diff --git a/src/DIRAC/ConfigurationSystem/Client/PathFinder.py b/src/DIRAC/ConfigurationSystem/Client/PathFinder.py
index 941cf8dec41..95737405d09 100755
--- a/src/DIRAC/ConfigurationSystem/Client/PathFinder.py
+++ b/src/DIRAC/ConfigurationSystem/Client/PathFinder.py
@@ -33,14 +33,23 @@ def divideFullName(entityName, componentName=None):
 
 
 def getSystemInstance(system, setup=False):
-    """Find system instance name
+    """Find system instance name.
 
     :param str system: system name
     :param str setup: setup name
 
-    :return: str
+    :return: str: instance name. If the system option is present
+       in the /DIRAC/Setups/<setup> section but is not given a value,
+       an empty string is returned
     """
-    optionPath = Path.cfgPath("/DIRAC/Setups", setup or getDIRACSetup(), system)
+
+    # If noSetupFlag is set to True, we do not have system instances in the configuration
+    noSetupFlag = gConfigurationData.extractOptionFromCFG("/DIRAC/NoSetup")
+    if noSetupFlag == "True":
+        return ""
+
+    setupToUse = setup or getDIRACSetup()
+    optionPath = Path.cfgPath("/DIRAC/Setups", setupToUse, system)
     instance = gConfigurationData.extractOptionFromCFG(optionPath)
     if not instance:
         raise RuntimeError(f"Option {optionPath} is not defined")
diff --git a/src/DIRAC/WorkloadManagementSystem/Agent/StalledJobAgent.py b/src/DIRAC/WorkloadManagementSystem/Agent/StalledJobAgent.py
index f95b74021b8..5d745e0e409 100755
--- a/src/DIRAC/WorkloadManagementSystem/Agent/StalledJobAgent.py
+++ b/src/DIRAC/WorkloadManagementSystem/Agent/StalledJobAgent.py
@@ -16,7 +16,7 @@
 from DIRAC import S_ERROR, S_OK, gConfig
 from DIRAC.AccountingSystem.Client.Types.Job import Job
 from DIRAC.ConfigurationSystem.Client.Helpers import cfgPath
-from DIRAC.ConfigurationSystem.Client.PathFinder import getSystemInstance
+from DIRAC.ConfigurationSystem.Client.PathFinder import getSystemSection
 from DIRAC.Core.Base.AgentModule import AgentModule
 from DIRAC.Core.Utilities import DErrno
 from DIRAC.Core.Utilities.ClassAd.ClassAdLight import ClassAd
@@ -55,9 +55,6 @@ def initialize(self):
         if not self.am_getOption("Enable", True):
             self.log.info("Stalled Job Agent running in disabled mode")
 
-        wms_instance = getSystemInstance("WorkloadManagement")
-        if not wms_instance:
-            return S_ERROR("Can not get the WorkloadManagement system instance")
         self.stalledJobsTolerantSites = self.am_getOption("StalledJobsTolerantSites", [])
         self.stalledJobsToleranceTime = self.am_getOption("StalledJobsToleranceTime", 0)
 
@@ -67,7 +64,7 @@ def initialize(self):
         self.matchedTime = self.am_getOption("MatchedTime", self.matchedTime)
         self.rescheduledTime = self.am_getOption("RescheduledTime", self.rescheduledTime)
 
-        wrapperSection = cfgPath("Systems", "WorkloadManagement", wms_instance, "JobWrapper")
+        wrapperSection = f"{getSystemSection('WorkloadManagement')}/JobWrapper"
 
         failedTime = self.am_getOption("FailedTimeHours", 6)
         watchdogCycle = gConfig.getValue(cfgPath(wrapperSection, "CheckingTime"), 30 * 60)
diff --git a/src/DIRAC/WorkloadManagementSystem/Agent/test/Test_Agent_StalledJobAgent.py b/src/DIRAC/WorkloadManagementSystem/Agent/test/Test_Agent_StalledJobAgent.py
index 615c55065a7..dbf4ce2fbf7 100644
--- a/src/DIRAC/WorkloadManagementSystem/Agent/test/Test_Agent_StalledJobAgent.py
+++ b/src/DIRAC/WorkloadManagementSystem/Agent/test/Test_Agent_StalledJobAgent.py
@@ -25,11 +25,11 @@ def sja(mocker):
     )
     mocker.patch("DIRAC.WorkloadManagementSystem.Agent.StalledJobAgent.JobDB")
     mocker.patch("DIRAC.WorkloadManagementSystem.Agent.StalledJobAgent.JobLoggingDB")
-    mocker.patch("DIRAC.WorkloadManagementSystem.Agent.StalledJobAgent.getSystemInstance", side_effect=mockNone)
+    mocker.patch("DIRAC.WorkloadManagementSystem.Agent.StalledJobAgent.getSystemSection", side_effect=mockNone)
     mocker.patch("DIRAC.WorkloadManagementSystem.Agent.StalledJobAgent.JobMonitoringClient", return_value=MagicMock())
     mocker.patch("DIRAC.WorkloadManagementSystem.Agent.StalledJobAgent.PilotManagerClient", return_value=MagicMock())
     mocker.patch("DIRAC.WorkloadManagementSystem.Agent.StalledJobAgent.WMSClient", return_value=MagicMock())
-    mocker.patch("DIRAC.WorkloadManagementSystem.Agent.StalledJobAgent.getSystemInstance", return_value="/bof/bih")
+    mocker.patch("DIRAC.WorkloadManagementSystem.Agent.StalledJobAgent.getSystemSection", return_value="/bof/bih")
 
     stalledJobAgent = StalledJobAgent()
     stalledJobAgent._AgentModule__configDefaults = mockAM
diff --git a/src/DIRAC/WorkloadManagementSystem/JobWrapper/Watchdog.py b/src/DIRAC/WorkloadManagementSystem/JobWrapper/Watchdog.py
index c2a0ef50ad6..7ff8a46d3b8 100755
--- a/src/DIRAC/WorkloadManagementSystem/JobWrapper/Watchdog.py
+++ b/src/DIRAC/WorkloadManagementSystem/JobWrapper/Watchdog.py
@@ -25,7 +25,7 @@
 
 from DIRAC import S_ERROR, S_OK, gLogger
 from DIRAC.ConfigurationSystem.Client.Config import gConfig
-from DIRAC.ConfigurationSystem.Client.PathFinder import getSystemInstance
+from DIRAC.ConfigurationSystem.Client.PathFinder import getSystemSection
 from DIRAC.Core.Utilities import MJF
 from DIRAC.Core.Utilities.Os import getDiskSpace
 from DIRAC.Core.Utilities.Profiler import Profiler
@@ -104,13 +104,7 @@ def initialize(self):
         else:
             self.initialized = True
 
-        setup = gConfig.getValue("/DIRAC/Setup", "")
-        if not setup:
-            return S_ERROR("Can not get the DIRAC Setup value")
-        wms_instance = getSystemInstance("WorkloadManagement")
-        if not wms_instance:
-            return S_ERROR("Can not get the WorkloadManagement system instance")
-        self.section = f"/Systems/WorkloadManagement/{wms_instance}/JobWrapper"
+        self.section = f"{getSystemSection('WorkloadManagement')}/JobWrapper"
 
         self.log.verbose("Watchdog initialization")
         # Test control flags
diff --git a/src/DIRAC/WorkloadManagementSystem/JobWrapper/test/Test_JobWrapper.py b/src/DIRAC/WorkloadManagementSystem/JobWrapper/test/Test_JobWrapper.py
index b13d7c6ce2f..4fb1521f718 100644
--- a/src/DIRAC/WorkloadManagementSystem/JobWrapper/test/Test_JobWrapper.py
+++ b/src/DIRAC/WorkloadManagementSystem/JobWrapper/test/Test_JobWrapper.py
@@ -92,7 +92,7 @@ def test_execute(mocker, executable, args, src, expectedResult):
         "DIRAC.WorkloadManagementSystem.JobWrapper.JobWrapper.getSystemSection", side_effect=getSystemSectionMock
     )
     mocker.patch(
-        "DIRAC.WorkloadManagementSystem.JobWrapper.Watchdog.getSystemInstance", side_effect=getSystemSectionMock
+        "DIRAC.WorkloadManagementSystem.JobWrapper.Watchdog.getSystemSection", side_effect=getSystemSectionMock
     )
 
     if src: