Index: llvm/trunk/lib/LTO/LTO.cpp
===================================================================
--- llvm/trunk/lib/LTO/LTO.cpp
+++ llvm/trunk/lib/LTO/LTO.cpp
@@ -472,6 +472,36 @@
   return Error::success();
 }
 
+// Checks whether the given global value is in a non-prevailing comdat
+// (comdat containing values the linker indicated were not prevailing,
+// which we then dropped to available_externally), and if so, removes
+// it from the comdat. This is called for all global values to ensure the
+// comdat is empty rather than leaving an incomplete comdat. It is needed for
+// regular LTO modules, in case we are in a mixed-LTO mode (both regular
+// and thin LTO modules) compilation. Since the regular LTO module will be
+// linked first in the final native link, we want to make sure the linker
+// doesn't select any of these incomplete comdats that would be left
+// in the regular LTO module without this cleanup.
+static void
+handleNonPrevailingComdat(GlobalValue &GV,
+                          std::set<const Comdat *> &NonPrevailingComdats) {
+  Comdat *C = GV.getComdat();
+  if (!C)
+    return;
+
+  if (!NonPrevailingComdats.count(C))
+    return;
+
+  // Additionally need to drop externally visible global values from the comdat
+  // to available_externally, so that there aren't multiply defined linker
+  // errors.
+  if (!GV.hasLocalLinkage())
+    GV.setLinkage(GlobalValue::AvailableExternallyLinkage);
+
+  if (auto GO = dyn_cast<GlobalObject>(&GV))
+    GO->setComdat(nullptr);
+}
+
 // Add a regular LTO object to the link.
 // The resulting module needs to be linked into the combined LTO module with
 // linkRegularLTO.
@@ -523,6 +553,7 @@
   };
   Skip();
 
+  std::set<const Comdat *> NonPrevailingComdats;
   for (const InputFile::Symbol &Sym : Syms) {
     assert(ResI != ResE);
     SymbolResolution Res = *ResI++;
@@ -557,6 +588,8 @@
         // module (in linkRegularLTO), based on whether it is undefined.
         Mod.Keep.push_back(GV);
         GV->setLinkage(GlobalValue::AvailableExternallyLinkage);
+        if (GV->hasComdat())
+          NonPrevailingComdats.insert(GV->getComdat());
         cast<GlobalObject>(GV)->setComdat(nullptr);
       }
     }
@@ -574,6 +607,9 @@
 
     // FIXME: use proposed local attribute for FinalDefinitionInLinkageUnit.
   }
+  if (!M.getComdatSymbolTable().empty())
+    for (GlobalValue &GV : M.global_values())
+      handleNonPrevailingComdat(GV, NonPrevailingComdats);
   assert(MsymI == MsymE);
   return std::move(Mod);
 }
Index: llvm/trunk/test/LTO/Resolution/X86/Inputs/comdat-mixed-lto.ll
===================================================================
--- llvm/trunk/test/LTO/Resolution/X86/Inputs/comdat-mixed-lto.ll
+++ llvm/trunk/test/LTO/Resolution/X86/Inputs/comdat-mixed-lto.ll
@@ -0,0 +1,23 @@
+; ModuleID = 'comdat-mixed-lto1.o'
+source_filename = "comdat-mixed-lto1.cpp"
+target datalayout = "e-m:e-i64:64-f80:128-n8:16:32:64-S128"
+target triple = "x86_64-unknown-linux-gnu"
+
+%"class.Test::ptr" = type { i32 }
+
+$C = comdat any
+
+@C = linkonce_odr global %"class.Test::ptr" zeroinitializer, comdat, align 4
+@llvm.global_ctors = appending global [1 x { i32, void ()*, i8* }] [{ i32, void ()*, i8* } { i32 65535, void ()* @__cxx_global_var_init, i8* bitcast (%"class.Test::ptr"* @C to i8*) }]
+
+define void @testglobfunc() #1 section ".text.startup" comdat($C) {
+entry:
+  ret void
+}
+
+; Function Attrs: noinline uwtable
+define internal void @__cxx_global_var_init() #1 section ".text.startup" comdat($C) {
+entry:
+  store i32 0, i32* getelementptr inbounds (%"class.Test::ptr", %"class.Test::ptr"* @C, i32 0, i32 0), align 4
+  ret void
+}
Index: llvm/trunk/test/LTO/Resolution/X86/comdat-mixed-lto.ll
===================================================================
--- llvm/trunk/test/LTO/Resolution/X86/comdat-mixed-lto.ll
+++ llvm/trunk/test/LTO/Resolution/X86/comdat-mixed-lto.ll
@@ -0,0 +1,42 @@
+; Test of comdat handling with mixed thinlto and regular lto compilation.
+
+; This module is compiled with ThinLTO
+; RUN: opt -module-summary -o %t1.o %s
+; Input module compiled for regular LTO
+; RUN: opt -o %t2.o %p/Inputs/comdat-mixed-lto.ll
+
+; The copy of C from this module is prevailing. The copy of C from the
+; regular LTO module is not prevailing, and will be dropped to
+; available_externally.
+; RUN: llvm-lto2 run -r=%t1.o,C,pl -r=%t2.o,C,l -r=%t2.o,testglobfunc,lxp -r=%t1.o,testglobfunc,lx -o %t3 %t1.o %t2.o -save-temps
+
+; The Input module (regular LTO) is %t3.0. Check to make sure that we removed
+; __cxx_global_var_init and testglobfunc from comdat. Also check to ensure
+; that testglobfunc was dropped to available_externally. Otherwise we would
+; have linker multiply defined errors as it is no longer in a comdat and
+; would clash with the copy from this module.
+; RUN: llvm-dis %t3.0.0.preopt.bc -o - | FileCheck %s
+; CHECK: define internal void @__cxx_global_var_init() section ".text.startup" {
+; CHECK: define available_externally void @testglobfunc() section ".text.startup" {
+
+; ModuleID = 'comdat-mixed-lto.o'
+source_filename = "comdat-mixed-lto.cpp"
+target datalayout = "e-m:e-i64:64-f80:128-n8:16:32:64-S128"
+target triple = "x86_64-unknown-linux-gnu"
+
+%"class.Test::ptr" = type { i32 }
+
+$C = comdat any
+
+@C = linkonce_odr global %"class.Test::ptr" zeroinitializer, comdat, align 4
+@llvm.global_ctors = appending global [1 x { i32, void ()*, i8* }] [{ i32, void ()*, i8* } { i32 65535, void ()* @__cxx_global_var_init, i8* bitcast (%"class.Test::ptr"* @C to i8*) }]
+define void @testglobfunc() #1 section ".text.startup" comdat($C) {
+entry:
+  ret void
+}
+
+; Function Attrs: noinline uwtable
+define internal void @__cxx_global_var_init() #1 section ".text.startup" comdat($C) {
+entry:
+  ret void
+}