Merge branch 'origin/release-2020' into master

[alexxy/gromacs.git] / src / gromacs / nbnxm / nbnxm_setup.cpp

diff --git a/src/gromacs/nbnxm/nbnxm_setup.cpp b/src/gromacs/nbnxm/nbnxm_setup.cpp
index 26a9bba0da94ffef9ec382aec0e1dd9f8b3581b3..e7994d84bac46560035ffc9b5e3d746a0dbd0cdc 100644 (file)
--- a/src/gromacs/nbnxm/nbnxm_setup.cpp
+++ b/src/gromacs/nbnxm/nbnxm_setup.cpp
@@ -49,15 +49,16 @@
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/mdtypes/forcerec.h"
 #include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/mdtypes/interaction_const.h"
+#include "gromacs/nbnxm/atomdata.h"
 #include "gromacs/nbnxm/gpu_data_mgmt.h"
 #include "gromacs/nbnxm/nbnxm.h"
 #include "gromacs/nbnxm/pairlist_tuning.h"
 #include "gromacs/simd/simd.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/logger.h"
 
-#include "atomdata.h"
-#include "gpu_types.h"
 #include "grid.h"
 #include "nbnxm_geometry.h"
 #include "nbnxm_simd.h"
@@ -320,7 +321,7 @@ namespace Nbnxm
 {
 
 /*! \brief Gets and returns the minimum i-list count for balacing based on the GPU used or env.var. when set */
-static int getMinimumIlistCountForGpuBalancing(gmx_nbnxn_gpu_t* nbnxmGpu)
+static int getMinimumIlistCountForGpuBalancing(NbnxmGpu* nbnxmGpu)
 {
     int minimumIlistCount;
 
@@ -356,25 +357,24 @@ static int getMinimumIlistCountForGpuBalancing(gmx_nbnxn_gpu_t* nbnxmGpu)
     return minimumIlistCount;
 }
 
-std::unique_ptr<nonbonded_verlet_t> init_nb_verlet(const gmx::MDLogger&     mdlog,
-                                                   gmx_bool                 bFEP_NonBonded,
-                                                   const t_inputrec*        ir,
-                                                   const t_forcerec*        fr,
-                                                   const t_commrec*         cr,
-                                                   const gmx_hw_info_t&     hardwareInfo,
-                                                   const gmx_device_info_t* deviceInfo,
-                                                   const gmx_mtop_t*        mtop,
-                                                   matrix                   box,
-                                                   gmx_wallcycle*           wcycle)
+std::unique_ptr<nonbonded_verlet_t> init_nb_verlet(const gmx::MDLogger& mdlog,
+                                                   const t_inputrec*    ir,
+                                                   const t_forcerec*    fr,
+                                                   const t_commrec*     cr,
+                                                   const gmx_hw_info_t& hardwareInfo,
+                                                   const bool           useGpuForNonbonded,
+                                                   const gmx::DeviceStreamManager* deviceStreamManager,
+                                                   const gmx_mtop_t*               mtop,
+                                                   matrix                          box,
+                                                   gmx_wallcycle*                  wcycle)
 {
     const bool emulateGpu = (getenv("GMX_EMULATE_GPU") != nullptr);
-    const bool useGpu     = deviceInfo != nullptr;
 
-    GMX_RELEASE_ASSERT(!(emulateGpu && useGpu),
+    GMX_RELEASE_ASSERT(!(emulateGpu && useGpuForNonbonded),
                        "When GPU emulation is active, there cannot be a GPU assignment");
 
     NonbondedResource nonbondedResource;
-    if (useGpu)
+    if (useGpuForNonbonded)
     {
         nonbondedResource = NonbondedResource::Gpu;
     }
@@ -390,10 +390,10 @@ std::unique_ptr<nonbonded_verlet_t> init_nb_verlet(const gmx::MDLogger&     mdlo
     Nbnxm::KernelSetup kernelSetup = pick_nbnxn_kernel(mdlog, fr->use_simd_kernels, hardwareInfo,
                                                        nonbondedResource, ir, fr->bNonbonded);
 
-    const bool haveMultipleDomains = (DOMAINDECOMP(cr) && cr->dd->nnodes > 1);
+    const bool haveMultipleDomains = havePPDomainDecomposition(cr);
 
-    PairlistParams pairlistParams(kernelSetup.kernelType, bFEP_NonBonded, ir->rlist,
-                                  havePPDomainDecomposition(cr));
+    bool           bFEP_NonBonded = (fr->efep != efepNO) && haveFepPerturbedNBInteractions(mtop);
+    PairlistParams pairlistParams(kernelSetup.kernelType, bFEP_NonBonded, ir->rlist, haveMultipleDomains);
 
     setupDynamicPairlistPruning(mdlog, ir, mtop, box, fr->ic, &pairlistParams);
 
@@ -423,7 +423,8 @@ std::unique_ptr<nonbonded_verlet_t> init_nb_verlet(const gmx::MDLogger&     mdlo
         enbnxninitcombrule = enbnxninitcombruleNONE;
     }
 
-    auto pinPolicy = (useGpu ? gmx::PinningPolicy::PinnedIfSupported : gmx::PinningPolicy::CannotBePinned);
+    auto pinPolicy = (useGpuForNonbonded ? gmx::PinningPolicy::PinnedIfSupported
+                                         : gmx::PinningPolicy::CannotBePinned);
 
     auto nbat = std::make_unique<nbnxn_atomdata_t>(pinPolicy);
 
@@ -438,15 +439,18 @@ std::unique_ptr<nonbonded_verlet_t> init_nb_verlet(const gmx::MDLogger&     mdlo
     }
     nbnxn_atomdata_init(mdlog, nbat.get(), kernelSetup.kernelType, enbnxninitcombrule, fr->ntype,
                         fr->nbfp, mimimumNumEnergyGroupNonbonded,
-                        (useGpu || emulateGpu) ? 1 : gmx_omp_nthreads_get(emntNonbonded));
+                        (useGpuForNonbonded || emulateGpu) ? 1 : gmx_omp_nthreads_get(emntNonbonded));
 
-    gmx_nbnxn_gpu_t* gpu_nbv                          = nullptr;
-    int              minimumIlistCountForGpuBalancing = 0;
-    if (useGpu)
+    NbnxmGpu* gpu_nbv                          = nullptr;
+    int       minimumIlistCountForGpuBalancing = 0;
+    if (useGpuForNonbonded)
     {
         /* init the NxN GPU data; the last argument tells whether we'll have
          * both local and non-local NB calculation on GPU */
-        gpu_nbv = gpu_init(deviceInfo, fr->ic, pairlistParams, nbat.get(), cr->nodeid, haveMultipleDomains);
+        GMX_RELEASE_ASSERT(
+                (deviceStreamManager != nullptr),
+                "Device stream manager should be initialized in order to use GPU for non-bonded.");
+        gpu_nbv = gpu_init(*deviceStreamManager, fr->ic, pairlistParams, nbat.get(), haveMultipleDomains);
 
         minimumIlistCountForGpuBalancing = getMinimumIlistCountForGpuBalancing(gpu_nbv);
     }
@@ -455,7 +459,7 @@ std::unique_ptr<nonbonded_verlet_t> init_nb_verlet(const gmx::MDLogger&     mdlo
                                                        minimumIlistCountForGpuBalancing);
 
     auto pairSearch = std::make_unique<PairSearch>(
-            ir->ePBC, EI_TPI(ir->eI), DOMAINDECOMP(cr) ? &cr->dd->nc : nullptr,
+            ir->pbcType, EI_TPI(ir->eI), DOMAINDECOMP(cr) ? &cr->dd->numCells : nullptr,
             DOMAINDECOMP(cr) ? domdec_zones(cr->dd) : nullptr, pairlistParams.pairlistType,
             bFEP_NonBonded, gmx_omp_nthreads_get(emntPairsearch), pinPolicy);
 
@@ -469,7 +473,7 @@ nonbonded_verlet_t::nonbonded_verlet_t(std::unique_ptr<PairlistSets>     pairlis
                                        std::unique_ptr<PairSearch>       pairSearch,
                                        std::unique_ptr<nbnxn_atomdata_t> nbat_in,
                                        const Nbnxm::KernelSetup&         kernelSetup,
-                                       gmx_nbnxn_gpu_t*                  gpu_nbv_ptr,
+                                       NbnxmGpu*                         gpu_nbv_ptr,
                                        gmx_wallcycle*                    wcycle) :
     pairlistSets_(std::move(pairlistSets)),
     pairSearch_(std::move(pairSearch)),