Confirmed on x86_64-linux-gnu, I'm reducing that.

Apparently, it's a very old issue, started with GCC 5.1.0:

$ cat 1.ii
namespace xercesc_2_7 {
class XercesDOMParser {
  void resetEntities();
};
void XercesDOMParser::resetEntities() {}
} // namespace xercesc_2_7

$ cat 2.ii
namespace xercesc_2_7 {
class XMLErrorReporter {
public:
  virtual ~XMLErrorReporter();
};
class XMLEntityHandler {
  virtual void resetEntities();
};
class AbstractDOMParser : XMLErrorReporter, XMLEntityHandler {};
class XercesDOMParser : AbstractDOMParser {
  void resetEntities();
};
inline void XercesDOMParser::resetEntities() {}
} // namespace xercesc_2_7

$ g++ -flto=16 -O2 -fno-inline 1.ii 2.ii
2.ii:10:7: warning: type 'struct XercesDOMParser' violates the C++ One Definition Rule [-Wodr]
   10 | class XercesDOMParser : AbstractDOMParser {
      |       ^
1.ii:2:7: note: a type with different bases is defined in another translation unit
    2 | class XercesDOMParser {
      |       ^
2.ii:13:13: warning: type of 'resetEntities' does not match original declaration [-Wlto-type-mismatch]
   13 | inline void XercesDOMParser::resetEntities() {}
      |             ^
1.ii:5:6: note: 'resetEntities' was previously declared here
    5 | void XercesDOMParser::resetEntities() {}
      |      ^
lto1: error: Alias and target's section differs
_ZN11xercesc_2_715XercesDOMParser13resetEntitiesEv/0 (resetEntities) @0x7f80058ea580
  Type: function definition analyzed
  Visibility: externally_visible prevailing_def_ironly public
  Address is taken.
  References: 
  Referring: *.LTHUNK0/2 (alias)_ZTVN11xercesc_2_715XercesDOMParserE/4 (addr)
  Read from file: /tmp/cc2Oyr2J.o
  Function flags: count:1073741824 (estimated locally)
  Called by: 
  Calls: 
lto1: error: Alias and target's comdat groups differs
_ZN11xercesc_2_715XercesDOMParser13resetEntitiesEv/0 (resetEntities) @0x7f80058ea580
  Type: function definition analyzed
  Visibility: externally_visible prevailing_def_ironly public
  Address is taken.
  References: 
  Referring: *.LTHUNK0/2 (alias)_ZTVN11xercesc_2_715XercesDOMParserE/4 (addr)
  Read from file: /tmp/cc2Oyr2J.o
  Function flags: count:1073741824 (estimated locally)
  Called by: 
  Calls: 
*.LTHUNK0/2 (*.LTHUNK0) @0x7f80058ea840
  Type: function definition analyzed alias
  Visibility: comdat_group:_ZN11xercesc_2_715XercesDOMParser13resetEntitiesEv section:.text._ZN11xercesc_2_715XercesDOMParser13resetEntitiesEv (implicit_section) artificial
  Same comdat group as: _ZThn8_N11xercesc_2_715XercesDOMParser13resetEntitiesEv/3
  References: _ZN11xercesc_2_715XercesDOMParser13resetEntitiesEv/0 (alias)
  Referring: 
  Read from file: /tmp/ccixDNgJ.o
  Function flags:
  Called by: _ZThn8_N11xercesc_2_715XercesDOMParser13resetEntitiesEv/3 (can throw external) 
  Calls: 
during IPA pass: pure-const
lto1: internal compiler error: verify_cgraph_node failed
0x88e42e cgraph_node::verify_node()
	/home/marxin/Programming/gcc/gcc/cgraph.c:3411
0x880d8c symtab_node::verify()
	/home/marxin/Programming/gcc/gcc/symtab.c:1268
0x8824ff symtab_node::verify_symtab_nodes()
	/home/marxin/Programming/gcc/gcc/symtab.c:1288
0xaf0f5f symtab_node::checking_verify_symtab_nodes()
	/home/marxin/Programming/gcc/gcc/cgraph.h:648
0xaf0f5f symbol_table::remove_unreachable_nodes(_IO_FILE*)
	/home/marxin/Programming/gcc/gcc/ipa.c:667
0x80c54e read_cgraph_and_symbols(unsigned int, char const**)
	/home/marxin/Programming/gcc/gcc/lto/lto-common.c:2910
0x7f2da2 lto_main()
	/home/marxin/Programming/gcc/gcc/lto/lto.c:629
Please submit a full bug report,
with preprocessed source if appropriate.
Please include the complete backtrace with any bug report.
See <https://gcc.gnu.org/bugs/> for instructions.
lto-wrapper: fatal error: g++ returned 1 exit status
compilation terminated.
/usr/bin/ld: error: lto-wrapper failed
collect2: error: ld returned 1 exit status

It's related to PR92599. It's also an ODR violation that leads to the ICE.

(In reply to Martin Liška from comment #3)
> It's related to PR92599. It's also an ODR violation that leads to the ICE.

So it must be something different. There are source files which do not violate ODR:

$ cat 1.ii
unsigned short a;
namespace xercesc_2_7 {
class MemoryManager;
class XMemory {};
class XMLErrorReporter {
  virtual void resetErrors();
};
class XMLBuffer {};
class XMLBufferMgr {
  unsigned fBufCount;
  MemoryManager *fMemoryManager;
  XMLBuffer **fBufList;
};
template <class> class RefVectorOf;
class XMLStringPool;
class GrammarResolver;
class XMLValidator;
template <class> class ValueStackOf;
class XMLEntityHandler;
class ErrorHandler;
class XMLScanner {
public:
  XMLEntityHandler *fEntityHandler;
};
class SGXMLScanner : XMLScanner {
  int *resolveSystemId();
};
class XMLDocumentHandler {
  virtual void endEntityReference();
};
class XMLEntityHandler {
public:
  virtual bool expandSystemId(const unsigned short *, XMLBuffer &);
};
class PSVIHandler {
  virtual void handleElementPSVI();
};
class DOMNode;
class DOMEntity;
class DocTypeHandler {
  virtual void startIntSubset();
};
class DOMDocumentImpl;
class DOMDocumentTypeImpl;
class XMLGrammarPool;
class AbstractDOMParser : XMemory,
                          XMLDocumentHandler,
                          XMLErrorReporter,
                          XMLEntityHandler,
                          DocTypeHandler,
                          PSVIHandler {
  bool fCreateEntityReferenceNodes;
  bool fIncludeIgnorableWhitespace;
  bool fWithinElement;
  bool fParseInProgress;
  bool fCreateCommentNodes;
  bool fDocumentAdoptedByUser;
  bool fCreateSchemaInfo;
  XMLScanner *fScanner;
  unsigned short *fImplementationFeatures;
  DOMNode *fCurrentParent;
  DOMNode *fCurrentNode;
  DOMEntity *fCurrentEntity;
  DOMDocumentImpl *fDocument;
  ValueStackOf<DOMNode *> *fNodeStack;
  DOMDocumentTypeImpl *fDocumentType;
  RefVectorOf<DOMDocumentImpl> *fDocumentVector;
  GrammarResolver *fGrammarResolver;
  XMLStringPool *fURIStringPool;
  XMLValidator *fValidator;
  MemoryManager *fMemoryManager;
  XMLGrammarPool *fGrammarPool;
  XMLBufferMgr fBufMgr;
  XMLBuffer &fInternalSubset;
  PSVIHandler *fPSVIHandler;
};
class EntityResolver;
class XMLEntityResolver;
class XercesDOMParser : AbstractDOMParser {
  virtual void error();
  bool expandSystemId(const unsigned short *, XMLBuffer &);
  EntityResolver *fEntityResolver;
  XMLEntityResolver *fXMLEntityResolver;
  ErrorHandler *fErrorHandler;
};
inline bool XercesDOMParser::expandSystemId(const unsigned short *,
                                            XMLBuffer &) { return false; }
int *SGXMLScanner::resolveSystemId() {
  XMLBuffer b;
  fEntityHandler->expandSystemId(&a, b);
  return 0;
}
} // namespace xercesc_2_7

$ cat 2.ii
namespace xercesc_2_7 {
class DOMNode;
class DOMEntity;
class MemoryManager;
class XMemory {};
class XMLErrorReporter {
public:
  virtual ~XMLErrorReporter();
};
template <class> class RefVectorOf;
class XMLDocumentHandler {
  virtual void XMLDecl();
};
class XMLBuffer;
class XMLEntityHandler {
  virtual bool expandSystemId(const unsigned short *, XMLBuffer &);
};
template <class> class ValueStackOf;
class GrammarResolver;
class XMLStringPool;
class DocTypeHandler {
public:
  virtual ~DocTypeHandler();
};
class XMLBufferMgr {
  unsigned fBufCount;
  MemoryManager *fMemoryManager;
  XMLBuffer **fBufList;
};
class PSVIHandler {
  virtual void handlePartialElementPSVI();
};
class XMLScanner;
class XMLValidator;
class DOMDocumentImpl;
class DOMDocumentTypeImpl;
class XMLGrammarPool;
class AbstractDOMParser : XMemory,
                          XMLDocumentHandler,
                          XMLErrorReporter,
                          XMLEntityHandler,
                          DocTypeHandler,
                          PSVIHandler {
  bool fCreateEntityReferenceNodes;
  bool fIncludeIgnorableWhitespace;
  bool fWithinElement;
  bool fParseInProgress;
  bool fCreateCommentNodes;
  bool fDocumentAdoptedByUser;
  bool fCreateSchemaInfo;
  XMLScanner *fScanner;
  unsigned short *fImplementationFeatures;
  DOMNode *fCurrentParent;
  DOMNode *fCurrentNode;
  DOMEntity *fCurrentEntity;
  DOMDocumentImpl *fDocument;
  ValueStackOf<DOMNode *> *fNodeStack;
  DOMDocumentTypeImpl *fDocumentType;
  RefVectorOf<DOMDocumentImpl> *fDocumentVector;
  GrammarResolver *fGrammarResolver;
  XMLStringPool *fURIStringPool;
  XMLValidator *fValidator;
  MemoryManager *fMemoryManager;
  XMLGrammarPool *fGrammarPool;
  XMLBufferMgr fBufMgr;
  XMLBuffer &fInternalSubset;
  PSVIHandler *fPSVIHandler;
};
class EntityResolver;
class ErrorHandler;
class XMLEntityResolver;
class XercesDOMParser : AbstractDOMParser {
  bool expandSystemId(const unsigned short *, XMLBuffer &);
  EntityResolver *fEntityResolver;
  XMLEntityResolver *fXMLEntityResolver;
  ErrorHandler *fErrorHandler;
};
inline bool XercesDOMParser::expandSystemId(const unsigned short *,
                                            XMLBuffer &) { return false; }
} // namespace xercesc_2_7

$ g++-9 -O2 -flto -fno-inline -shared -fPIC 1.ii 2.ii -fchecking
lto1: error: Two symbols with same comdat_group are not linked by the same_comdat_group list.
_ZN11xercesc_2_715XercesDOMParser14expandSystemIdEPKtRNS_9XMLBufferE/7 (expandSystemId) @0x7f9cfcb50b40
  Type: function definition analyzed
  Visibility: externally_visible undef public weak comdat comdat_group:_ZN11xercesc_2_715XercesDOMParser14expandSystemIdEPKtRNS_9XMLBufferE one_only section:.text._ZN11xercesc_2_715XercesDOMParser14expandSystemIdEPKtRNS_9XMLBufferE (implicit_section) virtual
  Address is taken.
  References: 
  Referring: *.LTHUNK0/2 (alias)_ZTVN11xercesc_2_715XercesDOMParserE/10 (addr)
  Read from file: /tmp/cchvQQd7.o
  Function flags: count:1073741824 (estimated locally)
  Called by: 
  Calls: 
_ZThn16_N11xercesc_2_715XercesDOMParser14expandSystemIdEPKtRNS_9XMLBufferE/3 (_ZThn16_N11xercesc_2_715XercesDOMParser14expandSystemIdEPKtRNS_9XMLBufferE) @0x7f9cfcb50870
  Type: function definition analyzed
  Visibility: externally_visible prevailing_def_ironly_exp public weak comdat comdat_group:_ZN11xercesc_2_715XercesDOMParser14expandSystemIdEPKtRNS_9XMLBufferE one_only section:.text._ZN11xercesc_2_715XercesDOMParser14expandSystemIdEPKtRNS_9XMLBufferE (implicit_section) virtual artificial
  Same comdat group as: *.LTHUNK0/2
  Address is taken.
  References: 
  Referring: _ZTVN11xercesc_2_715XercesDOMParserE/10 (addr)
  Read from file: /tmp/cceOf484.o
  Function flags: calls_comdat_local merged_comdat
  Thunk fixed offset -16 virtual value 0 indirect_offset 0 has virtual offset 0
  Called by: 
  Calls: *.LTHUNK0/2 
(null):0: confused by earlier errors, bailing out
lto-wrapper: fatal error: g++-9 returned 1 exit status
compilation terminated.
/usr/lib64/gcc/x86_64-suse-linux/9/../../../../x86_64-suse-linux/bin/ld: error: lto-wrapper failed
collect2: error: ld returned 1 exit status

Started with r267359.

Created attachment 47621 [details]
Clean up test-case

So the now the diff of the source file is minimal:

$ diff -u 1.ii 2.ii
--- 1.ii	2020-01-09 17:14:33.000405474 +0100
+++ 2.ii	2020-01-09 17:14:33.000405474 +0100
@@ -79,7 +79,6 @@
 class ErrorHandler;
 class XMLEntityResolver;
 class XercesDOMParser : AbstractDOMParser {
-  virtual void error_that_causes_ice();
   bool expandSystemId(const unsigned short *, XMLBuffer &);
   EntityResolver *fEntityResolver;
   XMLEntityResolver *fXMLEntityResolver;
@@ -87,10 +86,4 @@
 };
 inline bool XercesDOMParser::expandSystemId(const unsigned short *,
                                             XMLBuffer &) { return false; }
-int *SGXMLScanner::resolveSystemId() {
-  unsigned short a;
-  XMLBuffer b;
-  fEntityHandler->expandSystemId(&a, b);
-  return 0;
-}
 } // namespace xercesc_2_7

Honza, does it explain now better?

Well, because the source files differs, the comdat group differs and the loosing one has fewer symbols in it.  So we end up keeping some symbols from the other comdat group that happens to have same name.  The compilation is bound to fail, so I guess question is how best to silence the ICE.  I suppose we may get around by dissoling comdat groups of all UNDEF symbols

(In reply to Jan Hubicka from comment #6)
> Well, because the source files differs, the comdat group differs and the
> loosing one has fewer symbols in it.  So we end up keeping some symbols from
> the other comdat group that happens to have same name.  The compilation is
> bound to fail, so I guess question is how best to silence the ICE.  I
> suppose we may get around by dissoling comdat groups of all UNDEF symbols

Btw. is this a violation of ODR? Maybe, we could provide a warning for such a situation?

GCC 9.3.0 has been released, adjusting target milestone.

GCC 9.4 is being released, retargeting bugs to GCC 9.5.

The undefined testcase is almost definitely a dup of bug 87501. I have not looked into it otherwise.

GCC 9 branch is being closed

GCC 10.4 is being released, retargeting bugs to GCC 10.5.

GCC 10 branch is being closed.