* 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>
+#include <string.h>
#ifdef HAVE_UNISTD_H
#include <unistd.h>
#endif
-#include <string.h>
-#include <assert.h>
#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
#include "copyrite.h"
#include "force.h"
#include "mdrun.h"
#include "constr.h"
#include "mvdata.h"
#include "checkpoint.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
#include "sighandler.h"
#include "txtdump.h"
#include "gmx_detect_hardware.h"
#include "gmx_omp_nthreads.h"
#include "gromacs/gmxpreprocess/calc_verletbuf.h"
-#include "gmx_fatal_collective.h"
#include "membed.h"
-#include "macros.h"
#include "gmx_thread_affinity.h"
#include "inputrec.h"
+#include "main.h"
+#include "gromacs/essentialdynamics/edsam.h"
#include "gromacs/fileio/tpxio.h"
+#include "gromacs/math/vec.h"
#include "gromacs/mdlib/nbnxn_search.h"
#include "gromacs/mdlib/nbnxn_consts.h"
-#include "gromacs/timing/wallcycle.h"
-#include "gromacs/utility/gmxmpi.h"
-#include "gromacs/utility/gmxomp.h"
-#include "gromacs/swap/swapcoords.h"
-#include "gromacs/essentialdynamics/edsam.h"
+#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pulling/pull.h"
#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"
#ifdef GMX_FAHCORE
#include "corewrap.h"
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
{
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 =
{
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)
{
/* 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 &&
/* 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])
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";
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)
{
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",
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);
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);
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)
{
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;
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;
}
}
- /* Check for externally set OpenMP affinity and turn off internal
- * pinning if any is found. We need to do this check early to tell
- * thread-MPI whether it should do pinning when spawning threads.
- * TODO: the above no longer holds, we should move these checks down
- */
- gmx_omp_check_thread_affinity(fplog, cr, hw_opt);
-
/* Check and update the hardware options for internal consistency */
check_and_update_hw_opt_1(hw_opt, SIMMASTER(cr));
+ /* Early check for externally set process affinity. */
+ gmx_check_thread_affinity_set(fplog, cr,
+ hw_opt, hwinfo->nthreads_hw_avail, FALSE);
if (SIMMASTER(cr))
{
-#ifdef GMX_THREAD_MPI
- /* Early check for externally set process affinity.
- * With thread-MPI this is needed as pinning might get turned off,
- * which needs to be known before starting thread-MPI.
- * With thread-MPI hw_opt is processed here on the master rank
- * and passed to the other ranks later, so we only do this on master.
- */
- gmx_check_thread_affinity_set(fplog,
- NULL,
- hw_opt, hwinfo->nthreads_hw_avail, FALSE);
-#endif
#ifdef GMX_THREAD_MPI
if (cr->npmenodes > 0 && hw_opt->nthreads_tmpi <= 0)
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,
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);
}
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);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff