Merge "Merge branch release-5-0"

diff --git a/cmake/gmxCFlags.cmake b/cmake/gmxCFlags.cmake
index 5940751ace32b98e2001185152eec33a2d8e47c1..47f596ab9d55bace50b3d4f0b593cacb9d4972ef 100644 (file)
--- a/cmake/gmxCFlags.cmake
+++ b/cmake/gmxCFlags.cmake
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
+# Copyright (c) 2009,2010,2011,2012,2013,2014,2015, 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.
@@ -249,18 +249,18 @@ MACRO(gmx_c_flags)
     endif()
 
     # xlc
-    # The suppressions below stop information messages about -O3
-    # causing non-strict IEEE compliance that changes the semantics of
-    # the program (duh; 1500-036), warnings about correct PBC-related use of
-    # maximum array indices of DIM-sized C arrays (1500-010).
+    # The suppressions below stop
+    # 1500-036: (I) about -O3 causing non-strict IEEE compliance that changes the semantics of the program (duh)
+    # 1500-010: (W) about correct PBC-related use of maximum array indices of DIM-sized C arrays
+    # 1500-030: (I) Additional optimization may be attained by recompiling and specifying MAXMEM option with a value greater than 8192.
     if (CMAKE_C_COMPILER_ID MATCHES "XL")
         GMX_TEST_CFLAG(CFLAGS_OPT "-qarch=auto -qtune=auto" GMXC_CFLAGS)
         GMX_TEST_CFLAG(CFLAGS_LANG "-qlanglvl=extc99" GMXC_CFLAGS)
-        GMX_TEST_CFLAG(CFLAGS_LANG "-qsuppress=1500-036 -qsuppress=1500-010" GMXC_CFLAGS)
+        GMX_TEST_CFLAG(CFLAGS_LANG "-qsuppress=1500-036 -qsuppress=1500-010 -qsuppress=1500-030" GMXC_CFLAGS)
     endif()
     if (CMAKE_CXX_COMPILER_ID MATCHES "XL")
         GMX_TEST_CXXFLAG(CXXFLAGS_OPT "-qarch=auto -qtune=auto" GMXC_CXXFLAGS)
-        GMX_TEST_CXXFLAG(CFLAGS_LANG "-qsuppress=1500-036 -qsuppress=1500-010" GMXC_CXXFLAGS)
+        GMX_TEST_CXXFLAG(CFLAGS_LANG "-qsuppress=1500-036 -qsuppress=1500-010 -qsuppress=1500-030" GMXC_CXXFLAGS)
     endif()
 
     # msvc

diff --git a/src/gromacs/domdec/domdec.cpp b/src/gromacs/domdec/domdec.cpp
index 3ed2d3dc1a4f4d3fc8b7714063caf898205a5c09..c9bfb95cf985f28f58cc5a0f6acf58df747ebc78 100644 (file)
--- a/src/gromacs/domdec/domdec.cpp
+++ b/src/gromacs/domdec/domdec.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2005,2006,2007,2008,2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2005,2006,2007,2008,2009,2010,2011,2012,2013,2014,2015, 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.
@@ -8715,7 +8715,7 @@ static void set_zones_size(gmx_domdec_t *dd,
         /* To determine the bounding box for a zone we need to find
          * the extreme corners of 4, 2 or 1 corners.
          */
-        nc = 1 << (ddbox->npbcdim - 1);
+        nc = 1 << (ddbox->nboundeddim - 1);
 
         for (c = 0; c < nc; c++)
         {

diff --git a/src/gromacs/domdec/domdec_box.cpp b/src/gromacs/domdec/domdec_box.cpp
index 8dc0e518f80a75decf8f02b0333e6da8ea6735c3..170e36b97621577895ef910d82cb3c966474102d 100644 (file)
--- a/src/gromacs/domdec/domdec_box.cpp
+++ b/src/gromacs/domdec/domdec_box.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2009,2010,2014, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2014,2015, 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.
@@ -146,7 +146,7 @@ static void set_tric_dir(ivec *dd_nc, gmx_ddbox_t *ddbox, matrix box)
                 if (dd_nc != NULL && (*dd_nc)[j] > 1 && (*dd_nc)[d] == 1)
                 {
                     gmx_fatal(FARGS, "Domain decomposition has not been implemented for box vectors that have non-zero components in directions that do not use domain decomposition: ncells = %d %d %d, box vector[%d] = %f %f %f",
-                              dd_nc[XX], dd_nc[YY], dd_nc[ZZ],
+                              (*dd_nc)[XX], (*dd_nc)[YY], (*dd_nc)[ZZ],
                               j+1, box[j][XX], box[j][YY], box[j][ZZ]);
                 }
             }

diff --git a/src/gromacs/gmxlib/copyrite.cpp b/src/gromacs/gmxlib/copyrite.cpp
index 3c1eea513d75d5ce8780cfe2bab4a0c4f6f91ddc..73e6c45732f51bb2215c81638287f13860494b71 100644 (file)
--- a/src/gromacs/gmxlib/copyrite.cpp
+++ b/src/gromacs/gmxlib/copyrite.cpp
@@ -628,11 +628,15 @@ const char *ShortProgram(void)
 
 const char *Program(void)
 {
+    const char *programName = NULL;
+
     try
     {
-        return gmx::getProgramContext().fullBinaryPath();
+        programName = gmx::getProgramContext().fullBinaryPath();
     }
     GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+
+    return programName;
 }
 
 

diff --git a/src/gromacs/mdlib/nbnxn_search.c b/src/gromacs/mdlib/nbnxn_search.c
index bac66a24e56ddd9c20e8f64291fffc47b7bb7deb..14573e913c8ebceca426491cdbaee3b12e1cda5a 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_search.c
+++ b/src/gromacs/mdlib/nbnxn_search.c
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015, 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.
@@ -3558,7 +3558,7 @@ static void make_fep_list_supersub(const nbnxn_search_t    nbs,
                 nlist->gid[nri]      = 0;
                 nlist->shift[nri]    = nbl_sci->shift & NBNXN_CI_SHIFT;
 
-                bFEP_i = (gridi->fep[c_abs - gridi->cell0] & (1 << i));
+                bFEP_i = (gridi->fep[c_abs - gridi->cell0*GPU_NSUBCELL] & (1 << i));
 
                 xi = nbat->x[ind_i*nbat->xstride+XX] + shx;
                 yi = nbat->x[ind_i*nbat->xstride+YY] + shy;

diff --git a/src/programs/mdrun/md.cpp b/src/programs/mdrun/md.cpp
index bc1a7a2267e61b1a4fbfd996140be359dcffb9cc..f0c9a73553f74c314baf0f33dfb13da7d5a53a33 100644 (file)
--- a/src/programs/mdrun/md.cpp
+++ b/src/programs/mdrun/md.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, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014,2015, 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.
@@ -209,7 +209,8 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
     gmx_bool          bVV, bTemp, bPres, bTrotter;
     gmx_bool          bUpdateDoLR;
     real              dvdl_constr;
-    rvec             *cbuf = NULL;
+    rvec             *cbuf        = NULL;
+    int               cbuf_nalloc = 0;
     matrix            lastbox;
     int               lamnew  = 0;
     /* for FEP */
@@ -253,11 +254,7 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
     /* md-vv uses averaged full step velocities for T-control
        md-vv-avek uses averaged half step velocities for T-control (but full step ekin for P control)
        md uses averaged half step kinetic energies to determine temperature unless defined otherwise by GMX_EKIN_AVE_VEL; */
-    bVV = EI_VV(ir->eI);
-    if (bVV) /* to store the initial velocities while computing virial */
-    {
-        snew(cbuf, top_global->natoms);
-    }
+    bVV      = EI_VV(ir->eI);
     bTrotter = (bVV && (IR_NPT_TROTTER(ir) || IR_NPH_TROTTER(ir) || IR_NVT_TROTTER(ir)));
 
     if (bRerunMD)
@@ -1071,6 +1068,8 @@ 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############### */
         {
+            rvec *vbuf = NULL;
+
             wallcycle_start(wcycle, ewcUPDATE);
             if (ir->eI == eiVV && bInitStep)
             {
@@ -1080,7 +1079,8 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
                  * revert back to the initial coordinates
                  * so that the input is actually the initial step.
                  */
-                copy_rvecn(state->v, cbuf, 0, state->natoms); /* should make this better for parallelizing? */
+                snew(vbuf, state->natoms);
+                copy_rvecn(state->v, vbuf, 0, state->natoms); /* should make this better for parallelizing? */
             }
             else
             {
@@ -1207,9 +1207,10 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
                 }
             }
             /* if it's the initial step, we performed this first step just to get the constraint virial */
-            if (bInitStep && ir->eI == eiVV)
+            if (ir->eI == eiVV && bInitStep)
             {
-                copy_rvecn(cbuf, state->v, 0, state->natoms);
+                copy_rvecn(vbuf, state->v, 0, state->natoms);
+                sfree(vbuf);
             }
             wallcycle_stop(wcycle, ewcUPDATE);
         }
@@ -1406,6 +1407,12 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
 
                 if (ir->eI == eiVVAK)
                 {
+                    /* We probably only need md->homenr, not state->natoms */
+                    if (state->natoms > cbuf_nalloc)
+                    {
+                        cbuf_nalloc = state->natoms;
+                        srenew(cbuf, cbuf_nalloc);
+                    }
                     copy_rvecn(state->x, cbuf, 0, state->natoms);
                 }
                 bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));