Index: llvm/trunk/lib/Transforms/Instrumentation/GCOVProfiling.cpp
===================================================================
--- llvm/trunk/lib/Transforms/Instrumentation/GCOVProfiling.cpp
+++ llvm/trunk/lib/Transforms/Instrumentation/GCOVProfiling.cpp
@@ -494,6 +494,11 @@
     // LTO, we'll generate the same .gcno files.
 
     auto *CU = cast<DICompileUnit>(CU_Nodes->getOperand(i));
+
+    // Skip module skeleton (and module) CUs.
+    if (CU->getDWOId())
+      continue;
+
     std::error_code EC;
     raw_fd_ostream out(mangleName(CU, "gcno"), EC, sys::fs::F_None);
     std::string EdgeDestinations;
@@ -853,6 +858,11 @@
   if (CU_Nodes) {
     for (unsigned i = 0, e = CU_Nodes->getNumOperands(); i != e; ++i) {
       auto *CU = cast<DICompileUnit>(CU_Nodes->getOperand(i));
+
+      // Skip module skeleton (and module) CUs.
+      if (CU->getDWOId())
+        continue;
+
       std::string FilenameGcda = mangleName(CU, "gcda");
       uint32_t CfgChecksum = FileChecksums.empty() ? 0 : FileChecksums[i];
       Builder.CreateCall(StartFile,
Index: llvm/trunk/test/Transforms/GCOVProfiling/modules.ll
===================================================================
--- llvm/trunk/test/Transforms/GCOVProfiling/modules.ll
+++ llvm/trunk/test/Transforms/GCOVProfiling/modules.ll
@@ -0,0 +1,12 @@
+; RUN: opt -insert-gcov-profiling -o - < %s | llvm-dis | FileCheck -check-prefix=EMIT-ARCS %s
+
+; EMIT-ARCS-NOT: call void @llvm_gcda_start_file
+
+!llvm.dbg.cu = !{!0}
+!llvm.module.flags = !{!3, !4}
+
+!0 = distinct !DICompileUnit(language: DW_LANG_C99, file: !1, producer: "LLVM", isOptimized: false, runtimeVersion: 2, splitDebugFilename: "my.dwo", emissionKind: 1, enums: !2, retainedTypes: !2, subprograms: !2, globals: !2, imports: !2, dwoId: 43981)
+!1 = !DIFile(filename: "<stdin>", directory: "/")
+!2 = !{}
+!3 = !{i32 2, !"Dwarf Version", i32 4}
+!4 = !{i32 2, !"Debug Info Version", i32 3}