Calorimeter/CaloRec/python/CaloCellGetter.py

-# Copyright (C) 2002-2019 CERN for the benefit of the ATLAS collaboration
+# Copyright (C) 2002-2020 CERN for the benefit of the ATLAS collaboration
 
 # specifies Calo cell making
 # so far only handle the RawChannel->CaloCell step
@@ -141,7 +141,7 @@ class CaloCellGetter (Configured)  :
                         if 'doTileOpt2' not in dir():
                             from RecExConfig.AutoConfiguration import GetRunNumber
                             rn = GetRunNumber()
-                            if rn > 0 and rn < 171194:  
+                            if not athenaCommonFlags.isOnline() and rn > 0 and rn < 171194:
                                 doTileOpt2 = True
                             elif jobproperties.Beam.beamType()=='collisions':
                                 doTileOpt2 = False # use OF without iterations for collisions

Control/AthenaConfiguration/python/ComponentAccumulator.py

@@ -121,6 +121,8 @@ class ComponentAccumulator(object):
              log = logging.getLogger("ComponentAccumulator")
              log.error("This ComponentAccumulator was never merged!")
              log.error(self._inspect())
+             import traceback
+             traceback.print_stack()
          if getattr(self,'_privateTools',None) is not None:
              log = logging.getLogger("ComponentAccumulator")
              log.error("Deleting a ComponentAccumulator with dangling private tool(s)")

DataQuality/DataQualityUtils/scripts/physval_make_web_display.py

@@ -27,6 +27,10 @@ worst = DQAlgorithm(id='WorstCaseSummary',libname='libdqm_summaries.so')
 algorithmparameters = [DQAlgorithmParameter('AuxAlgName--Chi2Test_Chi2_per_NDF', 1),
                        DQAlgorithmParameter('RepeatAlgorithm--ResultsNEntries', 1)]
 
+# this will be used if no references are provided
+norefalgorithm = DQAlgorithm(id='GatherData',
+                             libname='libdqm_algorithms.so')
+
 # Edit this to change thresholds
 thresh = make_thresholds('Chi2_per_NDF', 1.0, 1.50, 'Chi2Thresholds')
 
@@ -58,11 +62,7 @@ def recurse(rdir, dqregion, ignorepath, modelrefs=[], displaystring='Draw=PE', d
             elif regex:
                 if not regex.match(name): continue
             dqpargs = { 'id' : ('' if fpath else 'top_level/') + name,
-                        'algorithm': repeatalgorithm,
                         'inputdatasource': (startpath + '/' if startpath else '') + name,
-                        'algorithmparameters': algorithmparameters,
-                        #'thresholds': chi2thresh,
-                        'thresholds': thresh,
                         }
             if modelrefs:
                 lnewrefs = []
@@ -70,7 +70,13 @@ def recurse(rdir, dqregion, ignorepath, modelrefs=[], displaystring='Draw=PE', d
                     newref = DQReference(manglefunc(mref.getReference().replace('same_name', (startpath + '/' if startpath else '') + name), mref.id))
                     newref.addAnnotation('info', mref.id)
                     lnewrefs.append(newref)
-                dqpargs['references'] = lnewrefs
+                dqpargs.update({'algorithm': repeatalgorithm,
+                                'algorithmparameters': algorithmparameters,
+                                'thresholds': thresh,
+                                'references': lnewrefs
+                                })
+            else:
+                dqpargs['algorithm'] = norefalgorithm
             dqpar = dqregion.newDQParameter( **dqpargs)
             drawstrs = []
             if not options.normalize: drawstrs.append('NoNorm')

Database/APR/ImplicitCollection/CMakeLists.txt

@@ -11,7 +11,7 @@ atlas_add_library( ImplicitCollection
                    src/*.cpp
                    NO_PUBLIC_HEADERS
                    PRIVATE_INCLUDE_DIRS ${CORAL_INCLUDE_DIRS}
-                   PRIVATE_LINK_LIBRARIES ${CORAL_LIBRARIES} CollectionBase POOLCore PersistencySvc PersistentDataModel StorageSvc )
+                   PRIVATE_LINK_LIBRARIES ${CORAL_LIBRARIES} AthenaKernel CollectionBase POOLCore PersistencySvc PersistentDataModel StorageSvc )
 
 # Component list generation:
 atlas_generate_componentslist( ImplicitCollection )

Database/APR/RootCollection/CMakeLists.txt

@@ -20,8 +20,8 @@ atlas_add_library( RootCollection
                    INCLUDE_DIRS ${ROOT_INCLUDE_DIRS}
                    PRIVATE_INCLUDE_DIRS ${CORAL_INCLUDE_DIRS}
                    LINK_LIBRARIES ${ROOT_LIBRARIES} RootUtilsPyROOT
-                   PRIVATE_LINK_LIBRARIES ${CORAL_LIBRARIES} CollectionBase
-                   GaudiKernel POOLCore PersistencySvc PersistentDataModel RootUtils )
+                   PRIVATE_LINK_LIBRARIES ${CORAL_LIBRARIES} AthenaKernel CollectionBase
+                   FileCatalog GaudiKernel POOLCore PersistencySvc PersistentDataModel RootUtils )
 
 atlas_add_library( RootCollectionComponents
                    NO_PUBLIC_HEADERS

Database/APR/RootStorageSvc/src/RootTreeContainer.cpp

@@ -206,7 +206,11 @@ DbStatus RootTreeContainer::writeObject( ActionList::value_type& action )
                    if( dsc.rows_written ) {
                       // catch up with the rows written by other branches
                       newBrDsc.object = nullptr;
-                      newBrDsc.branch->SetAddress( nullptr );
+                      // As of root 6.22, calling SetAddress with nullptr
+                      // may not work as expected if the address had
+                      // previously been set to something non-null.
+                      // So we need to create the temp object ourselves.
+                      newBrDsc.branch->SetAddress( newBrDsc.dummyAddr() );
                       for( size_t r=0; r<dsc.rows_written; ++r ) {
                          num_bytes += newBrDsc.branch->BackFill();
                       }
@@ -261,8 +265,12 @@ DbStatus RootTreeContainer::writeObject( ActionList::value_type& action )
       BranchDesc& dsc = descMapElem.second;
       if( !dsc.written ) {
          dsc.object = nullptr;
-         dsc.branch->SetAddress( nullptr );
-         // cout << "   Branch " <<  SG::AuxTypeRegistry::instance().getName(descMapElem.first) << " filled out with NULL" << endl;
+         // As of root 6.22, calling SetAddress with nullptr
+         // may not work as expected if the address had
+         // previously been set to something non-null.
+         // So we need to create the temp object ourselves.
+         dsc.branch->SetAddress( dsc.dummyAddr() );
+         // cout << "   aaa Branch " <<  SG::AuxTypeRegistry::instance().getName(descMapElem.first) << " filled out with NULL" << endl;
          if( isBranchContainer() && !m_treeFillMode ) {
             size_t bytes_out = dsc.branch->Fill();
             num_bytes += bytes_out;

Database/APR/RootStorageSvc/src/RootTreeContainer.h

 /*
-  Copyright (C) 2002-2019 CERN for the benefit of the ATLAS collaboration
+  Copyright (C) 2002-2020 CERN for the benefit of the ATLAS collaboration
 */
 
 //====================================================================
@@ -22,6 +22,7 @@
 #include <map>
 #include <vector>
 #include <set>
+#include <functional>
 
 // Forward declarations
 class TObject;
@@ -76,6 +77,13 @@ namespace pool  {
       bool              is_basic_type = false;
       bool              written = false;
       
+      // Dummy object instance; used when there was no request to write
+      // this branch but we need to write it anyway (for example,
+      // a dynamic variable that wasn't written on this event).
+      using dummy_ptr_t = std::unique_ptr<void, std::function<void(void*)> >;
+      dummy_ptr_t dummyptr;
+      void* dummy = 0;
+      
       BranchDesc()
             : clazz(nullptr), 
               branch(nullptr),
@@ -99,6 +107,20 @@ namespace pool  {
       {}
       // difference for branch.setAddress() for objects and basic types, used by Aux dynamic 
       void*     objectAddr() { return is_basic_type? object : &object; }
+
+      void*     dummyAddr()
+      {
+        if (clazz) {
+          if (!dummy) {
+            using std::placeholders::_1;
+            std::function<void(void*)> del = std::bind (&TClass::Destructor, clazz, _1, false);
+            dummyptr = dummy_ptr_t (clazz->New(), std::move(del));
+            dummy = dummyptr.get();
+          }
+          return &dummy;
+        }
+        return nullptr;
+      }
     };
 
     /// Definition of the branch container

Database/AthenaPOOL/RootConversions/RootConversions/ATLAS_CHECK_THREAD_SAFETY

+Database/AthenaPOOL/RootConversions

Database/AthenaPOOL/RootConversions/RootConversions/TConverterRegistry.h

 // This file's extension implies that it's C, but it's really -*- C++ -*-.
 
 /*
-  Copyright (C) 2002-2017 CERN for the benefit of the ATLAS collaboration
+  Copyright (C) 2002-2020 CERN for the benefit of the ATLAS collaboration
 */
-
-// $Id: TConverterRegistry.h,v 1.4 2008-11-04 12:42:10 ssnyder Exp $
 /**
  * @file TConverterRegistry.h
  * @author scott snyder <snyder@bnl.gov>
@@ -30,6 +28,7 @@
 
 #include <string>
 #include <map>
+#include <mutex>
 #include "Rtypes.h"
 class TVirtualConverter;
 class TMemberStreamer;
@@ -116,6 +115,10 @@ private:
   /// Map of registered converters.
   MapType fMap;
 
+  /// Protect access to the map.
+  mutable std::mutex fMutex;
+  using lock_t = std::lock_guard<std::mutex>;
+
   /// Streamer converters.
 #ifndef __CLING__
   typedef std::map<std::string, TMemberStreamer*> SMapType;

Database/AthenaPOOL/RootConversions/RootConversions/TConvertingBranchElement.h

 // This file's extension implies that it's C, but it's really -*- C++ -*-.
 
 /*
-  Copyright (C) 2002-2017 CERN for the benefit of the ATLAS collaboration
+  Copyright (C) 2002-2020 CERN for the benefit of the ATLAS collaboration
 */
-
-// $Id: TConvertingBranchElement.h,v 1.7 2008-04-25 20:35:13 ssnyder Exp $
 /**
  * @file TConvertingBranchElement.h
  * @author scott snyder <snyder@bnl.gov>
@@ -55,6 +53,8 @@
 # pragma clang diagnostic pop
 #endif
 
+#include <atomic>
+
 class TVirtualConverter;
 
 /**
@@ -212,7 +212,7 @@ private:
   bool               fConvDontReset;     //! Flag that the next read should
                                          //  not reset the buffer pointer.
                                          //  See GetEntry().
-  static bool        fgDoDel;            //! If true, try to delete the
+  static std::atomic<bool> fgDoDel;      //! If true, try to delete the
                                          //  branch object when the branch
                                          //  is deleted.
 

Database/AthenaPOOL/RootConversions/RootConversions/TConvertingStreamerInfo.h

 // This file's extension implies that it's C, but it's really -*- C++ -*-.
 
 /*
-  Copyright (C) 2002-2017 CERN for the benefit of the ATLAS collaboration
+  Copyright (C) 2002-2020 CERN for the benefit of the ATLAS collaboration
 */
-
-// $Id: TConvertingStreamerInfo.h,v 1.1 2008-03-21 21:08:01 ssnyder Exp $
 /**
  * @file RootConversions/TConvertingStreamerInfo.h
  * @author scott snyder <snyder@bnl.gov>
@@ -129,7 +127,7 @@ private:
   ErrorHandlerFunc_t m_oldhand;
 
   /// Hook to get this object back from the static @c errhand.
-  static TConvertingStreamerInfo* s_self;
+  static thread_local TConvertingStreamerInfo* s_self;
 
 
   TConvertingStreamerInfo& operator= (const TConvertingStreamerInfo&);

Database/AthenaPOOL/RootConversions/RootConversions/TVirtualConverter.h

 // This file's extension implies that it's C, but it's really -*- C++ -*-.
 
 /*
-  Copyright (C) 2002-2017 CERN for the benefit of the ATLAS collaboration
+  Copyright (C) 2002-2020 CERN for the benefit of the ATLAS collaboration
 */
-
-// $Id: TVirtualConverter.h,v 1.5 2007-12-04 02:11:02 ssnyder Exp $
 /**
  * @file TVirtualConverter.h
  * @author scott snyder <snyder@bnl.gov>
@@ -163,12 +161,12 @@ public:
   /**
    * @brief Return the transient class, to which we're converting.
    */
-  TClass* GetTransClass () const;
+  TClass* GetTransClass ();
 
   /**
    * @brief Return the persistent class, from which we're converting.
    */
-  TClass* GetPersClass() const;
+  TClass* GetPersClass();
 
   /**
    * @brief Return the checksum of the class from which we're converting.

Database/AthenaPOOL/RootConversions/src/TConverterRegistry.cxx

 /*
-  Copyright (C) 2002-2017 CERN for the benefit of the ATLAS collaboration
+  Copyright (C) 2002-2020 CERN for the benefit of the ATLAS collaboration
 */
-
-// $Id: TConverterRegistry.cxx,v 1.6 2008-11-04 12:42:10 ssnyder Exp $
 /**
  * @file TConverterRegistry.cxx
  * @author scott snyder <snyder@bnl.gov>
@@ -17,6 +15,7 @@
 #include "RootConversions/TConverterRegistry.h"
 #include "RootConversions/TVirtualConverter.h"
 #include "RootConversions/TConverterStreamer.h"
+#include "CxxUtils/checker_macros.h"
 #include "TMemberStreamer.h"
 #include "TClass.h"
 #include "TROOT.h"
@@ -51,6 +50,7 @@ void TConverterRegistry::AddConverter (TVirtualConverter* conv)
 void TConverterRegistry::AddConverter (TVirtualConverter* conv,
                                        bool takeown)
 {
+  lock_t lock (fMutex);
   // Make sure the branch element is properly initialized.
   TConvertingBranchElement_init();
 
@@ -100,6 +100,7 @@ bool TConverterRegistry::AddConverter (const char* convname)
 TVirtualConverter* TConverterRegistry::GetConverter (const char* name,
                                                      int checksum) const
 {
+  lock_t lock (fMutex);
   MapType::const_iterator i = fMap.find (name);
   if (i != fMap.end()) {
     CheckSumMap::const_iterator i2 = i->second.find (checksum);
@@ -114,6 +115,7 @@ void TConverterRegistry::AddStreamerConverter (const std::string& from_type,
                                                const std::string& to_type,
                                                TMemberStreamer* streamer)
 {
+  lock_t lock (fMutex);
   std::string key = from_type + "-" + to_type;
   SMapType::const_iterator i = fSMap.find (key);
   if (i != fSMap.end())
@@ -126,6 +128,7 @@ TMemberStreamer*
 TConverterRegistry::GetStreamerConverter (const std::string& from_type,
                                           const std::string& to_type) const
 {
+  lock_t lock (fMutex);
   std::string key = from_type + "-" + to_type;
   SMapType::const_iterator i = fSMap.find (key);
   if (i != fSMap.end())
@@ -141,7 +144,7 @@ TConverterRegistry* TConverterRegistry::Instance()
 {
   // Do it like this so that the object gets destroyed automatically
   // at program termination.
-  static TConverterRegistry instance;
+  static TConverterRegistry instance ATLAS_THREAD_SAFE;
   return &instance;
 }
 

Database/AthenaPOOL/RootConversions/src/TConvertingBranchElement.cxx

@@ -32,7 +32,7 @@
 #include <cstdlib>
 
 
-bool TConvertingBranchElement::fgDoDel = false;
+std::atomic<bool> TConvertingBranchElement::fgDoDel = false;
 
 
 namespace {
@@ -1062,7 +1062,7 @@ void TConvertingBranchElement::ReadLeavesMemberBranchCountConverting(TBuffer& b)
    // For split-class branch, base class branch, data member branch, or top-level branch.
    // which do have a branch count and are not a counter.
    
-   R__ASSERT(fStreamerType != TVirtualStreamerInfo::kCounter);
+   assert(fStreamerType != TVirtualStreamerInfo::kCounter);
 
    ValidateAddress();
    if (fObject == 0)

Database/AthenaPOOL/RootConversions/src/TConvertingStreamerInfo.cxx

 /*
-  Copyright (C) 2002-2017 CERN for the benefit of the ATLAS collaboration
+  Copyright (C) 2002-2020 CERN for the benefit of the ATLAS collaboration
 */
-
-// $Id: TConvertingStreamerInfo.cxx,v 1.5 2009-05-12 19:09:54 ssnyder Exp $
 /**
  * @file RootConversions/src/TConvertingStreamerInfo.cxx
  * @author scott snyder <snyder@bnl.gov>
@@ -13,6 +11,7 @@
 
 #include "RootConversions/TConvertingStreamerInfo.h"
 #include "RootConversions/TConverterRegistry.h"
+#include "CxxUtils/checker_macros.h"
 #include "TStreamerElement.h"
 #include "TMemberStreamer.h"
 #include "TROOT.h"
@@ -22,10 +21,11 @@
 #include <vector>
 #include <cassert>
 #include <memory>
+#include <mutex>
 
 
 /// Hook to get this object back from the static @c errhand.
-TConvertingStreamerInfo* TConvertingStreamerInfo::s_self;
+thread_local TConvertingStreamerInfo* TConvertingStreamerInfo::s_self;
 
 
 /**
@@ -42,7 +42,10 @@ TConvertingStreamerInfo::TConvertingStreamerInfo()
  */
 void TConvertingStreamerInfo::Initialize()
 {
-  static bool initialized = false;
+  static bool initialized ATLAS_THREAD_SAFE = false;
+  static std::mutex initmutex;
+  std::lock_guard<std::mutex> lock (initmutex);
+
   if (initialized)
     return;
   initialized = true;

Database/AthenaPOOL/RootConversions/src/TVirtualConverter.cxx

@@ -212,7 +212,7 @@ TVirtualConverter::~TVirtualConverter()
 /**
  * @brief Return the transient class, to which we're converting.
  */
-TClass* TVirtualConverter::GetTransClass() const
+TClass* TVirtualConverter::GetTransClass()
 {
   return fTransClass;
 }
@@ -221,7 +221,7 @@ TClass* TVirtualConverter::GetTransClass() const
 /**
  * @brief Return the persistent class, from which we're converting.
  */
-TClass* TVirtualConverter::GetPersClass() const
+TClass* TVirtualConverter::GetPersClass()
 {
   return fPersClass;
 }
@@ -381,8 +381,7 @@ void TVirtualConverter::CheckStreamInfos()
         // class), and add it to the persistent class's list.
         TStreamerInfo* new_si =(TStreamerInfo*)(trans_sis->At(v)->Clone());
         new_si->SetClass (fPersClass);
-        // MN: consider using ROOT6  TClass::RegisterStreamerInfo(info)?
-        const_cast<TObjArray*>(pers_sis)->AddAtAndExpand (new_si, v);
+        fPersClass->RegisterStreamerInfo (new_si);
       }
     }
 

Database/IOVDbAthenaPool/CMakeLists.txt

-################################################################################
-# Package: IOVDbAthenaPool
-################################################################################
+# Copyright (C) 2002-2020 CERN for the benefit of the ATLAS collaboration
 
 # Declare the package name:
 atlas_subdir( IOVDbAthenaPool )
 
-# Declare the package's dependencies:
-atlas_depends_on_subdirs( PUBLIC
-                          Database/AthenaPOOL/AthenaPoolUtilities
-                          PRIVATE
-                          Database/AthenaPOOL/AthenaPoolCnvSvc
-                          Database/IOVDbDataModel
-                          Database/IOVDbTPCnv )
-
 # Component(s) in the package:
 atlas_add_poolcnv_library( IOVDbAthenaPoolPoolCnv
                            src/*.cxx
                            FILES IOVDbDataModel/IOVMetaDataContainer.h
-                           LINK_LIBRARIES AthenaPoolUtilities AthenaPoolCnvSvcLib IOVDbDataModel IOVDbTPCnv )
-
+                           LINK_LIBRARIES AthenaPoolCnvSvcLib IOVDbDataModel IOVDbTPCnv )

Database/IOVDbDataModel/CMakeLists.txt

-################################################################################
-# Package: IOVDbDataModel
-################################################################################
+# Copyright (C) 2002-2020 CERN for the benefit of the ATLAS collaboration
 
 # Declare the package name:
 atlas_subdir( IOVDbDataModel )
 
-# Declare the package's dependencies:
-atlas_depends_on_subdirs( PUBLIC
-                          Control/AthenaKernel
-                          Database/AthenaPOOL/AthenaPoolUtilities
-                          GaudiKernel
-                          PRIVATE
-                          Control/RootUtils )
-
-# External dependencies:
-find_package( ROOT COMPONENTS Core Tree MathCore Hist RIO pthread )
-
 # Component(s) in the package:
 atlas_add_library( IOVDbDataModel
                    src/*.cxx
                    PUBLIC_HEADERS IOVDbDataModel
-                   PRIVATE_INCLUDE_DIRS ${ROOT_INCLUDE_DIRS}
-                   LINK_LIBRARIES AthenaKernel AthenaPoolUtilities GaudiKernel RootUtilsPyROOT
-                   PRIVATE_LINK_LIBRARIES ${ROOT_LIBRARIES} RootUtils )
+                   LINK_LIBRARIES AthenaKernel AthenaPoolUtilities GaudiKernel RootUtils )
 
 atlas_add_dictionary( IOVDbDataModelDict
                       IOVDbDataModel/IOVDbDataModelDict.h
                       IOVDbDataModel/selection.xml
-                      INCLUDE_DIRS ${ROOT_INCLUDE_DIRS}
-                      LINK_LIBRARIES ${ROOT_LIBRARIES} AthenaKernel AthenaPoolUtilities GaudiKernel RootUtils RootUtilsPyROOT IOVDbDataModel )
-
+                      LINK_LIBRARIES IOVDbDataModel )