header file not found on spacemacs

[kurogane1031]

Observed behavior

I am attempting to include cuda library in my code, but all the files related to it is not found. The illustration of the error is as follow. There is no problem with standard c++ library.

compile_commands.json generated using bear make

[
    {
        "arguments": [
            "clang++-10", 
            "-c", 
            "-std=c++14", 
            "-g", 
            "-O2", 
            "-ftime-trace", 
            "-I.", 
            "-I/usr/local/cuda-10.0/include", 
            "-I/usr/include/eigen3/", 
            "-o", 
            "main.cpp.o", 
            "main.cpp"
        ], 
        "directory": "/home/userz/develop/Path_Planning_Stacks/testz", 
        "file": "main.cpp"
    }
]

Expected behavior

I expect ccls will be able to locate any third party (for this example is cuda header files) related library. There might be some steps that I did wrong and I appreciate if someone can guide me through

Steps to reproduce

I have attempted several method as follow

1. delete ccls folder, download and compile the ccls using pre-built binaries
   cmake -H. -BRelease -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=/home/userz/.program_files/clang+llvm-10.0.0-x86_64-linux-gnu-ubuntu-18.04

2. delete ccls folder, download and compile the ccls using clang-10 from apt install
cmake -H. -BRelease -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=/usr/lib/llvm-10 -DLLVM_INCLUDE_DIR=/usr/lib/llvm-10/include -DLLVM_BUILD_INCLUDE_DIR=/usr/include/llvm-10

3. similar as 2. but adding flag -DSYSTEM_CLANG=ON.

4. remove compile_commands.json and use only .ccls with the following

clang
%cpp -std=c++14
-I.
-I/usr/local/cuda-10.0/include

5. use compile_commands.json and .ccls with following

%compile_commands.json
%cpp -std=c++14
%cpp -stdlib=c++14
%cpp %cu -I/usr/local/cuda-10.0/include

6. delete .ccls-cache and re-execute ccls -index="."

System information

snippet of dotspacemacs-configuration-layers

     (auto-completion :variables auto-completion-tab-key-behavior 'nil)
     cmake
     (c-c++ :variables
            c-c++-enable-clang-support t
            c-c++-enable-google-style t
            c-c++-lsp-executable "/home/userz/.program_files/ccls/Release/ccls"
            c-c++-backend 'lsp-ccls
            c-c++-lsp-semantic-highlight-method 'font-lock
            c-c++-lsp-enable-semantic-highlight 'rainbow
              )

.
├── apf.cu
├── apf.cu.o
├── apf.hpp
├── .ccls
├── .ccls-cache
│   ├── @@home@userz@develop@Path_Planning_Stacks@testz
│   │   ├── @usr@include@features.h
│   │   ├── @usr@include@features.h.blob
│   │   ├── @usr@include@limits.h
│   │   ├── @usr@include@limits.h.blob
│   │   ├── @usr@include@linux@limits.h
│   │   ├── @usr@include@linux@limits.h.blob
│   │   ├── @usr@include@stdc-predef.h
│   │   ├── @usr@include@stdc-predef.h.blob
│   │   ├── @usr@include@stdio.h
│   │   ├── @usr@include@stdio.h.blob
│   │   ├── @usr@include@x86_64-linux-gnu@bits@_G_config.h
│   │   ├── @usr@include@x86_64-linux-gnu@bits@_G_config.h.blob
│   │   ├── @usr@include@x86_64-linux-gnu@bits@libc-header-start.h
│   │   ├── @usr@include@x86_64-linux-gnu@bits@libc-header-start.h.blob
│   │   ├── @usr@include@x86_64-linux-gnu@bits@libio.h
│   │   ├── @usr@include@x86_64-linux-gnu@bits@libio.h.blob
│   │   ├── @usr@include@x86_64-linux-gnu@bits@local_lim.h
│   │   ├── @usr@include@x86_64-linux-gnu@bits@local_lim.h.blob
│   │   ├── @usr@include@x86_64-linux-gnu@bits@long-double.h
│   │   ├── @usr@include@x86_64-linux-gnu@bits@long-double.h.blob
│   │   ├── @usr@include@x86_64-linux-gnu@bits@posix1_lim.h
│   │   ├── @usr@include@x86_64-linux-gnu@bits@posix1_lim.h.blob
│   │   ├── @usr@include@x86_64-linux-gnu@bits@posix2_lim.h
│   │   ├── @usr@include@x86_64-linux-gnu@bits@posix2_lim.h.blob
│   │   ├── @usr@include@x86_64-linux-gnu@bits@stdio.h
│   │   ├── @usr@include@x86_64-linux-gnu@bits@stdio.h.blob
│   │   ├── @usr@include@x86_64-linux-gnu@bits@stdio_lim.h
│   │   ├── @usr@include@x86_64-linux-gnu@bits@stdio_lim.h.blob
│   │   ├── @usr@include@x86_64-linux-gnu@bits@sys_errlist.h
│   │   ├── @usr@include@x86_64-linux-gnu@bits@sys_errlist.h.blob
│   │   ├── @usr@include@x86_64-linux-gnu@bits@types@__FILE.h
│   │   ├── @usr@include@x86_64-linux-gnu@bits@types@FILE.h
│   │   ├── @usr@include@x86_64-linux-gnu@bits@types@__FILE.h.blob
│   │   ├── @usr@include@x86_64-linux-gnu@bits@types@FILE.h.blob
│   │   ├── @usr@include@x86_64-linux-gnu@bits@types.h
│   │   ├── @usr@include@x86_64-linux-gnu@bits@types.h.blob
│   │   ├── @usr@include@x86_64-linux-gnu@bits@typesizes.h
│   │   ├── @usr@include@x86_64-linux-gnu@bits@typesizes.h.blob
│   │   ├── @usr@include@x86_64-linux-gnu@bits@types@__mbstate_t.h
│   │   ├── @usr@include@x86_64-linux-gnu@bits@types@__mbstate_t.h.blob
│   │   ├── @usr@include@x86_64-linux-gnu@bits@uio_lim.h
│   │   ├── @usr@include@x86_64-linux-gnu@bits@uio_lim.h.blob
│   │   ├── @usr@include@x86_64-linux-gnu@bits@wordsize.h
│   │   ├── @usr@include@x86_64-linux-gnu@bits@wordsize.h.blob
│   │   ├── @usr@include@x86_64-linux-gnu@bits@xopen_lim.h
│   │   ├── @usr@include@x86_64-linux-gnu@bits@xopen_lim.h.blob
│   │   ├── @usr@include@x86_64-linux-gnu@gnu@stubs-64.h
│   │   ├── @usr@include@x86_64-linux-gnu@gnu@stubs-64.h.blob
│   │   ├── @usr@include@x86_64-linux-gnu@gnu@stubs.h
│   │   ├── @usr@include@x86_64-linux-gnu@gnu@stubs.h.blob
│   │   ├── @usr@include@x86_64-linux-gnu@sys@cdefs.h
│   │   ├── @usr@include@x86_64-linux-gnu@sys@cdefs.h.blob
│   │   ├── @usr@lib@llvm-10@lib@clang@10.0.0@include@limits.h
│   │   ├── @usr@lib@llvm-10@lib@clang@10.0.0@include@limits.h.blob
│   │   ├── @usr@lib@llvm-10@lib@clang@10.0.0@include@stdarg.h
│   │   ├── @usr@lib@llvm-10@lib@clang@10.0.0@include@stdarg.h.blob
│   │   ├── @usr@lib@llvm-10@lib@clang@10.0.0@include@stddef.h
│   │   ├── @usr@lib@llvm-10@lib@clang@10.0.0@include@stddef.h.blob
│   │   ├── @usr@lib@llvm-10@lib@clang@10.0.0@include@__stddef_max_align_t.h
│   │   ├── @usr@lib@llvm-10@lib@clang@10.0.0@include@__stddef_max_align_t.h.blob
│   │   ├── @usr@local@cuda-10.0@include@builtin_types.h
│   │   ├── @usr@local@cuda-10.0@include@builtin_types.h.blob
│   │   ├── @usr@local@cuda-10.0@include@channel_descriptor.h
│   │   ├── @usr@local@cuda-10.0@include@channel_descriptor.h.blob
│   │   ├── @usr@local@cuda-10.0@include@crt@host_config.h
│   │   ├── @usr@local@cuda-10.0@include@crt@host_config.h.blob
│   │   ├── @usr@local@cuda-10.0@include@crt@host_defines.h
│   │   ├── @usr@local@cuda-10.0@include@crt@host_defines.h.blob
│   │   ├── @usr@local@cuda-10.0@include@cuda_device_runtime_api.h
│   │   ├── @usr@local@cuda-10.0@include@cuda_device_runtime_api.h.blob
│   │   ├── @usr@local@cuda-10.0@include@cuda_runtime_api.h
│   │   ├── @usr@local@cuda-10.0@include@cuda_runtime_api.h.blob
│   │   ├── @usr@local@cuda-10.0@include@cuda_runtime.h
│   │   ├── @usr@local@cuda-10.0@include@cuda_runtime.h.blob
│   │   ├── @usr@local@cuda-10.0@include@device_launch_parameters.h
│   │   ├── @usr@local@cuda-10.0@include@device_launch_parameters.h.blob
│   │   ├── @usr@local@cuda-10.0@include@device_types.h
│   │   ├── @usr@local@cuda-10.0@include@device_types.h.blob
│   │   ├── @usr@local@cuda-10.0@include@driver_functions.h
│   │   ├── @usr@local@cuda-10.0@include@driver_functions.h.blob
│   │   ├── @usr@local@cuda-10.0@include@driver_types.h
│   │   ├── @usr@local@cuda-10.0@include@driver_types.h.blob
│   │   ├── @usr@local@cuda-10.0@include@library_types.h
│   │   ├── @usr@local@cuda-10.0@include@library_types.h.blob
│   │   ├── @usr@local@cuda-10.0@include@surface_types.h
│   │   ├── @usr@local@cuda-10.0@include@surface_types.h.blob
│   │   ├── @usr@local@cuda-10.0@include@texture_types.h
│   │   ├── @usr@local@cuda-10.0@include@texture_types.h.blob
│   │   ├── @usr@local@cuda-10.0@include@vector_functions.h
│   │   ├── @usr@local@cuda-10.0@include@vector_functions.h.blob
│   │   ├── @usr@local@cuda-10.0@include@vector_functions.hpp
│   │   ├── @usr@local@cuda-10.0@include@vector_functions.hpp.blob
│   │   ├── @usr@local@cuda-10.0@include@vector_types.h
│   │   └── @usr@local@cuda-10.0@include@vector_types.h.blob
│   └── @home@userz@develop@Path_Planning_Stacks@testz
│       ├── apf.hpp
│       ├── apf.hpp.blob
│       ├── main.cpp
│       └── main.cpp.blob
├── compile_commands.json
├── .git
│   ├── branches
│   ├── config
│   ├── description
│   ├── HEAD
│   ├── hooks
│   │   ├── applypatch-msg.sample
│   │   ├── commit-msg.sample
│   │   ├── fsmonitor-watchman.sample
│   │   ├── post-update.sample
│   │   ├── pre-applypatch.sample
│   │   ├── pre-commit.sample
│   │   ├── pre-merge-commit.sample
│   │   ├── prepare-commit-msg.sample
│   │   ├── pre-push.sample
│   │   ├── pre-rebase.sample
│   │   ├── pre-receive.sample
│   │   └── update.sample
│   ├── info
│   │   └── exclude
│   ├── objects
│   │   ├── info
│   │   └── pack
│   └── refs
│       ├── heads
│       └── tags
├── main.cpp
├── main.cpp.json
├── main.cpp.o
├── Makefile
└── run

clang++ -fsyntax-only -v -xc++ /dev/null

clang version 10.0.0-4ubuntu1~18.04.1 
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/bin
Found candidate GCC installation: /usr/bin/../lib/gcc/i686-linux-gnu/8
Found candidate GCC installation: /usr/bin/../lib/gcc/x86_64-linux-gnu/7
Found candidate GCC installation: /usr/bin/../lib/gcc/x86_64-linux-gnu/7.5.0
Found candidate GCC installation: /usr/bin/../lib/gcc/x86_64-linux-gnu/8
Found candidate GCC installation: /usr/lib/gcc/i686-linux-gnu/8
Found candidate GCC installation: /usr/lib/gcc/x86_64-linux-gnu/7
Found candidate GCC installation: /usr/lib/gcc/x86_64-linux-gnu/7.5.0
Found candidate GCC installation: /usr/lib/gcc/x86_64-linux-gnu/8
Selected GCC installation: /usr/bin/../lib/gcc/x86_64-linux-gnu/7.5.0
Candidate multilib: .;@m64
Selected multilib: .;@m64
Found CUDA installation: /usr/local/cuda-10.0, version 10.0
 (in-process)
 "/usr/lib/llvm-10/bin/clang" -cc1 -triple x86_64-pc-linux-gnu -fsyntax-only -disable-free -disable-llvm-verifier -discard-value-names -main-file-name null -mrelocation-model static -mthread-model posix -mframe-pointer=all -fmath-errno -fno-rounding-math -masm-verbose -mconstructor-aliases -munwind-tables -target-cpu x86-64 -dwarf-column-info -fno-split-dwarf-inlining -debugger-tuning=gdb -v -resource-dir /usr/lib/llvm-10/lib/clang/10.0.0 -internal-isystem /usr/bin/../lib/gcc/x86_64-linux-gnu/7.5.0/../../../../include/c++/7.5.0 -internal-isystem /usr/bin/../lib/gcc/x86_64-linux-gnu/7.5.0/../../../../include/x86_64-linux-gnu/c++/7.5.0 -internal-isystem /usr/bin/../lib/gcc/x86_64-linux-gnu/7.5.0/../../../../include/x86_64-linux-gnu/c++/7.5.0 -internal-isystem /usr/bin/../lib/gcc/x86_64-linux-gnu/7.5.0/../../../../include/c++/7.5.0/backward -internal-isystem /usr/local/include -internal-isystem /usr/lib/llvm-10/lib/clang/10.0.0/include -internal-externc-isystem /usr/include/x86_64-linux-gnu -internal-externc-isystem /include -internal-externc-isystem /usr/include -fdeprecated-macro -fdebug-compilation-dir /home/userz/develop/Path_Planning_Stacks/testz -ferror-limit 19 -fmessage-length 0 -fgnuc-version=4.2.1 -fobjc-runtime=gcc -fcxx-exceptions -fexceptions -fdiagnostics-show-option -fcolor-diagnostics -faddrsig -x c++ /dev/null
clang -cc1 version 10.0.0 based upon LLVM 10.0.0 default target x86_64-pc-linux-gnu
ignoring nonexistent directory "/include"
ignoring duplicate directory "/usr/bin/../lib/gcc/x86_64-linux-gnu/7.5.0/../../../../include/x86_64-linux-gnu/c++/7.5.0"
#include "..." search starts here:
#include <...> search starts here:
 /usr/bin/../lib/gcc/x86_64-linux-gnu/7.5.0/../../../../include/c++/7.5.0
 /usr/bin/../lib/gcc/x86_64-linux-gnu/7.5.0/../../../../include/x86_64-linux-gnu/c++/7.5.0
 /usr/bin/../lib/gcc/x86_64-linux-gnu/7.5.0/../../../../include/c++/7.5.0/backward
 /usr/local/include
 /usr/lib/llvm-10/lib/clang/10.0.0/include
 /usr/include/x86_64-linux-gnu
 /usr/include
End of search list.

ccls.log

22:48:15 ccls           initialize.cc:274 I initialize in directory /home/userz/develop/Path_Planning_Stacks/testz with uri file:///home/userz/develop/Path_Planning_Stacks/testz/.
22:48:15 ccls           initialize.cc:297 I initializationOptions: {"compilationDatabaseCommand":"","compilationDatabaseDirectory":"","cache":{"directory":".ccls-cache","format":"binary","hierarchicalPath":false,"retainInMemory":2},"capabilities":{"documentOnTypeFormattingProvider":{"firstTriggerCharacter":"}","moreTriggerCharacter":[]},"foldingRangeProvider":true,"workspace":{"workspaceFolders":{"supported":true,"changeNotifications":true}}},"clang":{"excludeArgs":[],"extraArgs":[],"pathMappings":[],"resourceDir":""},"client":{"diagnosticsRelatedInformation":true,"hierarchicalDocumentSymbolSupport":true,"linkSupport":true,"snippetSupport":true},"codeLens":{"localVariables":true},"completion":{"caseSensitivity":2,"detailedLabel":true,"dropOldRequests":true,"duplicateOptional":true,"filterAndSort":true,"include":{"blacklist":[],"maxPathSize":30,"suffixWhitelist":[".h",".hpp",".hh",".inc"],"whitelist":[]},"maxNum":100,"placeholder":true},"diagnostics":{"blacklist":[],"onChange":1000,"onOpen":0,"onSave":0,"spellChecking":true,"whitelist":[]},"highlight":{"largeFileSize":2097152,"lsRanges":false,"blacklist":[],"whitelist":[]},"index":{"blacklist":[],"comments":2,"initialNoLinkage":false,"initialBlacklist":[],"initialWhitelist":[],"maxInitializerLines":5,"multiVersion":0,"multiVersionBlacklist":[],"multiVersionWhitelist":[],"name":{"suppressUnwrittenScope":false},"onChange":false,"parametersInDeclarations":true,"threads":0,"trackDependency":2,"whitelist":[]},"request":{"timeout":5000},"session":{"maxNum":10},"workspaceSymbol":{"caseSensitivity":1,"maxNum":1000,"sort":true},"xref":{"maxNum":2000}}
22:48:15 ccls           initialize.cc:329 I use -resource-dir=/usr/lib/llvm-10/lib/clang/10.0.0
22:48:15 ccls           initialize.cc:361 I workspace folder: /home/userz/develop/Path_Planning_Stacks/testz/
22:48:15 ccls              project.cc:426 I loaded /home/userz/develop/Path_Planning_Stacks/testz/compile_commands.json
22:48:15 ccls              project.cc:284 I use /home/userz/develop/Path_Planning_Stacks/testz/.ccls: %compile_commands.json %cpp -std=c++14 %cpp -stdlib=c++14 %cpp %cu -I/usr/local/cuda-10.0/include
22:48:15 ccls           initialize.cc:386 I start 12 indexers
22:48:15 ccls           initialize.cc:394 I dispatch initial index requests
22:48:15 indexer0         pipeline.cc:386 I parse /home/userz/develop/Path_Planning_Stacks/testz/main.cpp
  clang++-10 --driver-mode=g++ -c -std=c++14 -g -O2 -ftime-trace -I. -I/usr/local/cuda-10.0/include -I/usr/include/eigen3/ -o main.cpp.o main.cpp -std=c++14 -stdlib=c++14 -I/usr/local/cuda-10.0/include -working-directory=/home/userz/develop/Path_Planning_Stacks/testz
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/include/x86_64-linux-gnu/bits/types/__FILE.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/include/x86_64-linux-gnu/bits/stdio_lim.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/include/stdio.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/local/cuda-10.0/include/device_launch_parameters.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/include/x86_64-linux-gnu/bits/stdio.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/local/cuda-10.0/include/vector_functions.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/local/cuda-10.0/include/driver_functions.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/lib/llvm-10/lib/clang/10.0.0/include/stdarg.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/local/cuda-10.0/include/cuda_device_runtime_api.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/include/x86_64-linux-gnu/bits/types/__mbstate_t.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/lib/llvm-10/lib/clang/10.0.0/include/limits.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/include/features.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/include/x86_64-linux-gnu/bits/types/FILE.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/local/cuda-10.0/include/surface_types.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/include/x86_64-linux-gnu/bits/libc-header-start.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/local/cuda-10.0/include/device_types.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/local/cuda-10.0/include/vector_functions.hpp (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/include/x86_64-linux-gnu/bits/wordsize.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/include/x86_64-linux-gnu/bits/uio_lim.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/include/x86_64-linux-gnu/bits/sys_errlist.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /home/userz/develop/Path_Planning_Stacks/testz/main.cpp (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/local/cuda-10.0/include/driver_types.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/include/x86_64-linux-gnu/bits/xopen_lim.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/local/cuda-10.0/include/vector_types.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/include/limits.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/include/x86_64-linux-gnu/bits/typesizes.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /home/userz/develop/Path_Planning_Stacks/testz/apf.hpp (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/include/x86_64-linux-gnu/bits/long-double.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/local/cuda-10.0/include/cuda_runtime.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/local/cuda-10.0/include/crt/host_config.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/local/cuda-10.0/include/builtin_types.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/include/x86_64-linux-gnu/bits/types.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/include/stdc-predef.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/include/x86_64-linux-gnu/sys/cdefs.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/lib/llvm-10/lib/clang/10.0.0/include/stddef.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/include/x86_64-linux-gnu/gnu/stubs.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/include/x86_64-linux-gnu/gnu/stubs-64.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/local/cuda-10.0/include/crt/host_defines.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/include/x86_64-linux-gnu/bits/posix1_lim.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/include/x86_64-linux-gnu/bits/local_lim.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/include/linux/limits.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/include/x86_64-linux-gnu/bits/posix2_lim.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/lib/llvm-10/lib/clang/10.0.0/include/__stddef_max_align_t.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/include/x86_64-linux-gnu/bits/libio.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/local/cuda-10.0/include/texture_types.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/include/x86_64-linux-gnu/bits/_G_config.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/local/cuda-10.0/include/library_types.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/local/cuda-10.0/include/channel_descriptor.h (delta: 0)
22:48:15 indexer0         pipeline.cc:397 I store index for /usr/local/cuda-10.0/include/cuda_runtime_api.h (delta: 0)

M-x company-diag

Emacs 26.3 (x86_64-pc-linux-gnu) of 2019-09-17 on lcy01-amd64-030
Company 0.9.12

company-backends: (company-capf company-c-headers
              (company-semantic company-dabbrev-code company-gtags company-etags company-keywords)
              company-files company-dabbrev)

Used backend: company-capf
Value of c-a-p-f: (tags-completion-at-point-function)
Major mode: c++-mode
Prefix: ""
Completions:

• ccls version (git describe --tags --long): 99f0b402a7584f92de12f0af164ad7e0c772fcd2
• clang version: 10.0.0
• OS: ubuntu 18.04
• Editor: spacemacs
• Language client (and version):

[kurogane1031]

Found the issue. It seems that I need to remove my root directory index in order to solve this issue.
Solution from emacs-lsp/emacs-ccls#40