dev-manual/build-system.rst
dev-manual/commitstyle.rst
dev-manual/documentation-generation.rst
+ dev-manual/contribute.rst
dev-manual/doxygen.rst
dev-manual/error-handling.rst
dev-manual/formatting.rst
release-notes/2018/major/removed-features.rst
release-notes/2018/major/portability.rst
release-notes/2018/major/miscellaneous.rst
+ release-notes/2016/2016.5.rst
+ release-notes/2016/2016.4.rst
+ release-notes/2016/2016.3.rst
+ release-notes/2016/2016.2.rst
+ release-notes/2016/2016.1.rst
+ release-notes/2016/major/highlights.rst
+ release-notes/2016/major/new-features.rst
+ release-notes/2016/major/performance.rst
+ release-notes/2016/major/tools.rst
+ release-notes/2016/major/bugs-fixed.rst
+ release-notes/2016/major/removed-features.rst
+ release-notes/2016/major/miscellaneous.rst
+ release-notes/older/index.rst
user-guide/index.rst
user-guide/cutoff-schemes.rst
user-guide/getting-started.rst
class GetIrTest : public ::testing::Test
{
public:
- GetIrTest() : fileManager_(), data_(), checker_(data_.rootChecker()),
- ir_(), mdModules_(), opts_(),
+ GetIrTest() : fileManager_(), ir_(), mdModules_(), opts_(),
wi_(init_warning(FALSE, 0)), wiGuard_(wi_)
{
get_ir(inputMdpFilename.c_str(), outputMdpFilename.c_str(),
&mdModules_, &ir_, &opts_, WriteMdpHeader::no, wi_);
- bool failure = warning_errors_exist(wi_);
- checker_.checkBoolean(failure, "Error parsing mdp file");
+
+ // Now check
+ bool failure = warning_errors_exist(wi_);
+ TestReferenceData data;
+ TestReferenceChecker checker(data.rootChecker());
+ checker.checkBoolean(failure, "Error parsing mdp file");
warning_reset(wi_);
auto outputMdpContents = TextReader::readFileToString(outputMdpFilename);
- checker_.checkString(outputMdpContents, "OutputMdpFile");
+ checker.checkString(outputMdpContents, "OutputMdpFile");
}
TestFileManager fileManager_;
- TestReferenceData data_;
- TestReferenceChecker checker_;
t_inputrec ir_;
MDModules mdModules_;
t_gromppopts opts_;
runTest(joinStrings(inputMdpFile, "\n"));
}
+ TEST_F(GetIrTest, DefineHandlesAssignmentOnRhs)
+ {
+ const char *inputMdpFile[] = {
+ "define = -DBOOL -DVAR=VALUE",
+ };
+ runTest(joinStrings(inputMdpFile, "\n"));
+ }
+
TEST_F(GetIrTest, EmptyInputWorks)
{
const char *inputMdpFile = "";
runTest(inputMdpFile);
}
+TEST_F(GetIrTest, TerminatesOnDuplicateOldAndNewKeys)
+{
+ const char *inputMdpFile[] = {"verlet-buffer-drift = 1.3", "verlet-buffer-tolerance = 2.7"};
+ EXPECT_DEATH_IF_SUPPORTED(runTest(joinStrings(inputMdpFile, "\n")), "A parameter is present with both");
+}
+
+TEST_F(GetIrTest, ImplicitSolventNoWorks)
+{
+ const char *inputMdpFile = "implicit-solvent = no";
+ runTest(inputMdpFile);
+}
+
+TEST_F(GetIrTest, ImplicitSolventYesWorks)
+{
+ const char *inputMdpFile = "implicit-solvent = yes";
+ EXPECT_DEATH_IF_SUPPORTED(runTest(inputMdpFile), "Invalid enum");
+}
+
} // namespace
} // namespace
--- /dev/null
-
-; IMPLICIT SOLVENT ALGORITHM
-implicit-solvent = No
-
-; GENERALIZED BORN ELECTROSTATICS
-; Algorithm for calculating Born radii
-gb-algorithm = Still
-; Frequency of calculating the Born radii inside rlist
-nstgbradii = 1
-; Cutoff for Born radii calculation; the contribution from atoms
-; between rlist and rgbradii is updated every nstlist steps
-rgbradii = 1
-; Dielectric coefficient of the implicit solvent
-gb-epsilon-solvent = 80
-; Salt concentration in M for Generalized Born models
-gb-saltconc = 0
-; Scaling factors used in the OBC GB model. Default values are OBC(II)
-gb-obc-alpha = 1
-gb-obc-beta = 0.8
-gb-obc-gamma = 4.85
-gb-dielectric-offset = 0.009
-sa-algorithm = Ace-approximation
-; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
-; The value -1 will set default value for Still/HCT/OBC GB-models.
-sa-surface-tension = -1
+ <?xml version="1.0"?>
+ <?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+ <ReferenceData>
+ <Bool Name="Error parsing mdp file">false</Bool>
+ <String Name="OutputMdpFile">
+ ; VARIOUS PREPROCESSING OPTIONS
+ ; Preprocessor information: use cpp syntax.
+ ; e.g.: -I/home/joe/doe -I/home/mary/roe
+ include =
+ ; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)
+ define = -DBOOL -DVAR=VALUE
+
+ ; RUN CONTROL PARAMETERS
+ integrator = md
+ ; Start time and timestep in ps
+ tinit = 0
+ dt = 0.001
+ nsteps = 0
+ ; For exact run continuation or redoing part of a run
+ init-step = 0
+ ; Part index is updated automatically on checkpointing (keeps files separate)
+ simulation-part = 1
+ ; mode for center of mass motion removal
+ comm-mode = Linear
+ ; number of steps for center of mass motion removal
+ nstcomm = 100
+ ; group(s) for center of mass motion removal
+ comm-grps =
+
+ ; LANGEVIN DYNAMICS OPTIONS
+ ; Friction coefficient (amu/ps) and random seed
+ bd-fric = 0
+ ld-seed = -1
+
+ ; ENERGY MINIMIZATION OPTIONS
+ ; Force tolerance and initial step-size
+ emtol = 10
+ emstep = 0.01
+ ; Max number of iterations in relax-shells
+ niter = 20
+ ; Step size (ps^2) for minimization of flexible constraints
+ fcstep = 0
+ ; Frequency of steepest descents steps when doing CG
+ nstcgsteep = 1000
+ nbfgscorr = 10
+
+ ; TEST PARTICLE INSERTION OPTIONS
+ rtpi = 0.05
+
+ ; OUTPUT CONTROL OPTIONS
+ ; Output frequency for coords (x), velocities (v) and forces (f)
+ nstxout = 0
+ nstvout = 0
+ nstfout = 0
+ ; Output frequency for energies to log file and energy file
+ nstlog = 1000
+ nstcalcenergy = 100
+ nstenergy = 1000
+ ; Output frequency and precision for .xtc file
+ nstxout-compressed = 0
+ compressed-x-precision = 1000
+ ; This selects the subset of atoms for the compressed
+ ; trajectory file. You can select multiple groups. By
+ ; default, all atoms will be written.
+ compressed-x-grps =
+ ; Selection of energy groups
+ energygrps =
+
+ ; NEIGHBORSEARCHING PARAMETERS
+ ; cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)
+ cutoff-scheme = Verlet
+ ; nblist update frequency
+ nstlist = 10
+ ; ns algorithm (simple or grid)
+ ns-type = Grid
+ ; Periodic boundary conditions: xyz, no, xy
+ pbc = xyz
+ periodic-molecules = no
+ ; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,
+ ; a value of -1 means: use rlist
+ verlet-buffer-tolerance = 0.005
+ ; nblist cut-off
+ rlist = 1
+ ; long-range cut-off for switched potentials
+
+ ; OPTIONS FOR ELECTROSTATICS AND VDW
+ ; Method for doing electrostatics
+ coulombtype = Cut-off
+ coulomb-modifier = Potential-shift-Verlet
+ rcoulomb-switch = 0
+ rcoulomb = 1
+ ; Relative dielectric constant for the medium and the reaction field
+ epsilon-r = 1
+ epsilon-rf = 0
+ ; Method for doing Van der Waals
+ vdw-type = Cut-off
+ vdw-modifier = Potential-shift-Verlet
+ ; cut-off lengths
+ rvdw-switch = 0
+ rvdw = 1
+ ; Apply long range dispersion corrections for Energy and Pressure
+ DispCorr = No
+ ; Extension of the potential lookup tables beyond the cut-off
+ table-extension = 1
+ ; Separate tables between energy group pairs
+ energygrp-table =
+ ; Spacing for the PME/PPPM FFT grid
+ fourierspacing = 0.12
+ ; FFT grid size, when a value is 0 fourierspacing will be used
+ fourier-nx = 0
+ fourier-ny = 0
+ fourier-nz = 0
+ ; EWALD/PME/PPPM parameters
+ pme-order = 4
+ ewald-rtol = 1e-05
+ ewald-rtol-lj = 0.001
+ lj-pme-comb-rule = Geometric
+ ewald-geometry = 3d
+ epsilon-surface = 0
++implicit-solvent = no
+
+ ; OPTIONS FOR WEAK COUPLING ALGORITHMS
+ ; Temperature coupling
+ tcoupl = No
+ nsttcouple = -1
+ nh-chain-length = 10
+ print-nose-hoover-chain-variables = no
+ ; Groups to couple separately
+ tc-grps =
+ ; Time constant (ps) and reference temperature (K)
+ tau-t =
+ ref-t =
+ ; pressure coupling
+ pcoupl = No
+ pcoupltype = Isotropic
+ nstpcouple = -1
+ ; Time constant (ps), compressibility (1/bar) and reference P (bar)
+ tau-p = 1
+ compressibility =
+ ref-p =
+ ; Scaling of reference coordinates, No, All or COM
+ refcoord-scaling = No
+
+ ; OPTIONS FOR QMMM calculations
+ QMMM = no
+ ; Groups treated Quantum Mechanically
+ QMMM-grps =
+ ; QM method
+ QMmethod =
+ ; QMMM scheme
+ QMMMscheme = normal
+ ; QM basisset
+ QMbasis =
+ ; QM charge
+ QMcharge =
+ ; QM multiplicity
+ QMmult =
+ ; Surface Hopping
+ SH =
+ ; CAS space options
+ CASorbitals =
+ CASelectrons =
+ SAon =
+ SAoff =
+ SAsteps =
+ ; Scale factor for MM charges
+ MMChargeScaleFactor = 1
+
+ ; SIMULATED ANNEALING
+ ; Type of annealing for each temperature group (no/single/periodic)
+ annealing =
+ ; Number of time points to use for specifying annealing in each group
+ annealing-npoints =
+ ; List of times at the annealing points for each group
+ annealing-time =
+ ; Temp. at each annealing point, for each group.
+ annealing-temp =
+
+ ; GENERATE VELOCITIES FOR STARTUP RUN
+ gen-vel = no
+ gen-temp = 300
+ gen-seed = -1
+
+ ; OPTIONS FOR BONDS
+ constraints = none
+ ; Type of constraint algorithm
+ constraint-algorithm = Lincs
+ ; Do not constrain the start configuration
+ continuation = no
+ ; Use successive overrelaxation to reduce the number of shake iterations
+ Shake-SOR = no
+ ; Relative tolerance of shake
+ shake-tol = 0.0001
+ ; Highest order in the expansion of the constraint coupling matrix
+ lincs-order = 4
+ ; Number of iterations in the final step of LINCS. 1 is fine for
+ ; normal simulations, but use 2 to conserve energy in NVE runs.
+ ; For energy minimization with constraints it should be 4 to 8.
+ lincs-iter = 1
+ ; Lincs will write a warning to the stderr if in one step a bond
+ ; rotates over more degrees than
+ lincs-warnangle = 30
+ ; Convert harmonic bonds to morse potentials
+ morse = no
+
+ ; ENERGY GROUP EXCLUSIONS
+ ; Pairs of energy groups for which all non-bonded interactions are excluded
+ energygrp-excl =
+
+ ; WALLS
+ ; Number of walls, type, atom types, densities and box-z scale factor for Ewald
+ nwall = 0
+ wall-type = 9-3
+ wall-r-linpot = -1
+ wall-atomtype =
+ wall-density =
+ wall-ewald-zfac = 3
+
+ ; COM PULLING
+ pull = no
+
+ ; AWH biasing
+ awh = no
+
+ ; ENFORCED ROTATION
+ ; Enforced rotation: No or Yes
+ rotation = no
+
+ ; Group to display and/or manipulate in interactive MD session
+ IMD-group =
+
+ ; NMR refinement stuff
+ ; Distance restraints type: No, Simple or Ensemble
+ disre = No
+ ; Force weighting of pairs in one distance restraint: Conservative or Equal
+ disre-weighting = Conservative
+ ; Use sqrt of the time averaged times the instantaneous violation
+ disre-mixed = no
+ disre-fc = 1000
+ disre-tau = 0
+ ; Output frequency for pair distances to energy file
+ nstdisreout = 100
+ ; Orientation restraints: No or Yes
+ orire = no
+ ; Orientation restraints force constant and tau for time averaging
+ orire-fc = 0
+ orire-tau = 0
+ orire-fitgrp =
+ ; Output frequency for trace(SD) and S to energy file
+ nstorireout = 100
+
+ ; Free energy variables
+ free-energy = no
+ couple-moltype =
+ couple-lambda0 = vdw-q
+ couple-lambda1 = vdw-q
+ couple-intramol = no
+ init-lambda = -1
+ init-lambda-state = -1
+ delta-lambda = 0
+ nstdhdl = 50
+ fep-lambdas =
+ mass-lambdas =
+ coul-lambdas =
+ vdw-lambdas =
+ bonded-lambdas =
+ restraint-lambdas =
+ temperature-lambdas =
+ calc-lambda-neighbors = 1
+ init-lambda-weights =
+ dhdl-print-energy = no
+ sc-alpha = 0
+ sc-power = 1
+ sc-r-power = 6
+ sc-sigma = 0.3
+ sc-coul = no
+ separate-dhdl-file = yes
+ dhdl-derivatives = yes
+ dh_hist_size = 0
+ dh_hist_spacing = 0.1
+
+ ; Non-equilibrium MD stuff
+ acc-grps =
+ accelerate =
+ freezegrps =
+ freezedim =
+ cos-acceleration = 0
+ deform =
+
+ ; simulated tempering variables
+ simulated-tempering = no
+ simulated-tempering-scaling = geometric
+ sim-temp-low = 300
+ sim-temp-high = 300
+
+ ; Ion/water position swapping for computational electrophysiology setups
+ ; Swap positions along direction: no, X, Y, Z
+ swapcoords = no
+ adress = no
+
+ ; User defined thingies
+ user1-grps =
+ user2-grps =
+ userint1 = 0
+ userint2 = 0
+ userint3 = 0
+ userint4 = 0
+ userreal1 = 0
+ userreal2 = 0
+ userreal3 = 0
+ userreal4 = 0
+ ; Electric fields
+ ; Format for electric-field-x, etc. is: four real variables:
+ ; amplitude (V/nm), frequency omega (1/ps), time for the pulse peak (ps),
+ ; and sigma (ps) width of the pulse. Omega = 0 means static field,
+ ; sigma = 0 means no pulse, leaving the field to be a cosine function.
+ electric-field-x = 0 0 0 0
+ electric-field-y = 0 0 0 0
+ electric-field-z = 0 0 0 0
+ </String>
+ </ReferenceData>
if (doNoseHoover || doPROffDiagonal || doAcceleration)
{
+ matrix stepM;
+ if (!doParrinelloRahman)
+ {
+ /* We should not apply PR scaling at this step */
+ clear_mat(stepM);
+ }
+ else
+ {
+ copy_mat(M, stepM);
+ }
+
if (!doAcceleration)
{
updateMDLeapfrogGeneral<AccelerationType::none>
(start, nrend, doNoseHoover, dt, dtPressureCouple,
- ir, md, ekind, box, x, xprime, v, f, nh_vxi, M);
+ ir, md, ekind, box, x, xprime, v, f, nh_vxi, stepM);
}
else if (ekind->bNEMD)
{
updateMDLeapfrogGeneral<AccelerationType::group>
(start, nrend, doNoseHoover, dt, dtPressureCouple,
- ir, md, ekind, box, x, xprime, v, f, nh_vxi, M);
+ ir, md, ekind, box, x, xprime, v, f, nh_vxi, stepM);
}
else
{
updateMDLeapfrogGeneral<AccelerationType::cosine>
(start, nrend, doNoseHoover, dt, dtPressureCouple,
- ir, md, ekind, box, x, xprime, v, f, nh_vxi, M);
+ ir, md, ekind, box, x, xprime, v, f, nh_vxi, stepM);
}
}
else
t_idef *idef,
tensor vir_part,
t_commrec *cr,
+ const gmx_multisim_t *ms,
t_nrnb *nrnb,
gmx_wallcycle_t wcycle,
gmx_update_t *upd,
if (EI_VV(inputrec->eI) && bFirstHalf)
{
constrain(nullptr, bLog, bEner, constr, idef,
- inputrec, cr, step, 1, 1.0, md,
+ inputrec, cr, ms, step, 1, 1.0, md,
as_rvec_array(state->x.data()), as_rvec_array(state->v.data()), as_rvec_array(state->v.data()),
bMolPBC, state->box,
state->lambda[efptBONDED], dvdlambda,
else
{
constrain(nullptr, bLog, bEner, constr, idef,
- inputrec, cr, step, 1, 1.0, md,
+ inputrec, cr, ms, step, 1, 1.0, md,
as_rvec_array(state->x.data()), as_rvec_array(upd->xp.data()), nullptr,
bMolPBC, state->box,
state->lambda[efptBONDED], dvdlambda,
wallcycle_start(wcycle, ewcCONSTR);
constrain(nullptr, bLog, bEner, constr, idef,
- inputrec, cr, step, 1, 0.5, md,
+ inputrec, cr, ms, step, 1, 0.5, md,
as_rvec_array(state->x.data()), as_rvec_array(upd->xp.data()), nullptr,
bMolPBC, state->box,
state->lambda[efptBONDED], dvdlambda,
namespace gmx
{
+/*! \brief Barrier for safe simultaneous thread access to mdrunner data
+ *
+ * Used to ensure that the master thread does not modify mdrunner during copy
+ * on the spawned threads. */
+static void threadMpiMdrunnerAccessBarrier()
+{
+#if GMX_THREAD_MPI
+ MPI_Barrier(MPI_COMM_WORLD);
+#endif
+}
+
void Mdrunner::reinitializeOnSpawnedThread()
{
// TODO This duplication is formally necessary if any thread might
// Mdrunner.
fnm = dup_tfn(nfile, fnm);
- cr = reinitialize_commrec_for_this_thread(cr);
+ threadMpiMdrunnerAccessBarrier();
- if (!MASTER(cr))
- {
- // Only the master rank writes to the log files
- fplog = nullptr;
- }
+ cr = reinitialize_commrec_for_this_thread(cr, ms);
+
+ GMX_RELEASE_ASSERT(!MASTER(cr), "reinitializeOnSpawnedThread should only be called on spawned threads");
+
+ // Only the master rank writes to the log file
+ fplog = nullptr;
}
/*! \brief The callback used for running on spawned threads.
* argument permitted to the thread-launch API call, copies it to make
* a new runner for this thread, reinitializes necessary data, and
* proceeds to the simulation. */
-static void mdrunner_start_fn(void *arg)
+static void mdrunner_start_fn(const void *arg)
{
try
{
auto masterMdrunner = reinterpret_cast<const gmx::Mdrunner *>(arg);
/* copy the arg list to make sure that it's thread-local. This
- doesn't copy pointed-to items, of course, but those are all
- const. */
+ doesn't copy pointed-to items, of course; fnm, cr and fplog
+ are reset in the call below, all others should be const. */
gmx::Mdrunner mdrunner = *masterMdrunner;
mdrunner.reinitializeOnSpawnedThread();
mdrunner.mdrunner();
* (including the main thread) for thread-parallel runs. This in turn
* calls mdrunner() for each thread. All options are the same as for
* mdrunner(). */
-t_commrec *Mdrunner::spawnThreads(int numThreadsToLaunch)
+t_commrec *Mdrunner::spawnThreads(int numThreadsToLaunch) const
{
/* first check whether we even need to start tMPI */
return cr;
}
- gmx::Mdrunner spawnedMdrunner = *this;
- // TODO This duplication is formally necessary if any thread might
- // modify any memory in fnm or the pointers it contains. If the
- // contents are ever provably const, then we can remove this
- // allocation (and memory leak).
- // TODO This should probably become part of a copy constructor for
- // Mdrunner.
- spawnedMdrunner.fnm = dup_tfn(this->nfile, fnm);
-
#if GMX_THREAD_MPI
/* now spawn new threads that start mdrunner_start_fn(), while
the main thread returns, we set thread affinity later */
if (tMPI_Init_fn(TRUE, numThreadsToLaunch, TMPI_AFFINITY_NONE,
- mdrunner_start_fn, static_cast<void*>(&spawnedMdrunner)) != TMPI_SUCCESS)
+ mdrunner_start_fn, static_cast<const void*>(this)) != TMPI_SUCCESS)
{
GMX_THROW(gmx::InternalError("Failed to spawn thread-MPI threads"));
}
+
+ threadMpiMdrunnerAccessBarrier();
#else
GMX_UNUSED_VALUE(mdrunner_start_fn);
#endif
- return reinitialize_commrec_for_this_thread(cr);
+ return reinitialize_commrec_for_this_thread(cr, ms);
}
} // namespace
/* CAUTION: threads may be started later on in this function, so
cr doesn't reflect the final parallel state right now */
- gmx::MDModules mdModules;
- t_inputrec inputrecInstance;
- t_inputrec *inputrec = &inputrecInstance;
+ std::unique_ptr<gmx::MDModules> mdModules(new gmx::MDModules);
+ t_inputrec inputrecInstance;
+ t_inputrec *inputrec = &inputrecInstance;
snew(mtop, 1);
if (mdrunOptions.continuationOptions.appendFiles)
gmx::LoggerOwner logOwner(buildLogger(fplog, cr));
gmx::MDLogger mdlog(logOwner.logger());
- hwinfo = gmx_detect_hardware(mdlog, cr);
+ hwinfo = gmx_detect_hardware(mdlog);
- gmx_print_detected_hardware(fplog, cr, mdlog, hwinfo);
+ gmx_print_detected_hardware(fplog, cr, ms, mdlog, hwinfo);
std::vector<int> gpuIdsToUse;
auto compatibleGpus = getCompatibleGpus(hwinfo->gpu_info);
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
// TODO: Error handling
- mdModules.assignOptionsToModules(*inputrec->params, nullptr);
+ mdModules->assignOptionsToModules(*inputrec->params, nullptr);
if (fplog != nullptr)
{
snew(fcd, 1);
/* This needs to be called before read_checkpoint to extend the state */
- init_disres(fplog, mtop, inputrec, cr, fcd, globalState.get(), replExParams.exchangeInterval > 0);
+ init_disres(fplog, mtop, inputrec, cr, ms, fcd, globalState.get(), replExParams.exchangeInterval > 0);
- init_orires(fplog, mtop, inputrec, cr, globalState.get(), &(fcd->orires));
+ init_orires(fplog, mtop, inputrec, cr, ms, globalState.get(), &(fcd->orires));
if (inputrecDeform(inputrec))
{
/* Initialize per-physical-node MPI process/thread ID and counters. */
gmx_init_intranode_counters(cr);
- if (cr->ms && cr->ms->nsim > 1 && !opt2bSet("-multidir", nfile, fnm))
- {
- GMX_LOG(mdlog.info).asParagraph().
- appendText("The -multi flag is deprecated, and may be removed in a future version. Please "
- "update your workflows to use -multidir instead.");
- }
#if GMX_MPI
- if (MULTISIM(cr))
+ if (isMultiSim(ms))
{
GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
"This is simulation %d out of %d running as a composite GROMACS\n"
"multi-simulation job. Setup for this simulation:\n",
- cr->ms->sim, cr->ms->nsim);
+ ms->sim, ms->nsim);
}
GMX_LOG(mdlog.warning).appendTextFormatted(
"Using %d MPI %s\n",
check_and_update_hw_opt_2(&hw_opt, inputrec->cutoff_scheme);
/* Check and update the number of OpenMP threads requested */
- checkAndUpdateRequestedNumOpenmpThreads(&hw_opt, *hwinfo, cr, pmeRunMode, *mtop);
+ checkAndUpdateRequestedNumOpenmpThreads(&hw_opt, *hwinfo, cr, ms, pmeRunMode, *mtop);
gmx_omp_nthreads_init(mdlog, cr,
hwinfo->nthreads_hw_avail,
{
// Produce the task assignment for this rank.
gpuTaskAssignment = runTaskAssignment(gpuIdsToUse, userGpuTaskAssignment, *hwinfo,
- mdlog, cr, gpuTasksOnThisRank);
+ mdlog, cr, ms, gpuTasksOnThisRank);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
{
MPI_Barrier(cr->mpi_comm_mysim);
}
- if (MULTISIM(cr))
+ if (isMultiSim(ms))
{
- MPI_Barrier(ms->mpi_comm_masters);
+ if (MASTER(cr))
+ {
- MPI_Barrier(cr->ms->mpi_comm_masters);
++ MPI_Barrier(ms->mpi_comm_masters);
+ }
+ /* We need another barrier to prevent non-master ranks from contiuing
+ * when an error occured in a different simulation.
+ */
+ MPI_Barrier(cr->mpi_comm_mysim);
}
#endif
checkHardwareOversubscription(numThreadsOnThisRank,
*hwinfo->hardwareTopology,
- cr, mdlog);
+ cr, ms, mdlog);
if (hw_opt.thread_affinity != threadaffOFF)
{
gmx_check_thread_affinity_set(mdlog, cr,
&hw_opt, hwinfo->nthreads_hw_avail, TRUE);
+ int numThreadsOnThisNode, intraNodeThreadOffset;
+ analyzeThreadsOnThisNode(cr, ms, nullptr, numThreadsOnThisRank, &numThreadsOnThisNode,
+ &intraNodeThreadOffset);
+
/* Set the CPU affinity */
gmx_set_thread_affinity(mdlog, cr, &hw_opt, *hwinfo->hardwareTopology,
- numThreadsOnThisRank, nullptr);
+ numThreadsOnThisRank, numThreadsOnThisNode,
+ intraNodeThreadOffset, nullptr);
}
if (mdrunOptions.timingOptions.resetStep > -1)
{
/* Initiate forcerecord */
fr = mk_forcerec();
- fr->forceProviders = mdModules.initForceProviders();
+ fr->forceProviders = mdModules->initForceProviders();
init_forcerec(fplog, mdlog, fr, fcd,
inputrec, mtop, cr, box,
opt2fn("-table", nfile, fnm),
}
/* Now do whatever the user wants us to do (how flexible...) */
- my_integrator(inputrec->eI) (fplog, cr, mdlog, nfile, fnm,
+ my_integrator(inputrec->eI) (fplog, cr, ms, mdlog, nfile, fnm,
oenv,
mdrunOptions,
vsite, constr,
- mdModules.outputProvider(),
+ mdModules->outputProvider(),
inputrec, mtop,
fcd,
globalState.get(),
inputrec, nrnb, wcycle, walltime_accounting,
fr ? fr->nbv : nullptr,
pmedata,
- EI_DYNAMICS(inputrec->eI) && !MULTISIM(cr));
+ EI_DYNAMICS(inputrec->eI) && !isMultiSim(ms));
// Free PME data
if (pmedata)
// As soon as we destroy GPU contexts after mdrunner() exits, these lines should go.
mdAtoms.reset(nullptr);
globalState.reset(nullptr);
+ mdModules.reset(nullptr); // destruct force providers here as they might also use the GPU
/* Free GPU memory and set a physical node tMPI barrier (which should eventually go away) */
- free_gpu_resources(fr, cr);
+ free_gpu_resources(fr, cr, ms);
free_gpu(nonbondedDeviceInfo);
free_gpu(pmeDeviceInfo);
if (MASTER(cr) && continuationOptions.appendFiles)
{
gmx_log_close(fplog);
+ fplog = nullptr;
}
rc = (int)gmx_get_stop_condition();
wait for that. */
if (PAR(cr) && MASTER(cr))
{
+ done_commrec(cr);
tMPI_Finalize();
}
#endif
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff