From: Mark Abraham <mark.j.abraham@gmail.com>
Date: Wed, 9 Jul 2014 20:36:31 +0000 (+0200)
Subject: Fix wallcycle counting with md-vv, sd and sd2
X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=d4aef0618508ea19abb0c0ab541c553fa5e92312;p=alexxy%2Fgromacs.git

Fix wallcycle counting with md-vv, sd and sd2

Previously the coordinate update for the first half of velocity Verlet
and (where applicable) the second half of the SD integrators was left
out of the walltime accounting, and showed up in the "Rest"
section. With this fix, the number of "update" steps reported depends
on exactly which flavour of which integrator is in use, because
there's also some number of calls to do constraining and/or energy
communication. Those numbers vary with either the flavour of
integrator, or the number of iterations MTTK actually needs.

Change-Id: Ib294455b7277caf89018c413d6c1c0ebf93c6ddb
---

diff --git a/src/gromacs/mdlib/update.c b/src/gromacs/mdlib/update.c
index 2bf5a7426b..e5a095baac 100644
--- a/src/gromacs/mdlib/update.c
+++ b/src/gromacs/mdlib/update.c
@@ -1663,6 +1663,7 @@ void update_constraints(FILE             *fplog,
 
     if (inputrec->eI == eiSD1 && bDoConstr && !bFirstHalf)
     {
+        wallcycle_start(wcycle, ewcUPDATE);
         xprime = get_xprime(state, upd);
 
         nth = gmx_omp_nthreads_get(emntUpdate);
@@ -1689,6 +1690,7 @@ void update_constraints(FILE             *fplog,
                           DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL);
         }
         inc_nrnb(nrnb, eNR_UPDATE, homenr);
+        wallcycle_stop(wcycle, ewcUPDATE);
 
         if (bDoConstr)
         {
@@ -1708,6 +1710,7 @@ void update_constraints(FILE             *fplog,
 
     if ((inputrec->eI == eiSD2) && !(bFirstHalf))
     {
+        wallcycle_start(wcycle, ewcUPDATE);
         xprime = get_xprime(state, upd);
 
         nth = gmx_omp_nthreads_get(emntUpdate);
@@ -1732,6 +1735,7 @@ void update_constraints(FILE             *fplog,
                           DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL);
         }
         inc_nrnb(nrnb, eNR_UPDATE, homenr);
+        wallcycle_stop(wcycle, ewcUPDATE);
 
         if (bDoConstr)
         {
diff --git a/src/programs/mdrun/md.c b/src/programs/mdrun/md.c
index 5fb9b70118..2b320246b5 100644
--- a/src/programs/mdrun/md.c
+++ b/src/programs/mdrun/md.c
@@ -1089,6 +1089,7 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
         if (bVV && !bStartingFromCpt && !bRerunMD)
         /*  ############### START FIRST UPDATE HALF-STEP FOR VV METHODS############### */
         {
+            wallcycle_start(wcycle, ewcUPDATE);
             if (ir->eI == eiVV && bInitStep)
             {
                 /* if using velocity verlet with full time step Ekin,
@@ -1163,11 +1164,13 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
                 bOK = TRUE;
                 if (!bRerunMD || rerun_fr.bV || bForceUpdate)     /* Why is rerun_fr.bV here?  Unclear. */
                 {
+                    wallcycle_stop(wcycle, ewcUPDATE);
                     update_constraints(fplog, step, NULL, ir, ekind, mdatoms,
                                        state, fr->bMolPBC, graph, f,
                                        &top->idef, shake_vir,
                                        cr, nrnb, wcycle, upd, constr,
                                        TRUE, bCalcVir, vetanew);
+                    wallcycle_start(wcycle, ewcUPDATE);
 
                     if (bCalcVir && bUpdateDoLR && ir->nstcalclr > 1)
                     {
@@ -1207,6 +1210,7 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
                    So we need information from the last step in the first half of the integration */
                 if (bGStat || do_per_step(step-1, nstglobalcomm))
                 {
+                    wallcycle_stop(wcycle, ewcUPDATE);
                     compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
                                     wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
                                     constr, NULL, FALSE, state->box,
@@ -1227,6 +1231,7 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
                        time step kinetic energy for the pressure (always true now, since we want accurate statistics).
                        b) If we are using EkinAveEkin for the kinetic energy for the temperature control, we still feed in
                        EkinAveVel because it's needed for the pressure */
+                    wallcycle_start(wcycle, ewcUPDATE);
                 }
                 /* temperature scaling and pressure scaling to produce the extended variables at t+dt */
                 if (!bInitStep)
@@ -1240,7 +1245,7 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
                     {
                         if (bExchanged)
                         {
-
+                            wallcycle_stop(wcycle, ewcUPDATE);
                             /* We need the kinetic energy at minus the half step for determining
                              * the full step kinetic energy and possibly for T-coupling.*/
                             /* This may not be quite working correctly yet . . . . */
@@ -1249,6 +1254,7 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
                                             constr, NULL, FALSE, state->box,
                                             top_global, &bSumEkinhOld,
                                             CGLO_RERUNMD | CGLO_GSTAT | CGLO_TEMPERATURE);
+                            wallcycle_start(wcycle, ewcUPDATE);
                         }
                     }
                 }
@@ -1278,6 +1284,7 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
             {
                 copy_rvecn(cbuf, state->v, 0, state->natoms);
             }
+            wallcycle_stop(wcycle, ewcUPDATE);
         }
 
         /* MRS -- now done iterating -- compute the conserved quantity */