Move bNonbonded flag from t_forcerec to SimulationWorkload

The flag to store whether nonbonded calculations are requested to be
skipped (set by env.var.) is move from t_forcerec to
SimulationWorkload. A minor side-effect of this change is that the
nbnxn module logs kernels choices when this option is set.

diff --git a/src/gromacs/mdlib/forcerec.cpp b/src/gromacs/mdlib/forcerec.cpp
index 1bd965839295e42b69ee6a5a5c23644775149b53..8dc12a3be3638a6265adbee7e55d5768924f2b92 100644 (file)
--- a/src/gromacs/mdlib/forcerec.cpp
+++ b/src/gromacs/mdlib/forcerec.cpp
@@ -1006,18 +1006,6 @@ void init_forcerec(FILE*                            fp,
     /* Free energy */
     fr->efep = ir->efep;
 
-    fr->bNonbonded = TRUE;
-    if (getenv("GMX_NO_NONBONDED") != nullptr)
-    {
-        /* turn off non-bonded calculations */
-        fr->bNonbonded = FALSE;
-        GMX_LOG(mdlog.warning)
-                .asParagraph()
-                .appendText(
-                        "Found environment variable GMX_NO_NONBONDED.\n"
-                        "Disabling nonbonded calculations.");
-    }
-
     if ((getenv("GMX_DISABLE_SIMD_KERNELS") != nullptr) || (getenv("GMX_NOOPTIMIZEDKERNELS") != nullptr))
     {
         fr->use_simd_kernels = FALSE;

diff --git a/src/gromacs/mdlib/sim_util.cpp b/src/gromacs/mdlib/sim_util.cpp
index 72160eda1a8b24c95a2eaac38376fed92b22765a..7d1109889be7d6dbeb9449d517b686dedfb44313 100644 (file)
--- a/src/gromacs/mdlib/sim_util.cpp
+++ b/src/gromacs/mdlib/sim_util.cpp
@@ -881,27 +881,26 @@ static DomainLifetimeWorkload setupDomainLifetimeWorkload(const t_inputrec&
 /*! \brief Set up force flag stuct from the force bitmask.
  *
  * \param[in]      legacyFlags          Force bitmask flags used to construct the new flags
- * \param[in]      isNonbondedOn        Global override, if false forces to turn off all nonbonded calculation.
  * \param[in]      simulationWork       Simulation workload description.
  * \param[in]      rankHasPmeDuty       If this rank computes PME.
  *
  * \returns New Stepworkload description.
  */
 static StepWorkload setupStepWorkload(const int                 legacyFlags,
-                                      const bool                isNonbondedOn,
                                       const SimulationWorkload& simulationWork,
                                       const bool                rankHasPmeDuty)
 {
     StepWorkload flags;
-    flags.stateChanged           = ((legacyFlags & GMX_FORCE_STATECHANGED) != 0);
-    flags.haveDynamicBox         = ((legacyFlags & GMX_FORCE_DYNAMICBOX) != 0);
-    flags.doNeighborSearch       = ((legacyFlags & GMX_FORCE_NS) != 0);
-    flags.computeVirial          = ((legacyFlags & GMX_FORCE_VIRIAL) != 0);
-    flags.computeEnergy          = ((legacyFlags & GMX_FORCE_ENERGY) != 0);
-    flags.computeForces          = ((legacyFlags & GMX_FORCE_FORCES) != 0);
-    flags.computeListedForces    = ((legacyFlags & GMX_FORCE_LISTED) != 0);
-    flags.computeNonbondedForces = ((legacyFlags & GMX_FORCE_NONBONDED) != 0) && isNonbondedOn;
-    flags.computeDhdl            = ((legacyFlags & GMX_FORCE_DHDL) != 0);
+    flags.stateChanged        = ((legacyFlags & GMX_FORCE_STATECHANGED) != 0);
+    flags.haveDynamicBox      = ((legacyFlags & GMX_FORCE_DYNAMICBOX) != 0);
+    flags.doNeighborSearch    = ((legacyFlags & GMX_FORCE_NS) != 0);
+    flags.computeVirial       = ((legacyFlags & GMX_FORCE_VIRIAL) != 0);
+    flags.computeEnergy       = ((legacyFlags & GMX_FORCE_ENERGY) != 0);
+    flags.computeForces       = ((legacyFlags & GMX_FORCE_FORCES) != 0);
+    flags.computeListedForces = ((legacyFlags & GMX_FORCE_LISTED) != 0);
+    flags.computeNonbondedForces =
+            ((legacyFlags & GMX_FORCE_NONBONDED) != 0) && simulationWork.computeNonbonded;
+    flags.computeDhdl = ((legacyFlags & GMX_FORCE_DHDL) != 0);
 
     if (simulationWork.useGpuBufferOps)
     {
@@ -1053,8 +1052,8 @@ void do_force(FILE*                               fplog,
     const SimulationWorkload& simulationWork = runScheduleWork->simulationWork;
 
 
-    runScheduleWork->stepWork    = setupStepWorkload(legacyFlags, fr->bNonbonded, simulationWork,
-                                                  thisRankHasDuty(cr, DUTY_PME));
+    runScheduleWork->stepWork =
+            setupStepWorkload(legacyFlags, simulationWork, thisRankHasDuty(cr, DUTY_PME));
     const StepWorkload& stepWork = runScheduleWork->stepWork;
 
 

diff --git a/src/gromacs/mdrun/runner.cpp b/src/gromacs/mdrun/runner.cpp
index 781ccea41c4566bfa13f489ecee1b07dee5c1bf2..e0802407fc68793ac5719d166dc30741e0b82138 100644 (file)
--- a/src/gromacs/mdrun/runner.cpp
+++ b/src/gromacs/mdrun/runner.cpp
@@ -1247,10 +1247,22 @@ int Mdrunner::mdrunner()
     const bool printHostName = (cr->nnodes > 1);
     gpuTaskAssignments.reportGpuUsage(mdlog, printHostName, useGpuForBonded, pmeRunMode, useGpuForUpdate);
 
+    const bool disableNonbondedCalculation = (getenv("GMX_NO_NONBONDED") != nullptr);
+    if (disableNonbondedCalculation)
+    {
+        /* turn off non-bonded calculations */
+        GMX_LOG(mdlog.warning)
+                .asParagraph()
+                .appendText(
+                        "Found environment variable GMX_NO_NONBONDED.\n"
+                        "Disabling nonbonded calculations.");
+    }
+
     MdrunScheduleWorkload runScheduleWork;
     // Also populates the simulation constant workload description.
-    runScheduleWork.simulationWork = createSimulationWorkload(
-            *inputrec, devFlags, useGpuForNonbonded, pmeRunMode, useGpuForBonded, useGpuForUpdate);
+    runScheduleWork.simulationWork =
+            createSimulationWorkload(*inputrec, disableNonbondedCalculation, devFlags,
+                                     useGpuForNonbonded, pmeRunMode, useGpuForBonded, useGpuForUpdate);
 
     std::unique_ptr<DeviceStreamManager> deviceStreamManager = nullptr;
 

diff --git a/src/gromacs/mdtypes/forcerec.h b/src/gromacs/mdtypes/forcerec.h
index b48bd0910d71383784743b37edf5ce12517bf100..9077b4b35deb4f0671a474081c14b79f5418dc9f 100644 (file)
--- a/src/gromacs/mdtypes/forcerec.h
+++ b/src/gromacs/mdtypes/forcerec.h
@@ -242,8 +242,7 @@ struct t_forcerec
 
     std::unique_ptr<gmx::WholeMoleculeTransform> wholeMoleculeTransform;
 
-    int      cutoff_scheme = 0;     /* group- or Verlet-style cutoff */
-    gmx_bool bNonbonded    = FALSE; /* true if nonbonded calculations are *not* turned off */
+    int cutoff_scheme = 0; /* group- or Verlet-style cutoff */
 
     /* The Nbnxm Verlet non-bonded machinery */
     std::unique_ptr<nonbonded_verlet_t> nbv;

diff --git a/src/gromacs/mdtypes/simulation_workload.h b/src/gromacs/mdtypes/simulation_workload.h
index 8f75ba7436b91c08bdfaf78f02e1f3ed2f17f3ca..0763e6f1258b7f847632d6376738a805bc565941 100644 (file)
--- a/src/gromacs/mdtypes/simulation_workload.h
+++ b/src/gromacs/mdtypes/simulation_workload.h
@@ -140,6 +140,8 @@ public:
 class SimulationWorkload
 {
 public:
+    //! Whether to compute nonbonded pair interactions
+    bool computeNonbonded = false;
     //! Whether total dipole needs to be computed
     bool computeMuTot = false;
     //! If we have calculation of short range nonbondeds on CPU

diff --git a/src/gromacs/nbnxm/nbnxm_setup.cpp b/src/gromacs/nbnxm/nbnxm_setup.cpp
index bcb0b7d92686ce35f54152d615c170e9c3472061..74086df3dea8b21e94ca2da97fdf639d1ece69ea 100644 (file)
--- a/src/gromacs/nbnxm/nbnxm_setup.cpp
+++ b/src/gromacs/nbnxm/nbnxm_setup.cpp
@@ -238,8 +238,7 @@ static KernelSetup pick_nbnxn_kernel(const gmx::MDLogger&     mdlog,
                                      gmx_bool                 use_simd_kernels,
                                      const gmx_hw_info_t&     hardwareInfo,
                                      const NonbondedResource& nonbondedResource,
-                                     const t_inputrec*        ir,
-                                     gmx_bool                 bDoNonbonded)
+                                     const t_inputrec*        ir)
 {
     KernelSetup kernelSetup;
 
@@ -248,12 +247,7 @@ static KernelSetup pick_nbnxn_kernel(const gmx::MDLogger&     mdlog,
         kernelSetup.kernelType         = KernelType::Cpu8x8x8_PlainC;
         kernelSetup.ewaldExclusionType = EwaldExclusionType::DecidedByGpuModule;
 
-        if (bDoNonbonded)
-        {
-            GMX_LOG(mdlog.warning)
-                    .asParagraph()
-                    .appendText("Emulating a GPU run on the CPU (slow)");
-        }
+        GMX_LOG(mdlog.warning).asParagraph().appendText("Emulating a GPU run on the CPU (slow)");
     }
     else if (nonbondedResource == NonbondedResource::Gpu)
     {
@@ -273,25 +267,22 @@ static KernelSetup pick_nbnxn_kernel(const gmx::MDLogger&     mdlog,
         }
     }
 
-    if (bDoNonbonded)
+    GMX_LOG(mdlog.info)
+            .asParagraph()
+            .appendTextFormatted("Using %s %dx%d nonbonded short-range kernels",
+                                 lookup_kernel_name(kernelSetup.kernelType),
+                                 IClusterSizePerKernelType[kernelSetup.kernelType],
+                                 JClusterSizePerKernelType[kernelSetup.kernelType]);
+
+    if (KernelType::Cpu4x4_PlainC == kernelSetup.kernelType
+        || KernelType::Cpu8x8x8_PlainC == kernelSetup.kernelType)
     {
-        GMX_LOG(mdlog.info)
+        GMX_LOG(mdlog.warning)
                 .asParagraph()
-                .appendTextFormatted("Using %s %dx%d nonbonded short-range kernels",
-                                     lookup_kernel_name(kernelSetup.kernelType),
-                                     IClusterSizePerKernelType[kernelSetup.kernelType],
-                                     JClusterSizePerKernelType[kernelSetup.kernelType]);
-
-        if (KernelType::Cpu4x4_PlainC == kernelSetup.kernelType
-            || KernelType::Cpu8x8x8_PlainC == kernelSetup.kernelType)
-        {
-            GMX_LOG(mdlog.warning)
-                    .asParagraph()
-                    .appendTextFormatted(
-                            "WARNING: Using the slow %s kernels. This should\n"
-                            "not happen during routine usage on supported platforms.",
-                            lookup_kernel_name(kernelSetup.kernelType));
-        }
+                .appendTextFormatted(
+                        "WARNING: Using the slow %s kernels. This should\n"
+                        "not happen during routine usage on supported platforms.",
+                        lookup_kernel_name(kernelSetup.kernelType));
     }
 
     GMX_RELEASE_ASSERT(kernelSetup.kernelType != KernelType::NotSet
@@ -387,8 +378,8 @@ std::unique_ptr<nonbonded_verlet_t> init_nb_verlet(const gmx::MDLogger& mdlog,
         nonbondedResource = NonbondedResource::Cpu;
     }
 
-    Nbnxm::KernelSetup kernelSetup = pick_nbnxn_kernel(mdlog, fr->use_simd_kernels, hardwareInfo,
-                                                       nonbondedResource, ir, fr->bNonbonded);
+    Nbnxm::KernelSetup kernelSetup =
+            pick_nbnxn_kernel(mdlog, fr->use_simd_kernels, hardwareInfo, nonbondedResource, ir);
 
     const bool haveMultipleDomains = havePPDomainDecomposition(cr);
 

diff --git a/src/gromacs/taskassignment/decidesimulationworkload.cpp b/src/gromacs/taskassignment/decidesimulationworkload.cpp
index ad9d3050edc601d9aee447fff78d0194f714dc96..60abedf026871e1b088dd6665cf844a861fb73b9 100644 (file)
--- a/src/gromacs/taskassignment/decidesimulationworkload.cpp
+++ b/src/gromacs/taskassignment/decidesimulationworkload.cpp
@@ -51,7 +51,8 @@
 namespace gmx
 {
 
-SimulationWorkload createSimulationWorkload(const t_inputrec&              inputrec,
+SimulationWorkload createSimulationWorkload(const t_inputrec& inputrec,
+                                            const bool        disableNonbondedCalculation,
                                             const DevelopmentFeatureFlags& devFlags,
                                             bool                           useGpuForNonbonded,
                                             PmeRunMode                     pmeRunMode,
@@ -59,10 +60,11 @@ SimulationWorkload createSimulationWorkload(const t_inputrec&              input
                                             bool                           useGpuForUpdate)
 {
     SimulationWorkload simulationWorkload;
-    simulationWorkload.computeMuTot    = inputrecNeedMutot(&inputrec);
-    simulationWorkload.useCpuNonbonded = !useGpuForNonbonded;
-    simulationWorkload.useGpuNonbonded = useGpuForNonbonded;
-    simulationWorkload.useCpuPme       = (pmeRunMode == PmeRunMode::CPU);
+    simulationWorkload.computeNonbonded = !disableNonbondedCalculation;
+    simulationWorkload.computeMuTot     = inputrecNeedMutot(&inputrec);
+    simulationWorkload.useCpuNonbonded  = !useGpuForNonbonded;
+    simulationWorkload.useGpuNonbonded  = useGpuForNonbonded;
+    simulationWorkload.useCpuPme        = (pmeRunMode == PmeRunMode::CPU);
     simulationWorkload.useGpuPme = (pmeRunMode == PmeRunMode::GPU || pmeRunMode == PmeRunMode::Mixed);
     simulationWorkload.useGpuPmeFft       = (pmeRunMode == PmeRunMode::Mixed);
     simulationWorkload.useGpuBonded       = useGpuForBonded;

diff --git a/src/gromacs/taskassignment/decidesimulationworkload.h b/src/gromacs/taskassignment/decidesimulationworkload.h
index 7dd87e60730b10ad1faa7843f8a530a78d2dc180..5cde42e10cbd150bf9910ae41a40830f1e9b64a1 100644 (file)
--- a/src/gromacs/taskassignment/decidesimulationworkload.h
+++ b/src/gromacs/taskassignment/decidesimulationworkload.h
@@ -59,6 +59,7 @@ struct DevelopmentFeatureFlags;
  * task on GPUs.
  *
  * \param[in] inputrec           The input record
+ * \param[in] disableNonbondedCalculation  Disable calculation of nonbonded forces
  * \param[in] devFlags           The development feature flags
  * \param[in] useGpuForNonbonded Whether we have short-range nonbonded interactions
  *                               calculations on GPU(s).
@@ -68,7 +69,8 @@ struct DevelopmentFeatureFlags;
  *                               GPU(s).
  * \returns Simulation lifetime constant workload description.
  */
-SimulationWorkload createSimulationWorkload(const t_inputrec&              inputrec,
+SimulationWorkload createSimulationWorkload(const t_inputrec& inputrec,
+                                            bool              disableNonbondedCalculation,
                                             const DevelopmentFeatureFlags& devFlags,
                                             bool                           useGpuForNonbonded,
                                             PmeRunMode                     pmeRunMode,