Merge branch release-5-1 into release-2016

Change-Id: Ib769849746a3e55f3e7ae4067f0b6f549e66bd2c

diff --git a/docs/user-guide/mdrun-performance.rst b/docs/user-guide/mdrun-performance.rst
index 1491d4140035057fc6df5af1ecc3ba2ad0f283c3..58689f4045a25fb0fd596fb15d51386b93b72bb6 100644 (file)
--- a/docs/user-guide/mdrun-performance.rst
+++ b/docs/user-guide/mdrun-performance.rst
@@ -352,9 +352,11 @@ There are further command-line parameters that are relevant in these
 cases.
 
 ``-tunepme``
-    Defaults to "on." If "on," will optimize various aspects of the
-    PME and DD algorithms, shifting load between ranks and/or GPUs to
-    maximize throughput
+    Defaults to "on." If "on," a Verlet-scheme simulation will
+    optimize various aspects of the PME and DD algorithms, shifting
+    load between ranks and/or GPUs to maximize throughput. Some
+    mdrun features are not compatible with this, and these ignore
+    this option.
 
 ``-dlb``
     Can be set to "auto," "no," or "yes."

diff --git a/src/gromacs/ewald/pme-load-balancing.cpp b/src/gromacs/ewald/pme-load-balancing.cpp
index a028c1cb987b011236930bf7075969c2d9996284..292624fb4d783b2c356701c8b72837d9e267be6d 100644 (file)
--- a/src/gromacs/ewald/pme-load-balancing.cpp
+++ b/src/gromacs/ewald/pme-load-balancing.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -163,6 +163,8 @@ void pme_loadbal_init(pme_load_balancing_t     **pme_lb_p,
                       gmx_bool                   bUseGPU,
                       gmx_bool                  *bPrinting)
 {
+    GMX_RELEASE_ASSERT(ir->cutoff_scheme != ecutsGROUP, "PME tuning is not supported with cutoff-scheme=group (because it contains bugs)");
+
     pme_load_balancing_t *pme_lb;
     real                  spm, sp;
     int                   d;
@@ -359,8 +361,13 @@ static gmx_bool pme_loadbal_increase_cutoff(pme_load_balancing_t *pme_lb,
     }
     else
     {
+        /* TODO Remove these lines and pme_lb->cutoff_scheme */
         tmpr_coulomb          = set->rcut_coulomb + pme_lb->rbuf_coulomb;
         tmpr_vdw              = pme_lb->rcut_vdw + pme_lb->rbuf_vdw;
+        /* Two (known) bugs with cutoff-scheme=group here:
+         * - This modification of rlist results in incorrect DD comunication.
+         * - We should set fr->bTwinRange = (fr->rlistlong > fr->rlist).
+         */
         set->rlist            = std::min(tmpr_coulomb, tmpr_vdw);
     }
 
@@ -768,7 +775,8 @@ pme_load_balance(pme_load_balancing_t      *pme_lb,
     /* TODO: centralize the code that sets the potentials shifts */
     if (ic->coulomb_modifier == eintmodPOTSHIFT)
     {
-        ic->sh_ewald = std::erfc(ic->ewaldcoeff_q*ic->rcoulomb);
+        GMX_RELEASE_ASSERT(ic->rcoulomb != 0, "Cutoff radius cannot be zero");
+        ic->sh_ewald = std::erfc(ic->ewaldcoeff_q*ic->rcoulomb) / ic->rcoulomb;
     }
     if (EVDW_PME(ic->vdwtype))
     {

diff --git a/src/gromacs/mdlib/forcerec.cpp b/src/gromacs/mdlib/forcerec.cpp
index 6b5a102f83a2f9adc68960e8b672e1c253384ca1..7c3a56e8133fb23a1148c1f2fdbb186376bf84e2 100644 (file)
--- a/src/gromacs/mdlib/forcerec.cpp
+++ b/src/gromacs/mdlib/forcerec.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -2056,9 +2056,10 @@ init_interaction_const(FILE                       *fp,
     ic->epsfac           = fr->epsfac;
     ic->ewaldcoeff_q     = fr->ewaldcoeff_q;
 
-    if (fr->coulomb_modifier == eintmodPOTSHIFT)
+    if (EEL_PME_EWALD(ic->eeltype) && ic->coulomb_modifier == eintmodPOTSHIFT)
     {
-        ic->sh_ewald = std::erfc(ic->ewaldcoeff_q*ic->rcoulomb);
+        GMX_RELEASE_ASSERT(ic->rcoulomb != 0, "Cutoff radius cannot be zero");
+        ic->sh_ewald = std::erfc(ic->ewaldcoeff_q*ic->rcoulomb) / ic->rcoulomb;
     }
     else
     {

diff --git a/src/programs/mdrun/md.cpp b/src/programs/mdrun/md.cpp
index 82618c0fcd8e8134f4379084e46fe1360ab7ccb9..bbb8e59754577e05b1f2fe1c3b6c5f253d1eaeaa 100644 (file)
--- a/src/programs/mdrun/md.cpp
+++ b/src/programs/mdrun/md.cpp
@@ -504,11 +504,11 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
                                         repl_ex_nst, repl_ex_nex, repl_ex_seed);
     }
 
-    /* PME tuning is only supported with PME for Coulomb. Is is not supported
-     * with only LJ PME, or for reruns.
-     */
+    /* PME tuning is only supported in the Verlet scheme, with PME for
+     * Coulomb. It is not supported with only LJ PME, or for
+     * reruns. */
     bPMETune = ((Flags & MD_TUNEPME) && EEL_PME(fr->eeltype) && !bRerunMD &&
-                !(Flags & MD_REPRODUCIBLE));
+                !(Flags & MD_REPRODUCIBLE) && ir->cutoff_scheme != ecutsGROUP);
     if (bPMETune)
     {
         pme_loadbal_init(&pme_loadbal, cr, fplog, ir, state->box,

diff --git a/src/programs/mdrun/mdrun.cpp b/src/programs/mdrun/mdrun.cpp
index 7829a823a444275ed73b151559277993c710e31e..798f7682742304554848fcc85b505101ffa6cad9 100644 (file)
--- a/src/programs/mdrun/mdrun.cpp
+++ b/src/programs/mdrun/mdrun.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -370,7 +370,7 @@ int gmx_mdrun(int argc, char *argv[])
         { "-nstlist", FALSE, etINT, {&nstlist},
           "Set nstlist when using a Verlet buffer tolerance (0 is guess)" },
         { "-tunepme", FALSE, etBOOL, {&bTunePME},
-          "Optimize PME load between PP/PME ranks or GPU/CPU" },
+          "Optimize PME load between PP/PME ranks or GPU/CPU (only with the Verlet cut-off scheme)" },
         { "-v",       FALSE, etBOOL, {&bVerbose},
           "Be loud and noisy" },
         { "-pforce",  FALSE, etREAL, {&pforce},