diff --git a/Compiler/FrontEnd/ComponentReference.mo b/Compiler/FrontEnd/ComponentReference.mo
index 78010ddca6..723912886e 100644
--- a/Compiler/FrontEnd/ComponentReference.mo
+++ b/Compiler/FrontEnd/ComponentReference.mo
@@ -2078,6 +2078,15 @@ algorithm
   outCref := makeCrefQual(DAE.previousNamePrefix, DAE.T_UNKNOWN_DEFAULT, {}, inCref);
 end crefPrefixPrevious;
 
+public function crefRemovePrePrefix
+  input output DAE.ComponentRef cref;
+algorithm
+  cref := match cref
+    case DAE.CREF_QUAL(ident=DAE.preNamePrefix) then cref.componentRef;
+    else cref;
+  end match;
+end crefRemovePrePrefix;
+
 public function crefPrefixStart "public function crefPrefixStart
   Appends $START to a cref, so a => $START.a"
   input DAE.ComponentRef inCref;
diff --git a/Compiler/SimCode/SimCodeUtil.mo b/Compiler/SimCode/SimCodeUtil.mo
index 31eae9b1c9..4dcd6850fa 100644
--- a/Compiler/SimCode/SimCodeUtil.mo
+++ b/Compiler/SimCode/SimCodeUtil.mo
@@ -8565,14 +8565,9 @@ algorithm
     outHT := List.fold(vars.intConstVars, addSimVarToHashTable, outHT);
     outHT := List.fold(vars.boolConstVars, addSimVarToHashTable, outHT);
     outHT := List.fold(vars.stringConstVars, addSimVarToHashTable, outHT);
-    if Config.simCodeTarget()=="Cpp" then
-      // Not needed in the hashtable (actually breaks code generation
-      // due to bad indexes, no information that they are seed variables
-      // and so on...
-      outHT := List.fold(vars.sensitivityVars, addSimVarToHashTable, outHT);
-      outHT := List.fold(vars.jacobianVars, addSimVarToHashTable, outHT);
-      outHT := List.fold(vars.seedVars, addSimVarToHashTable, outHT);
-    end if;
+    outHT := List.fold(vars.sensitivityVars, addSimVarToHashTable, outHT);
+    outHT := List.fold(vars.jacobianVars, addSimVarToHashTable, outHT);
+    outHT := List.fold(vars.seedVars, addSimVarToHashTable, outHT);
     outHT := List.fold(vars.realOptimizeConstraintsVars, addSimVarToHashTable, outHT);
     outHT := List.fold(vars.realOptimizeFinalConstraintsVars, addSimVarToHashTable, outHT);
   else
@@ -13321,16 +13316,8 @@ algorithm
         sv = BaseHashTable.get(cref, crefToSimVarHT);
         sv = match sv.aliasvar
           case SimCodeVar.NOALIAS() then sv;
-          /* The C++ runtime generates a different set of variables... */
-          case _ guard Config.simCodeTarget() == "Cpp" then sv;
-          case SimCodeVar.ALIAS(varName=cref)
-            algorithm
-              Error.addSourceMessage(Error.COMPILER_WARNING, {getInstanceName() + " got an alias variable " + ComponentReference.printComponentRefStr(inCref) + " to " + ComponentReference.printComponentRefStr(cref) + ", but before code generation these should have been removed"}, sv.source.info);
-           then cref2simvar(cref, simCode);
-          case SimCodeVar.NEGATEDALIAS(varName=cref)
-            algorithm
-              Error.addSourceMessage(Error.INTERNAL_ERROR, {getInstanceName() + " got a negated alias variable " + ComponentReference.printComponentRefStr(inCref) + " to " + ComponentReference.printComponentRefStr(cref) + ", but before code generation these should have been removed"}, sv.source.info);
-            then sv;
+          case SimCodeVar.ALIAS(varName=cref) then cref2simvar(cref, simCode); /* Possibly not needed; can't really hurt that much though */
+          case SimCodeVar.NEGATEDALIAS() then sv;
         end match;
       then sv;
 
@@ -13338,11 +13325,7 @@ algorithm
       equation
         //print("cref2simvar: " + ComponentReference.printComponentRefStr(inCref) + " not found!\n");
         badcref = ComponentReference.makeCrefIdent("ERROR_cref2simvar_failed " + ComponentReference.printComponentRefStr(inCref), DAE.T_REAL_DEFAULT, {});
-        /* Todo: This also generates an error for example itearation variables, so i commented  out
-        "Template did not find the simulation variable for "+ ComponentReference.printComponentRefStr(cref) + ". ";
-        Error.addInternalError(errstr, sourceInfo());*/
-      then
-         SimCodeVar.SIMVAR(badcref, BackendDAE.VARIABLE(), "", "", "", -2, NONE(), NONE(), NONE(), NONE(), false, DAE.T_REAL_DEFAULT, false, NONE(), SimCodeVar.NOALIAS(), DAE.emptyElementSource, SimCodeVar.INTERNAL(), NONE(), {}, false, true, false, NONE(), NONE());
+       then SimCodeVar.SIMVAR(badcref, BackendDAE.VARIABLE(), "", "", "", -2, NONE(), NONE(), NONE(), NONE(), false, DAE.T_REAL_DEFAULT, false, NONE(), SimCodeVar.NOALIAS(), DAE.emptyElementSource, SimCodeVar.INTERNAL(), NONE(), {}, false, true, false, NONE(), NONE());
   end matchcontinue;
 end cref2simvar;
 
diff --git a/Compiler/Template/CodegenC.tpl b/Compiler/Template/CodegenC.tpl
index 70c90b096f..e5481b5372 100644
--- a/Compiler/Template/CodegenC.tpl
+++ b/Compiler/Template/CodegenC.tpl
@@ -1618,8 +1618,9 @@ template functionInput(SimCode simCode, ModelInfo modelInfo, String modelNamePre
 
       <%vars.inputVars |> SIMVAR(__) hasindex i0 =>
         match cref2simvar(name, simCode)
-        case SIMVAR(__) then
+        case SIMVAR(aliasvar=NOALIAS()) then
         'data->simulationInfo->inputVars[<%i0%>] = data->modelData-><%expTypeShort(type_)%>VarsData[<%index%>].attribute.start;'
+        else error(sourceInfo(), 'Cannot get attributes of alias variable <%crefStr(name)%>. Alias variables should have been replaced by the compiler before SimCode')
         ;separator="\n"
       %>
 
@@ -1633,8 +1634,9 @@ template functionInput(SimCode simCode, ModelInfo modelInfo, String modelNamePre
 
       <%vars.inputVars |> SIMVAR(__) hasindex i0 =>
         match cref2simvar(name, simCode)
-        case SIMVAR(__) then
+        case SIMVAR(aliasvar=NOALIAS()) then
         'data->modelData-><%expTypeShort(type_)%>VarsData[<%index%>].attribute.start = data->simulationInfo->inputVars[<%i0%>];'
+        else error(sourceInfo(), 'Cannot get attributes of alias variable <%crefStr(name)%>. Alias variables should have been replaced by the compiler before SimCode')
         ;separator="\n"
       %>
 
@@ -1647,8 +1649,9 @@ template functionInput(SimCode simCode, ModelInfo modelInfo, String modelNamePre
 
       <%vars.inputVars |> simVar as SIMVAR(__) hasindex i0 =>
         match cref2simvar(name, simCode)
-        case SIMVAR(__) then
+        case SIMVAR(aliasvar=NOALIAS()) then
         'names[<%i0%>] = (char *) data->modelData-><%expTypeShort(type_)%>VarsData[<%index%>].info.name;'
+        else error(sourceInfo(), 'Cannot get attributes of alias variable <%crefStr(name)%>. Alias variables should have been replaced by the compiler before SimCode')
         ;separator="\n"
       %>
 
@@ -2944,10 +2947,11 @@ template functionUpdateBoundParameters(list<SimEqSystem> simpleParameterEquation
       <<
       <%cref(cref)%> = <%daeExpSimpleLiteral(exp)%>;
       <%match cref2simvar(cref, simCode)
-        case SIMVAR(varKind=PARAM()) then
+        case SIMVAR(aliasvar=NOALIAS(), varKind=PARAM()) then
           'data->modelData-><%expTypeShort(type_)%>ParameterData[<%index%>].time_unvarying = 1;'
-        case SIMVAR(__) then
-          'data->modelData-><%expTypeShort(type_)%>VarsData[<%index%>].time_unvarying = 1;'%>
+        case SIMVAR(aliasvar=NOALIAS()) then
+          'data->modelData-><%expTypeShort(type_)%>VarsData[<%index%>].time_unvarying = 1;'
+        else error(sourceInfo(), 'Cannot get attributes of alias variable <%crefStr(cref)%>. Alias variables should have been replaced by the compiler before SimCode')%>
       >> ; separator="\n" %>
     <%fncalls%>
     TRACE_POP
@@ -4459,12 +4463,6 @@ template crefShortType(ComponentRef cr) "template crefType
   end match
 end crefShortType;
 
-template crefIndexInArray(ComponentRef cr, SimCode simCode)
-::=
-  match cref2simvar(cr, simCode)
-  case SIMVAR(__) then index
-end crefIndexInArray;
-
 template functionAssertsforCheck(list<SimEqSystem> algAndEqAssertsEquations, String modelNamePrefix) "template functionAssertsforCheck
   Generates function in simulation file.
   This is a helper of template simulationFile."
diff --git a/Compiler/Template/CodegenCFunctions.tpl b/Compiler/Template/CodegenCFunctions.tpl
index b36b18f44b..59901558fa 100644
--- a/Compiler/Template/CodegenCFunctions.tpl
+++ b/Compiler/Template/CodegenCFunctions.tpl
@@ -4100,10 +4100,14 @@ template crefToCStr(ComponentRef cr, Integer ix, Boolean isPre, Boolean isStart)
   case SIMVAR(varKind=ALG_STATE_OLD(), index=index)
   then
     'data->simulationInfo->inlineData->algOldVars[<%index%>]'
+  case SIMVAR(aliasvar=ALIAS(varName=varName)) then crefToCStr(varName, ix, isPre, isStart)
+  case SIMVAR(aliasvar=NEGATEDALIAS(varName=varName), type_=T_BOOL()) then '!(<%crefToCStr(varName, ix, isPre, isStart)%>)'
+  case SIMVAR(aliasvar=NEGATEDALIAS(varName=varName)) then '-(<%crefToCStr(varName, ix, isPre, isStart)%>)'
   case SIMVAR(varKind=JAC_VAR())
   case SIMVAR(varKind=JAC_DIFF_VAR())
   case SIMVAR(varKind=SEED_VAR())
   case SIMVAR(varKind=DAE_RESIDUAL_VAR())
+  case SIMVAR(varKind=DAE_RESIDUAL_VAR())
   case SIMVAR(index=-2)
   then
     if intEq(ix,0) then (if isPre then "$P$PRE")+crefDefine(cr)
@@ -6980,11 +6984,11 @@ end varAttributes;
 
 template crefAttributes(ComponentRef cr)
 ::=
-  match cref2simvar(cr, getSimCode())
+  match cref2simvar(crefRemovePrePrefix(cr), getSimCode())
   case var as SIMVAR(index=-1, varKind=JAC_VAR()) then "dummyREAL_ATTRIBUTE"
-  case var as SIMVAR(index=-1) then error(sourceInfo(), 'varAttributes got index=-1 for <%crefStr(name)%>')
   case var as SIMVAR(__) then
-  'data->modelData-><%varArrayName(var)%>Data[<%index%>].attribute /* <%escapeCComments(crefStrNoUnderscore(name))%> */'
+    if intLt(index,0) then error(sourceInfo(), 'varAttributes got negative index=<%index%> for <%crefStr(name)%>') else
+    'data->modelData-><%varArrayName(var)%>Data[<%index%>].attribute /* <%escapeCComments(crefStrNoUnderscore(name))%> */'
 end crefAttributes;
 
 annotation(__OpenModelica_Interface="backend");
diff --git a/Compiler/Template/SimCodeTV.mo b/Compiler/Template/SimCodeTV.mo
index 8fd33118ca..c6c2cdf4e4 100644
--- a/Compiler/Template/SimCodeTV.mo
+++ b/Compiler/Template/SimCodeTV.mo
@@ -3244,6 +3244,10 @@ package ComponentReference
     output DAE.ComponentRef outCR;
   end popCref;
 
+  function crefRemovePrePrefix
+    input DAE.ComponentRef inCR;
+    output DAE.ComponentRef outCR;
+  end crefRemovePrePrefix;
 end ComponentReference;
 
 package Expression