holywen/.claude.json.tmp.19248.1758515690672
[DEBUG] Preserving file permissions: 100664
[DEBUG] Temp file written successfully, size: 53478 bytes
[DEBUG] Applied original permissions to temp file
[DEBUG] Renaming /home/holywen/.claude.json.tmp.19248.1758515690672 to /home/holywen/.claude.json
[DEBUG] File /home/holywen/.claude.json written atomically

[DEBUG] MCP server "sequential-thinking": Successfully connected to stdio server in 1182ms
[DEBUG] MCP server "sequential-thinking": Connection established with capabilities: {"hasTools":true,"hasPrompts":false,"hasResources":false,"serverVersion":{"name":"sequential-thinking-server","version":"0.2.0"}}
[DEBUG] MCP server "magic": Successfully connected to stdio server in 1320ms
[DEBUG] MCP server "magic": Connection established with capabilities: {"hasTools":true,"hasPrompts":false,"hasResources":false,"serverVersion":{"name":"21st-magic","version":"0.0.46"}}

[DEBUG] MCP server "context7": Successfully connected to stdio server in 1411ms
[DEBUG] MCP server "context7": Connection established with capabilities: {"hasTools":true,"hasPrompts":false,"hasResources":false,"serverVersion":{"name":"Context7","version":"1.0.17"}}
[DEBUG] MCP server "playwright": Starting connection with timeout of 60000ms
[DEBUG] MCP server "morphllm-fast-apply": Starting connection with timeout of 60000ms
[DEBUG] MCP server "filesystem": Starting connection with timeout of 60000ms

[DEBUG] MCP server "filesystem": Successfully connected to stdio server in 987ms
[DEBUG] MCP server "filesystem": Connection established with capabilities: {"hasTools":true,"hasPrompts":false,"hasResources":false,"serverVersion":{"name":"secure-filesystem-server","version":"0.2.0"}}
[DEBUG] MCP server "filesystem": Received ListRoots request from server

───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

 Try "edit packages.html to..."
───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
[DEBUG] MCP server "morphllm-fast-apply": Successfully connected to stdio server in 1256ms
[DEBUG] MCP server "morphllm-fast-apply": Connection established with capabilities: {"hasTools":true,"hasPrompts":false,"hasResources":false,"serverVersion":{"name":"secure-filesystem-server","version":"0.2.0"}}
[DEBUG] MCP server "morphllm-fast-apply": Received ListRoots request from server

───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
[DEBUG] MCP server "playwright": Successfully connected to stdio server in 1318ms
[DEBUG] MCP server "playwright": Connection established with capabilities: {"hasTools":true,"hasPrompts":false,"hasResources":false,"serverVersion":{"name":"Playwright","version":"0.0.39"}}
[DEBUG] MCP server "fetch": Starting connection with timeout of 60000ms
[DEBUG] MCP server "serena": Starting connection with timeout of 60000ms
[DEBUG] MCP server "ide": Starting connection with timeout of 60000ms
[DEBUG] MCP server "ide": Successfully connected to ws-ide server in 50ms
[DEBUG] MCP server "ide": Connection established with capabilities: {"hasTools":true,"hasPrompts":false,"hasResources":false,"serverVersion":{"name":"Claude Code JetBrains Plugin","version":"0.1.11-beta"}}

───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

 Try "edit packages.html to..."
───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
? for shortcuts ◯
Debug mode
[ERROR] MCP server "fetch" Server stderr: Server started with options: respect-robots-txt
[ERROR] MCP server "fetch" Server stderr: Failed to scan existing downloads: Error: ENOENT: no such file or directory, scandir '/home/holywen/Downloads/mcp-fetch'
at async Object.readdir (node:internal/fs/promises:957:18)
at async scanAndRegisterExistingFiles (file:///home/holywen/.npm/_npx/e5ec6e1360b435a5/node_modules/@kazuph/mcp-fetch/dist/index.js:40:26)
[DEBUG] MCP server "fetch": Successfully connected to stdio server in 1662ms
[DEBUG] MCP server "fetch": Connection established with capabilities: {"hasTools":true,"hasPrompts":false,"hasResources":true,"serverVersion":{"name":"mcp-fetch","version":"1.4.2"}}
[DEBUG] MCP server "serena": Connection failed after 2077ms: MCP error -32000: Connection closed

[MischaPanch]

Claude should save dedicated logs for Serena as well. Unfortunately, from just the logs above I can't see what the problem is, just that it didn't start.

Pls run the health check and the manual startup of the server. If they work, the only sources of errors can be in CC's MCP config or in some side effects due to many MCP Servers being present. Maybe you need a global path to uvx or something like that.

Manual startup:

uvx --from git+https://github.com/oraios/serena serena start-mcp-server --context ide-assistant --project $(pwd)

Health check

uvx --from git+https://github.com/oraios/serena project health-check

both from the project dir

[opcode81]

Do Serena's logs (~/.serena/logs) indicate normal startup?

[holywen]

The Manual startup works, from both Terminal out of Idea or in the Terminal of Idea. It does bring up the browser window now.

For the second command, the output is:

holywen@dellxps15:~/IdeaProjects/acm-express$ uvx --from git+https://github.com/oraios/serena project health-check
An executable named `project` is not provided by package `serena-agent`.
The following executables are available:
- index-project
- serena
- serena-mcp-server

[holywen]

~/.serna/logs showed some error:

holywen@dellxps15:~/.serena/logs/2025-09-24$ cat mcp_20250924-065221.txt 
INFO  2025-09-24 06:52:21,341 [MainThread] serena.cli:start_mcp_server:172 - Initializing Serena MCP server
INFO  2025-09-24 06:52:21,342 [MainThread] serena.cli:start_mcp_server:173 - Storing logs in /home/holywen/.serena/logs/2025-09-24/mcp_20250924-065221.txt
INFO  2025-09-24 06:52:21,343 [MainThread] serena.config.serena_config:from_config_file:413 - Loading Serena configuration from /home/holywen/.serena/serena_config.yml
INFO  2025-09-24 06:52:21,360 [MainThread] serena.agent:__init__:195 - Serena web dashboard started at http://127.0.0.1:24282/dashboard/index.html
ERROR 2025-09-24 06:52:21,360 [MainThread] serena.agent:show_fatal_exception_safe:49 - Fatal exception: [Errno 9] Bad file descriptor
Traceback (most recent call last):
  File "/home/holywen/.cache/uv/archive-v0/8uVc2rJl77PD_3XRZSfNQ/lib/python3.12/site-packages/serena/mcp.py", line 288, in create_mcp_server
    self._instantiate_agent(config, modes_instances)
  File "/home/holywen/.cache/uv/archive-v0/8uVc2rJl77PD_3XRZSfNQ/lib/python3.12/site-packages/serena/mcp.py", line 330, in _instantiate_agent
    self.agent = SerenaAgent(
                 ^^^^^^^^^^^^
  File "/home/holywen/.cache/uv/archive-v0/8uVc2rJl77PD_3XRZSfNQ/lib/python3.12/site-packages/serena/agent.py", line 200, in __init__
    process.start()
  File "/usr/lib/python3.12/multiprocessing/process.py", line 121, in start
    self._popen = self._Popen(self)
                  ^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/multiprocessing/context.py", line 224, in _Popen
    return _default_context.get_context().Process._Popen(process_obj)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/multiprocessing/context.py", line 282, in _Popen
    return Popen(process_obj)
           ^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/multiprocessing/popen_fork.py", line 16, in __init__
    util._flush_std_streams()
  File "/usr/lib/python3.12/multiprocessing/util.py", line 442, in _flush_std_streams
    sys.stderr.flush()
OSError: [Errno 9] Bad file descriptor

[MischaPanch]

Serena may not work with python 3.12, you should use 3.11

[MischaPanch]

In fact, we have specified requires-python = ">=3.11, <3.12" but unfortunately uvx --from ignores that

[MischaPanch]

For the second command, the output is:

Sry, my bad, missed a serena. The correct command is

uvx --from git+https://github.com/oraios/serena serena project health-check

[holywen]

Health check failed:

holywen@dellxps15:~/IdeaProjects/acm-express$ uvx --from git+https://github.com/oraios/serena serena project health-check
INFO  2025-09-24 07:09:20,712 serena.util.file_system:start:329 - Loading of .gitignore files starting ...
INFO  2025-09-24 07:09:20,713 serena.util.file_system:_load_gitignore_files:148 - Processing .gitignore file: /home/holywen/IdeaProjects/acm-express/.gitignore
INFO  2025-09-24 07:09:20,719 serena.util.file_system:_load_gitignore_files:148 - Processing .gitignore file: /home/holywen/IdeaProjects/acm-express/.serena/.gitignore
INFO  2025-09-24 07:09:20,722 serena.util.file_system:stop:336 - Loading of .gitignore files completed in 0.009 seconds
INFO  2025-09-24 07:09:20,722 sensai.util.logging:add_file_logger:161 - Logging to /home/holywen/IdeaProjects/acm-express/.serena/logs/health-checks/health_check_20250924-070920.log ...
INFO  2025-09-24 07:09:20,723 serena.cli:health_check:557 - Starting health check for project: /home/holywen/IdeaProjects/acm-express
INFO  2025-09-24 07:09:20,723 serena.cli:health_check:561 - Creating SerenaAgent with disabled dashboard...
INFO  2025-09-24 07:09:20,739 serena.agent:__init__:204 - Starting Serena server (version=0.1.4-ca5fad09-dirty, process id=38668, parent process id=38599)
INFO  2025-09-24 07:09:20,739 serena.agent:__init__:205 - Configuration file: None
INFO  2025-09-24 07:09:20,739 serena.agent:__init__:206 - Available projects: 
INFO  2025-09-24 07:09:20,739 serena.agent:__init__:207 - Loaded tools (36): read_file, create_text_file, list_dir, find_file, replace_regex, delete_lines, replace_lines, insert_at_line, search_for_pattern, restart_language_server, get_symbols_overview, find_symbol, find_referencing_symbols, replace_symbol_body, insert_after_symbol, insert_before_symbol, write_memory, read_memory, list_memories, delete_memory, execute_shell_command, activate_project, remove_project, switch_modes, get_current_config, check_onboarding_performed, onboarding, think_about_collected_information, think_about_task_adherence, think_about_whether_you_are_done, summarize_changes, prepare_for_new_conversation, initial_instructions, jet_brains_find_symbol, jet_brains_find_referencing_symbols, jet_brains_get_symbols_overview
INFO  2025-09-24 07:09:20,739 serena.config.serena_config:apply:106 - SerenaAgentContext[name='desktop-app'] included 1 tools: switch_modes
INFO  2025-09-24 07:09:20,741 serena.agent:__init__:221 - Number of exposed tools: 26
INFO  2025-09-24 07:09:20,763 serena.agent:_update_active_tools:401 - Active tools (26): activate_project, check_onboarding_performed, create_text_file, delete_memory, execute_shell_command, find_file, find_referencing_symbols, find_symbol, get_current_config, get_symbols_overview, insert_after_symbol, insert_before_symbol, list_dir, list_memories, onboarding, prepare_for_new_conversation, read_file, read_memory, replace_regex, replace_symbol_body, search_for_pattern, switch_modes, think_about_collected_information, think_about_task_adherence, think_about_whether_you_are_done, write_memory
INFO  2025-09-24 07:09:20,767 serena.util.file_system:start:329 - Loading of .gitignore files starting ...
INFO  2025-09-24 07:09:20,767 serena.util.file_system:_load_gitignore_files:148 - Processing .gitignore file: /home/holywen/IdeaProjects/acm-express/.gitignore
INFO  2025-09-24 07:09:20,769 serena.util.file_system:_load_gitignore_files:148 - Processing .gitignore file: /home/holywen/IdeaProjects/acm-express/.serena/.gitignore
INFO  2025-09-24 07:09:20,772 serena.util.file_system:stop:336 - Loading of .gitignore files completed in 0.005 seconds
INFO  2025-09-24 07:09:20,773 serena.agent:load_project_from_path_or_name:476 - Added new project acm-express for path /home/holywen/IdeaProjects/acm-express
INFO  2025-09-24 07:09:20,773 serena.agent:_activate_project:441 - Activating acm-express at /home/holywen/IdeaProjects/acm-express
INFO  2025-09-24 07:09:20,773 serena.agent:_update_active_tools:401 - Active tools (26): activate_project, check_onboarding_performed, create_text_file, delete_memory, execute_shell_command, find_file, find_referencing_symbols, find_symbol, get_current_config, get_symbols_overview, insert_after_symbol, insert_before_symbol, list_dir, list_memories, onboarding, prepare_for_new_conversation, read_file, read_memory, replace_regex, replace_symbol_body, search_for_pattern, switch_modes, think_about_collected_information, think_about_task_adherence, think_about_whether_you_are_done, write_memory
INFO  2025-09-24 07:09:20,773 serena.agent:issue_task:420 - Scheduling Task-1[init_language_server]
INFO  2025-09-24 07:09:20,774 serena.agent:start:329 - Task-1[init_language_server] starting ...
INFO  2025-09-24 07:09:20,774 serena.cli:health_check:564 - SerenaAgent created successfully
INFO  2025-09-24 07:09:20,774 serena.agent:start:329 - Language server initialization starting ...
INFO  2025-09-24 07:09:20,774 serena.cli:health_check:567 - Searching for analyzable files...
INFO  2025-09-24 07:09:20,774 serena.project:create_language_server:303 - Creating language server instance for /home/holywen/IdeaProjects/acm-express.
INFO  2025-09-24 07:09:20,804 serena.cli:health_check:576 - Found analyzable file: config/wechat.php
INFO  2025-09-24 07:09:20,804 serena.cli:health_check:594 - Testing GetSymbolsOverviewTool on file: config/wechat.php
INFO  2025-09-24 07:09:20,805 serena.agent:issue_task:420 - Scheduling Task-2[<lambda>]
INFO  2025-09-24 07:09:20,889 solidlsp:load_cache:1576 - Loading document symbols cache from /home/holywen/IdeaProjects/acm-express/.serena/cache/php/document_symbols_cache_v23-06-25.pkl
INFO  2025-09-24 07:09:20,908 solidlsp:load_cache:1580 - Loaded 56 document symbols from cache.
INFO  2025-09-24 07:09:20,910 serena.agent:reset_language_server:594 - Starting the language server for acm-express
INFO  2025-09-24 07:09:20,910 solidlsp:start:1622 - Starting language server with language php for /home/holywen/IdeaProjects/acm-express
INFO  2025-09-24 07:09:20,911 solidlsp:_start_server:163 - Starting Intelephense server process
INFO  2025-09-24 07:09:20,911 solidlsp.ls_handler:start:189 - Starting language server process via command: /home/holywen/.serena/language_servers/static/Intelephense/php-lsp/node_modules/.bin/intelephense --stdio
INFO  2025-09-24 07:09:20,936 solidlsp:_start_server:167 - Sending initialize request from LSP client to LSP server and awaiting response
INFO  2025-09-24 07:09:21,491 solidlsp:window_log_message:153 - LSP: window/logMessage: {"type": 3, "message": "Initialising intelephense 1.14.4"}
INFO  2025-09-24 07:09:21,498 solidlsp:window_log_message:153 - LSP: window/logMessage: {"type": 3, "message": "Reading state from /tmp/intelephense/55ab1a8d."}
INFO  2025-09-24 07:09:21,845 solidlsp:window_log_message:153 - LSP: window/logMessage: {"type": 3, "message": "Initialised in 356 ms"}
INFO  2025-09-24 07:09:21,846 solidlsp:_start_server:172 - After sent initialize params
INFO  2025-09-24 07:09:21,846 serena.agent:stop:336 - Language server initialization completed in 1.072 seconds
INFO  2025-09-24 07:09:21,846 serena.agent:stop:336 - Task-1[init_language_server] completed in 1.073 seconds
INFO  2025-09-24 07:09:21,846 serena.agent:start:329 - Task-2[<lambda>] starting ...
INFO  2025-09-24 07:09:21,848 serena.agent:stop:336 - Task-2[<lambda>] completed in 0.002 seconds
INFO  2025-09-24 07:09:21,848 serena.cli:health_check:597 - GetSymbolsOverviewTool returned 0 symbols
ERROR 2025-09-24 07:09:21,848 serena.cli:health_check:600 - No symbols found in file config/wechat.php
❌ Health check failed: No symbols found in target file
Log saved to: /home/holywen/IdeaProjects/acm-express/.serena/logs/health-checks/health_check_20250924-070920.log
Log saved to: /home/holywen/IdeaProjects/acm-express/.serena/logs/health-checks/health_check_20250924-070920.log

[holywen]

In fact, we have specified requires-python = ">=3.11, <3.12" but unfortunately uvx --from ignores that

Switched to 3.11 and still get the same error:

holywen@dellxps15:~/.serena/logs/2025-09-24$ cat mcp_20250924-071745.txt 
INFO  2025-09-24 07:17:45,475 [MainThread] serena.cli:start_mcp_server:172 - Initializing Serena MCP server
INFO  2025-09-24 07:17:45,475 [MainThread] serena.cli:start_mcp_server:173 - Storing logs in /home/holywen/.serena/logs/2025-09-24/mcp_20250924-071745.txt
INFO  2025-09-24 07:17:45,477 [MainThread] serena.config.serena_config:from_config_file:413 - Loading Serena configuration from /home/holywen/.serena/serena_config.yml
INFO  2025-09-24 07:17:45,494 [MainThread] serena.agent:__init__:195 - Serena web dashboard started at http://127.0.0.1:24282/dashboard/index.html
ERROR 2025-09-24 07:17:45,494 [MainThread] serena.agent:show_fatal_exception_safe:49 - Fatal exception: [Errno 9] Bad file descriptor
Traceback (most recent call last):
  File "/home/holywen/.cache/uv/archive-v0/EJivxv3mJ5f00RZqIv0Zv/lib/python3.11/site-packages/serena/mcp.py", line 288, in create_mcp_server
    self._instantiate_agent(config, modes_instances)
  File "/home/holywen/.cache/uv/archive-v0/EJivxv3mJ5f00RZqIv0Zv/lib/python3.11/site-packages/serena/mcp.py", line 330, in _instantiate_agent
    self.agent = SerenaAgent(
                 ^^^^^^^^^^^^
  File "/home/holywen/.cache/uv/archive-v0/EJivxv3mJ5f00RZqIv0Zv/lib/python3.11/site-packages/serena/agent.py", line 200, in __init__
    process.start()
  File "/usr/lib/python3.11/multiprocessing/process.py", line 121, in start
    self._popen = self._Popen(self)
                  ^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.11/multiprocessing/context.py", line 224, in _Popen
    return _default_context.get_context().Process._Popen(process_obj)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.11/multiprocessing/context.py", line 281, in _Popen
    return Popen(process_obj)
           ^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.11/multiprocessing/popen_fork.py", line 16, in __init__
    util._flush_std_streams()
  File "/usr/lib/python3.11/multiprocessing/util.py", line 442, in _flush_std_streams
    sys.stderr.flush()
OSError: [Errno 9] Bad file descriptor

[holywen]

I tried disable the WebUI , and now in the .serna/logs file, there is no error, but still not able to connect to the MCP server.

Here is the latest startup log, it looks like the server has started successfully:

holywen@dellxps15:~/.serena/logs/2025-09-27$ cat mcp_20250927-081543.txt 
INFO  2025-09-27 08:15:43,178 [MainThread] serena.cli:start_mcp_server:172 - Initializing Serena MCP server
INFO  2025-09-27 08:15:43,178 [MainThread] serena.cli:start_mcp_server:173 - Storing logs in /home/holywen/.serena/logs/2025-09-27/mcp_20250927-081543.txt
INFO  2025-09-27 08:15:43,181 [MainThread] serena.config.serena_config:from_config_file:413 - Loading Serena configuration from /home/holywen/.serena/serena_config.yml
INFO  2025-09-27 08:15:43,205 [MainThread] serena.agent:__init__:204 - Starting Serena server (version=0.1.4-56b15680-dirty, process id=15530, parent process id=15472)
INFO  2025-09-27 08:15:43,205 [MainThread] serena.agent:__init__:205 - Configuration file: /home/holywen/.serena/serena_config.yml
INFO  2025-09-27 08:15:43,205 [MainThread] serena.agent:__init__:206 - Available projects: acm-express
INFO  2025-09-27 08:15:43,205 [MainThread] serena.agent:__init__:207 - Loaded tools (36): read_file, create_text_file, list_dir, find_file, replace_regex, delete_lines, replace_lines, insert_at_line, search_for_pattern, restart_language_server, get_symbols_overview, find_symbol, find_referencing_symbols, replace_symbol_body, insert_after_symbol, insert_before_symbol, write_memory, read_memory, list_memories, delete_memory, execute_shell_command, activate_project, remove_project, switch_modes, get_current_config, check_onboarding_performed, onboarding, think_about_collected_information, think_about_task_adherence, think_about_whether_you_are_done, summarize_changes, prepare_for_new_conversation, initial_instructions, jet_brains_find_symbol, jet_brains_find_referencing_symbols, jet_brains_get_symbols_overview
INFO  2025-09-27 08:15:43,205 [MainThread] serena.config.serena_config:start:329 - Loading project instance for RegisteredProject[project_root=/home/holywen/IdeaProjects/acm-express, project_config=ProjectConfig[project_name='acm-express']] starting ...
INFO  2025-09-27 08:15:43,206 [MainThread] serena.util.file_system:start:329 - Loading of .gitignore files starting ...
INFO  2025-09-27 08:15:43,206 [MainThread] serena.util.file_system:_load_gitignore_files:148 - Processing .gitignore file: /home/holywen/IdeaProjects/acm-express/.gitignore
INFO  2025-09-27 08:15:43,212 [MainThread] serena.util.file_system:_load_gitignore_files:148 - Processing .gitignore file: /home/holywen/IdeaProjects/acm-express/.serena/.gitignore
INFO  2025-09-27 08:15:43,215 [MainThread] serena.util.file_system:stop:336 - Loading of .gitignore files completed in 0.009 seconds
INFO  2025-09-27 08:15:43,215 [MainThread] serena.config.serena_config:stop:336 - Loading project instance for RegisteredProject[project_root=/home/holywen/IdeaProjects/acm-express, project_config=ProjectConfig[project_name='acm-express']] completed in 0.010 seconds
INFO  2025-09-27 08:15:43,215 [MainThread] serena.agent:load_project_from_path_or_name:473 - Found registered project 'acm-express' at path /home/holywen/IdeaProjects/acm-express
INFO  2025-09-27 08:15:43,216 [MainThread] serena.config.serena_config:apply:108 - SerenaAgentContext[name='ide-assistant'] excluded 5 tools: create_text_file, read_file, execute_shell_command, prepare_for_new_conversation, replace_regex
INFO  2025-09-27 08:15:43,216 [MainThread] serena.config.serena_config:apply:108 - ToolInclusionDefinition(excluded_tools=['activate_project', 'get_current_config'], included_optional_tools=()) excluded 2 tools: activate_project, get_current_config
INFO  2025-09-27 08:15:43,217 [MainThread] serena.agent:__init__:221 - Number of exposed tools: 18
INFO  2025-09-27 08:15:43,232 [MainThread] serena.agent:_update_active_tools:401 - Active tools (18): check_onboarding_performed, delete_memory, find_file, find_referencing_symbols, find_symbol, get_symbols_overview, insert_after_symbol, insert_before_symbol, list_dir, list_memories, onboarding, read_memory, replace_symbol_body, search_for_pattern, think_about_collected_information, think_about_task_adherence, think_about_whether_you_are_done, write_memory
INFO  2025-09-27 08:15:43,232 [MainThread] serena.agent:load_project_from_path_or_name:473 - Found registered project 'acm-express' at path /home/holywen/IdeaProjects/acm-express
INFO  2025-09-27 08:15:43,232 [MainThread] serena.agent:_activate_project:441 - Activating acm-express at /home/holywen/IdeaProjects/acm-express
INFO  2025-09-27 08:15:43,233 [MainThread] serena.agent:_update_active_tools:401 - Active tools (18): check_onboarding_performed, delete_memory, find_file, find_referencing_symbols, find_symbol, get_symbols_overview, insert_after_symbol, insert_before_symbol, list_dir, list_memories, onboarding, read_memory, replace_symbol_body, search_for_pattern, think_about_collected_information, think_about_task_adherence, think_about_whether_you_are_done, write_memory
INFO  2025-09-27 08:15:43,233 [MainThread] serena.agent:issue_task:420 - Scheduling Task-1[init_language_server]
INFO  2025-09-27 08:15:43,234 [SerenaAgentExecutor_0] serena.agent:start:329 - Task-1[init_language_server] starting ...
INFO  2025-09-27 08:15:43,234 [MainThread] serena.agent:create_system_prompt:373 - Generating system prompt with available_tools=(see exposed tools), available_markers={'InsertBeforeSymbolTool', 'ToolMarkerSymbolicEdit', 'FindReferencingSymbolsTool', 'FindSymbolTool', 'ReplaceSymbolBodyTool', 'ToolMarkerSymbolicRead', 'GetSymbolsOverviewTool', 'ToolMarkerCanEdit', 'InsertAfterSymbolTool'}
INFO  2025-09-27 08:15:43,234 [SerenaAgentExecutor_0] serena.agent:start:329 - Language server initialization starting ...
INFO  2025-09-27 08:15:43,237 [MainThread] serena.agent:create_system_prompt:380 - System prompt:
You are a professional coding agent concerned with one particular codebase. You have 
access to semantic coding tools on which you rely heavily for all your work, as well as collection of memory 
files containing general information about the codebase. You operate in a resource-efficient and intelligent manner, always
keeping in mind to not read or generate content that is not needed for the task at hand.

When reading code in order to answer a user question or task, you should try reading only the necessary code. 
Some tasks may require you to understand the architecture of large parts of the codebase, while for others,
it may be enough to read a small set of symbols or a single file.
Generally, you should avoid reading entire files unless it is absolutely necessary, instead relying on
intelligent step-by-step acquisition of information. However, if you already read a file, it does not make
sense to further analyse it with the symbolic tools (except for the `find_referencing_symbols` tool), 
as you already have the information.

I WILL BE SERIOUSLY UPSET IF YOU READ ENTIRE FILES WITHOUT NEED!

CONSIDER INSTEAD USING THE OVERVIEW TOOL AND SYMBOLIC TOOLS TO READ ONLY THE NECESSARY CODE FIRST!
I WILL BE EVEN MORE UPSET IF AFTER HAVING READ AN ENTIRE FILE YOU KEEP READING THE SAME CONTENT WITH THE SYMBOLIC TOOLS!
THE PURPOSE OF THE SYMBOLIC TOOLS IS TO HAVE TO READ LESS CODE, NOT READ THE SAME CONTENT MULTIPLE TIMES!


You can achieve the intelligent reading of code by using the symbolic tools for getting an overview of symbols and
the relations between them, and then only reading the bodies of symbols that are necessary to answer the question 
or complete the task. 
You can use the standard tools like list_dir, find_file and search_for_pattern if you need to.
When tools allow it, you pass the `relative_path` parameter to restrict the search to a specific file or directory.
For some tools, `relative_path` can only be a file path, so make sure to properly read the tool descriptions.

If you are unsure about a symbol's name or location (to the extent that substring_matching for the symbol name is not enough), you can use the `search_for_pattern` tool, which allows fast
and flexible search for patterns in the codebase.This way you can first find candidates for symbols or files,
and then proceed with the symbolic tools.



Symbols are identified by their `name_path and `relative_path`, see the description of the `find_symbol` tool for more details
on how the `name_path` matches symbols.
You can get information about available symbols by using the `get_symbols_overview` tool for finding top-level symbols in a file,
or by using `find_symbol` if you already know the symbol's name path. You generally try to read as little code as possible
while still solving your task, meaning you only read the bodies when you need to, and after you have found the symbol you want to edit.
For example, if you are working with python code and already know that you need to read the body of the constructor of the class Foo, you can directly
use `find_symbol` with the name path `Foo/__init__` and `include_body=True`. If you don't know yet which methods in `Foo` you need to read or edit,
you can use `find_symbol` with the name path `Foo`, `include_body=False` and `depth=1` to get all (top-level) methods of `Foo` before proceeding
to read the desired methods with `include_body=True`
You can understand relationships between symbols by using the `find_referencing_symbols` tool.



You generally have access to memories and it may be useful for you to read them, but also only if they help you
to answer the question or complete the task. You can infer which memories are relevant to the current task by reading
the memory names and descriptions.


The context and modes of operation are described below. From them you can infer how to interact with your user
and which tasks and kinds of interactions are expected of you.

Context description:
You are running in IDE assistant context where file operations, basic (line-based) edits and reads, 
and shell commands are handled by your own, internal tools.
The initial instructions and the current config inform you on which tools are available to you,
and how to use them.
Don't attempt to use any excluded tools, instead rely on your own internal tools
for achieving the basic file or shell operations.

If serena's tools can be used for achieving your task, 
you should prioritize them. In particular, it is important that you avoid reading entire source code files,
unless it is strictly necessary! Instead, for exploring and reading code in a token-efficient manner, 
you should use serena's overview and symbolic search tools. 
Before reading a full file, it is usually best to first explore the file using the symbol_overview tool, 
and then make targeted reads using find_symbol and other symbolic tools.
For non-code files or for reads where you don't know the symbol's name path, you can use the pattern searching tool,
and read full files only as a last resort.

Modes descriptions:

- You are operating in interactive mode. You should engage with the user throughout the task, asking for clarification
whenever anything is unclear, insufficiently specified, or ambiguous.

Break down complex tasks into smaller steps and explain your thinking at each stage. When you're uncertain about
a decision, present options to the user and ask for guidance rather than making assumptions.

Focus on providing informative results for intermediate steps so the user can follow along with your progress and
provide feedback as needed.

- You are operating in editing mode. You can edit files with the provided tools
to implement the requested changes to the code base while adhering to the project's code style and patterns.
Use symbolic editing tools whenever possible for precise code modifications.
If no editing task has yet been provided, wait for the user to provide one.

When writing new code, think about where it belongs best. Don't generate new files if you don't plan on actually
integrating them into the codebase, instead use the editing tools to insert the code directly into the existing files in that case.

You have two main approaches for editing code - editing by regex and editing by symbol.
The symbol-based approach is appropriate if you need to adjust an entire symbol, e.g. a method, a class, a function, etc.
But it is not appropriate if you need to adjust just a few lines of code within a symbol, for that you should
use the regex-based approach that is described below.

Let us first discuss the symbol-based approach.
Symbols are identified by their name path and relative file path, see the description of the `find_symbol` tool for more details
on how the `name_path` matches symbols.
You can get information about available symbols by using the `get_symbols_overview` tool for finding top-level symbols in a file,
or by using `find_symbol` if you already know the symbol's name path. You generally try to read as little code as possible
while still solving your task, meaning you only read the bodies when you need to, and after you have found the symbol you want to edit.
Before calling symbolic reading tools, you should have a basic understanding of the repository structure that you can get from memories
or by using the `list_dir` and `find_file` tools (or similar).
For example, if you are working with python code and already know that you need to read the body of the constructor of the class Foo, you can directly
use `find_symbol` with the name path `Foo/__init__` and `include_body=True`. If you don't know yet which methods in `Foo` you need to read or edit,
you can use `find_symbol` with the name path `Foo`, `include_body=False` and `depth=1` to get all (top-level) methods of `Foo` before proceeding
to read the desired methods with `include_body=True`.
In particular, keep in mind the description of the `replace_symbol_body` tool. If you want to add some new code at the end of the file, you should
use the `insert_after_symbol` tool with the last top-level symbol in the file. If you want to add an import, often a good strategy is to use
`insert_before_symbol` with the first top-level symbol in the file.
You can understand relationships between symbols by using the `find_referencing_symbols` tool. If not explicitly requested otherwise by a user,
you make sure that when you edit a symbol, it is either done in a backward-compatible way, or you find and adjust the references as needed.
The `find_referencing_symbols` tool will give you code snippets around the references, as well as symbolic information.
You will generally be able to use the info from the snippets and the regex-based approach to adjust the references as well.
You can assume that all symbol editing tools are reliable, so you don't need to verify the results if the tool returns without error.



INFO  2025-09-27 08:15:43,238 [SerenaAgentExecutor_0] serena.project:create_language_server:303 - Creating language server instance for /home/holywen/IdeaProjects/acm-express.
INFO  2025-09-27 08:15:43,240 [MainThread] serena.cli:start_mcp_server:191 - Starting MCP server …
INFO  2025-09-27 08:15:43,282 [MainThread] serena.mcp:_set_mcp_tools:240 - Starting MCP server with 18 tools: ['list_dir', 'find_file', 'search_for_pattern', 'get_symbols_overview', 'find_symbol', 'find_referencing_symbols', 'replace_symbol_body', 'insert_after_symbol', 'insert_before_symbol', 'write_memory', 'read_memory', 'list_memories', 'delete_memory', 'check_onboarding_performed', 'onboarding', 'think_about_collected_information', 'think_about_task_adherence', 'think_about_whether_you_are_done']
INFO  2025-09-27 08:15:43,282 [MainThread] serena.mcp:server_lifespan:347 - MCP server lifetime setup complete
INFO  2025-09-27 08:15:43,380 [SerenaAgentExecutor_0] solidlsp:load_cache:1576 - Loading document symbols cache from /home/holywen/IdeaProjects/acm-express/.serena/cache/php/document_symbols_cache_v23-06-25.pkl
INFO  2025-09-27 08:15:43,414 [SerenaAgentExecutor_0] solidlsp:load_cache:1580 - Loaded 108 document symbols from cache.
INFO  2025-09-27 08:15:43,416 [SerenaAgentExecutor_0] serena.agent:reset_language_server:594 - Starting the language server for acm-express
INFO  2025-09-27 08:15:43,417 [SerenaAgentExecutor_0] solidlsp:start:1622 - Starting language server with language php for /home/holywen/IdeaProjects/acm-express
INFO  2025-09-27 08:15:43,417 [SerenaAgentExecutor_0] solidlsp:_start_server:163 - Starting Intelephense server process
INFO  2025-09-27 08:15:43,418 [SerenaAgentExecutor_0] solidlsp.ls_handler:start:189 - Starting language server process via command: /home/holywen/.serena/language_servers/static/Intelephense/php-lsp/node_modules/.bin/intelephense --stdio
INFO  2025-09-27 08:15:43,441 [SerenaAgentExecutor_0] solidlsp:_start_server:167 - Sending initialize request from LSP client to LSP server and awaiting response
INFO  2025-09-27 08:15:44,064 [LSP-stdout-reader] solidlsp:window_log_message:153 - LSP: window/logMessage: {"type": 3, "message": "Initialising intelephense 1.14.4"}
INFO  2025-09-27 08:15:44,068 [LSP-stdout-reader] solidlsp:window_log_message:153 - LSP: window/logMessage: {"type": 3, "message": "Reading state from /tmp/intelephense/55ab1a8d."}
INFO  2025-09-27 08:15:44,078 [LSP-stdout-reader] solidlsp:window_log_message:153 - LSP: window/logMessage: {"type": 3, "message": "Initialised in 15 ms"}
INFO  2025-09-27 08:15:44,079 [SerenaAgentExecutor_0] solidlsp:_start_server:172 - After sent initialize params
INFO  2025-09-27 08:15:44,079 [SerenaAgentExecutor_0] serena.agent:stop:336 - Language server initialization completed in 0.845 seconds
INFO  2025-09-27 08:15:44,079 [SerenaAgentExecutor_0] serena.agent:stop:336 - Task-1[init_language_server] completed in 0.846 seconds
holywen@dellxps15:~/.serena/logs/2025-09-27$ 

[MischaPanch]

Yes, everything looks good in the logs and we can't reproduce this. Sorry, I don't know what causes this