Clangd hidden C++ module state?

[rdong8]

I'm working on a project that uses C++20 modules and everything was going smoothly until I started getting undefined identifier errors for symbols defined in imported modules. I tried clearing .cache/ and build/ and re-configuring and building, and also stripped out almost everything from the project until it was just a main file and a simple module exporting one function and was still getting these errors. But after copying the code over to another directory and reconfiguring and building the project, clangd was able to pick up all modules just fine. Additionally, the errors went away after disabling and then re-enabling the clangd extension. Is there some state that clangd stores outside of the source directory that could be causing issues?

src/main.cpp:

import mod;

auto main() -> int
{
    foo();
}

src/foo.cppm:

export module mod;

export auto foo() -> void
{
}

CMakeLists.txt:

cmake_minimum_required(VERSION 4.2 FATAL_ERROR)

set(CMAKE_COLOR_DIAGNOSTICS ON)
set(CMAKE_CXX_STANDARD 26)
set(CMAKE_CXX_EXTENSIONS OFF)
set(CMAKE_CXX_SCAN_FOR_MODULES ON)
set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
set_property(GLOBAL PROPERTY USE_FOLDERS ON)

project(example
    LANGUAGES CXX
)

add_library(mod)
target_sources(mod
    PUBLIC FILE_SET CXX_MODULES FILES
        src/mod.cppm
)

add_executable(main)
target_sources(main
    PUBLIC
        src/main.cpp
)
target_link_libraries(main
    PRIVATE
        mod
)

Commands:

cmake -B build/ -S . -G "Ninja Multi-Config" -DCMAKE_CXX_COMPILER=clang++-21
cmake --build build/

Logs
Please attach the clangd log from the "Output" window if you can.
If possible, run with --log=verbose - note that the logs will include the contents of open files!

Logs

V[15:59:33.486] <<< {"id":14,"jsonrpc":"2.0","method":"shutdown"}

I[15:59:33.486] <-- shutdown(14)
I[15:59:33.486] --> reply:shutdown(14) 0 ms
V[15:59:33.486] >>> {"id":14,"jsonrpc":"2.0","result":null}

V[15:59:33.548] <<< {"jsonrpc":"2.0","method":"exit"}

I[15:59:33.549] <-- exit
I[15:59:33.549] LSP finished, exiting with status 0
I[15:59:33.555] clangd version 21.1.8 (https://github.com/llvm/llvm-project 2078da43e25a4623cab2d0d60decddf709aaea28)
I[15:59:33.555] Features: linux+grpc
I[15:59:33.555] PID: 41281
I[15:59:33.555] Working directory: /u4/rydong/cs444/cs-444-compiler
I[15:59:33.555] argv[0]: /u4/rydong/.vscode-server/data/User/globalStorage/llvm-vs-code-extensions.vscode-clangd/install/21.1.8/clangd_21.1.8/bin/clangd
I[15:59:33.555] argv[1]: --experimental-modules-support
I[15:59:33.555] argv[2]: --log=verbose
V[15:59:33.555] User config file is /u4/rydong/.config/clangd/config.yaml
I[15:59:33.555] Starting LSP over stdin/stdout
V[15:59:33.556] <<< {"id":0,"jsonrpc":"2.0","method":"initialize","params":{"capabilities":{"general":{"markdown":{"parser":"marked","version":"1.1.0"},"positionEncodings":["utf-16"],"regularExpressions":{"engine":"ECMAScript","version":"ES2020"},"staleRequestSupport":{"cancel":true,"retryOnContentModified":["textDocument/semanticTokens/full","textDocument/semanticTokens/range","textDocument/semanticTokens/full/delta"]}},"notebookDocument":{"synchronization":{"dynamicRegistration":true,"executionSummarySupport":true}},"textDocument":{"callHierarchy":{"dynamicRegistration":true},"codeAction":{"codeActionLiteralSupport":{"codeActionKind":{"valueSet":["","quickfix","refactor","refactor.extract","refactor.inline","refactor.rewrite","source","source.organizeImports"]}},"dataSupport":true,"disabledSupport":true,"dynamicRegistration":true,"honorsChangeAnnotations":true,"isPreferredSupport":true,"resolveSupport":{"properties":["edit"]}},"codeLens":{"dynamicRegistration":true},"colorProvider":{"dynamicRegistration":true},"completion":{"completionItem":{"commitCharactersSupport":true,"deprecatedSupport":true,"documentationFormat":["markdown","plaintext"],"insertReplaceSupport":true,"insertTextModeSupport":{"valueSet":[1,2]},"labelDetailsSupport":true,"preselectSupport":true,"resolveSupport":{"properties":["documentation","detail","additionalTextEdits"]},"snippetSupport":true,"tagSupport":{"valueSet":[1]}},"completionItemKind":{"valueSet":[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25]},"completionList":{"itemDefaults":["commitCharacters","editRange","insertTextFormat","insertTextMode","data"]},"contextSupport":true,"dynamicRegistration":true,"editsNearCursor":true,"insertTextMode":2},"declaration":{"dynamicRegistration":true,"linkSupport":true},"definition":{"dynamicRegistration":true,"linkSupport":true},"diagnostic":{"dynamicRegistration":true,"relatedDocumentSupport":false},"documentHighlight":{"dynamicRegistration":true},"documentLink":{"dynamicRegistration":true,"tooltipSupport":true},"documentSymbol":{"dynamicRegistration":true,"hierarchicalDocumentSymbolSupport":true,"labelSupport":true,"symbolKind":{"valueSet":[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26]},"tagSupport":{"valueSet":[1]}},"foldingRange":{"dynamicRegistration":true,"foldingRange":{"collapsedText":false},"foldingRangeKind":{"valueSet":["comment","imports","region"]},"lineFoldingOnly":true,"rangeLimit":5000},"formatting":{"dynamicRegistration":true},"hover":{"contentFormat":["markdown","plaintext"],"dynamicRegistration":true},"implementation":{"dynamicRegistration":true,"linkSupport":true},"inactiveRegionsCapabilities":{"inactiveRegions":true},"inlayHint":{"dynamicRegistration":true,"resolveSupport":{"properties":["tooltip","textEdits","label.tooltip","label.location","label.command"]}},"inlineValue":{"dynamicRegistration":true},"linkedEditingRange":{"dynamicRegistration":true},"onTypeFormatting":{"dynamicRegistration":true},"publishDiagnostics":{"codeDescriptionSupport":true,"dataSupport":true,"relatedInformation":true,"tagSupport":{"valueSet":[1,2]},"versionSupport":false},"rangeFormatting":{"dynamicRegistration":true,"rangesSupport":true},"references":{"dynamicRegistration":true},"rename":{"dynamicRegistration":true,"honorsChangeAnnotations":true,"prepareSupport":true,"prepareSupportDefaultBehavior":1},"selectionRange":{"dynamicRegistration":true},"semanticTokens":{"augmentsSyntaxTokens":true,"dynamicRegistration":true,"formats":["relative"],"multilineTokenSupport":false,"overlappingTokenSupport":false,"requests":{"full":{"delta":true},"range":true},"serverCancelSupport":true,"tokenModifiers":["declaration","definition","readonly","static","deprecated","abstract","async","modification","documentation","defaultLibrary"],"tokenTypes":["namespace","type","class","enum","interface","struct","typeParameter","parameter","variable","property","enumMember","event","function","method","macro","keyword","modifier","comment","string","number","regexp","operator","decorator"]},"signatureHelp":{"contextSupport":true,"dynamicRegistration":true,"signatureInformation":{"activeParameterSupport":true,"documentationFormat":["markdown","plaintext"],"parameterInformation":{"labelOffsetSupport":true}}},"synchronization":{"didSave":true,"dynamicRegistration":true,"willSave":true,"willSaveWaitUntil":true},"typeDefinition":{"dynamicRegistration":true,"linkSupport":true},"typeHierarchy":{"dynamicRegistration":true}},"window":{"showDocument":{"support":true},"showMessage":{"messageActionItem":{"additionalPropertiesSupport":true}},"workDoneProgress":true},"workspace":{"applyEdit":true,"codeLens":{"refreshSupport":true},"configuration":true,"diagnostics":{"refreshSupport":true},"didChangeConfiguration":{"dynamicRegistration":true},"didChangeWatchedFiles":{"dynamicRegistration":true,"relativePatternSupport":true},"executeCommand":{"dynamicRegistration":true},"fileOperations":{"didCreate":true,"didDelete":true,"didRename":true,"dynamicRegistration":true,"willCreate":true,"willDelete":true,"willRename":true},"foldingRange":{"refreshSupport":true},"inlayHint":{"refreshSupport":true},"inlineValue":{"refreshSupport":true},"semanticTokens":{"refreshSupport":true},"symbol":{"dynamicRegistration":true,"resolveSupport":{"properties":["location.range"]},"symbolKind":{"valueSet":[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26]},"tagSupport":{"valueSet":[1]}},"workspaceEdit":{"changeAnnotationSupport":{"groupsOnLabel":true},"documentChanges":true,"failureHandling":"textOnlyTransactional","normalizesLineEndings":true,"resourceOperations":["create","rename","delete"]},"workspaceFolders":true}},"clientInfo":{"name":"Visual Studio Code","version":"1.108.2"},"initializationOptions":{"clangdFileStatus":true,"fallbackFlags":[]},"locale":"en","processId":36295,"rootPath":"/u4/rydong/cs444/cs-444-compiler","rootUri":"file:///u4/rydong/cs444/cs-444-compiler","trace":"off","workspaceFolders":[{"name":"cs-444-compiler","uri":"file:///u4/rydong/cs444/cs-444-compiler"}]}}

I[15:59:33.556] <-- initialize(0)
I[15:59:33.569] --> reply:initialize(0) 12 ms
V[15:59:33.569] >>> {"id":0,"jsonrpc":"2.0","result":{"capabilities":{"astProvider":true,"callHierarchyProvider":true,"clangdInlayHintsProvider":true,"codeActionProvider":{"codeActionKinds":["quickfix","refactor","info"]},"compilationDatabase":{"automaticReload":true},"completionProvider":{"resolveProvider":false,"triggerCharacters":[".","<",">",":","\"","/","*"]},"declarationProvider":true,"definitionProvider":true,"documentFormattingProvider":true,"documentHighlightProvider":true,"documentLinkProvider":{"resolveProvider":false},"documentOnTypeFormattingProvider":{"firstTriggerCharacter":"\n","moreTriggerCharacter":[]},"documentRangeFormattingProvider":{"rangesSupport":true},"documentSymbolProvider":true,"executeCommandProvider":{"commands":["clangd.applyFix","clangd.applyRename","clangd.applyTweak"]},"foldingRangeProvider":true,"hoverProvider":true,"implementationProvider":true,"inactiveRegionsProvider":true,"inlayHintProvider":true,"memoryUsageProvider":true,"positionEncoding":"utf-16","referencesProvider":true,"renameProvider":{"prepareProvider":true},"selectionRangeProvider":true,"semanticTokensProvider":{"full":{"delta":true},"legend":{"tokenModifiers":["declaration","definition","deprecated","deduced","readonly","static","abstract","virtual","dependentName","defaultLibrary","usedAsMutableReference","usedAsMutablePointer","constructorOrDestructor","userDefined","functionScope","classScope","fileScope","globalScope"],"tokenTypes":["variable","variable","parameter","function","method","function","property","variable","class","interface","enum","enumMember","type","type","unknown","namespace","typeParameter","concept","type","macro","modifier","operator","bracket","label","comment"]},"range":false},"signatureHelpProvider":{"triggerCharacters":["(",")","{","}","<",">",","]},"standardTypeHierarchyProvider":true,"textDocumentSync":{"change":2,"openClose":true,"save":true},"typeDefinitionProvider":true,"typeHierarchyProvider":true,"workspaceSymbolProvider":true},"offsetEncoding":"utf-16","serverInfo":{"name":"clangd","version":"clangd version 21.1.8 (https://github.com/llvm/llvm-project 2078da43e25a4623cab2d0d60decddf709aaea28) linux+grpc x86_64-unknown-linux-gnu"}}}

V[15:59:33.571] <<< {"jsonrpc":"2.0","method":"initialized","params":{}}

I[15:59:33.571] <-- initialized
V[15:59:33.573] <<< {"jsonrpc":"2.0","method":"textDocument/didOpen","params":{"textDocument":{"languageId":"cpp","text":"import mod;\n\nauto main() -> int\n{\n    foo();\n}\n","uri":"file:///u4/rydong/cs444/cs-444-compiler/src/main.cpp","version":374}}}

I[15:59:33.573] <-- textDocument/didOpen
I[15:59:33.576] Loaded compilation database from /u4/rydong/cs444/cs-444-compiler/build/compile_commands.json
V[15:59:33.576] Broadcasting compilation database from /u4/rydong/cs444/cs-444-compiler
I[15:59:33.577] --> window/workDoneProgress/create(0)
V[15:59:33.577] >>> {"id":0,"jsonrpc":"2.0","method":"window/workDoneProgress/create","params":{"token":"backgroundIndexProgress"}}

I[15:59:33.577] Enqueueing 2 commands for indexing
V[15:59:33.577] <<< {"id":0,"jsonrpc":"2.0","result":null}

I[15:59:33.577] <-- reply(0)
I[15:59:33.577] --> $/progress
I[15:59:33.577] ASTWorker building file /u4/rydong/cs444/cs-444-compiler/src/main.cpp version 374 with command 
[/u4/rydong/cs444/cs-444-compiler/build]
/usr/lib/llvm-21/bin/clang++-21 --driver-mode=g++ "-DCMAKE_INTDIR=\"Debug\"" -g -std=c++26 -fcolor-diagnostics -gmodules -fmodule-file=mod=CMakeFiles/mod.dir/Debug/mod.pcm -o CMakeFiles/main.dir/Debug/src/main.cpp.o -c -resource-dir=/u4/rydong/.vscode-server/data/User/globalStorage/llvm-vs-code-extensions.vscode-clangd/install/21.1.8/clangd_21.1.8/lib/clang/21 -- /u4/rydong/cs444/cs-444-compiler/src/main.cpp
V[15:59:33.577] >>> {"jsonrpc":"2.0","method":"$/progress","params":{"token":"backgroundIndexProgress","value":{"kind":"begin","percentage":0,"title":"indexing"}}}

I[15:59:33.577] --> $/progress
V[15:59:33.577] >>> {"jsonrpc":"2.0","method":"$/progress","params":{"token":"backgroundIndexProgress","value":{"kind":"report","message":"0/1","percentage":0}}}

V[15:59:33.578] BackgroundIndex: building version 1 after loading index from disk
V[15:59:33.578] BackgroundIndex: serving version 1 (13140 bytes)
I[15:59:33.579] --> $/progress
V[15:59:33.579] >>> {"jsonrpc":"2.0","method":"$/progress","params":{"token":"backgroundIndexProgress","value":{"kind":"report","message":"0/1","percentage":0}}}

I[15:59:33.579] --> $/progress
V[15:59:33.579] >>> {"jsonrpc":"2.0","method":"$/progress","params":{"token":"backgroundIndexProgress","value":{"kind":"end"}}}

V[15:59:33.580] Ignored diagnostic. argument unused during compilation: '-c'
V[15:59:33.582] Driver produced command: cc1 -cc1 -triple x86_64-unknown-linux-gnu -fsyntax-only -disable-free -clear-ast-before-backend -disable-llvm-verifier -discard-value-names -main-file-name main.cpp -mrelocation-model pic -pic-level 2 -pic-is-pie -mframe-pointer=all -fmath-errno -ffp-contract=on -fno-rounding-math -mconstructor-aliases -funwind-tables=2 -target-cpu x86-64 -tune-cpu generic -dwarf-ext-refs -fmodule-format=obj -debug-info-kind=constructor -dwarf-version=5 -debugger-tuning=gdb -fdebug-compilation-dir=/u4/rydong/cs444/cs-444-compiler/build -fcoverage-compilation-dir=/u4/rydong/cs444/cs-444-compiler/build -resource-dir /u4/rydong/.vscode-server/data/User/globalStorage/llvm-vs-code-extensions.vscode-clangd/install/21.1.8/clangd_21.1.8/lib/clang/21 -D "CMAKE_INTDIR=\"Debug\"" -internal-isystem /usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14 -internal-isystem /usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/x86_64-linux-gnu/c++/14 -internal-isystem /usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/backward -internal-isystem /u4/rydong/.vscode-server/data/User/globalStorage/llvm-vs-code-extensions.vscode-clangd/install/21.1.8/clangd_21.1.8/lib/clang/21/include -internal-isystem /usr/local/include -internal-isystem /usr/lib/gcc/x86_64-linux-gnu/14/../../../../x86_64-linux-gnu/include -internal-externc-isystem /usr/include/x86_64-linux-gnu -internal-externc-isystem /include -internal-externc-isystem /usr/include -std=c++26 -fdeprecated-macro -ferror-limit 19 -fgnuc-version=4.2.1 -fno-implicit-modules -fmodule-file=mod=CMakeFiles/mod.dir/Debug/mod.pcm -fskip-odr-check-in-gmf -fcxx-exceptions -fexceptions -no-round-trip-args -faddrsig -D__GCC_HAVE_DWARF2_CFI_ASM=1 -x c++ /u4/rydong/cs444/cs-444-compiler/src/main.cpp
I[15:59:33.582] --> textDocument/clangd.fileStatus
V[15:59:33.582] >>> {"jsonrpc":"2.0","method":"textDocument/clangd.fileStatus","params":{"state":"parsing includes, running Update","uri":"file:///u4/rydong/cs444/cs-444-compiler/src/main.cpp"}}

V[15:59:33.582] Building first preamble for /u4/rydong/cs444/cs-444-compiler/src/main.cpp version 374
[Error - 3:59:33 PM] Server process exited with code 0.
I[15:59:33.597] Built preamble of size 253732 for file /u4/rydong/cs444/cs-444-compiler/src/main.cpp version 374 in 0.01 seconds
V[15:59:33.620] Ignored diagnostic. argument unused during compilation: '-c'
V[15:59:33.626] Ignored diagnostic. unable to open output file '/tmp/clangd/module_files/mod.cppm17647138007654665420-40-7b-fb-88-73-34/mod.pcm': 'Permission denied'
V[15:59:33.626] Failed to compile /u4/rydong/cs444/cs-444-compiler/src/mod.cppm with command: /usr/lib/llvm-21/bin/clang++-21 --driver-mode=g++ -DCMAKE_INTDIR="Debug" -g -std=c++26 -fcolor-diagnostics -gmodules -x c++-module -fmodule-output=CMakeFiles/mod.dir/Debug/mod.pcm -o CMakeFiles/mod.dir/Debug/src/mod.cppm.o -c -resource-dir=/u4/rydong/.vscode-server/data/User/globalStorage/llvm-vs-code-extensions.vscode-clangd/install/21.1.8/clangd_21.1.8/lib/clang/21 -- /u4/rydong/cs444/cs-444-compiler/src/mod.cppm.
E[15:59:33.626] Failed to build module mod; due to Failed to compile /u4/rydong/cs444/cs-444-compiler/src/mod.cppm. Use '--log=verbose' to view detailed failure reasons.
I[15:59:33.626] Built prerequisite modules for file /u4/rydong/cs444/cs-444-compiler/src/main.cpp in 0.03 seconds
I[15:59:33.627] --> workspace/semanticTokens/refresh(1)
V[15:59:33.627] >>> {"id":1,"jsonrpc":"2.0","method":"workspace/semanticTokens/refresh","params":null}

V[15:59:33.627] indexed preamble AST for /u4/rydong/cs444/cs-444-compiler/src/main.cpp version 374:
  symbol slab: 0 symbols, 120 bytes
  ref slab: 0 symbols, 0 refs, 128 bytes
  relations slab: 0 relations, 24 bytes
V[15:59:33.627] <<< {"id":1,"jsonrpc":"2.0","result":null}

I[15:59:33.627] <-- reply(1)
I[15:59:33.630] Indexing c++23 standard library in the context of /u4/rydong/cs444/cs-444-compiler/src/main.cpp
V[15:59:33.644] Trying to fix unresolved name "foo" in scopes: []
V[15:59:33.645] Dex query tree: false
V[15:59:33.647] indexed file AST for /u4/rydong/cs444/cs-444-compiler/src/main.cpp version 374:
  symbol slab: 1 symbols, 4448 bytes
  ref slab: 1 symbols, 1 refs, 4248 bytes
  relations slab: 0 relations, 24 bytes
V[15:59:33.647] Build dynamic index for main-file symbols with estimated memory usage of 11520 bytes
I[15:59:33.647] --> textDocument/publishDiagnostics
V[15:59:33.647] >>> {"jsonrpc":"2.0","method":"textDocument/publishDiagnostics","params":{"diagnostics":[{"code":"ast_file_different_branch","message":"Module file 'CMakeFiles/mod.dir/Debug/mod.pcm' built from a different branch ((++20251221032922+2078da43e25a-1~exp1~20251221153059.70)) than the compiler ((https://github.com/llvm/llvm-project 2078da43e25a4623cab2d0d60decddf709aaea28))","range":{"end":{"character":6,"line":0},"start":{"character":0,"line":0}},"relatedInformation":[],"severity":1,"source":"clang"},{"code":"undeclared_var_use","message":"Use of undeclared identifier 'foo'","range":{"end":{"character":7,"line":4},"start":{"character":4,"line":4}},"relatedInformation":[],"severity":1,"source":"clang"}],"uri":"file:///u4/rydong/cs444/cs-444-compiler/src/main.cpp","version":374}}

I[15:59:33.647] --> textDocument/inactiveRegions
V[15:59:33.647] >>> {"jsonrpc":"2.0","method":"textDocument/inactiveRegions","params":{"regions":[],"textDocument":{"uri":"file:///u4/rydong/cs444/cs-444-compiler/src/main.cpp"}}}

I[15:59:33.648] --> textDocument/clangd.fileStatus
V[15:59:33.648] >>> {"jsonrpc":"2.0","method":"textDocument/clangd.fileStatus","params":{"state":"idle","uri":"file:///u4/rydong/cs444/cs-444-compiler/src/main.cpp"}}

V[15:59:35.091] Ignored diagnostic. /usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/backward/backward_warning.h:32:2:This file includes at least one deprecated or antiquated header which   may be removed without further notice at a future date. Please use a   non-deprecated interface with equivalent functionality instead. For a   listing of replacement headers and interfaces, consult the file   backward_warning.h. To disable this warning use -Wno-deprecated.
V[15:59:35.650] indexed preamble AST for /u4/rydong/cs444/cs-444-compiler/src/main.cpp version :
  symbol slab: 29695 symbols, 9330576 bytes
  ref slab: 0 symbols, 0 refs, 128 bytes
  relations slab: 710 relations, 17432 bytes
I[15:59:35.689] Indexed c++23 standard library: 17387 symbols, 12308 filtered
V[15:59:35.726] Build dynamic index for header symbols with estimated memory usage of 10226076 bytes
V[15:59:41.786] <<< {"id":1,"jsonrpc":"2.0","method":"textDocument/codeAction","params":{"context":{"diagnostics":[{"code":"ast_file_different_branch","message":"Module file 'CMakeFiles/mod.dir/Debug/mod.pcm' built from a different branch ((++20251221032922+2078da43e25a-1~exp1~20251221153059.70)) than the compiler ((https://github.com/llvm/llvm-project 2078da43e25a4623cab2d0d60decddf709aaea28))","range":{"end":{"character":6,"line":0},"start":{"character":0,"line":0}},"relatedInformation":[],"severity":1,"source":"clang"}],"triggerKind":2},"range":{"end":{"character":0,"line":0},"start":{"character":0,"line":0}},"textDocument":{"uri":"file:///u4/rydong/cs444/cs-444-compiler/src/main.cpp"}}}

I[15:59:41.786] <-- textDocument/codeAction(1)
V[15:59:41.786] <<< {"id":2,"jsonrpc":"2.0","method":"textDocument/documentSymbol","params":{"textDocument":{"uri":"file:///u4/rydong/cs444/cs-444-compiler/src/main.cpp"}}}

I[15:59:41.786] <-- textDocument/documentSymbol(2)
V[15:59:41.786] ASTWorker running codeAction on version 374 of /u4/rydong/cs444/cs-444-compiler/src/main.cpp
I[15:59:41.787] --> reply:textDocument/codeAction(1) 0 ms
V[15:59:41.787] >>> {"id":1,"jsonrpc":"2.0","result":[]}

V[15:59:41.787] ASTWorker running DocumentSymbols on version 374 of /u4/rydong/cs444/cs-444-compiler/src/main.cpp
I[15:59:41.787] --> reply:textDocument/documentSymbol(2) 0 ms
V[15:59:41.787] >>> {"id":2,"jsonrpc":"2.0","result":[{"detail":"auto () -> int","kind":12,"name":"main","range":{"end":{"character":1,"line":5},"start":{"character":0,"line":2}},"selectionRange":{"end":{"character":9,"line":2},"start":{"character":5,"line":2}}}]}

I[15:59:41.787] --> textDocument/clangd.fileStatus
V[15:59:41.787] >>> {"jsonrpc":"2.0","method":"textDocument/clangd.fileStatus","params":{"state":"idle","uri":"file:///u4/rydong/cs444/cs-444-compiler/src/main.cpp"}}

V[15:59:41.793] <<< {"id":3,"jsonrpc":"2.0","method":"textDocument/inlayHint","params":{"range":{"end":{"character":0,"line":6},"start":{"character":0,"line":0}},"textDocument":{"uri":"file:///u4/rydong/cs444/cs-444-compiler/src/main.cpp"}}}

I[15:59:41.793] <-- textDocument/inlayHint(3)
V[15:59:41.793] <<< {"id":4,"jsonrpc":"2.0","method":"textDocument/documentLink","params":{"textDocument":{"uri":"file:///u4/rydong/cs444/cs-444-compiler/src/main.cpp"}}}

I[15:59:41.793] <-- textDocument/documentLink(4)
V[15:59:41.793] ASTWorker running InlayHints on version 374 of /u4/rydong/cs444/cs-444-compiler/src/main.cpp
I[15:59:41.793] --> reply:textDocument/inlayHint(3) 0 ms
V[15:59:41.793] >>> {"id":3,"jsonrpc":"2.0","result":[]}

V[15:59:41.793] ASTWorker running DocumentLinks on version 374 of /u4/rydong/cs444/cs-444-compiler/src/main.cpp
I[15:59:41.793] --> reply:textDocument/documentLink(4) 0 ms
V[15:59:41.793] >>> {"id":4,"jsonrpc":"2.0","result":[]}

I[15:59:41.793] --> textDocument/clangd.fileStatus
V[15:59:41.793] >>> {"jsonrpc":"2.0","method":"textDocument/clangd.fileStatus","params":{"state":"idle","uri":"file:///u4/rydong/cs444/cs-444-compiler/src/main.cpp"}}

V[15:59:41.877] <<< {"id":5,"jsonrpc":"2.0","method":"textDocument/documentHighlight","params":{"position":{"character":6,"line":4},"textDocument":{"uri":"file:///u4/rydong/cs444/cs-444-compiler/src/main.cpp"}}}

I[15:59:41.877] <-- textDocument/documentHighlight(5)
V[15:59:41.877] ASTWorker running Highlights on version 374 of /u4/rydong/cs444/cs-444-compiler/src/main.cpp
I[15:59:41.878] --> reply:textDocument/documentHighlight(5) 0 ms
V[15:59:41.878] >>> {"id":5,"jsonrpc":"2.0","result":[]}

I[15:59:41.878] --> textDocument/clangd.fileStatus
V[15:59:41.878] >>> {"jsonrpc":"2.0","method":"textDocument/clangd.fileStatus","params":{"state":"idle","uri":"file:///u4/rydong/cs444/cs-444-compiler/src/main.cpp"}}

V[15:59:41.925] <<< {"id":6,"jsonrpc":"2.0","method":"textDocument/inlayHint","params":{"range":{"end":{"character":0,"line":6},"start":{"character":0,"line":0}},"textDocument":{"uri":"file:///u4/rydong/cs444/cs-444-compiler/src/main.cpp"}}}

I[15:59:41.925] <-- textDocument/inlayHint(6)
V[15:59:41.925] ASTWorker running InlayHints on version 374 of /u4/rydong/cs444/cs-444-compiler/src/main.cpp
I[15:59:41.925] --> reply:textDocument/inlayHint(6) 0 ms
V[15:59:41.925] >>> {"id":6,"jsonrpc":"2.0","result":[]}

I[15:59:41.925] --> textDocument/clangd.fileStatus
V[15:59:41.925] >>> {"jsonrpc":"2.0","method":"textDocument/clangd.fileStatus","params":{"state":"idle","uri":"file:///u4/rydong/cs444/cs-444-compiler/src/main.cpp"}}

V[15:59:41.974] <<< {"id":7,"jsonrpc":"2.0","method":"textDocument/foldingRange","params":{"textDocument":{"uri":"file:///u4/rydong/cs444/cs-444-compiler/src/main.cpp"}}}

I[15:59:41.974] <-- textDocument/foldingRange(7)
I[15:59:41.975] --> reply:textDocument/foldingRange(7) 0 ms
V[15:59:41.975] >>> {"id":7,"jsonrpc":"2.0","result":[{"endLine":4,"kind":"region","startCharacter":1,"startLine":3}]}

V[15:59:42.009] <<< {"id":8,"jsonrpc":"2.0","method":"textDocument/codeAction","params":{"context":{"diagnostics":[{"code":"undeclared_var_use","message":"Use of undeclared identifier 'foo'","range":{"end":{"character":7,"line":4},"start":{"character":4,"line":4}},"relatedInformation":[],"severity":1,"source":"clang"}],"triggerKind":2},"range":{"end":{"character":6,"line":4},"start":{"character":6,"line":4}},"textDocument":{"uri":"file:///u4/rydong/cs444/cs-444-compiler/src/main.cpp"}}}

I[15:59:42.009] <-- textDocument/codeAction(8)
V[15:59:42.009] ASTWorker running codeAction on version 374 of /u4/rydong/cs444/cs-444-compiler/src/main.cpp
I[15:59:42.010] --> reply:textDocument/codeAction(8) 0 ms
V[15:59:42.010] >>> {"id":8,"jsonrpc":"2.0","result":[]}

I[15:59:42.010] --> textDocument/clangd.fileStatus
V[15:59:42.010] >>> {"jsonrpc":"2.0","method":"textDocument/clangd.fileStatus","params":{"state":"idle","uri":"file:///u4/rydong/cs444/cs-444-compiler/src/main.cpp"}}

V[15:59:42.079] <<< {"id":9,"jsonrpc":"2.0","method":"textDocument/semanticTokens/full","params":{"textDocument":{"uri":"file:///u4/rydong/cs444/cs-444-compiler/src/main.cpp"}}}

I[15:59:42.079] <-- textDocument/semanticTokens/full(9)
V[15:59:42.079] <<< {"id":10,"jsonrpc":"2.0","method":"textDocument/foldingRange","params":{"textDocument":{"uri":"file:///u4/rydong/cs444/cs-444-compiler/src/main.cpp"}}}

I[15:59:42.079] <-- textDocument/foldingRange(10)
V[15:59:42.079] ASTWorker running SemanticHighlights on version 374 of /u4/rydong/cs444/cs-444-compiler/src/main.cpp
I[15:59:42.080] --> reply:textDocument/semanticTokens/full(9) 0 ms
V[15:59:42.080] >>> {"id":9,"jsonrpc":"2.0","result":{"data":[2,5,4,3,131075,2,4,3,14,256],"resultId":"1"}}

I[15:59:42.080] --> textDocument/clangd.fileStatus
V[15:59:42.080] >>> {"jsonrpc":"2.0","method":"textDocument/clangd.fileStatus","params":{"state":"idle","uri":"file:///u4/rydong/cs444/cs-444-compiler/src/main.cpp"}}

I[15:59:42.080] --> reply:textDocument/foldingRange(10) 0 ms
V[15:59:42.080] >>> {"id":10,"jsonrpc":"2.0","result":[{"endLine":4,"kind":"region","startCharacter":1,"startLine":3}]}

V[15:59:42.414] <<< {"id":11,"jsonrpc":"2.0","method":"textDocument/hover","params":{"position":{"character":10,"line":4},"textDocument":{"uri":"file:///u4/rydong/cs444/cs-444-compiler/src/main.cpp"}}}

I[15:59:42.414] <-- textDocument/hover(11)
V[15:59:42.414] ASTWorker running Hover on version 374 of /u4/rydong/cs444/cs-444-compiler/src/main.cpp
I[15:59:42.414] --> reply:textDocument/hover(11) 0 ms
V[15:59:42.414] >>> {"id":11,"jsonrpc":"2.0","result":null}

I[15:59:42.414] --> textDocument/clangd.fileStatus
V[15:59:42.414] >>> {"jsonrpc":"2.0","method":"textDocument/clangd.fileStatus","params":{"state":"idle","uri":"file:///u4/rydong/cs444/cs-444-compiler/src/main.cpp"}}

System information
Clangd version (from the log, or clangd --version): bundled with extension: clangd version 21.1.8 (https://github.com/llvm/llvm-project 2078da43e25a4623cab2d0d60decddf709aaea28)
clangd extension version: 0.4.0
Operating system: Ubuntu 24.04.3

[HighCommander4]

This line of the log is suspicious:

V[15:59:33.626] Ignored diagnostic. unable to open output file '/tmp/clangd/module_files/mod.cppm17647138007654665420-40-7b-fb-88-73-34/mod.pcm': 'Permission denied'

So to answer your question, pre-compiled module (pcm) files stored in /tmp/clangd/module_files could be the state you were wondering about.

If there is a permission issue with accessing /tmp, a solution could be to run clangd with the environment variable TMPDIR set to a different value (then $TMPDIR/clangd/module_files will be used).

[rdong8]

I am getting these issues even without seeing that line in the log.

I am using Conan to install dependencies, one of which is LLVM. I see this in the log:

I[10:04:22.218] ASTWorker building file /u4/rydong/projects/cs-444-compiler/src/parser/ast_builder.cppm version 2 with command 
[/u4/rydong/projects/cs-444-compiler/build]
/usr/lib/llvm-21/bin/clang++-21 --driver-mode=g++ "-DJOOSC_LR1_PATH=\"/u4/rydong/projects/cs-444-compiler/build/src/parser/resources/grammar.lr1\"" -DSPDLOG_COMPILED_LIB -DSPDLOG_USE_STD_FORMAT "-DCMAKE_INTDIR=\"Debug\"" -I/u4/rydong/projects/cs-444-compiler/src/parser -I/u4/rydong/projects/cs-444-compiler/src/. -I/u4/rydong/projects/cs-444-compiler/src/scanner -I/u4/rydong/projects/cs-444-compiler/src/utility -isystem /u4/rydong/.conan2/p/b/spdlo728049d6155b1/p/include -isystem /u4/rydong/.conan2/p/b/llvm-488a6dbf5ea17/p/include -isystem /u4/rydong/.conan2/p/magic2b79a91bc8c6c/p/include --gcc-toolchain=/usr/local/gcc-15.2.0 -m64 -stdlib=libstdc++ -g -std=c++26 -fcolor-diagnostics -glldb -fno-omit-frame-pointer -fno-sanitize-merge -D_FORTIFY_SOURCE=3 -Og -U_FORTIFY_SOURCE -Wall -Wcast-align -Wconversion -Wdouble-promotion -Wextra -Wformat=2 -Wimplicit-fallthrough -Wnon-virtual-dtor -Wnull-dereference -Wold-style-cast -Woverloaded-virtual -Wpedantic -Wshadow -Wsign-conversion -Wunused -fsanitize=address,leak,undefined -fno-sanitize-recover=all -Werror -x c++-module -fmodule-output=src/parser/CMakeFiles/parser.dir/Debug/joosc.parser.ast_builder.pcm -fmodule-file=joosc.parser.ast=src/parser/CMakeFiles/parser.dir/Debug/joosc.parser.ast.pcm -fmodule-file=joosc.parser.parse_tree=src/parser/CMakeFiles/parser.dir/Debug/joosc.parser.parse_tree.pcm -o src/parser/CMakeFiles/parser.dir/Debug/ast_builder.cppm.o -c -resource-dir=/u4/rydong/.vscode-server/data/User/globalStorage/llvm-vs-code-extensions.vscode-clangd/install/21.1.8/clangd_21.1.8/lib/clang/21 -- /u4/rydong/projects/cs-444-compiler/src/parser/ast_builder.cppm

Then later, I see this. The include directory here is wrong/out of date (notice it differs from the one above):

V[10:04:22.651] Background-index: Couldn't read /u4/rydong/.conan2/p/b/llvm-6ddb42522a7f7/p/include/llvm/Support/ErrorHandling.h to validate stored index: No such file or directory

I'm not sure where it's getting this from. Disabling/re-enabling or uninstalling/reinstalling the extension no longer seems to fix it.

compile_commands.json

clangd.log

[HighCommander4]

I'm not familiar with conan. Why are there two different directories beginning with /u4/rydong/.conan2/p/b/llvm-? Do both of them exist at the time clangd is started?

[rdong8]

I believe Conan makes a hash of the compiler version, flags, and anything else that could affect the build, then caches the built dependencies keyed by the hash, so whenever you change any options it will rebuild everything. The LLVM in the compile commands file does actually exist, but the one it is looking for when it errors does not (I think this might be an old build or something that was cleaned from the cache).

[HighCommander4]

Ah, I just noticed the message is coming from the background index. So probably what happened is:

• on a previous run, clangd built its background index, and recorded that some of the indexed headers were located in the old llvm- directory
• some compile flags changed, causing conan to creat a new llvm- directory (and I guess delete the old one)
• on a subsequent run, clangd tries to load the background index, notices that some of the header files don't exist, and prints this "Couldn't read" message about them

Anyways, the "Couldn't read" messages should be harmless. Their only consequence should be that clangd needs to reindex the affected headers, which is to be expected. If you want to silence them, closing clangd, deleting the background index (based on the logs should be at /u4/rydong/projects/cs-444-compiler/build/.cache/clangd/index), and restarting clangd should do it.

[rdong8]

ok I think I figured it out, it is related to the TMPDIR thing you mentioned earlier. We're using a multi-user dev machine and it seems like everyone's /tmp/clangd/module_files might be conflicting with each other. Setting TMPDIR to /tmp/$USER instead seems to fix everything. Thank you for the help!