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38 /* IMPORTANT FOR DEVELOPERS:
40 * Triclinic pme stuff isn't entirely trivial, and we've experienced
41 * some bugs during development (many of them due to me). To avoid
42 * this in the future, please check the following things if you make
43 * changes in this file:
45 * 1. You should obtain identical (at least to the PME precision)
46 * energies, forces, and virial for
47 * a rectangular box and a triclinic one where the z (or y) axis is
48 * tilted a whole box side. For instance you could use these boxes:
50 * rectangular triclinic
55 * 2. You should check the energy conservation in a triclinic box.
57 * It might seem an overkill, but better safe than sorry.
77 #include "gromacs/domdec/domdec.h"
78 #include "gromacs/ewald/pme.h"
79 #include "gromacs/ewald/pme_coordinate_receiver_gpu.h"
80 #include "gromacs/ewald/pme_force_sender_gpu.h"
81 #include "gromacs/fft/parallel_3dfft.h"
82 #include "gromacs/fileio/pdbio.h"
83 #include "gromacs/gmxlib/network.h"
84 #include "gromacs/gmxlib/nrnb.h"
85 #include "gromacs/gpu_utils/device_stream_manager.h"
86 #include "gromacs/gpu_utils/hostallocator.h"
87 #include "gromacs/math/gmxcomplex.h"
88 #include "gromacs/math/units.h"
89 #include "gromacs/math/vec.h"
90 #include "gromacs/mdtypes/commrec.h"
91 #include "gromacs/mdtypes/forceoutput.h"
92 #include "gromacs/mdtypes/inputrec.h"
93 #include "gromacs/mdtypes/simulation_workload.h"
94 #include "gromacs/mdtypes/state_propagator_data_gpu.h"
95 #include "gromacs/timing/cyclecounter.h"
96 #include "gromacs/timing/wallcycle.h"
97 #include "gromacs/utility/fatalerror.h"
98 #include "gromacs/utility/futil.h"
99 #include "gromacs/utility/gmxmpi.h"
100 #include "gromacs/utility/gmxomp.h"
101 #include "gromacs/utility/smalloc.h"
103 #include "pme_gpu_internal.h"
104 #include "pme_output.h"
105 #include "pme_pp_communication.h"
107 /*! \brief Master PP-PME communication data structure */
110 MPI_Comm mpi_comm_mysim; /**< MPI communicator for this simulation */
111 std::vector<PpRanks> ppRanks; /**< The PP partner ranks */
112 int peerRankId; /**< The peer PP rank id */
114 /**< Vectors of A- and B-state parameters used to transfer vectors to PME ranks */
115 gmx::PaddedHostVector<real> chargeA;
116 std::vector<real> chargeB;
117 std::vector<real> sqrt_c6A;
118 std::vector<real> sqrt_c6B;
119 std::vector<real> sigmaA;
120 std::vector<real> sigmaB;
122 gmx::HostVector<gmx::RVec> x; /**< Vector of atom coordinates to transfer to PME ranks */
123 std::vector<gmx::RVec> f; /**< Vector of atom forces received from PME ranks */
125 /**< Vectors of MPI objects used in non-blocking communication between multiple PP ranks per PME rank */
126 std::vector<MPI_Request> req;
127 std::vector<MPI_Status> stat;
130 /*! \brief object for receiving coordinates using communications operating on GPU memory space */
131 std::unique_ptr<gmx::PmeCoordinateReceiverGpu> pmeCoordinateReceiverGpu;
132 /*! \brief object for sending PME force using communications operating on GPU memory space */
133 std::unique_ptr<gmx::PmeForceSenderGpu> pmeForceSenderGpu;
135 /*! \brief whether GPU direct communications are active for PME-PP transfers */
136 bool useGpuDirectComm = false;
139 /*! \brief Initialize the PME-only side of the PME <-> PP communication */
140 static std::unique_ptr<gmx_pme_pp> gmx_pme_pp_init(const t_commrec* cr)
142 auto pme_pp = std::make_unique<gmx_pme_pp>();
147 pme_pp->mpi_comm_mysim = cr->mpi_comm_mysim;
148 MPI_Comm_rank(cr->mpi_comm_mygroup, &rank);
149 auto ppRanks = get_pme_ddranks(cr, rank);
150 pme_pp->ppRanks.reserve(ppRanks.size());
151 for (const auto& ppRankId : ppRanks)
153 pme_pp->ppRanks.push_back({ ppRankId, 0 });
155 // The peer PP rank is the last one.
156 pme_pp->peerRankId = pme_pp->ppRanks.back().rankId;
157 pme_pp->req.resize(eCommType_NR * pme_pp->ppRanks.size());
158 pme_pp->stat.resize(eCommType_NR * pme_pp->ppRanks.size());
160 GMX_UNUSED_VALUE(cr);
166 static void reset_pmeonly_counters(gmx_wallcycle* wcycle,
167 gmx_walltime_accounting_t walltime_accounting,
172 /* Reset all the counters related to performance over the run */
173 wallcycle_stop(wcycle, WallCycleCounter::Run);
174 wallcycle_reset_all(wcycle);
176 wallcycle_start(wcycle, WallCycleCounter::Run);
177 walltime_accounting_reset_time(walltime_accounting, step);
185 static gmx_pme_t* gmx_pmeonly_switch(std::vector<gmx_pme_t*>* pmedata,
186 const ivec grid_size,
190 const t_inputrec* ir)
192 GMX_ASSERT(pmedata, "Bad PME tuning list pointer");
193 for (auto& pme : *pmedata)
195 GMX_ASSERT(pme, "Bad PME tuning list element pointer");
196 if (gmx_pme_grid_matches(*pme, grid_size))
198 /* Here we have found an existing PME data structure that suits us.
199 * However, in the GPU case, we have to reinitialize it - there's only one GPU structure.
200 * This should not cause actual GPU reallocations, at least (the allocated buffers are never shrunk).
201 * So, just some grid size updates in the GPU kernel parameters.
202 * TODO: this should be something like gmx_pme_update_split_params()
204 gmx_pme_reinit(&pme, cr, pme, ir, grid_size, ewaldcoeff_q, ewaldcoeff_lj);
209 const auto& pme = pmedata->back();
210 gmx_pme_t* newStructure = nullptr;
211 // Copy last structure with new grid params
212 gmx_pme_reinit(&newStructure, cr, pme, ir, grid_size, ewaldcoeff_q, ewaldcoeff_lj);
213 pmedata->push_back(newStructure);
217 /*! \brief Called by PME-only ranks to receive coefficients and coordinates
219 * \param[in] pme PME data structure.
220 * \param[in,out] pme_pp PME-PP communication structure.
221 * \param[out] natoms Number of received atoms.
222 * \param[out] box System box, if received.
223 * \param[out] maxshift_x Maximum shift in X direction, if received.
224 * \param[out] maxshift_y Maximum shift in Y direction, if received.
225 * \param[out] lambda_q Free-energy lambda for electrostatics, if received.
226 * \param[out] lambda_lj Free-energy lambda for Lennard-Jones, if received.
227 * \param[out] computeEnergyAndVirial Set to true if this is an energy/virial calculation
228 * step, otherwise set to false.
229 * \param[out] step MD integration step number.
230 * \param[out] grid_size PME grid size, if received.
231 * \param[out] ewaldcoeff_q Ewald cut-off parameter for electrostatics, if received.
232 * \param[out] ewaldcoeff_lj Ewald cut-off parameter for Lennard-Jones, if received.
233 * \param[in] useGpuForPme Flag on whether PME is on GPU.
234 * \param[in] stateGpu GPU state propagator object.
235 * \param[in] runMode PME run mode.
237 * \retval pmerecvqxX All parameters were set, chargeA and chargeB can be NULL.
238 * \retval pmerecvqxFINISH No parameters were set.
239 * \retval pmerecvqxSWITCHGRID Only grid_size and *ewaldcoeff were set.
240 * \retval pmerecvqxRESETCOUNTERS *step was set.
242 static int gmx_pme_recv_coeffs_coords(struct gmx_pme_t* pme,
250 gmx_bool* computeEnergyAndVirial,
256 gmx::StatePropagatorDataGpu* stateGpu,
257 PmeRunMode gmx_unused runMode)
264 bool atomSetChanged = false;
268 gmx_pme_comm_n_box_t cnb;
271 /* Receive the send count, box and time step from the peer PP node */
272 MPI_Recv(&cnb, sizeof(cnb), MPI_BYTE, pme_pp->peerRankId, eCommType_CNB, pme_pp->mpi_comm_mysim, MPI_STATUS_IGNORE);
279 "PME only rank receiving:%s%s%s%s%s\n",
280 (cnb.flags & PP_PME_CHARGE) ? " charges" : "",
281 (cnb.flags & PP_PME_COORD) ? " coordinates" : "",
282 (cnb.flags & PP_PME_FINISH) ? " finish" : "",
283 (cnb.flags & PP_PME_SWITCHGRID) ? " switch grid" : "",
284 (cnb.flags & PP_PME_RESETCOUNTERS) ? " reset counters" : "");
287 pme_pp->useGpuDirectComm = ((cnb.flags & PP_PME_GPUCOMMS) != 0);
288 GMX_ASSERT(!pme_pp->useGpuDirectComm || (pme_pp->pmeForceSenderGpu != nullptr),
289 "The use of GPU direct communication for PME-PP is enabled, "
290 "but the PME GPU force reciever object does not exist");
292 if (cnb.flags & PP_PME_FINISH)
294 status = pmerecvqxFINISH;
297 if (cnb.flags & PP_PME_SWITCHGRID)
299 /* Special case, receive the new parameters and return */
300 copy_ivec(cnb.grid_size, *grid_size);
301 *ewaldcoeff_q = cnb.ewaldcoeff_q;
302 *ewaldcoeff_lj = cnb.ewaldcoeff_lj;
304 status = pmerecvqxSWITCHGRID;
307 if (cnb.flags & PP_PME_RESETCOUNTERS)
309 /* Special case, receive the step (set above) and return */
310 status = pmerecvqxRESETCOUNTERS;
313 if (cnb.flags & (PP_PME_CHARGE | PP_PME_SQRTC6 | PP_PME_SIGMA))
315 atomSetChanged = true;
317 /* Receive the send counts from the other PP nodes */
318 for (auto& sender : pme_pp->ppRanks)
320 if (sender.rankId == pme_pp->peerRankId)
322 sender.numAtoms = cnb.natoms;
326 MPI_Irecv(&sender.numAtoms,
327 sizeof(sender.numAtoms),
331 pme_pp->mpi_comm_mysim,
332 &pme_pp->req[messages++]);
335 MPI_Waitall(messages, pme_pp->req.data(), pme_pp->stat.data());
339 for (const auto& sender : pme_pp->ppRanks)
341 nat += sender.numAtoms;
344 if (cnb.flags & PP_PME_CHARGE)
346 pme_pp->chargeA.resizeWithPadding(nat);
348 if (cnb.flags & PP_PME_CHARGEB)
350 pme_pp->chargeB.resize(nat);
352 if (cnb.flags & PP_PME_SQRTC6)
354 pme_pp->sqrt_c6A.resize(nat);
356 if (cnb.flags & PP_PME_SQRTC6B)
358 pme_pp->sqrt_c6B.resize(nat);
360 if (cnb.flags & PP_PME_SIGMA)
362 pme_pp->sigmaA.resize(nat);
364 if (cnb.flags & PP_PME_SIGMAB)
366 pme_pp->sigmaB.resize(nat);
368 pme_pp->x.resize(nat);
369 pme_pp->f.resize(nat);
371 /* maxshift is sent when the charges are sent */
372 *maxshift_x = cnb.maxshift_x;
373 *maxshift_y = cnb.maxshift_y;
375 /* Receive the charges in place */
376 for (int q = 0; q < eCommType_NR; q++)
380 if (!(cnb.flags & (PP_PME_CHARGE << q)))
386 case eCommType_ChargeA: bufferPtr = pme_pp->chargeA.data(); break;
387 case eCommType_ChargeB: bufferPtr = pme_pp->chargeB.data(); break;
388 case eCommType_SQRTC6A: bufferPtr = pme_pp->sqrt_c6A.data(); break;
389 case eCommType_SQRTC6B: bufferPtr = pme_pp->sqrt_c6B.data(); break;
390 case eCommType_SigmaA: bufferPtr = pme_pp->sigmaA.data(); break;
391 case eCommType_SigmaB: bufferPtr = pme_pp->sigmaB.data(); break;
392 default: gmx_incons("Wrong eCommType");
395 for (const auto& sender : pme_pp->ppRanks)
397 if (sender.numAtoms > 0)
399 MPI_Irecv(bufferPtr + nat,
400 sender.numAtoms * sizeof(real),
404 pme_pp->mpi_comm_mysim,
405 &pme_pp->req[messages++]);
406 nat += sender.numAtoms;
410 "Received from PP rank %d: %d %s\n",
413 (q == eCommType_ChargeA || q == eCommType_ChargeB) ? "charges"
421 if (cnb.flags & PP_PME_COORD)
425 gmx_pme_reinit_atoms(pme, nat, pme_pp->chargeA, pme_pp->chargeB);
428 stateGpu->reinit(nat, nat);
429 pme_gpu_set_device_x(pme, stateGpu->getCoordinates());
431 if (pme_pp->useGpuDirectComm)
433 GMX_ASSERT(runMode == PmeRunMode::GPU,
434 "GPU Direct PME-PP communication has been enabled, "
435 "but PME run mode is not PmeRunMode::GPU\n");
437 // This rank will have its data accessed directly by PP rank, so needs to send the remote addresses.
438 pme_pp->pmeCoordinateReceiverGpu->sendCoordinateBufferAddressToPpRanks(
439 stateGpu->getCoordinates());
440 pme_pp->pmeForceSenderGpu->setForceSendBuffer(pme_gpu_get_device_f(pme));
445 /* The box, FE flag and lambda are sent along with the coordinates
447 copy_mat(cnb.box, box);
448 *lambda_q = cnb.lambda_q;
449 *lambda_lj = cnb.lambda_lj;
450 *computeEnergyAndVirial = ((cnb.flags & PP_PME_ENER_VIR) != 0U);
453 /* Receive the coordinates in place */
455 for (const auto& sender : pme_pp->ppRanks)
457 if (sender.numAtoms > 0)
459 if (pme_pp->useGpuDirectComm)
463 pme_pp->pmeCoordinateReceiverGpu->receiveCoordinatesSynchronizerFromPpCudaDirect(
468 pme_pp->pmeCoordinateReceiverGpu->launchReceiveCoordinatesFromPpCudaMpi(
469 stateGpu->getCoordinates(), nat, sender.numAtoms * sizeof(rvec), sender.rankId);
474 MPI_Irecv(pme_pp->x[nat],
475 sender.numAtoms * sizeof(rvec),
479 pme_pp->mpi_comm_mysim,
480 &pme_pp->req[messages++]);
482 nat += sender.numAtoms;
486 "Received from PP rank %d: %d "
494 if (pme_pp->useGpuDirectComm)
496 pme_pp->pmeCoordinateReceiverGpu->synchronizeOnCoordinatesFromPpRanks();
502 /* Wait for the coordinates and/or charges to arrive */
503 MPI_Waitall(messages, pme_pp->req.data(), pme_pp->stat.data());
505 } while (status == -1);
507 GMX_UNUSED_VALUE(pme);
508 GMX_UNUSED_VALUE(pme_pp);
509 GMX_UNUSED_VALUE(box);
510 GMX_UNUSED_VALUE(maxshift_x);
511 GMX_UNUSED_VALUE(maxshift_y);
512 GMX_UNUSED_VALUE(lambda_q);
513 GMX_UNUSED_VALUE(lambda_lj);
514 GMX_UNUSED_VALUE(computeEnergyAndVirial);
515 GMX_UNUSED_VALUE(step);
516 GMX_UNUSED_VALUE(grid_size);
517 GMX_UNUSED_VALUE(ewaldcoeff_q);
518 GMX_UNUSED_VALUE(ewaldcoeff_lj);
519 GMX_UNUSED_VALUE(useGpuForPme);
520 GMX_UNUSED_VALUE(stateGpu);
525 if (status == pmerecvqxX)
533 /*! \brief Send the PME mesh force, virial and energy to the PP-only ranks. */
534 static void gmx_pme_send_force_vir_ener(const gmx_pme_t& pme,
536 const PmeOutput& output,
542 gmx_pme_comm_vir_ene_t cve;
543 int messages, ind_start, ind_end;
546 /* Now the evaluated forces have to be transferred to the PP nodes */
549 for (const auto& receiver : pme_pp->ppRanks)
552 ind_end = ind_start + receiver.numAtoms;
553 if (pme_pp->useGpuDirectComm)
555 GMX_ASSERT((pme_pp->pmeForceSenderGpu != nullptr),
556 "The use of GPU direct communication for PME-PP is enabled, "
557 "but the PME GPU force reciever object does not exist");
561 pme_pp->pmeForceSenderGpu->sendFToPpCudaDirect(receiver.rankId, receiver.numAtoms);
565 pme_pp->pmeForceSenderGpu->sendFToPpCudaMpi(pme_gpu_get_device_f(&pme),
567 receiver.numAtoms * sizeof(rvec),
569 &pme_pp->req[messages]);
576 void* sendbuf = const_cast<void*>(static_cast<const void*>(output.forces_[ind_start]));
579 receiver.numAtoms * sizeof(rvec),
583 pme_pp->mpi_comm_mysim,
584 &pme_pp->req[messages]);
589 /* send virial and energy to our last PP node */
590 copy_mat(output.coulombVirial_, cve.vir_q);
591 copy_mat(output.lennardJonesVirial_, cve.vir_lj);
592 cve.energy_q = output.coulombEnergy_;
593 cve.energy_lj = output.lennardJonesEnergy_;
594 cve.dvdlambda_q = dvdlambda_q;
595 cve.dvdlambda_lj = dvdlambda_lj;
596 /* check for the signals to send back to a PP node */
597 cve.stop_cond = gmx_get_stop_condition();
603 fprintf(debug, "PME rank sending to PP rank %d: virial and energy\n", pme_pp->peerRankId);
605 MPI_Isend(&cve, sizeof(cve), MPI_BYTE, pme_pp->peerRankId, 1, pme_pp->mpi_comm_mysim, &pme_pp->req[messages++]);
607 /* Wait for the forces to arrive */
608 MPI_Waitall(messages, pme_pp->req.data(), pme_pp->stat.data());
610 GMX_RELEASE_ASSERT(false, "Invalid call to gmx_pme_send_force_vir_ener");
611 GMX_UNUSED_VALUE(pme);
612 GMX_UNUSED_VALUE(pme_pp);
613 GMX_UNUSED_VALUE(output);
614 GMX_UNUSED_VALUE(dvdlambda_q);
615 GMX_UNUSED_VALUE(dvdlambda_lj);
616 GMX_UNUSED_VALUE(cycles);
620 int gmx_pmeonly(struct gmx_pme_t* pme,
623 gmx_wallcycle* wcycle,
624 gmx_walltime_accounting_t walltime_accounting,
627 bool useGpuPmePpCommunication,
628 const gmx::DeviceStreamManager* deviceStreamManager)
635 int maxshift_x = 0, maxshift_y = 0;
636 real dvdlambda_q, dvdlambda_lj;
639 bool computeEnergyAndVirial = false;
642 /* This data will only use with PME tuning, i.e. switching PME grids */
643 std::vector<gmx_pme_t*> pmedata;
644 pmedata.push_back(pme);
646 auto pme_pp = gmx_pme_pp_init(cr);
648 std::unique_ptr<gmx::StatePropagatorDataGpu> stateGpu;
649 // TODO the variable below should be queried from the task assignment info
650 const bool useGpuForPme = (runMode == PmeRunMode::GPU) || (runMode == PmeRunMode::Mixed);
654 deviceStreamManager != nullptr,
655 "Device stream manager can not be nullptr when using GPU in PME-only rank.");
656 GMX_RELEASE_ASSERT(deviceStreamManager->streamIsValid(gmx::DeviceStreamType::Pme),
657 "Device stream can not be nullptr when using GPU in PME-only rank");
658 changePinningPolicy(&pme_pp->chargeA, pme_get_pinning_policy());
659 changePinningPolicy(&pme_pp->x, pme_get_pinning_policy());
660 if (useGpuPmePpCommunication)
662 pme_pp->pmeCoordinateReceiverGpu = std::make_unique<gmx::PmeCoordinateReceiverGpu>(
663 deviceStreamManager->stream(gmx::DeviceStreamType::Pme),
664 pme_pp->mpi_comm_mysim,
666 pme_pp->pmeForceSenderGpu =
667 std::make_unique<gmx::PmeForceSenderGpu>(pme_gpu_get_f_ready_synchronizer(pme),
668 pme_pp->mpi_comm_mysim,
669 deviceStreamManager->context(),
672 // TODO: Special PME-only constructor is used here. There is no mechanism to prevent from using the other constructor here.
673 // This should be made safer.
674 stateGpu = std::make_unique<gmx::StatePropagatorDataGpu>(
675 &deviceStreamManager->stream(gmx::DeviceStreamType::Pme),
676 deviceStreamManager->context(),
677 GpuApiCallBehavior::Async,
678 pme_gpu_get_block_size(pme),
685 do /****** this is a quasi-loop over time steps! */
687 /* The reason for having a loop here is PME grid tuning/switching */
690 /* Domain decomposition */
692 real ewaldcoeff_q = 0, ewaldcoeff_lj = 0;
693 ret = gmx_pme_recv_coeffs_coords(pme,
701 &computeEnergyAndVirial,
710 if (ret == pmerecvqxSWITCHGRID)
712 /* Switch the PME grid to newGridSize */
713 pme = gmx_pmeonly_switch(&pmedata, newGridSize, ewaldcoeff_q, ewaldcoeff_lj, cr, ir);
716 if (ret == pmerecvqxRESETCOUNTERS)
718 /* Reset the cycle and flop counters */
719 reset_pmeonly_counters(wcycle, walltime_accounting, mynrnb, step, useGpuForPme);
721 } while (ret == pmerecvqxSWITCHGRID || ret == pmerecvqxRESETCOUNTERS);
723 if (ret == pmerecvqxFINISH)
725 /* We should stop: break out of the loop */
731 wallcycle_start(wcycle, WallCycleCounter::Run);
732 walltime_accounting_start_time(walltime_accounting);
735 wallcycle_start(wcycle, WallCycleCounter::PmeMesh);
740 // TODO Make a struct of array refs onto these per-atom fields
741 // of pme_pp (maybe box, energy and virial, too; and likewise
742 // from mdatoms for the other call to gmx_pme_do), so we have
743 // fewer lines of code and less parameter passing.
744 gmx::StepWorkload stepWork;
745 stepWork.computeVirial = computeEnergyAndVirial;
746 stepWork.computeEnergy = computeEnergyAndVirial;
747 stepWork.computeForces = true;
748 PmeOutput output = { {}, false, 0, { { 0 } }, 0, 0, { { 0 } }, 0 };
751 stepWork.haveDynamicBox = false;
752 stepWork.useGpuPmeFReduction = pme_pp->useGpuDirectComm;
753 // TODO this should be set properly by gmx_pme_recv_coeffs_coords,
754 // or maybe use inputrecDynamicBox(ir), at the very least - change this when this codepath is tested!
755 pme_gpu_prepare_computation(pme, box, wcycle, stepWork);
756 if (!pme_pp->useGpuDirectComm)
758 stateGpu->copyCoordinatesToGpu(gmx::ArrayRef<gmx::RVec>(pme_pp->x), gmx::AtomLocality::All);
760 // On the separate PME rank we do not need a synchronizer as we schedule everything in a single stream
761 // TODO: with pme on GPU the receive should make a list of synchronizers and pass it here #3157
762 auto xReadyOnDevice = nullptr;
764 pme_gpu_launch_spread(pme, xReadyOnDevice, wcycle, lambda_q);
765 pme_gpu_launch_complex_transforms(pme, wcycle, stepWork);
766 pme_gpu_launch_gather(pme, wcycle, lambda_q);
767 output = pme_gpu_wait_finish_task(pme, computeEnergyAndVirial, lambda_q, wcycle);
768 pme_gpu_reinit_computation(pme, wcycle);
772 GMX_ASSERT(pme_pp->x.size() == static_cast<size_t>(natoms),
773 "The coordinate buffer should have size natoms");
790 output.coulombVirial_,
791 output.lennardJonesVirial_,
792 &output.coulombEnergy_,
793 &output.lennardJonesEnergy_,
799 output.forces_ = pme_pp->f;
802 cycles = wallcycle_stop(wcycle, WallCycleCounter::PmeMesh);
803 gmx_pme_send_force_vir_ener(*pme, pme_pp.get(), output, dvdlambda_q, dvdlambda_lj, cycles);
806 } /***** end of quasi-loop, we stop with the break above */
809 walltime_accounting_end_time(walltime_accounting);