Converted runner.c to C++

Used std::max, eliminated unused variables, used const char *, used
size_t instead of int, declared constant variable of type float
rather than type double.

Moved declaration of cr_old to where it is used.

Renamed variables relating to automated nstlist choice to better
reflect what is actually going on.

Added some assertions to help static analysis and humans understand
what is going on. This is a problem because static analysis can't
reason correctly about cr and fr while we continue to pass them
everywhere as non-const.

Change-Id: I1afe0c5e96c0ccdc6b46f772f8746402af471234

diff --git a/src/gromacs/utility/smalloc.h b/src/gromacs/utility/smalloc.h
index ea91947cf738910e83a4f5aa200f514272156a5c..91e2ebe89eb9d4d8e4dc1e514f95bfdeb2b36b88 100644 (file)
--- a/src/gromacs/utility/smalloc.h
+++ b/src/gromacs/utility/smalloc.h
@@ -330,6 +330,10 @@ void gmx_snew_aligned_impl(const char *name, const char *file, int line,
 
 #endif
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 /*! \brief
  * Frees memory referenced by \p ptr.
  *
@@ -388,4 +392,8 @@ int over_alloc_dd(int n);
 /** Over allocation for large data types: complex structs */
 #define over_alloc_large(n) (int)(OVER_ALLOC_FAC*(n) + 1000)
 
+#ifdef __cplusplus
+}
+#endif
+
 #endif

diff --git a/src/programs/mdrun/runner.c b/src/programs/mdrun/runner.cpp
similarity index 97%
rename from src/programs/mdrun/runner.c
rename to src/programs/mdrun/runner.cpp
index b6777c65069c77d8a1c0bf4b6697ddf5d6e5e6be..3bccd5a1b6daf0179d585c6937daf48c18d69d1a 100644 (file)
--- a/src/programs/mdrun/runner.c
+++ b/src/programs/mdrun/runner.cpp
@@ -34,10 +34,13 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
+
 #ifdef HAVE_CONFIG_H
 #include <config.h>
 #endif
 
+#include <algorithm>
+
 #include <assert.h>
 #include <signal.h>
 #include <stdlib.h>
@@ -73,7 +76,6 @@
 #include "gmx_omp_nthreads.h"
 #include "gromacs/gmxpreprocess/calc_verletbuf.h"
 #include "membed.h"
-#include "macros.h"
 #include "gmx_thread_affinity.h"
 #include "inputrec.h"
 #include "main.h"
@@ -88,6 +90,7 @@
 #include "gromacs/pulling/pull_rotation.h"
 #include "gromacs/swap/swapcoords.h"
 #include "gromacs/timing/wallcycle.h"
+#include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/gmxmpi.h"
 #include "gromacs/utility/smalloc.h"
 
@@ -296,7 +299,7 @@ static int get_tmpi_omp_thread_division(const gmx_hw_info_t *hwinfo,
     else if (hw_opt->nthreads_omp > 0)
     {
         /* Here we could oversubscribe, when we do, we issue a warning later */
-        nthreads_tmpi = max(1, nthreads_tot/hw_opt->nthreads_omp);
+        nthreads_tmpi = std::max(1, nthreads_tot/hw_opt->nthreads_omp);
     }
     else
     {
@@ -315,8 +318,6 @@ static int get_tmpi_omp_thread_division(const gmx_hw_info_t *hwinfo,
         const int nthreads_omp_always_faster             =  4;
         const int nthreads_omp_always_faster_Nehalem     = 12;
         const int nthreads_omp_always_faster_SandyBridge = 16;
-        const int first_model_Nehalem                    = 0x1A;
-        const int first_model_SandyBridge                = 0x2A;
         gmx_bool  bIntel_Family6;
 
         bIntel_Family6 =
@@ -357,8 +358,6 @@ static int get_nthreads_mpi(const gmx_hw_info_t *hwinfo,
 {
     int      nthreads_hw, nthreads_tot_max, nthreads_tmpi, nthreads_new, ngpu;
     int      min_atoms_per_mpi_thread;
-    char    *env;
-    char     sbuf[STRLEN];
     gmx_bool bCanUseGPU;
 
     if (hw_opt->nthreads_tmpi > 0)
@@ -433,7 +432,7 @@ static int get_nthreads_mpi(const gmx_hw_info_t *hwinfo,
     {
         /* the thread number was chosen automatically, but there are too many
            threads (too few atoms per thread) */
-        nthreads_new = max(1, mtop->natoms/min_atoms_per_mpi_thread);
+        nthreads_new = std::max(1, mtop->natoms/min_atoms_per_mpi_thread);
 
         /* Avoid partial use of Hyper-Threading */
         if (gmx_cpuid_x86_smt(hwinfo->cpuid_info) == GMX_CPUID_X86_SMT_ENABLED &&
@@ -481,7 +480,7 @@ static int get_nthreads_mpi(const gmx_hw_info_t *hwinfo,
 /* We determine the extra cost of the non-bonded kernels compared to
  * a reference nstlist value of 10 (which is the default in grompp).
  */
-static const int    nbnxn_reference_nstlist = 10;
+static const int    nbnxnReferenceNstlist = 10;
 /* The values to try when switching  */
 const int           nstlist_try[] = { 20, 25, 40 };
 #define NNSTL  sizeof(nstlist_try)/sizeof(nstlist_try[0])
@@ -510,9 +509,9 @@ static void increase_nstlist(FILE *fp, t_commrec *cr,
     float                  listfac_ok, listfac_max;
     int                    nstlist_orig, nstlist_prev;
     verletbuf_list_setup_t ls;
-    real                   rlist_nstlist10, rlist_inc, rlist_ok, rlist_max;
+    real                   rlistWithReferenceNstlist, rlist_inc, rlist_ok, rlist_max;
     real                   rlist_new, rlist_prev;
-    int                    nstlist_ind = 0;
+    size_t                 nstlist_ind = 0;
     t_state                state_tmp;
     gmx_bool               bBox, bDD, bCont;
     const char            *nstl_gpu = "\nFor optimal performance with a GPU nstlist (now %d) should be larger.\nThe optimum depends on your CPU and GPU resources.\nYou might want to try several nstlist values.\n";
@@ -521,6 +520,7 @@ static void increase_nstlist(FILE *fp, t_commrec *cr,
     const char            *box_err  = "Can not increase nstlist because the box is too small";
     const char            *dd_err   = "Can not increase nstlist because of domain decomposition limitations";
     char                   buf[STRLEN];
+    const float            oneThird = 1.0f / 3.0f;
 
     if (nstlist_cmdline <= 0)
     {
@@ -606,19 +606,19 @@ static void increase_nstlist(FILE *fp, t_commrec *cr,
     verletbuf_get_list_setup(bGPU, &ls);
 
     /* Allow rlist to make the list a given factor larger than the list
-     * would be with nstlist=10.
+     * would be with the reference value for nstlist (10).
      */
     nstlist_prev = ir->nstlist;
-    ir->nstlist  = 10;
+    ir->nstlist  = nbnxnReferenceNstlist;
     calc_verlet_buffer_size(mtop, det(box), ir, -1, &ls, NULL,
-                            &rlist_nstlist10);
+                            &rlistWithReferenceNstlist);
     ir->nstlist  = nstlist_prev;
 
     /* Determine the pair list size increase due to zero interactions */
     rlist_inc = nbnxn_get_rlist_effective_inc(ls.cluster_size_j,
                                               mtop->natoms/det(box));
-    rlist_ok  = (rlist_nstlist10 + rlist_inc)*pow(listfac_ok, 1.0/3.0) - rlist_inc;
-    rlist_max = (rlist_nstlist10 + rlist_inc)*pow(listfac_max, 1.0/3.0) - rlist_inc;
+    rlist_ok  = (rlistWithReferenceNstlist + rlist_inc)*pow(listfac_ok, oneThird) - rlist_inc;
+    rlist_max = (rlistWithReferenceNstlist + rlist_inc)*pow(listfac_max, oneThird) - rlist_inc;
     if (debug)
     {
         fprintf(debug, "nstlist tuning: rlist_inc %.3f rlist_ok %.3f rlist_max %.3f\n",
@@ -762,7 +762,7 @@ static void convert_to_verlet_scheme(FILE *fplog,
                                      t_inputrec *ir,
                                      gmx_mtop_t *mtop, real box_vol)
 {
-    char *conv_mesg = "Converting input file with group cut-off scheme to the Verlet cut-off scheme";
+    const char *conv_mesg = "Converting input file with group cut-off scheme to the Verlet cut-off scheme";
 
     md_print_warn(NULL, fplog, "%s\n", conv_mesg);
 
@@ -845,7 +845,7 @@ static void convert_to_verlet_scheme(FILE *fplog,
             rlist_fac       = 1 + verlet_buffer_ratio_nodynamics;
         }
         ir->verletbuf_tol   = -1;
-        ir->rlist           = rlist_fac*max(ir->rvdw, ir->rcoulomb);
+        ir->rlist           = rlist_fac*std::max(ir->rvdw, ir->rcoulomb);
     }
 
     gmx_mtop_remove_chargegroups(mtop);
@@ -1051,7 +1051,7 @@ static void free_gpu_resources(const t_forcerec *fr,
     gmx_bool bIsPPrankUsingGPU;
     char     gpu_err_str[STRLEN];
 
-    bIsPPrankUsingGPU = (cr->duty & DUTY_PP) && fr->nbv != NULL && fr->nbv->bUseGPU;
+    bIsPPrankUsingGPU = (cr->duty & DUTY_PP) && fr != NULL && fr->nbv != NULL && fr->nbv->bUseGPU;
 
     if (bIsPPrankUsingGPU)
     {
@@ -1094,13 +1094,11 @@ int mdrunner(gmx_hw_opt_t *hw_opt,
              const char *deviceOptions, int imdport, unsigned long Flags)
 {
     gmx_bool                  bForceUseGPU, bTryUseGPU;
-    double                    nodetime = 0, realtime;
     t_inputrec               *inputrec;
     t_state                  *state = NULL;
     matrix                    box;
     gmx_ddbox_t               ddbox = {0};
     int                       npme_major, npme_minor;
-    real                      tmpr1, tmpr2;
     t_nrnb                   *nrnb;
     gmx_mtop_t               *mtop          = NULL;
     t_mdatoms                *mdatoms       = NULL;
@@ -1111,16 +1109,13 @@ int mdrunner(gmx_hw_opt_t *hw_opt,
     gmx_pme_t                *pmedata       = NULL;
     gmx_vsite_t              *vsite         = NULL;
     gmx_constr_t              constr;
-    int                       i, m, nChargePerturbed = -1, nTypePerturbed = 0, status, nalloc;
-    char                     *gro;
+    int                       nChargePerturbed = -1, nTypePerturbed = 0, status;
     gmx_wallcycle_t           wcycle;
     gmx_bool                  bReadEkin;
-    int                       list;
     gmx_walltime_accounting_t walltime_accounting = NULL;
     int                       rc;
     gmx_int64_t               reset_counters;
     gmx_edsam_t               ed           = NULL;
-    t_commrec                *cr_old       = cr;
     int                       nthreads_pme = 1;
     int                       nthreads_pp  = 1;
     gmx_membed_t              membed       = NULL;
@@ -1257,6 +1252,7 @@ int mdrunner(gmx_hw_opt_t *hw_opt,
 
         if (hw_opt->nthreads_tmpi > 1)
         {
+            t_commrec *cr_old       = cr;
             /* now start the threads. */
             cr = mdrunner_start_threads(hw_opt, fplog, cr_old, nfile, fnm,
                                         oenv, bVerbose, bCompact, nstglobalcomm,
@@ -1734,6 +1730,7 @@ int mdrunner(gmx_hw_opt_t *hw_opt,
 
         if (DOMAINDECOMP(cr))
         {
+            GMX_RELEASE_ASSERT(fr, "fr was NULL while cr->duty was DUTY_PP");
             dd_init_bondeds(fplog, cr->dd, mtop, vsite, inputrec,
                             Flags & MD_DDBONDCHECK, fr->cginfo_mb);
 
@@ -1771,6 +1768,7 @@ int mdrunner(gmx_hw_opt_t *hw_opt,
     }
     else
     {
+        GMX_RELEASE_ASSERT(pmedata, "pmedata was NULL while cr->duty was not DUTY_PP");
         /* do PME only */
         walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntPME));
         gmx_pmeonly(*pmedata, cr, nrnb, wcycle, walltime_accounting, ewaldcoeff_q, ewaldcoeff_lj, inputrec);