diff --git a/Compiler/SimCode/SimCodeUtil.mo b/Compiler/SimCode/SimCodeUtil.mo
index 99a07d128f..c72f9bee44 100644
--- a/Compiler/SimCode/SimCodeUtil.mo
+++ b/Compiler/SimCode/SimCodeUtil.mo
@@ -1221,6 +1221,9 @@ algorithm
   try
     column::{} := symjac.columns;
     (eqs, modelInfo, tmpSymJacs) := addAlgebraicLoopsModelInfo(column.columnEqns, modelInfo);
+    // set partition index to number of clocks (max index) for now.
+    // TODO: use actual clock index to support multirate systems
+    tmpSymJacs := list(rewriteJacPartIdx(a, modelInfo.nSubClocks) for a in tmpSymJacs);
     outSymJacsInSymJacs := listAppend(tmpSymJacs, outSymJacsInSymJacs);
     column.columnEqns := eqs;
     symjac.columns := {column};
@@ -12806,6 +12809,7 @@ algorithm
       ({contSimJac}, outModelInfo, symJacs) := addAlgebraicLoopsModelInfoSymJacs({contSimJac}, inModelInfo);
       contPartSimDer := SOME(contSimJac);
       // set partition index to number of clocks (max index) for now
+      // TODO: use actual clock indices to support multirate systems
       symJacFMI := {rewriteJacPartIdx(contSimJac, inModelInfo.nSubClocks)};
     else
       contPartSimDer := NONE();
diff --git a/Compiler/Template/CodegenCpp.tpl b/Compiler/Template/CodegenCpp.tpl
index 9c099ba055..32120bbb3e 100644
--- a/Compiler/Template/CodegenCpp.tpl
+++ b/Compiler/Template/CodegenCpp.tpl
@@ -81,8 +81,8 @@ template translateModel(SimCode simCode)
         let()= textFile(simulationWriteOutputCppFile(simCode , &extraFuncs , &extraFuncsDecl, "", stateDerVectorName, false),'OMCpp<%fileNamePrefix%>WriteOutput.cpp')
         let()= textFile(simulationFactoryFile(simCode , &extraFuncs , &extraFuncsDecl, ""),'OMCpp<%fileNamePrefix%>FactoryExport.cpp')
         let()= textFile(simulationMainRunScript(simCode , &extraFuncs , &extraFuncsDecl, "", "", "", "exec"), '<%fileNamePrefix%><%simulationMainRunScriptSuffix(simCode , &extraFuncs , &extraFuncsDecl, "")%>')
-        let jac =  (jacobianMatrixes |> JAC_MATRIX(columns=mat) =>
-          (mat |> JAC_COLUMN(columnEqns=eqs) => algloopfiles(eqs, simCode, &extraFuncs, &extraFuncsDecl, "", contextAlgloopJacobian, 0, stateDerVectorName, false) ;separator="")
+        let jac =  (jacobianMatrixes |> JAC_MATRIX(columns=mat, partitionIndex=partIdx) =>
+          (mat |> JAC_COLUMN(columnEqns=eqs) => algloopfiles(eqs, simCode, &extraFuncs, &extraFuncsDecl, "", contextAlgloopJacobian, partIdx, stateDerVectorName, false) ;separator="")
          ;separator="")
         let alg = algloopfiles(listAppend(allEquations, initialEquations), simCode, &extraFuncs, &extraFuncsDecl, "", contextAlgloop, 0, stateDerVectorName, false)
         let clk = getSubPartitions(clockedPartitions) |> subPartition hasindex i fromindex 1 =>