Index: llvm/include/llvm/ProfileData/InstrProf.h
===================================================================
--- llvm/include/llvm/ProfileData/InstrProf.h
+++ llvm/include/llvm/ProfileData/InstrProf.h
@@ -1143,8 +1143,8 @@
 
 // Create a COMDAT variable INSTR_PROF_RAW_VERSION_VAR to make the runtime
 // aware this is an ir_level profile so it can set the version flag.
-void createIRLevelProfileFlagVar(Module &M, bool IsCS,
-                                 bool InstrEntryBBEnabled);
+GlobalVariable *createIRLevelProfileFlagVar(Module &M, bool IsCS,
+                                            bool InstrEntryBBEnabled);
 
 // Create the variable for the profile file name.
 void createProfileFileNameVar(Module &M, StringRef InstrProfileOutput);
Index: llvm/lib/ProfileData/InstrProf.cpp
===================================================================
--- llvm/lib/ProfileData/InstrProf.cpp
+++ llvm/lib/ProfileData/InstrProf.cpp
@@ -1098,10 +1098,14 @@
 bool isIRPGOFlagSet(const Module *M) {
   auto IRInstrVar =
       M->getNamedGlobal(INSTR_PROF_QUOTE(INSTR_PROF_RAW_VERSION_VAR));
-  if (!IRInstrVar || IRInstrVar->isDeclaration() ||
-      IRInstrVar->hasLocalLinkage())
+  if (!IRInstrVar || IRInstrVar->hasLocalLinkage())
     return false;
 
+  // For CSPGO, this variable might be marked as non-prevailing and we only
+  // have the decl.
+  if (IRInstrVar->isDeclaration())
+    return true;
+
   // Check if the flag is set.
   if (!IRInstrVar->hasInitializer())
     return false;
@@ -1137,8 +1141,8 @@
 
 // Create a COMDAT variable INSTR_PROF_RAW_VERSION_VAR to make the runtime
 // aware this is an ir_level profile so it can set the version flag.
-void createIRLevelProfileFlagVar(Module &M, bool IsCS,
-                                 bool InstrEntryBBEnabled) {
+GlobalVariable *createIRLevelProfileFlagVar(Module &M, bool IsCS,
+                                            bool InstrEntryBBEnabled) {
   const StringRef VarName(INSTR_PROF_QUOTE(INSTR_PROF_RAW_VERSION_VAR));
   Type *IntTy64 = Type::getInt64Ty(M.getContext());
   uint64_t ProfileVersion = (INSTR_PROF_RAW_VERSION | VARIANT_MASK_IR_PROF);
@@ -1155,6 +1159,7 @@
     IRLevelVersionVariable->setLinkage(GlobalValue::ExternalLinkage);
     IRLevelVersionVariable->setComdat(M.getOrInsertComdat(VarName));
   }
+  return IRLevelVersionVariable;
 }
 
 // Create the variable for the profile file name.
Index: llvm/lib/Transforms/Instrumentation/PGOInstrumentation.cpp
===================================================================
--- llvm/lib/Transforms/Instrumentation/PGOInstrumentation.cpp
+++ llvm/lib/Transforms/Instrumentation/PGOInstrumentation.cpp
@@ -110,6 +110,7 @@
 #include "llvm/Support/raw_ostream.h"
 #include "llvm/Transforms/Instrumentation.h"
 #include "llvm/Transforms/Utils/BasicBlockUtils.h"
+#include "llvm/Transforms/Utils/ModuleUtils.h"
 #include <algorithm>
 #include <cassert>
 #include <cstdint>
@@ -464,7 +465,8 @@
 private:
   bool runOnModule(Module &M) override {
     createProfileFileNameVar(M, InstrProfileOutput);
-    createIRLevelProfileFlagVar(M, /* IsCS */ true, PGOInstrumentEntry);
+    appendToCompilerUsed(
+        M, createIRLevelProfileFlagVar(M, /* IsCS */ true, PGOInstrumentEntry));
     return false;
   }
   std::string InstrProfileOutput;
@@ -1632,7 +1634,8 @@
 PreservedAnalyses
 PGOInstrumentationGenCreateVar::run(Module &M, ModuleAnalysisManager &AM) {
   createProfileFileNameVar(M, CSInstrName);
-  createIRLevelProfileFlagVar(M, /* IsCS */ true, PGOInstrumentEntry);
+  appendToCompilerUsed(
+      M, createIRLevelProfileFlagVar(M, /* IsCS */ true, PGOInstrumentEntry));
   return PreservedAnalyses::all();
 }
 
Index: llvm/test/Transforms/PGOProfile/lto_cspgo_gen.ll
===================================================================
--- /dev/null
+++ llvm/test/Transforms/PGOProfile/lto_cspgo_gen.ll
@@ -0,0 +1,32 @@
+; REQUIRES: x86-registered-target
+
+; RUN: opt -passes='thinlto-pre-link<O2>' --cs-profilegen-file=alloc -cspgo-kind=cspgo-instr-gen-pipeline -module-summary %s -o %t.bc
+; RUN: llvm-dis %t.bc -o - | FileCheck %s --check-prefix=IRPGOPRE
+
+; RUN: llvm-lto2 run -lto-cspgo-profile-file=alloc -lto-cspgo-gen -save-temps -o %t %t.bc \
+; RUN:   -r=%t.bc,f,px \
+; RUN:   -r=%t.bc,__llvm_profile_filename,x \
+; RUN:   -r=%t.bc,__llvm_profile_raw_version,x
+; RUN: llvm-dis %t.0.0.preopt.bc -o - | FileCheck %s --check-prefix=IRPGOBE
+
+; IRPGOPRE: @__llvm_profile_raw_version = constant i64
+; IRPGOBE: @__llvm_profile_raw_version = external constant i64
+
+target datalayout = "e-m:e-p270:32:32-p271:32:32-p272:64:64-i64:64-f80:128-n8:16:32:64-S128"
+target triple = "x86_64-unknown-linux-gnu"
+
+$f = comdat any
+
+; Function Attrs: nofree norecurse nosync nounwind readnone uwtable willreturn mustprogress
+define i32 @f() local_unnamed_addr #0 {
+entry:
+  ret i32 1
+}
+
+attributes #0 = { "target-cpu"="x86-64" }
+
+!llvm.module.flags = !{!0, !1, !2}
+
+!0 = !{i32 1, !"wchar_size", i32 4}
+!1 = !{i32 7, !"uwtable", i32 1}
+!2 = !{i32 1, !"ThinLTO", i32 0}