CLion report Cannot get compiler information when opening openjdk project

I setup the dev env. according to Tips & Tricks: Develop OpenJDK in CLion with Pleasure. Unfortunately, CLion pop up error message "Cannot get compiler information" and stop indexing the project.

Compiler exited with error code 1: /usr/bin/clang++ -xc++ -include-pch /Users/<my user name>/workspace/jdk/build/macosx-x86_64-server-fastdebug/hotspot/variant-server/libjvm/objs/precompiled/precompiled.hpp.pch -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D_GNU_SOURCE -pipe -fno-rtti -fno-exceptions -fvisibility=hidden -fno-strict-aliasing -fno-omit-frame-pointer -flimit-debug-info -mno-omit-leaf-frame-pointer -mstack-alignment=16 -std=c++14 -DMAC_OS_X_VERSION_MIN_REQUIRED=10120 -mmacosx-version-min=10.12.0 -DLIBC=default -D_ALLBSD_SOURCE -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE -Wall -Wextra -Wformat=2 -Wpointer-arith -Wsign-compare -Wreorder -Wunused-function -Wundef -Wunused-value -Woverloaded-virtual -fPIC -DVM_LITTLE_ENDIAN -D_LP64=1 -fno-delete-null-pointer-checks -m64 -arch x86_64 -DASSERT -DCHECK_UNHANDLED_OOPS -DTARGET_ARCH_x86 -DINCLUDE_SUFFIX_OS=_bsd -DINCLUDE_SUFFIX_CPU=_x86 -DINCLUDE_SUFFIX_COMPILER=_gcc -DTARGET_COMPILER_gcc -DAMD64 -DHOTSPOT_LIB_ARCH=\"amd64\" -DCOMPILER1 -DCOMPILER2 -DDTRACE_ENABLED -I/Users/<my user name>/workspace/jdk/build/macosx-x86_64-server-fastdebug/hotspot/variant-server/gensrc/adfiles -I/Users/<my user name>/workspace/jdk/src/hotspot/share -I/Users/<my user name>/workspace/jdk/src/hotspot/os/bsd -I/Users/<my user name>/workspace/jdk/src/hotspot/os/posix -I/Users/<my user name>/workspace/jdk/src/hotspot/cpu/x86 -I/Users/<my user name>/workspace/jdk/src/hotspot/os_cpu/bsd_x86 -I/Users/<my user name>/workspace/jdk/build/macosx-x86_64-server-fastdebug/hotspot/variant-server/gensrc -I/Users/<my user name>/workspace/jdk/src/hotspot/share/precompiled -I/Users/<my user name>/workspace/jdk/src/hotspot/share/include -I/Users/<my user name>/workspace/jdk/src/hotspot/os/posix/include -I/Users/<my user name>/workspace/jdk/build/macosx-x86_64-server-fastdebug/support/modules_include/java.base -I/Users/<my user name>/workspace/jdk/build/macosx-x86_64-server-fastdebug/support/modules_include/java.base/darwin -I/Users/<my user name>/workspace/jdk/src/java.base/share/native/libjimage -m64 -I/Users/<my user name>/workspace/jdk/build/macosx-x86_64-server-fastdebug/hotspot/variant-server/gensrc/adfiles -I/Users/<my user name>/workspace/jdk/src/hotspot/share -I/Users/<my user name>/workspace/jdk/src/hotspot/os/bsd -I/Users/<my user name>/workspace/jdk/src/hotspot/os/posix -I/Users/<my user name>/workspace/jdk/src/hotspot/cpu/x86 -I/Users/<my user name>/workspace/jdk/src/hotspot/os_cpu/bsd_x86 -I/Users/<my user name>/workspace/jdk/build/macosx-x86_64-server-fastdebug/hotspot/variant-server/gensrc -g -Wno-unknown-warning-option -Wno-unused-parameter -Wno-unused -Wno-tautological-compare -Wno-undefined-var-template -Wno-sometimes-uninitialized -Wno-unknown-pragmas -Wno-delete-non-virtual-dtor -Wno-missing-braces -Wno-char-subscripts -Wno-ignored-qualifiers -Wno-missing-field-initializers -Wno-mismatched-tags -Wno-shift-negative-value -Wno-misleading-indentation -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.1.sdk -iframework /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.1.sdk/System/Library/Frameworks -O3 -c -fpch-preprocess -v -dD -E
Apple clang version 13.0.0 (clang-1300.0.29.30)
Target: x86_64-apple-darwin20.6.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
 "/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang" -cc1 -triple x86_64-apple-macosx10.12.0 -Wundef-prefix=TARGET_OS_ -Wdeprecated-objc-isa-usage -Werror=deprecated-objc-isa-usage -Werror=implicit-function-declaration -E -disable-free -disable-llvm-verifier -discard-value-names -main-file-name compiler-file13266851965654859621 -mrelocation-model pic -pic-level 2 -fno-delete-null-pointer-checks -mframe-pointer=all -relaxed-aliasing -fno-strict-return -fno-rounding-math -munwind-tables -faligned-alloc-unavailable -target-sdk-version=12.1 -fvisibility-inlines-hidden-static-local-var -target-cpu penryn -tune-cpu generic -debug-info-kind=limited -dwarf-version=4 -debugger-tuning=lldb -target-linker-version 711 -v -resource-dir /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/13.0.0 -include-pch /Users/<my user name>/workspace/jdk/build/macosx-x86_64-server-fastdebug/hotspot/variant-server/libjvm/objs/precompiled/precompiled.hpp.pch -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.1.sdk -iframework /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.1.sdk/System/Library/Frameworks -D __STDC_FORMAT_MACROS -D __STDC_LIMIT_MACROS -D __STDC_CONSTANT_MACROS -D _GNU_SOURCE -D MAC_OS_X_VERSION_MIN_REQUIRED=10120 -D LIBC=default -D _ALLBSD_SOURCE -D _DARWIN_C_SOURCE -D _XOPEN_SOURCE -D VM_LITTLE_ENDIAN -D _LP64=1 -D ASSERT -D CHECK_UNHANDLED_OOPS -D TARGET_ARCH_x86 -D INCLUDE_SUFFIX_OS=_bsd -D INCLUDE_SUFFIX_CPU=_x86 -D INCLUDE_SUFFIX_COMPILER=_gcc -D TARGET_COMPILER_gcc -D AMD64 -D "HOTSPOT_LIB_ARCH=\"amd64\"" -D COMPILER1 -D COMPILER2 -D DTRACE_ENABLED -I /Users/<my user name>/workspace/jdk/build/macosx-x86_64-server-fastdebug/hotspot/variant-server/gensrc/adfiles -I /Users/<my user name>/workspace/jdk/src/hotspot/share -I /Users/<my user name>/workspace/jdk/src/hotspot/os/bsd -I /Users/<my user name>/workspace/jdk/src/hotspot/os/posix -I /Users/<my user name>/workspace/jdk/src/hotspot/cpu/x86 -I /Users/<my user name>/workspace/jdk/src/hotspot/os_cpu/bsd_x86 -I /Users/<my user name>/workspace/jdk/build/macosx-x86_64-server-fastdebug/hotspot/variant-server/gensrc -I /Users/<my user name>/workspace/jdk/src/hotspot/share/precompiled -I /Users/<my user name>/workspace/jdk/src/hotspot/share/include -I /Users/<my user name>/workspace/jdk/src/hotspot/os/posix/include -I /Users/<my user name>/workspace/jdk/build/macosx-x86_64-server-fastdebug/support/modules_include/java.base -I /Users/<my user name>/workspace/jdk/build/macosx-x86_64-server-fastdebug/support/modules_include/java.base/darwin -I /Users/<my user name>/workspace/jdk/src/java.base/share/native/libjimage -I /Users/<my user name>/workspace/jdk/build/macosx-x86_64-server-fastdebug/hotspot/variant-server/gensrc/adfiles -I /Users/<my user name>/workspace/jdk/src/hotspot/share -I /Users/<my user name>/workspace/jdk/src/hotspot/os/bsd -I /Users/<my user name>/workspace/jdk/src/hotspot/os/posix -I /Users/<my user name>/workspace/jdk/src/hotspot/cpu/x86 -I /Users/<my user name>/workspace/jdk/src/hotspot/os_cpu/bsd_x86 -I /Users/<my user name>/workspace/jdk/build/macosx-x86_64-server-fastdebug/hotspot/variant-server/gensrc -D ___CIDR_DEFINITIONS_END -I/usr/local/include -stdlib=libc++ -internal-isystem /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.1.sdk/usr/include/c++/v1 -internal-isystem /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.1.sdk/usr/local/include -internal-isystem /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/13.0.0/include -internal-externc-isystem /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.1.sdk/usr/include -internal-externc-isystem /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include -O3 -Wall -Wextra -Wformat=2 -Wpointer-arith -Wsign-compare -Wreorder -Wunused-function -Wundef -Wunused-value -Woverloaded-virtual -Wno-unknown-warning-option -Wno-unused-parameter -Wno-unused -Wno-tautological-compare -Wno-undefined-var-template -Wno-sometimes-uninitialized -Wno-unknown-pragmas -Wno-delete-non-virtual-dtor -Wno-missing-braces -Wno-char-subscripts -Wno-ignored-qualifiers -Wno-missing-field-initializers -Wno-mismatched-tags -Wno-shift-negative-value -Wno-misleading-indentation -Wno-reorder-init-list -Wno-implicit-int-float-conversion -Wno-c99-designator -Wno-final-dtor-non-final-class -Wno-extra-semi-stmt -Wno-misleading-indentation -Wno-quoted-include-in-framework-header -Wno-implicit-fallthrough -Wno-enum-enum-conversion -Wno-enum-float-conversion -Wno-elaborated-enum-base -std=c++14 -fdeprecated-macro -fdebug-compilation-dir /Users/<my user name>/workspace/jdk/make/hotspot -ferror-limit 19 -fvisibility hidden -stack-protector 1 -mstack-alignment=16 -mdarwin-stkchk-strong-link -fblocks -fencode-extended-block-signature -fno-rtti -fregister-global-dtors-with-atexit -fgnuc-version=4.2.1 -fno-cxx-modules -fmax-type-align=16 -fcommon -vectorize-loops -vectorize-slp -dD -clang-vendor-feature=+nullptrToBoolConversion -clang-vendor-feature=+messageToSelfInClassMethodIdReturnType -clang-vendor-feature=+disableInferNewAvailabilityFromInit -clang-vendor-feature=+disableNeonImmediateRangeCheck -clang-vendor-feature=+disableNonDependentMemberExprInCurrentInstantiation -fno-odr-hash-protocols -clang-vendor-feature=+revert09abecef7bbf -mllvm -disable-aligned-alloc-awareness=1 -mllvm -enable-dse-memoryssa=0 -o - -x c++ /private/var/folders/m8/l221nxd908q5k3q23m_pqwyr0000gn/T/compiler-file13266851965654859621
clang -cc1 version 13.0.0 (clang-1300.0.29.30) default target x86_64-apple-darwin20.6.0
error: unable to read PCH file /Users/<my user name>/workspace/jdk/build/macosx-x86_64-server-fastdebug/hotspot/variant-server/libjvm/objs/precompiled/precompiled.hpp.pch: 'No such file or directory'
ignoring nonexistent directory "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.1.sdk/usr/local/include"
ignoring nonexistent directory "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.1.sdk/Library/Frameworks"
ignoring duplicate directory "/Users/<my user name>/workspace/jdk/build/macosx-x86_64-server-fastdebug/hotspot/variant-server/gensrc/adfiles"
ignoring duplicate directory "/Users/<my user name>/workspace/jdk/src/hotspot/share"
ignoring duplicate directory "/Users/<my user name>/workspace/jdk/src/hotspot/os/bsd"
ignoring duplicate directory "/Users/<my user name>/workspace/jdk/src/hotspot/os/posix"
ignoring duplicate directory "/Users/<my user name>/workspace/jdk/src/hotspot/cpu/x86"
ignoring duplicate directory "/Users/<my user name>/workspace/jdk/src/hotspot/os_cpu/bsd_x86"
ignoring duplicate directory "/Users/<my user name>/workspace/jdk/build/macosx-x86_64-server-fastdebug/hotspot/variant-server/gensrc"
ignoring duplicate directory "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.1.sdk/System/Library/Frameworks"
#include "..." search starts here:
#include <...> search starts here:
 /Users/<my user name>/workspace/jdk/build/macosx-x86_64-server-fastdebug/hotspot/variant-server/gensrc/adfiles
 /Users/<my user name>/workspace/jdk/src/hotspot/share
 /Users/<my user name>/workspace/jdk/src/hotspot/os/bsd
 /Users/<my user name>/workspace/jdk/src/hotspot/os/posix
 /Users/<my user name>/workspace/jdk/src/hotspot/cpu/x86
 /Users/<my user name>/workspace/jdk/src/hotspot/os_cpu/bsd_x86
 /Users/<my user name>/workspace/jdk/build/macosx-x86_64-server-fastdebug/hotspot/variant-server/gensrc
 /Users/<my user name>/workspace/jdk/src/hotspot/share/precompiled
 /Users/<my user name>/workspace/jdk/src/hotspot/share/include
 /Users/<my user name>/workspace/jdk/src/hotspot/os/posix/include
 /Users/<my user name>/workspace/jdk/build/macosx-x86_64-server-fastdebug/support/modules_include/java.base
 /Users/<my user name>/workspace/jdk/build/macosx-x86_64-server-fastdebug/support/modules_include/java.base/darwin
 /Users/<my user name>/workspace/jdk/src/java.base/share/native/libjimage
 /usr/local/include
 /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.1.sdk/System/Library/Frameworks (framework directory)
 /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.1.sdk/usr/include/c++/v1
 /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/13.0.0/include
 /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.1.sdk/usr/include
 /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include
End of search list.
1 error generated.

I didn't find out the root cause. However, I did find out the direct reason for this failure. The generated compile_commands.json contains incorrect command.

{
  "directory": "/Users/<my user name>/workspace/jdk/make/hotspot",
  "file": "/Users/<my user name>/workspace/jdk/src/hotspot/share/compiler/abstractCompiler.cpp",
  "command": "/usr/bin/clang++ -include-pch /Users/<my user name>/workspace/jdk/build/macosx-x86_64-server-fastdebug/hotspot/variant-server/libjvm/objs/precompiled/precompiled.hpp.pch -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D_GNU_SOURCE -pipe -fno-rtti -fno-exceptions -fvisibility=hidden -fno-strict-aliasing -fno-omit-frame-pointer -flimit-debug-info -mno-omit-leaf-frame-pointer -mstack-alignment=16 -std=c++14 -DMAC_OS_X_VERSION_MIN_REQUIRED=10120 -mmacosx-version-min=10.12.0 -DLIBC=default -D_ALLBSD_SOURCE -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE -Wall -Wextra -Wformat=2 -Wpointer-arith -Wsign-compare -Wreorder -Wunused-function -Wundef -Wunused-value -Woverloaded-virtual -fPIC -DVM_LITTLE_ENDIAN -D_LP64=1 -fno-delete-null-pointer-checks -m64 -arch x86_64 -DASSERT -DCHECK_UNHANDLED_OOPS -DTARGET_ARCH_x86 -DINCLUDE_SUFFIX_OS=_bsd -DINCLUDE_SUFFIX_CPU=_x86 -DINCLUDE_SUFFIX_COMPILER=_gcc -DTARGET_COMPILER_gcc -DAMD64 -DHOTSPOT_LIB_ARCH='\"amd64\"' -DCOMPILER1 -DCOMPILER2 -DDTRACE_ENABLED -I/Users/<my user name>/workspace/jdk/build/macosx-x86_64-server-fastdebug/hotspot/variant-server/gensrc/adfiles -I/Users/<my user name>/workspace/jdk/src/hotspot/share -I/Users/<my user name>/workspace/jdk/src/hotspot/os/bsd -I/Users/<my user name>/workspace/jdk/src/hotspot/os/posix -I/Users/<my user name>/workspace/jdk/src/hotspot/cpu/x86 -I/Users/<my user name>/workspace/jdk/src/hotspot/os_cpu/bsd_x86 -I/Users/<my user name>/workspace/jdk/build/macosx-x86_64-server-fastdebug/hotspot/variant-server/gensrc -I/Users/<my user name>/workspace/jdk/src/hotspot/share/precompiled -I/Users/<my user name>/workspace/jdk/src/hotspot/share/include -I/Users/<my user name>/workspace/jdk/src/hotspot/os/posix/include -I/Users/<my user name>/workspace/jdk/build/macosx-x86_64-server-fastdebug/support/modules_include/java.base -I/Users/<my user name>/workspace/jdk/build/macosx-x86_64-server-fastdebug/support/modules_include/java.base/darwin -I/Users/<my user name>/workspace/jdk/src/java.base/share/native/libjimage -m64 -arch x86_64 -I/Users/<my user name>/workspace/jdk/build/macosx-x86_64-server-fastdebug/hotspot/variant-server/gensrc/adfiles -I/Users/<my user name>/workspace/jdk/src/hotspot/share -I/Users/<my user name>/workspace/jdk/src/hotspot/os/bsd -I/Users/<my user name>/workspace/jdk/src/hotspot/os/posix -I/Users/<my user name>/workspace/jdk/src/hotspot/cpu/x86 -I/Users/<my user name>/workspace/jdk/src/hotspot/os_cpu/bsd_x86 -I/Users/<my user name>/workspace/jdk/build/macosx-x86_64-server-fastdebug/hotspot/variant-server/gensrc -g -Wno-unknown-warning-option -Wno-unused-parameter -Wno-unused -Wno-tautological-compare -Wno-undefined-var-template -Wno-sometimes-uninitialized -Wno-unknown-pragmas -Wno-delete-non-virtual-dtor -Wno-missing-braces -Wno-char-subscripts -Wno-ignored-qualifiers -Wno-missing-field-initializers -Wno-mismatched-tags -Wno-shift-negative-value -Wno-misleading-indentation -Werror -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.1.sdk -iframework /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.1.sdk/System/Library/Frameworks -O3 -c -o /Users/<my user name>/workspace/jdk/build/macosx-x86_64-server-fastdebug/hotspot/variant-server/libjvm/objs/abstractCompiler.o /Users/<my user name>/workspace/jdk/src/hotspot/share/compiler/abstractCompiler.cpp"
}

And in the command field, you will see something like -include-pch /Users/<my user name>/workspace/jdk/build/macosx-x86_64-server-fastdebug/hotspot/variant-server/libjvm/objs/precompiled/precompiled.hpp.pch

Well actually, the precompiled.hpp.pch is not generated.

As a workaround, I add extra argument --disable-precompiled-headers:

bash configure --with-debug-level=fastdebug --disable-precompiled-headers

That makes compile_commands.json does not configure -include-pch argument, and CLion can continue to open the project and index source code.