* Any remaining vsites are assigned to a separate master thread task.
*/
+using gmx::ArrayRef;
using gmx::RVec;
-static void init_ilist(t_ilist* ilist)
-{
- for (int i = 0; i < F_NRE; i++)
- {
- ilist[i].nr = 0;
- ilist[i].nalloc = 0;
- ilist[i].iatoms = nullptr;
- }
-}
-
/*! \brief List of atom indices belonging to a task */
struct AtomIndex
{
struct InterdependentTask
{
//! The interaction lists, only vsite entries are used
- t_ilist ilist[F_NRE];
+ InteractionLists ilist;
//! Thread/task-local force buffer
std::vector<RVec> force;
//! The atom indices of the vsites of our task
//! Flags if elements in force are spread to or not
std::vector<bool> use;
//! The number of entries set to true in use
- int nuse;
+ int nuse = 0;
//! Array of atoms indices, size nthreads, covering all nuse set elements in use
std::vector<AtomIndex> atomIndex;
//! List of tasks (force blocks) this task spread forces to
std::vector<int> spreadTask;
//! List of tasks that write to this tasks force block range
std::vector<int> reduceTask;
-
- InterdependentTask()
- {
- init_ilist(ilist);
- nuse = 0;
- }
};
/*! \brief Vsite thread task data structure */
//! End of atom range of this task
int rangeEnd;
//! The interaction lists, only vsite entries are used
- t_ilist ilist[F_NRE];
+ std::array<InteractionList, F_NRE> ilist;
//! Local fshift accumulation buffer
rvec fshift[SHIFTS];
//! Local virial dx*df accumulation buffer
{
rangeStart = -1;
rangeEnd = -1;
- init_ilist(ilist);
clear_rvecs(SHIFTS, fshift);
clear_mat(dxdf);
useInterdependentTask = false;
*
* \param[in] ilist The interaction list
*/
-template<typename T>
-static int vsiteIlistNrCount(const T* ilist)
+static int vsiteIlistNrCount(ArrayRef<const InteractionList> ilist)
{
int nr = 0;
for (int ftype = c_ftypeVsiteStart; ftype < c_ftypeVsiteEnd; ftype++)
}
-static int constr_vsiten(const t_iatom* ia, const t_iparams ip[], rvec* x, const t_pbc* pbc)
+static int constr_vsiten(const t_iatom* ia, ArrayRef<const t_iparams> ip, rvec* x, const t_pbc* pbc)
{
rvec x1, dx;
dvec dsum;
}
}
-static void construct_vsites_thread(rvec x[],
- real dt,
- rvec* v,
- const t_iparams ip[],
- const t_ilist ilist[],
- const t_pbc* pbc_null)
+static void construct_vsites_thread(rvec x[],
+ real dt,
+ rvec* v,
+ ArrayRef<const t_iparams> ip,
+ ArrayRef<const InteractionList> ilist,
+ const t_pbc* pbc_null)
{
real inv_dt;
if (v != nullptr)
for (int ftype = c_ftypeVsiteStart; ftype < c_ftypeVsiteEnd; ftype++)
{
- if (ilist[ftype].nr == 0)
+ if (ilist[ftype].empty())
{
continue;
}
{ // TODO remove me
int nra = interaction_function[ftype].nratoms;
int inc = 1 + nra;
- int nr = ilist[ftype].nr;
+ int nr = ilist[ftype].size();
- const t_iatom* ia = ilist[ftype].iatoms;
+ const t_iatom* ia = ilist[ftype].iatoms.data();
for (int i = 0; i < nr;)
{
}
}
-void construct_vsites(const gmx_vsite_t* vsite,
- rvec x[],
- real dt,
- rvec* v,
- const t_iparams ip[],
- const t_ilist ilist[],
- PbcType pbcType,
- gmx_bool bMolPBC,
- const t_commrec* cr,
- const matrix box)
+void construct_vsites(const gmx_vsite_t* vsite,
+ rvec x[],
+ real dt,
+ rvec* v,
+ ArrayRef<const t_iparams> ip,
+ ArrayRef<const InteractionList> ilist,
+ PbcType pbcType,
+ gmx_bool bMolPBC,
+ const t_commrec* cr,
+ const matrix box)
{
const bool useDomdec = (vsite != nullptr && vsite->useDomdec);
GMX_ASSERT(!useDomdec || (cr != nullptr && DOMAINDECOMP(cr)),
{
const gmx_molblock_t& molb = mtop.molblock[mb];
const gmx_moltype_t& molt = mtop.moltype[molb.type];
- if (vsiteIlistNrCount(molt.ilist.data()) > 0)
+ if (vsiteIlistNrCount(molt.ilist) > 0)
{
int atomOffset = mtop.moleculeBlockIndices[mb].globalAtomStart;
for (int mol = 0; mol < molb.nmol; mol++)
{
- t_ilist ilist[F_NRE];
- for (int ftype = c_ftypeVsiteStart; ftype < c_ftypeVsiteEnd; ftype++)
- {
- ilist[ftype].nr = molt.ilist[ftype].size();
- ilist[ftype].iatoms = const_cast<t_iatom*>(molt.ilist[ftype].iatoms.data());
- }
-
construct_vsites(nullptr, as_rvec_array(x.data()) + atomOffset, 0.0, nullptr,
- mtop.ffparams.iparams.data(), ilist, PbcType::No, TRUE, nullptr, nullptr);
+ mtop.ffparams.iparams, molt.ilist, PbcType::No, TRUE, nullptr, nullptr);
atomOffset += molt.atoms.nr;
}
}
}
-static int spread_vsiten(const t_iatom ia[],
- const t_iparams ip[],
- const rvec x[],
- rvec f[],
- rvec fshift[],
- const t_pbc* pbc,
- const t_graph* g)
+static int spread_vsiten(const t_iatom ia[],
+ ArrayRef<const t_iparams> ip,
+ const rvec x[],
+ rvec f[],
+ rvec fshift[],
+ const t_pbc* pbc,
+ const t_graph* g)
{
rvec xv, dx, fi;
int n3, av, i, ai;
}
-static int vsite_count(const t_ilist* ilist, int ftype)
+static int vsite_count(ArrayRef<const InteractionList> ilist, int ftype)
{
if (ftype == F_VSITEN)
{
- return ilist[ftype].nr / 3;
+ return ilist[ftype].size() / 3;
}
else
{
- return ilist[ftype].nr / (1 + interaction_function[ftype].nratoms);
+ return ilist[ftype].size() / (1 + interaction_function[ftype].nratoms);
}
}
-static void spread_vsite_f_thread(const rvec x[],
- rvec f[],
- rvec* fshift,
- gmx_bool VirCorr,
- matrix dxdf,
- t_iparams ip[],
- const t_ilist ilist[],
- const t_graph* g,
- const t_pbc* pbc_null)
+static void spread_vsite_f_thread(const rvec x[],
+ rvec f[],
+ rvec* fshift,
+ gmx_bool VirCorr,
+ matrix dxdf,
+ ArrayRef<const t_iparams> ip,
+ ArrayRef<const InteractionList> ilist,
+ const t_graph* g,
+ const t_pbc* pbc_null)
{
const PbcMode pbcMode = getPbcMode(pbc_null);
/* We need another pbc pointer, as with charge groups we switch per vsite */
* higher type vsites from lower types */
for (int ftype = c_ftypeVsiteEnd - 1; ftype >= c_ftypeVsiteStart; ftype--)
{
- if (ilist[ftype].nr == 0)
+ if (ilist[ftype].empty())
{
continue;
}
{ // TODO remove me
int nra = interaction_function[ftype].nratoms;
int inc = 1 + nra;
- int nr = ilist[ftype].nr;
+ int nr = ilist[ftype].size();
- const t_iatom* ia = ilist[ftype].iatoms;
+ const t_iatom* ia = ilist[ftype].iatoms.data();
if (pbcMode == PbcMode::all)
{
void spread_vsite_f(const gmx_vsite_t* vsite,
const rvec* gmx_restrict x,
rvec* gmx_restrict f,
- rvec* gmx_restrict fshift,
- gmx_bool VirCorr,
- matrix vir,
- t_nrnb* nrnb,
- const t_idef* idef,
- PbcType pbcType,
- gmx_bool bMolPBC,
- const t_graph* g,
- const matrix box,
- const t_commrec* cr,
- gmx_wallcycle* wcycle)
+ rvec* gmx_restrict fshift,
+ gmx_bool VirCorr,
+ matrix vir,
+ t_nrnb* nrnb,
+ const InteractionDefinitions& idef,
+ PbcType pbcType,
+ gmx_bool bMolPBC,
+ const t_graph* g,
+ const matrix box,
+ const t_commrec* cr,
+ gmx_wallcycle* wcycle)
{
wallcycle_start(wcycle, ewcVSITESPREAD);
const bool useDomdec = vsite->useDomdec;
{
clear_mat(dxdf);
}
- spread_vsite_f_thread(x, f, fshift, VirCorr, dxdf, idef->iparams, idef->il, g, pbc_null);
+ spread_vsite_f_thread(x, f, fshift, VirCorr, dxdf, idef.iparams, idef.il, g, pbc_null);
if (VirCorr)
{
clear_mat(vsite->tData[vsite->nthreads]->dxdf);
}
spread_vsite_f_thread(x, f, fshift, VirCorr, vsite->tData[vsite->nthreads]->dxdf,
- idef->iparams, vsite->tData[vsite->nthreads]->ilist, g, pbc_null);
+ idef.iparams, vsite->tData[vsite->nthreads]->ilist, g, pbc_null);
#pragma omp parallel num_threads(vsite->nthreads)
{
copy_rvec(f[idTask->vsite[i]], idTask->force[idTask->vsite[i]]);
}
spread_vsite_f_thread(x, as_rvec_array(idTask->force.data()), fshift_t, VirCorr,
- tData.dxdf, idef->iparams, tData.idTask.ilist, g, pbc_null);
+ tData.dxdf, idef.iparams, tData.idTask.ilist, g, pbc_null);
/* We need a barrier before reducing forces below
* that have been produced by a different thread above.
}
/* Spread the vsites that spread locally only */
- spread_vsite_f_thread(x, f, fshift_t, VirCorr, tData.dxdf, idef->iparams,
+ spread_vsite_f_thread(x, f, fshift_t, VirCorr, tData.dxdf, idef.iparams,
tData.ilist, g, pbc_null);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
dd_move_f_vsites(cr->dd, f, fshift);
}
- inc_nrnb(nrnb, eNR_VSITE2, vsite_count(idef->il, F_VSITE2));
- inc_nrnb(nrnb, eNR_VSITE2FD, vsite_count(idef->il, F_VSITE2FD));
- inc_nrnb(nrnb, eNR_VSITE3, vsite_count(idef->il, F_VSITE3));
- inc_nrnb(nrnb, eNR_VSITE3FD, vsite_count(idef->il, F_VSITE3FD));
- inc_nrnb(nrnb, eNR_VSITE3FAD, vsite_count(idef->il, F_VSITE3FAD));
- inc_nrnb(nrnb, eNR_VSITE3OUT, vsite_count(idef->il, F_VSITE3OUT));
- inc_nrnb(nrnb, eNR_VSITE4FD, vsite_count(idef->il, F_VSITE4FD));
- inc_nrnb(nrnb, eNR_VSITE4FDN, vsite_count(idef->il, F_VSITE4FDN));
- inc_nrnb(nrnb, eNR_VSITEN, vsite_count(idef->il, F_VSITEN));
+ inc_nrnb(nrnb, eNR_VSITE2, vsite_count(idef.il, F_VSITE2));
+ inc_nrnb(nrnb, eNR_VSITE2FD, vsite_count(idef.il, F_VSITE2FD));
+ inc_nrnb(nrnb, eNR_VSITE3, vsite_count(idef.il, F_VSITE3));
+ inc_nrnb(nrnb, eNR_VSITE3FD, vsite_count(idef.il, F_VSITE3FD));
+ inc_nrnb(nrnb, eNR_VSITE3FAD, vsite_count(idef.il, F_VSITE3FAD));
+ inc_nrnb(nrnb, eNR_VSITE3OUT, vsite_count(idef.il, F_VSITE3OUT));
+ inc_nrnb(nrnb, eNR_VSITE4FD, vsite_count(idef.il, F_VSITE4FD));
+ inc_nrnb(nrnb, eNR_VSITE4FDN, vsite_count(idef.il, F_VSITE4FDN));
+ inc_nrnb(nrnb, eNR_VSITEN, vsite_count(idef.il, F_VSITEN));
wallcycle_stop(wcycle, ewcVSITESPREAD);
}
* taskIndex[] is set for all vsites in our range, either to our local tasks
* or to the single last task as taskIndex[]=2*nthreads.
*/
-static void assignVsitesToThread(VsiteThread* tData,
- int thread,
- int nthread,
- int natperthread,
- gmx::ArrayRef<int> taskIndex,
- const t_ilist* ilist,
- const t_iparams* ip,
- const unsigned short* ptype)
+static void assignVsitesToThread(VsiteThread* tData,
+ int thread,
+ int nthread,
+ int natperthread,
+ gmx::ArrayRef<int> taskIndex,
+ ArrayRef<const InteractionList> ilist,
+ ArrayRef<const t_iparams> ip,
+ const unsigned short* ptype)
{
for (int ftype = c_ftypeVsiteStart; ftype < c_ftypeVsiteEnd; ftype++)
{
- tData->ilist[ftype].nr = 0;
- tData->idTask.ilist[ftype].nr = 0;
+ tData->ilist[ftype].clear();
+ tData->idTask.ilist[ftype].clear();
- int nral1 = 1 + NRAL(ftype);
- int inc = nral1;
- t_iatom* iat = ilist[ftype].iatoms;
- for (int i = 0; i < ilist[ftype].nr;)
+ int nral1 = 1 + NRAL(ftype);
+ int inc = nral1;
+ const int* iat = ilist[ftype].iatoms.data();
+ for (int i = 0; i < ilist[ftype].size();)
{
if (ftype == F_VSITEN)
{
if (task == thread || task == nthread + thread)
{
/* Copy this vsite to the thread data struct of thread */
- t_ilist* il_task;
+ InteractionList* il_task;
if (task == thread)
{
il_task = &tData->ilist[ftype];
{
il_task = &tData->idTask.ilist[ftype];
}
- /* Ensure we have sufficient memory allocated */
- if (il_task->nr + inc > il_task->nalloc)
- {
- il_task->nalloc = over_alloc_large(il_task->nr + inc);
- srenew(il_task->iatoms, il_task->nalloc);
- }
/* Copy the vsite data to the thread-task local array */
- for (int j = i; j < i + inc; j++)
- {
- il_task->iatoms[il_task->nr++] = iat[j];
- }
+ il_task->push_back(iat[i], nral1 - 1, iat + i + 1);
if (task == nthread + thread)
{
/* This vsite write outside our own task force block.
}
/*! \brief Assign all vsites with taskIndex[]==task to task tData */
-static void assignVsitesToSingleTask(VsiteThread* tData,
- int task,
- gmx::ArrayRef<const int> taskIndex,
- const t_ilist* ilist,
- const t_iparams* ip)
+static void assignVsitesToSingleTask(VsiteThread* tData,
+ int task,
+ gmx::ArrayRef<const int> taskIndex,
+ ArrayRef<const InteractionList> ilist,
+ ArrayRef<const t_iparams> ip)
{
for (int ftype = c_ftypeVsiteStart; ftype < c_ftypeVsiteEnd; ftype++)
{
- tData->ilist[ftype].nr = 0;
- tData->idTask.ilist[ftype].nr = 0;
+ tData->ilist[ftype].clear();
+ tData->idTask.ilist[ftype].clear();
- int nral1 = 1 + NRAL(ftype);
- int inc = nral1;
- t_iatom* iat = ilist[ftype].iatoms;
- t_ilist* il_task = &tData->ilist[ftype];
+ int nral1 = 1 + NRAL(ftype);
+ int inc = nral1;
+ const int* iat = ilist[ftype].iatoms.data();
+ InteractionList* il_task = &tData->ilist[ftype];
- for (int i = 0; i < ilist[ftype].nr;)
+ for (int i = 0; i < ilist[ftype].size();)
{
if (ftype == F_VSITEN)
{
/* Check if the vsite is assigned to our task */
if (taskIndex[iat[1 + i]] == task)
{
- /* Ensure we have sufficient memory allocated */
- if (il_task->nr + inc > il_task->nalloc)
- {
- il_task->nalloc = over_alloc_large(il_task->nr + inc);
- srenew(il_task->iatoms, il_task->nalloc);
- }
/* Copy the vsite data to the thread-task local array */
- for (int j = i; j < i + inc; j++)
- {
- il_task->iatoms[il_task->nr++] = iat[j];
- }
+ il_task->push_back(iat[i], inc - 1, iat + i + 1);
}
i += inc;
}
}
-void split_vsites_over_threads(const t_ilist* ilist, const t_iparams* ip, const t_mdatoms* mdatoms, gmx_vsite_t* vsite)
+void split_vsites_over_threads(ArrayRef<const InteractionList> ilist,
+ ArrayRef<const t_iparams> ip,
+ const t_mdatoms* mdatoms,
+ gmx_vsite_t* vsite)
{
int vsite_atom_range, natperthread;
{ // TODO remove me
if (ftype != F_VSITEN)
{
- int nral1 = 1 + NRAL(ftype);
- const t_iatom* iat = ilist[ftype].iatoms;
- for (int i = 0; i < ilist[ftype].nr; i += nral1)
+ int nral1 = 1 + NRAL(ftype);
+ ArrayRef<const int> iat = ilist[ftype].iatoms;
+ for (int i = 0; i < ilist[ftype].size(); i += nral1)
{
for (int j = i + 1; j < i + nral1; j++)
{
{
int vs_ind_end;
- const t_iatom* iat = ilist[ftype].iatoms;
+ ArrayRef<const int> iat = ilist[ftype].iatoms;
int i = 0;
- while (i < ilist[ftype].nr)
+ while (i < ilist[ftype].size())
{
/* The 3 below is from 1+NRAL(ftype)=3 */
vs_ind_end = i + ip[iat[i]].vsiten.n * 3;
for (int ftype = c_ftypeVsiteStart; ftype < c_ftypeVsiteEnd; ftype++)
{
- if (ilist[ftype].nr > 0)
+ if (!ilist[ftype].empty())
{
fprintf(debug, "%-20s thread dist:", interaction_function[ftype].longname);
for (int th = 0; th < vsite->nthreads + 1; th++)
{
- fprintf(debug, " %4d %4d ", vsite->tData[th]->ilist[ftype].nr,
- vsite->tData[th]->idTask.ilist[ftype].nr);
+ fprintf(debug, " %4d %4d ", vsite->tData[th]->ilist[ftype].size(),
+ vsite->tData[th]->idTask.ilist[ftype].size());
}
fprintf(debug, "\n");
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff