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37 * \brief Implements GPU halo exchange using CUDA.
40 * \author Alan Gray <alang@nvidia.com>
42 * \ingroup module_domdec
46 #include "gpuhaloexchange_impl.cuh"
55 #include "gromacs/domdec/domdec.h"
56 #include "gromacs/domdec/domdec_struct.h"
57 #include "gromacs/domdec/gpuhaloexchange.h"
58 #include "gromacs/gpu_utils/cudautils.cuh"
59 #include "gromacs/gpu_utils/device_context.h"
60 #include "gromacs/gpu_utils/devicebuffer.h"
61 #include "gromacs/gpu_utils/gpueventsynchronizer.cuh"
62 #include "gromacs/gpu_utils/typecasts.cuh"
63 #include "gromacs/gpu_utils/vectype_ops.cuh"
64 #include "gromacs/math/vectypes.h"
65 #include "gromacs/pbcutil/ishift.h"
66 #include "gromacs/timing/wallcycle.h"
67 #include "gromacs/utility/gmxmpi.h"
69 #include "domdec_internal.h"
74 //! Number of CUDA threads in a block
75 // TODO Optimize this through experimentation
76 constexpr static int c_threadsPerBlock = 256;
79 __global__ void packSendBufKernel(float3* __restrict__ dataPacked,
80 const float3* __restrict__ data,
81 const int* __restrict__ map,
83 const float3 coordinateShift)
85 int threadIndex = blockIdx.x * blockDim.x + threadIdx.x;
86 float3* gm_dataDest = &dataPacked[threadIndex];
87 const float3* gm_dataSrc = &data[map[threadIndex]];
89 if (threadIndex < mapSize)
93 *gm_dataDest = *gm_dataSrc + coordinateShift;
97 *gm_dataDest = *gm_dataSrc;
104 /*! \brief unpack non-local force data buffer on the GPU using pre-populated "map" containing index
105 * information \param[out] data full array of force values \param[in] dataPacked packed
106 * array of force values to be transferred \param[in] map array of indices defining mapping
107 * from full to packed array \param[in] mapSize number of elements in map array
109 template<bool accumulate>
110 __global__ void unpackRecvBufKernel(float3* __restrict__ data,
111 const float3* __restrict__ dataPacked,
112 const int* __restrict__ map,
116 int threadIndex = blockIdx.x * blockDim.x + threadIdx.x;
117 const float3* gm_dataSrc = &dataPacked[threadIndex];
118 float3* gm_dataDest = &data[map[threadIndex]];
120 if (threadIndex < mapSize)
124 *gm_dataDest += *gm_dataSrc;
128 *gm_dataDest = *gm_dataSrc;
135 void GpuHaloExchange::Impl::reinitHalo(float3* d_coordinatesBuffer, float3* d_forcesBuffer)
137 wallcycle_start(wcycle_, ewcDOMDEC);
138 wallcycle_sub_start(wcycle_, ewcsDD_GPU);
140 d_x_ = d_coordinatesBuffer;
141 d_f_ = d_forcesBuffer;
143 const gmx_domdec_comm_t& comm = *dd_->comm;
144 const gmx_domdec_comm_dim_t& cd = comm.cd[dimIndex_];
145 const gmx_domdec_ind_t& ind = cd.ind[pulse_];
147 numHomeAtoms_ = comm.atomRanges.numHomeAtoms(); // offset for data recieved by this rank
149 // Determine receive offset for the dimension index and pulse of this halo exchange object
152 int numAtomsTotal = numHomeAtoms_;
153 for (int i = 0; i <= dimIndex_; i++)
155 int pulseMax = (i == dimIndex_) ? pulse_ : (comm.cd[i].numPulses() - 1);
156 for (int p = 0; p <= pulseMax; p++)
158 atomOffset_ = numAtomsTotal;
159 const gmx_domdec_ind_t& indTemp = comm.cd[i].ind[p];
160 numAtomsTotal += indTemp.nrecv[numZoneTemp + 1];
162 numZone = numZoneTemp;
163 numZoneTemp += numZoneTemp;
166 int newSize = ind.nsend[numZone + 1];
168 GMX_ASSERT(cd.receiveInPlace, "Out-of-place receive is not yet supported in GPU halo exchange");
170 // reallocates only if needed
171 h_indexMap_.resize(newSize);
172 // reallocate on device only if needed
173 if (newSize > maxPackedBufferSize_)
175 reallocateDeviceBuffer(&d_indexMap_, newSize, &indexMapSize_, &indexMapSizeAlloc_, deviceContext_);
176 reallocateDeviceBuffer(&d_sendBuf_, newSize, &sendBufSize_, &sendBufSizeAlloc_, deviceContext_);
177 reallocateDeviceBuffer(&d_recvBuf_, newSize, &recvBufSize_, &recvBufSizeAlloc_, deviceContext_);
178 maxPackedBufferSize_ = newSize;
181 xSendSize_ = newSize;
183 MPI_Sendrecv(&xSendSize_,
196 fSendSize_ = xRecvSize_;
197 fRecvSize_ = xSendSize_;
201 GMX_ASSERT(ind.index.size() == h_indexMap_.size(),
202 "Size mismatch between domain decomposition communication index array and GPU "
203 "halo exchange index mapping array");
204 std::copy(ind.index.begin(), ind.index.end(), h_indexMap_.begin());
207 &d_indexMap_, h_indexMap_.data(), 0, newSize, nonLocalStream_, GpuApiCallBehavior::Async, nullptr);
211 // Exchange of remote addresses from neighboring ranks is needed only with CUDA-direct as cudamemcpy needs both src/dst pointer
212 // MPI calls such as MPI_send doesn't worry about receiving address, that is taken care by MPI_recv call in neighboring rank
215 // This rank will push data to its neighbor, so needs to know
216 // the remote receive address and similarly send its receive
217 // address to other neighbour. We can do this here in reinit fn
218 // since the pointers will not change until the next NS step.
220 // Coordinates buffer:
221 float3* recvPtr = &d_x_[atomOffset_];
222 MPI_Sendrecv(&recvPtr,
236 recvPtr = d_recvBuf_;
237 MPI_Sendrecv(&recvPtr,
252 wallcycle_sub_stop(wcycle_, ewcsDD_GPU);
253 wallcycle_stop(wcycle_, ewcDOMDEC);
258 void GpuHaloExchange::Impl::enqueueWaitRemoteCoordinatesReadyEvent(GpuEventSynchronizer* coordinatesReadyOnDeviceEvent)
260 GMX_ASSERT(coordinatesReadyOnDeviceEvent != nullptr,
261 "Co-ordinate Halo exchange requires valid co-ordinate ready event");
263 // Wait for event from receiving task that remote coordinates are ready, and enqueue that event to stream used
264 // for subsequent data push. This avoids a race condition with the remote data being written in the previous timestep.
265 // Similarly send event to task that will push data to this task.
266 GpuEventSynchronizer* remoteCoordinatesReadyOnDeviceEvent;
267 MPI_Sendrecv(&coordinatesReadyOnDeviceEvent,
268 sizeof(GpuEventSynchronizer*),
272 &remoteCoordinatesReadyOnDeviceEvent,
273 sizeof(GpuEventSynchronizer*),
279 remoteCoordinatesReadyOnDeviceEvent->enqueueWaitEvent(nonLocalStream_);
282 void GpuHaloExchange::Impl::communicateHaloCoordinates(const matrix box,
283 GpuEventSynchronizer* coordinatesReadyOnDeviceEvent)
286 wallcycle_start(wcycle_, ewcLAUNCH_GPU);
289 // ensure stream waits until coordinate data is available on device
290 coordinatesReadyOnDeviceEvent->enqueueWaitEvent(nonLocalStream_);
293 wallcycle_sub_start(wcycle_, ewcsLAUNCH_GPU_MOVEX);
295 // launch kernel to pack send buffer
296 KernelLaunchConfig config;
297 config.blockSize[0] = c_threadsPerBlock;
298 config.blockSize[1] = 1;
299 config.blockSize[2] = 1;
300 config.gridSize[0] = (xSendSize_ + c_threadsPerBlock - 1) / c_threadsPerBlock;
301 config.gridSize[1] = 1;
302 config.gridSize[2] = 1;
303 config.sharedMemorySize = 0;
305 const float3* sendBuf = d_sendBuf_;
306 const float3* d_x = d_x_;
307 const int* indexMap = d_indexMap_;
308 const int size = xSendSize_;
309 // The coordinateShift changes between steps when we have
310 // performed a DD partition, or have updated the box e.g. when
311 // performing pressure coupling. So, for simplicity, the box
312 // is used every step to pass the shift vector as an argument of
313 // the packing kernel.
314 const int boxDimensionIndex = dd_->dim[dimIndex_];
315 const float3 coordinateShift{ box[boxDimensionIndex][XX],
316 box[boxDimensionIndex][YY],
317 box[boxDimensionIndex][ZZ] };
319 // Avoid launching kernel when there is no work to do
322 auto kernelFn = usePBC_ ? packSendBufKernel<true> : packSendBufKernel<false>;
324 const auto kernelArgs = prepareGpuKernelArguments(
325 kernelFn, config, &sendBuf, &d_x, &indexMap, &size, &coordinateShift);
328 kernelFn, config, nonLocalStream_, nullptr, "Domdec GPU Apply X Halo Exchange", kernelArgs);
331 wallcycle_sub_stop(wcycle_, ewcsLAUNCH_GPU_MOVEX);
332 wallcycle_stop(wcycle_, ewcLAUNCH_GPU);
334 // Consider time spent in communicateHaloData as Comm.X counter
335 // ToDo: We need further refinement here as communicateHaloData includes launch time for cudamemcpyasync
336 wallcycle_start(wcycle_, ewcMOVEX);
338 // wait for remote co-ordinates is implicit with process-MPI as non-local stream is synchronized before MPI calls
339 // and MPI_Waitall call makes sure both neighboring ranks' non-local stream is synchronized before data transfer is initiated
340 if (GMX_THREAD_MPI && pulse_ == 0)
342 enqueueWaitRemoteCoordinatesReadyEvent(coordinatesReadyOnDeviceEvent);
345 float3* recvPtr = GMX_THREAD_MPI ? remoteXPtr_ : &d_x_[atomOffset_];
346 communicateHaloData(d_sendBuf_, xSendSize_, sendRankX_, recvPtr, xRecvSize_, recvRankX_);
348 wallcycle_stop(wcycle_, ewcMOVEX);
353 // The following method should be called after non-local buffer operations,
354 // and before the local buffer operations. It operates in the non-local stream.
355 void GpuHaloExchange::Impl::communicateHaloForces(bool accumulateForces)
357 // Consider time spent in communicateHaloData as Comm.F counter
358 // ToDo: We need further refinement here as communicateHaloData includes launch time for cudamemcpyasync
359 wallcycle_start(wcycle_, ewcMOVEF);
361 float3* recvPtr = GMX_THREAD_MPI ? remoteFPtr_ : d_recvBuf_;
363 // Communicate halo data (in non-local stream)
364 communicateHaloData(&(d_f_[atomOffset_]), fSendSize_, sendRankF_, recvPtr, fRecvSize_, recvRankF_);
366 wallcycle_stop(wcycle_, ewcMOVEF);
368 wallcycle_start_nocount(wcycle_, ewcLAUNCH_GPU);
369 wallcycle_sub_start(wcycle_, ewcsLAUNCH_GPU_MOVEF);
372 // If this is the last pulse and index (noting the force halo
373 // exchanges across multiple pulses and indices are called in
374 // reverse order) then perform the following preparation
376 if ((pulse_ == (dd_->comm->cd[dimIndex_].numPulses() - 1)) && (dimIndex_ == (dd_->ndim - 1)))
378 // ensure non-local stream waits for local stream, due to dependence on
379 // the previous H2D copy of CPU forces (if accumulateForces is true)
380 // or local force clearing.
381 GpuEventSynchronizer eventLocal;
382 eventLocal.markEvent(localStream_);
383 eventLocal.enqueueWaitEvent(nonLocalStream_);
386 // Unpack halo buffer into force array
388 KernelLaunchConfig config;
389 config.blockSize[0] = c_threadsPerBlock;
390 config.blockSize[1] = 1;
391 config.blockSize[2] = 1;
392 config.gridSize[0] = (fRecvSize_ + c_threadsPerBlock - 1) / c_threadsPerBlock;
393 config.gridSize[1] = 1;
394 config.gridSize[2] = 1;
395 config.sharedMemorySize = 0;
397 const float3* recvBuf = d_recvBuf_;
398 const int* indexMap = d_indexMap_;
399 const int size = fRecvSize_;
401 if (pulse_ > 0 || dd_->ndim > 1)
403 // We need to accumulate rather than set, since it is possible
404 // that, in this pulse/dim, a value could be written to a location
405 // corresponding to the halo region of a following pulse/dim.
406 accumulateForces = true;
411 auto kernelFn = accumulateForces ? unpackRecvBufKernel<true> : unpackRecvBufKernel<false>;
413 const auto kernelArgs =
414 prepareGpuKernelArguments(kernelFn, config, &d_f, &recvBuf, &indexMap, &size);
417 kernelFn, config, nonLocalStream_, nullptr, "Domdec GPU Apply F Halo Exchange", kernelArgs);
422 fReadyOnDevice_.markEvent(nonLocalStream_);
425 wallcycle_sub_stop(wcycle_, ewcsLAUNCH_GPU_MOVEF);
426 wallcycle_stop(wcycle_, ewcLAUNCH_GPU);
429 void GpuHaloExchange::Impl::communicateHaloData(float3* sendPtr,
438 // no need to explicitly sync with GMX_THREAD_MPI as all operations are
439 // anyway launched in correct stream
440 communicateHaloDataWithCudaDirect(sendPtr, sendSize, sendRank, recvPtr, recvRank);
444 communicateHaloDataWithCudaMPI(sendPtr, sendSize, sendRank, recvPtr, recvSize, recvRank);
448 void GpuHaloExchange::Impl::communicateHaloDataWithCudaMPI(float3* sendPtr,
455 // no need to wait for haloDataReadyOnDevice event if this rank is not sending any data
458 // wait for non local stream to complete all outstanding
459 // activities, to ensure that buffer is up-to-date in GPU memory
460 // before transferring to remote rank
462 // ToDo: Replace stream synchronize with event synchronize
463 nonLocalStream_.synchronize();
466 // perform halo exchange directly in device buffers
470 // recv remote data into halo region
471 MPI_Irecv(recvPtr, recvSize * DIM, MPI_FLOAT, recvRank, 0, mpi_comm_mysim_, &request);
473 // send data to remote halo region
474 MPI_Send(sendPtr, sendSize * DIM, MPI_FLOAT, sendRank, 0, mpi_comm_mysim_);
476 MPI_Wait(&request, MPI_STATUS_IGNORE);
480 void GpuHaloExchange::Impl::communicateHaloDataWithCudaDirect(float3* sendPtr,
489 // We asynchronously push data to remote rank. The remote
490 // destination pointer has already been set in the init fn. We
491 // don't need to worry about overwriting data the remote ranks
492 // still needs since the halo exchange is just done once per
493 // timestep, for each of X and F.
495 // send data to neighbor, if any data exists to send
498 stat = cudaMemcpyAsync(remotePtr,
500 sendSize * DIM * sizeof(float),
501 cudaMemcpyDeviceToDevice,
502 nonLocalStream_.stream());
504 CU_RET_ERR(stat, "cudaMemcpyAsync on GPU Domdec CUDA direct data transfer failed");
508 // ensure pushed data has arrived before remote rank progresses
509 // This rank records an event and sends it to the remote rank which has just been pushed data.
510 // This rank recieves event from remote rank which has pushed data here, and enqueues that event
512 GpuEventSynchronizer* haloDataTransferRemote;
514 GMX_ASSERT(haloDataTransferLaunched_ != nullptr,
515 "Halo exchange requires valid event to synchronize data transfer initiated in "
517 haloDataTransferLaunched_->markEvent(nonLocalStream_);
519 MPI_Sendrecv(&haloDataTransferLaunched_,
520 sizeof(GpuEventSynchronizer*),
524 &haloDataTransferRemote,
525 sizeof(GpuEventSynchronizer*),
532 haloDataTransferRemote->enqueueWaitEvent(nonLocalStream_);
534 GMX_UNUSED_VALUE(sendRank);
535 GMX_UNUSED_VALUE(recvRank);
539 GpuEventSynchronizer* GpuHaloExchange::Impl::getForcesReadyOnDeviceEvent()
541 return &fReadyOnDevice_;
544 /*! \brief Create Domdec GPU object */
545 GpuHaloExchange::Impl::Impl(gmx_domdec_t* dd,
547 MPI_Comm mpi_comm_mysim,
548 const DeviceContext& deviceContext,
549 const DeviceStream& localStream,
550 const DeviceStream& nonLocalStream,
552 gmx_wallcycle* wcycle) :
554 sendRankX_(dd->neighbor[dimIndex][1]),
555 recvRankX_(dd->neighbor[dimIndex][0]),
556 sendRankF_(dd->neighbor[dimIndex][0]),
557 recvRankF_(dd->neighbor[dimIndex][1]),
558 usePBC_(dd->ci[dd->dim[dimIndex]] == 0),
559 haloDataTransferLaunched_(GMX_THREAD_MPI ? new GpuEventSynchronizer() : nullptr),
560 mpi_comm_mysim_(mpi_comm_mysim),
561 deviceContext_(deviceContext),
562 localStream_(localStream),
563 nonLocalStream_(nonLocalStream),
568 if (usePBC_ && dd->unitCellInfo.haveScrewPBC)
570 gmx_fatal(FARGS, "Error: screw is not yet supported in GPU halo exchange\n");
573 changePinningPolicy(&h_indexMap_, gmx::PinningPolicy::PinnedIfSupported);
575 allocateDeviceBuffer(&d_fShift_, 1, deviceContext_);
578 GpuHaloExchange::Impl::~Impl()
580 freeDeviceBuffer(&d_indexMap_);
581 freeDeviceBuffer(&d_sendBuf_);
582 freeDeviceBuffer(&d_recvBuf_);
583 freeDeviceBuffer(&d_fShift_);
584 delete haloDataTransferLaunched_;
587 GpuHaloExchange::GpuHaloExchange(gmx_domdec_t* dd,
589 MPI_Comm mpi_comm_mysim,
590 const DeviceContext& deviceContext,
591 const DeviceStream& localStream,
592 const DeviceStream& nonLocalStream,
594 gmx_wallcycle* wcycle) :
595 impl_(new Impl(dd, dimIndex, mpi_comm_mysim, deviceContext, localStream, nonLocalStream, pulse, wcycle))
599 GpuHaloExchange::GpuHaloExchange(GpuHaloExchange&&) noexcept = default;
601 GpuHaloExchange& GpuHaloExchange::operator=(GpuHaloExchange&& other) noexcept
603 std::swap(impl_, other.impl_);
607 GpuHaloExchange::~GpuHaloExchange() = default;
609 void GpuHaloExchange::reinitHalo(DeviceBuffer<RVec> d_coordinatesBuffer, DeviceBuffer<RVec> d_forcesBuffer)
611 impl_->reinitHalo(asFloat3(d_coordinatesBuffer), asFloat3(d_forcesBuffer));
614 void GpuHaloExchange::communicateHaloCoordinates(const matrix box,
615 GpuEventSynchronizer* coordinatesReadyOnDeviceEvent)
617 impl_->communicateHaloCoordinates(box, coordinatesReadyOnDeviceEvent);
620 void GpuHaloExchange::communicateHaloForces(bool accumulateForces)
622 impl_->communicateHaloForces(accumulateForces);
625 GpuEventSynchronizer* GpuHaloExchange::getForcesReadyOnDeviceEvent()
627 return impl_->getForcesReadyOnDeviceEvent();