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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 environment variable to enable GPU P2P communication */
108 static const bool c_enableGpuPmePpComms =
109 GMX_GPU_CUDA && GMX_THREAD_MPI && (getenv("GMX_GPU_PME_PP_COMMS") != nullptr);
111 /*! \brief Master PP-PME communication data structure */
114 MPI_Comm mpi_comm_mysim; /**< MPI communicator for this simulation */
115 std::vector<PpRanks> ppRanks; /**< The PP partner ranks */
116 int peerRankId; /**< The peer PP rank id */
118 /**< Vectors of A- and B-state parameters used to transfer vectors to PME ranks */
119 gmx::PaddedHostVector<real> chargeA;
120 std::vector<real> chargeB;
121 std::vector<real> sqrt_c6A;
122 std::vector<real> sqrt_c6B;
123 std::vector<real> sigmaA;
124 std::vector<real> sigmaB;
126 gmx::HostVector<gmx::RVec> x; /**< Vector of atom coordinates to transfer to PME ranks */
127 std::vector<gmx::RVec> f; /**< Vector of atom forces received from PME ranks */
129 /**< Vectors of MPI objects used in non-blocking communication between multiple PP ranks per PME rank */
130 std::vector<MPI_Request> req;
131 std::vector<MPI_Status> stat;
134 /*! \brief object for receiving coordinates using communications operating on GPU memory space */
135 std::unique_ptr<gmx::PmeCoordinateReceiverGpu> pmeCoordinateReceiverGpu;
136 /*! \brief object for sending PME force using communications operating on GPU memory space */
137 std::unique_ptr<gmx::PmeForceSenderGpu> pmeForceSenderGpu;
139 /*! \brief whether GPU direct communications are active for PME-PP transfers */
140 bool useGpuDirectComm = false;
143 /*! \brief Initialize the PME-only side of the PME <-> PP communication */
144 static std::unique_ptr<gmx_pme_pp> gmx_pme_pp_init(const t_commrec* cr)
146 auto pme_pp = std::make_unique<gmx_pme_pp>();
151 pme_pp->mpi_comm_mysim = cr->mpi_comm_mysim;
152 MPI_Comm_rank(cr->mpi_comm_mygroup, &rank);
153 auto ppRanks = get_pme_ddranks(cr, rank);
154 pme_pp->ppRanks.reserve(ppRanks.size());
155 for (const auto& ppRankId : ppRanks)
157 pme_pp->ppRanks.push_back({ ppRankId, 0 });
159 // The peer PP rank is the last one.
160 pme_pp->peerRankId = pme_pp->ppRanks.back().rankId;
161 pme_pp->req.resize(eCommType_NR * pme_pp->ppRanks.size());
162 pme_pp->stat.resize(eCommType_NR * pme_pp->ppRanks.size());
164 GMX_UNUSED_VALUE(cr);
170 static void reset_pmeonly_counters(gmx_wallcycle_t wcycle,
171 gmx_walltime_accounting_t walltime_accounting,
176 /* Reset all the counters related to performance over the run */
177 wallcycle_stop(wcycle, ewcRUN);
178 wallcycle_reset_all(wcycle);
180 wallcycle_start(wcycle, ewcRUN);
181 walltime_accounting_reset_time(walltime_accounting, step);
189 static gmx_pme_t* gmx_pmeonly_switch(std::vector<gmx_pme_t*>* pmedata,
190 const ivec grid_size,
194 const t_inputrec* ir)
196 GMX_ASSERT(pmedata, "Bad PME tuning list pointer");
197 for (auto& pme : *pmedata)
199 GMX_ASSERT(pme, "Bad PME tuning list element pointer");
200 if (gmx_pme_grid_matches(*pme, grid_size))
202 /* Here we have found an existing PME data structure that suits us.
203 * However, in the GPU case, we have to reinitialize it - there's only one GPU structure.
204 * This should not cause actual GPU reallocations, at least (the allocated buffers are never shrunk).
205 * So, just some grid size updates in the GPU kernel parameters.
206 * TODO: this should be something like gmx_pme_update_split_params()
208 gmx_pme_reinit(&pme, cr, pme, ir, grid_size, ewaldcoeff_q, ewaldcoeff_lj);
213 const auto& pme = pmedata->back();
214 gmx_pme_t* newStructure = nullptr;
215 // Copy last structure with new grid params
216 gmx_pme_reinit(&newStructure, cr, pme, ir, grid_size, ewaldcoeff_q, ewaldcoeff_lj);
217 pmedata->push_back(newStructure);
221 /*! \brief Called by PME-only ranks to receive coefficients and coordinates
223 * \param[in] pme PME data structure.
224 * \param[in,out] pme_pp PME-PP communication structure.
225 * \param[out] natoms Number of received atoms.
226 * \param[out] box System box, if received.
227 * \param[out] maxshift_x Maximum shift in X direction, if received.
228 * \param[out] maxshift_y Maximum shift in Y direction, if received.
229 * \param[out] lambda_q Free-energy lambda for electrostatics, if received.
230 * \param[out] lambda_lj Free-energy lambda for Lennard-Jones, if received.
231 * \param[out] computeEnergyAndVirial Set to true if this is an energy/virial calculation
232 * step, otherwise set to false.
233 * \param[out] step MD integration step number.
234 * \param[out] grid_size PME grid size, if received.
235 * \param[out] ewaldcoeff_q Ewald cut-off parameter for electrostatics, if received.
236 * \param[out] ewaldcoeff_lj Ewald cut-off parameter for Lennard-Jones, if received.
237 * \param[in] useGpuForPme Flag on whether PME is on GPU.
238 * \param[in] stateGpu GPU state propagator object.
239 * \param[in] runMode PME run mode.
241 * \retval pmerecvqxX All parameters were set, chargeA and chargeB can be NULL.
242 * \retval pmerecvqxFINISH No parameters were set.
243 * \retval pmerecvqxSWITCHGRID Only grid_size and *ewaldcoeff were set.
244 * \retval pmerecvqxRESETCOUNTERS *step was set.
246 static int gmx_pme_recv_coeffs_coords(struct gmx_pme_t* pme,
254 gmx_bool* computeEnergyAndVirial,
260 gmx::StatePropagatorDataGpu* stateGpu,
261 PmeRunMode gmx_unused runMode)
267 unsigned int flags = 0;
269 bool atomSetChanged = false;
273 gmx_pme_comm_n_box_t cnb;
276 /* Receive the send count, box and time step from the peer PP node */
277 MPI_Recv(&cnb, sizeof(cnb), MPI_BYTE, pme_pp->peerRankId, eCommType_CNB, pme_pp->mpi_comm_mysim, MPI_STATUS_IGNORE);
279 /* We accumulate all received flags */
287 "PME only rank receiving:%s%s%s%s%s\n",
288 (cnb.flags & PP_PME_CHARGE) ? " charges" : "",
289 (cnb.flags & PP_PME_COORD) ? " coordinates" : "",
290 (cnb.flags & PP_PME_FINISH) ? " finish" : "",
291 (cnb.flags & PP_PME_SWITCHGRID) ? " switch grid" : "",
292 (cnb.flags & PP_PME_RESETCOUNTERS) ? " reset counters" : "");
295 pme_pp->useGpuDirectComm = ((cnb.flags & PP_PME_GPUCOMMS) != 0);
296 GMX_ASSERT(!pme_pp->useGpuDirectComm || (pme_pp->pmeForceSenderGpu != nullptr),
297 "The use of GPU direct communication for PME-PP is enabled, "
298 "but the PME GPU force reciever object does not exist");
300 if (cnb.flags & PP_PME_FINISH)
302 status = pmerecvqxFINISH;
305 if (cnb.flags & PP_PME_SWITCHGRID)
307 /* Special case, receive the new parameters and return */
308 copy_ivec(cnb.grid_size, *grid_size);
309 *ewaldcoeff_q = cnb.ewaldcoeff_q;
310 *ewaldcoeff_lj = cnb.ewaldcoeff_lj;
312 status = pmerecvqxSWITCHGRID;
315 if (cnb.flags & PP_PME_RESETCOUNTERS)
317 /* Special case, receive the step (set above) and return */
318 status = pmerecvqxRESETCOUNTERS;
321 if (cnb.flags & (PP_PME_CHARGE | PP_PME_SQRTC6 | PP_PME_SIGMA))
323 atomSetChanged = true;
325 /* Receive the send counts from the other PP nodes */
326 for (auto& sender : pme_pp->ppRanks)
328 if (sender.rankId == pme_pp->peerRankId)
330 sender.numAtoms = cnb.natoms;
334 MPI_Irecv(&sender.numAtoms,
335 sizeof(sender.numAtoms),
339 pme_pp->mpi_comm_mysim,
340 &pme_pp->req[messages++]);
343 MPI_Waitall(messages, pme_pp->req.data(), pme_pp->stat.data());
347 for (const auto& sender : pme_pp->ppRanks)
349 nat += sender.numAtoms;
352 if (cnb.flags & PP_PME_CHARGE)
354 pme_pp->chargeA.resizeWithPadding(nat);
356 if (cnb.flags & PP_PME_CHARGEB)
358 pme_pp->chargeB.resize(nat);
360 if (cnb.flags & PP_PME_SQRTC6)
362 pme_pp->sqrt_c6A.resize(nat);
364 if (cnb.flags & PP_PME_SQRTC6B)
366 pme_pp->sqrt_c6B.resize(nat);
368 if (cnb.flags & PP_PME_SIGMA)
370 pme_pp->sigmaA.resize(nat);
372 if (cnb.flags & PP_PME_SIGMAB)
374 pme_pp->sigmaB.resize(nat);
376 pme_pp->x.resize(nat);
377 pme_pp->f.resize(nat);
379 /* maxshift is sent when the charges are sent */
380 *maxshift_x = cnb.maxshift_x;
381 *maxshift_y = cnb.maxshift_y;
383 /* Receive the charges in place */
384 for (int q = 0; q < eCommType_NR; q++)
388 if (!(cnb.flags & (PP_PME_CHARGE << q)))
394 case eCommType_ChargeA: bufferPtr = pme_pp->chargeA.data(); break;
395 case eCommType_ChargeB: bufferPtr = pme_pp->chargeB.data(); break;
396 case eCommType_SQRTC6A: bufferPtr = pme_pp->sqrt_c6A.data(); break;
397 case eCommType_SQRTC6B: bufferPtr = pme_pp->sqrt_c6B.data(); break;
398 case eCommType_SigmaA: bufferPtr = pme_pp->sigmaA.data(); break;
399 case eCommType_SigmaB: bufferPtr = pme_pp->sigmaB.data(); break;
400 default: gmx_incons("Wrong eCommType");
403 for (const auto& sender : pme_pp->ppRanks)
405 if (sender.numAtoms > 0)
407 MPI_Irecv(bufferPtr + nat,
408 sender.numAtoms * sizeof(real),
412 pme_pp->mpi_comm_mysim,
413 &pme_pp->req[messages++]);
414 nat += sender.numAtoms;
418 "Received from PP rank %d: %d %s\n",
421 (q == eCommType_ChargeA || q == eCommType_ChargeB) ? "charges"
429 if (cnb.flags & PP_PME_COORD)
433 gmx_pme_reinit_atoms(pme, nat, pme_pp->chargeA.data(), pme_pp->chargeB.data());
436 stateGpu->reinit(nat, nat);
437 pme_gpu_set_device_x(pme, stateGpu->getCoordinates());
439 if (pme_pp->useGpuDirectComm)
441 GMX_ASSERT(runMode == PmeRunMode::GPU,
442 "GPU Direct PME-PP communication has been enabled, "
443 "but PME run mode is not PmeRunMode::GPU\n");
445 // This rank will have its data accessed directly by PP rank, so needs to send the remote addresses.
446 pme_pp->pmeCoordinateReceiverGpu->sendCoordinateBufferAddressToPpRanks(
447 stateGpu->getCoordinates());
448 pme_pp->pmeForceSenderGpu->sendForceBufferAddressToPpRanks(
449 reinterpret_cast<rvec*>(pme_gpu_get_device_f(pme)));
454 /* The box, FE flag and lambda are sent along with the coordinates
456 copy_mat(cnb.box, box);
457 *lambda_q = cnb.lambda_q;
458 *lambda_lj = cnb.lambda_lj;
459 *computeEnergyAndVirial = ((cnb.flags & PP_PME_ENER_VIR) != 0U);
462 /* Receive the coordinates in place */
464 for (const auto& sender : pme_pp->ppRanks)
466 if (sender.numAtoms > 0)
468 if (pme_pp->useGpuDirectComm)
470 pme_pp->pmeCoordinateReceiverGpu->launchReceiveCoordinatesFromPpCudaDirect(
475 MPI_Irecv(pme_pp->x[nat],
476 sender.numAtoms * sizeof(rvec),
480 pme_pp->mpi_comm_mysim,
481 &pme_pp->req[messages++]);
483 nat += sender.numAtoms;
487 "Received from PP rank %d: %d "
495 if (pme_pp->useGpuDirectComm)
497 pme_pp->pmeCoordinateReceiverGpu->enqueueWaitReceiveCoordinatesFromPpCudaDirect();
503 /* Wait for the coordinates and/or charges to arrive */
504 MPI_Waitall(messages, pme_pp->req.data(), pme_pp->stat.data());
506 } while (status == -1);
508 GMX_UNUSED_VALUE(pme);
509 GMX_UNUSED_VALUE(pme_pp);
510 GMX_UNUSED_VALUE(box);
511 GMX_UNUSED_VALUE(maxshift_x);
512 GMX_UNUSED_VALUE(maxshift_y);
513 GMX_UNUSED_VALUE(lambda_q);
514 GMX_UNUSED_VALUE(lambda_lj);
515 GMX_UNUSED_VALUE(computeEnergyAndVirial);
516 GMX_UNUSED_VALUE(step);
517 GMX_UNUSED_VALUE(grid_size);
518 GMX_UNUSED_VALUE(ewaldcoeff_q);
519 GMX_UNUSED_VALUE(ewaldcoeff_lj);
520 GMX_UNUSED_VALUE(useGpuForPme);
521 GMX_UNUSED_VALUE(stateGpu);
526 if (status == pmerecvqxX)
534 /*! \brief Send the PME mesh force, virial and energy to the PP-only ranks. */
535 static void gmx_pme_send_force_vir_ener(gmx_pme_pp* pme_pp,
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 void* sendbuf = const_cast<void*>(static_cast<const void*>(output.forces_[ind_start]));
554 if (pme_pp->useGpuDirectComm)
556 GMX_ASSERT((pme_pp->pmeForceSenderGpu != nullptr),
557 "The use of GPU direct communication for PME-PP is enabled, "
558 "but the PME GPU force reciever object does not exist");
559 pme_pp->pmeForceSenderGpu->sendFToPpCudaDirect(receiver.rankId);
565 receiver.numAtoms * sizeof(rvec),
569 pme_pp->mpi_comm_mysim,
570 &pme_pp->req[messages]);
575 /* send virial and energy to our last PP node */
576 copy_mat(output.coulombVirial_, cve.vir_q);
577 copy_mat(output.lennardJonesVirial_, cve.vir_lj);
578 cve.energy_q = output.coulombEnergy_;
579 cve.energy_lj = output.lennardJonesEnergy_;
580 cve.dvdlambda_q = dvdlambda_q;
581 cve.dvdlambda_lj = dvdlambda_lj;
582 /* check for the signals to send back to a PP node */
583 cve.stop_cond = gmx_get_stop_condition();
589 fprintf(debug, "PME rank sending to PP rank %d: virial and energy\n", pme_pp->peerRankId);
591 MPI_Isend(&cve, sizeof(cve), MPI_BYTE, pme_pp->peerRankId, 1, pme_pp->mpi_comm_mysim, &pme_pp->req[messages++]);
593 /* Wait for the forces to arrive */
594 MPI_Waitall(messages, pme_pp->req.data(), pme_pp->stat.data());
596 GMX_RELEASE_ASSERT(false, "Invalid call to gmx_pme_send_force_vir_ener");
597 GMX_UNUSED_VALUE(pme_pp);
598 GMX_UNUSED_VALUE(output);
599 GMX_UNUSED_VALUE(dvdlambda_q);
600 GMX_UNUSED_VALUE(dvdlambda_lj);
601 GMX_UNUSED_VALUE(cycles);
605 int gmx_pmeonly(struct gmx_pme_t* pme,
608 gmx_wallcycle* wcycle,
609 gmx_walltime_accounting_t walltime_accounting,
612 const gmx::DeviceStreamManager* deviceStreamManager)
619 int maxshift_x = 0, maxshift_y = 0;
620 real dvdlambda_q, dvdlambda_lj;
623 bool computeEnergyAndVirial = false;
626 /* This data will only use with PME tuning, i.e. switching PME grids */
627 std::vector<gmx_pme_t*> pmedata;
628 pmedata.push_back(pme);
630 auto pme_pp = gmx_pme_pp_init(cr);
632 std::unique_ptr<gmx::StatePropagatorDataGpu> stateGpu;
633 // TODO the variable below should be queried from the task assignment info
634 const bool useGpuForPme = (runMode == PmeRunMode::GPU) || (runMode == PmeRunMode::Mixed);
638 deviceStreamManager != nullptr,
639 "Device stream manager can not be nullptr when using GPU in PME-only rank.");
640 GMX_RELEASE_ASSERT(deviceStreamManager->streamIsValid(gmx::DeviceStreamType::Pme),
641 "Device stream can not be nullptr when using GPU in PME-only rank");
642 changePinningPolicy(&pme_pp->chargeA, pme_get_pinning_policy());
643 changePinningPolicy(&pme_pp->x, pme_get_pinning_policy());
644 if (c_enableGpuPmePpComms)
646 pme_pp->pmeCoordinateReceiverGpu = std::make_unique<gmx::PmeCoordinateReceiverGpu>(
647 deviceStreamManager->stream(gmx::DeviceStreamType::Pme),
648 pme_pp->mpi_comm_mysim,
650 pme_pp->pmeForceSenderGpu = std::make_unique<gmx::PmeForceSenderGpu>(
651 deviceStreamManager->stream(gmx::DeviceStreamType::Pme),
652 pme_pp->mpi_comm_mysim,
655 // TODO: Special PME-only constructor is used here. There is no mechanism to prevent from using the other constructor here.
656 // This should be made safer.
657 stateGpu = std::make_unique<gmx::StatePropagatorDataGpu>(
658 &deviceStreamManager->stream(gmx::DeviceStreamType::Pme),
659 deviceStreamManager->context(),
660 GpuApiCallBehavior::Async,
661 pme_gpu_get_block_size(pme),
668 do /****** this is a quasi-loop over time steps! */
670 /* The reason for having a loop here is PME grid tuning/switching */
673 /* Domain decomposition */
675 real ewaldcoeff_q = 0, ewaldcoeff_lj = 0;
676 ret = gmx_pme_recv_coeffs_coords(pme,
684 &computeEnergyAndVirial,
693 if (ret == pmerecvqxSWITCHGRID)
695 /* Switch the PME grid to newGridSize */
696 pme = gmx_pmeonly_switch(&pmedata, newGridSize, ewaldcoeff_q, ewaldcoeff_lj, cr, ir);
699 if (ret == pmerecvqxRESETCOUNTERS)
701 /* Reset the cycle and flop counters */
702 reset_pmeonly_counters(wcycle, walltime_accounting, mynrnb, step, useGpuForPme);
704 } while (ret == pmerecvqxSWITCHGRID || ret == pmerecvqxRESETCOUNTERS);
706 if (ret == pmerecvqxFINISH)
708 /* We should stop: break out of the loop */
714 wallcycle_start(wcycle, ewcRUN);
715 walltime_accounting_start_time(walltime_accounting);
718 wallcycle_start(wcycle, ewcPMEMESH);
723 // TODO Make a struct of array refs onto these per-atom fields
724 // of pme_pp (maybe box, energy and virial, too; and likewise
725 // from mdatoms for the other call to gmx_pme_do), so we have
726 // fewer lines of code and less parameter passing.
727 gmx::StepWorkload stepWork;
728 stepWork.computeVirial = computeEnergyAndVirial;
729 stepWork.computeEnergy = computeEnergyAndVirial;
730 stepWork.computeForces = true;
731 PmeOutput output = { {}, false, 0, { { 0 } }, 0, 0, { { 0 } }, 0 };
734 stepWork.haveDynamicBox = false;
735 stepWork.useGpuPmeFReduction = pme_pp->useGpuDirectComm;
736 // TODO this should be set properly by gmx_pme_recv_coeffs_coords,
737 // or maybe use inputrecDynamicBox(ir), at the very least - change this when this codepath is tested!
738 pme_gpu_prepare_computation(pme, box, wcycle, stepWork);
739 if (!pme_pp->useGpuDirectComm)
741 stateGpu->copyCoordinatesToGpu(gmx::ArrayRef<gmx::RVec>(pme_pp->x), gmx::AtomLocality::All);
743 // On the separate PME rank we do not need a synchronizer as we schedule everything in a single stream
744 // TODO: with pme on GPU the receive should make a list of synchronizers and pass it here #3157
745 auto xReadyOnDevice = nullptr;
747 pme_gpu_launch_spread(pme, xReadyOnDevice, wcycle, lambda_q);
748 pme_gpu_launch_complex_transforms(pme, wcycle, stepWork);
749 pme_gpu_launch_gather(pme, wcycle, lambda_q);
750 output = pme_gpu_wait_finish_task(pme, computeEnergyAndVirial, lambda_q, wcycle);
751 pme_gpu_reinit_computation(pme, wcycle);
755 GMX_ASSERT(pme_pp->x.size() == static_cast<size_t>(natoms),
756 "The coordinate buffer should have size natoms");
761 pme_pp->chargeA.data(),
762 pme_pp->chargeB.data(),
763 pme_pp->sqrt_c6A.data(),
764 pme_pp->sqrt_c6B.data(),
765 pme_pp->sigmaA.data(),
766 pme_pp->sigmaB.data(),
773 output.coulombVirial_,
774 output.lennardJonesVirial_,
775 &output.coulombEnergy_,
776 &output.lennardJonesEnergy_,
782 output.forces_ = pme_pp->f;
785 cycles = wallcycle_stop(wcycle, ewcPMEMESH);
786 gmx_pme_send_force_vir_ener(pme_pp.get(), output, dvdlambda_q, dvdlambda_lj, cycles);
789 } /***** end of quasi-loop, we stop with the break above */
792 walltime_accounting_end_time(walltime_accounting);