Fix GROMACS 2025 checkpoint notification ordering

patches/gromacs-2025.0.diff/src/gromacs/applied_forces/plumed/plumedMDModule.cpp

@@ -117,6 +117,16 @@ class PlumedMDModule final : public IMDModule
         notifier->simulationSetupNotifier_.subscribe(
                 [this](const StartingBehavior& startingBehavior)
                 { this->options_.setStartingBehavior(startingBehavior); });
+        // Set checkpoint status before PLUMED updates the current step.
+        notifier->checkpointingNotifier_.subscribe(
+                [this](const MDModulesCheckpointingSignal& checkpointingSignal)
+                {
+                    if (options_.active())
+                    {
+                        plumedForceProvider_->setCheckpointingThisStep(
+                                checkpointingSignal.isCheckpointingStep_);
+                    }
+                });
         //  writing checkpoint data
         notifier->checkpointingNotifier_.subscribe(
                 [this](MDModulesWriteCheckpointData /*checkpointData*/)

patches/gromacs-2025.0.diff/src/gromacs/applied_forces/plumed/plumedforceprovider.cpp

@@ -141,13 +141,33 @@ catch (const std::exception& ex)
             std::string("An error occurred while initializing the PLUMED force provider:\n") + ex.what()));
 }
 
+void PlumedForceProvider::setPlumedCheckpointing(bool isCheckpointingStep)
+{
+    if (plumedAPIversion_ > 3)
+    {
+        int checkpointing = isCheckpointingStep ? 1 : 0;
+        plumed_->cmd("doCheckPoint", &checkpointing);
+    }
+}
+
+void PlumedForceProvider::setCheckpointingThisStep(bool isCheckpointingStep)
+try
+{
+    hasCheckpointingStepNotifications_ = true;
+    setPlumedCheckpointing(isCheckpointingStep);
+}
+catch (const std::exception& ex)
+{
+    GMX_THROW(InternalError(
+            std::string("An error occurred while PLUMED was setting checkpoint status:\n") + ex.what()));
+}
+
 void PlumedForceProvider::writeCheckpointData()
 try
 {
-    if (plumedAPIversion_ > 3)
+    if (!hasCheckpointingStepNotifications_)
     {
-        int checkp = 1;
-        plumed_->cmd("doCheckPoint", &checkp);
+        setPlumedCheckpointing(true);
     }
 }
 catch (const std::exception& ex)

patches/gromacs-2025.0.diff/src/gromacs/applied_forces/plumed/plumedforceprovider.h

@@ -64,9 +64,20 @@ class PlumedForceProvider final : public IForceProvider
      */
     PlumedForceProvider(const PlumedOptions& options);
     ~PlumedForceProvider();
+    /*! \brief Set whether PLUMED is updating a checkpointing step.
+     *
+     * Receiving this notification also disables the later checkpoint-writing
+     * fallback used by the modular simulator.
+     *
+     * \param[in] isCheckpointingStep Whether GROMACS will write a checkpoint
+     *                                for the current step.
+     */
+    void setCheckpointingThisStep(bool isCheckpointingStep);
     /*! \brief Tells PLUMED to output the checkpoint data
      *
-     * If the PLUMED API version is not greater than 3 it will do nothing.
+     * This is a fallback for simulation paths that do not provide an early
+     * checkpoint-step notification. If the PLUMED API version is not greater
+     * than 3 it will do nothing.
      */
     void writeCheckpointData();
     /*! \brief Calculate the forces with PLUMED
@@ -77,9 +88,16 @@ class PlumedForceProvider final : public IForceProvider
                          ForceProviderOutput*      forceProviderOutput) override;
 
 private:
+    /*! \brief Pass checkpoint status to PLUMED.
+     *
+     * \param[in] isCheckpointingStep Whether the current step writes a checkpoint.
+     */
+    void setPlumedCheckpointing(bool isCheckpointingStep);
+
     std::unique_ptr<PLMD::Plumed> plumed_;
     int                           plumedAPIversion_;
     bool replex_;
+    bool hasCheckpointingStepNotifications_ = false;
 };
 
 } // namespace gmx