*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 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.
#include "gromacs/legacyheaders/sim_util.h"
#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/legacyheaders/vcm.h"
-#include "gromacs/legacyheaders/types/globsig.h"
#include "gromacs/timing/wallcycle.h"
#ifdef __cplusplus
extern "C" {
#endif
+struct gmx_signalling_t;
+
/* Define a number of flags to better control the information
* passed to compute_globals in md.c and global_stat.
*/
const t_inputrec *ir, int repl_ex_nst);
/* Determine the interval for inter-simulation communication */
-void init_global_signals(globsig_t *gs, const t_commrec *cr,
- const t_inputrec *ir, int repl_ex_nst);
-/* Constructor for globsig_t */
-
void copy_coupling_state(t_state *statea, t_state *stateb,
gmx_ekindata_t *ekinda, gmx_ekindata_t *ekindb, t_grpopts* opts);
/* Copy stuff from state A to state B */
t_nrnb *nrnb, t_vcm *vcm, gmx_wallcycle_t wcycle,
gmx_enerdata_t *enerd, tensor force_vir, tensor shake_vir, tensor total_vir,
tensor pres, rvec mu_tot, gmx_constr_t constr,
- globsig_t *gs, gmx_bool bInterSimGS,
+ struct gmx_signalling_t *gs, gmx_bool bInterSimGS,
matrix box, gmx_mtop_t *top_global, gmx_bool *bSumEkinhOld, int flags);
/* Compute global variables during integration */
#include "gromacs/legacyheaders/update.h"
#include "gromacs/legacyheaders/vcm.h"
#include "gromacs/legacyheaders/vsite.h"
-#include "gromacs/legacyheaders/types/globsig.h"
#include "gromacs/legacyheaders/types/membedt.h"
#include "gromacs/timing/wallcycle.h"
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2014, 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.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#ifndef _globsig_h
-#define _globsig_h
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-#if 0
-}
-/* Hack to make automatic indenting work */
-#endif
-
-/* simulation conditions to transmit. Keep in mind that they are
- transmitted to other nodes through an MPI_Reduce after
- casting them to a real (so the signals can be sent together with other
- data). This means that the only meaningful values are positive,
- negative or zero. */
-enum {
- eglsCHKPT, eglsSTOPCOND, eglsRESETCOUNTERS, eglsNR
-};
-
-typedef struct {
- int nstms; /* The frequency for intersimulation communication */
- int sig[eglsNR]; /* The signal set by one process in do_md */
- int set[eglsNR]; /* The communicated signal, equal for all processes */
-} globsig_t;
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif
#include "gromacs/legacyheaders/vcm.h"
#include "gromacs/legacyheaders/types/commrec.h"
#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/mdrun_signalling.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/snprintf.h"
-/* Is the signal in one simulation independent of other simulations? */
-gmx_bool gs_simlocal[eglsNR] = { FALSE, FALSE, TRUE };
-
/* check which of the multisim simulations has the shortest number of
steps and return that number of nsteps */
gmx_int64_t get_multisim_nsteps(const t_commrec *cr,
return nmin;
}
-void init_global_signals(globsig_t *gs, const t_commrec *cr,
- const t_inputrec *ir, int repl_ex_nst)
-{
- int i;
-
- if (MULTISIM(cr))
- {
- gs->nstms = multisim_nstsimsync(cr, ir, repl_ex_nst);
- if (debug)
- {
- fprintf(debug, "Syncing simulations for checkpointing and termination every %d steps\n", gs->nstms);
- }
- }
- else
- {
- gs->nstms = 1;
- }
-
- for (i = 0; i < eglsNR; i++)
- {
- gs->sig[i] = 0;
- gs->set[i] = 0;
- }
-}
-
void copy_coupling_state(t_state *statea, t_state *stateb,
gmx_ekindata_t *ekinda, gmx_ekindata_t *ekindb, t_grpopts* opts)
{
t_nrnb *nrnb, t_vcm *vcm, gmx_wallcycle_t wcycle,
gmx_enerdata_t *enerd, tensor force_vir, tensor shake_vir, tensor total_vir,
tensor pres, rvec mu_tot, gmx_constr_t constr,
- globsig_t *gs, gmx_bool bInterSimGS,
+ struct gmx_signalling_t *gs, gmx_bool bInterSimGS,
matrix box, gmx_mtop_t *top_global,
gmx_bool *bSumEkinhOld, int flags)
{
- int i, gsi;
- real gs_buf[eglsNR];
tensor corr_vir, corr_pres;
gmx_bool bEner, bPres, bTemp;
gmx_bool bStopCM, bGStat,
}
else
{
- if (gs != NULL)
- {
- for (i = 0; i < eglsNR; i++)
- {
- gs_buf[i] = gs->sig[i];
- }
- }
+ gmx::ArrayRef<real> signalBuffer = prepareSignalBuffer(gs);
if (PAR(cr))
{
wallcycle_start(wcycle, ewcMoveE);
global_stat(fplog, gstat, cr, enerd, force_vir, shake_vir, mu_tot,
ir, ekind, constr, bStopCM ? vcm : NULL,
- gs != NULL ? eglsNR : 0, gs_buf,
+ signalBuffer.size(), signalBuffer.data(),
top_global, state,
*bSumEkinhOld, flags);
wallcycle_stop(wcycle, ewcMoveE);
}
- if (gs != NULL)
- {
- if (MULTISIM(cr) && bInterSimGS)
- {
- if (MASTER(cr))
- {
- /* Communicate the signals between the simulations */
- gmx_sum_sim(eglsNR, gs_buf, cr->ms);
- }
- /* Communicate the signals form the master to the others */
- gmx_bcast(eglsNR*sizeof(gs_buf[0]), gs_buf, cr);
- }
- for (i = 0; i < eglsNR; i++)
- {
- if (bInterSimGS || gs_simlocal[i])
- {
- /* Set the communicated signal only when it is non-zero,
- * since signals might not be processed at each MD step.
- */
- gsi = (gs_buf[i] >= 0 ?
- (int)(gs_buf[i] + 0.5) :
- (int)(gs_buf[i] - 0.5));
- if (gsi != 0)
- {
- gs->set[i] = gsi;
- }
- /* Turn off the local signal */
- gs->sig[i] = 0;
- }
- }
- }
+ handleSignals(gs, cr, bInterSimGS);
*bSumEkinhOld = FALSE;
}
}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ *
+ * \brief This file defines functions for inter-rank signalling by mdrun.
+ *
+ * This handles details of responding to termination conditions,
+ * coordinating checkpoints, and coordinating multi-simulations.
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \ingroup module_mdlib
+ */
+
+#include "gmxpre.h"
+
+#include "mdrun_signalling.h"
+
+#include <algorithm>
+
+#include "gromacs/legacyheaders/md_support.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/real.h"
+
+void init_global_signals(struct gmx_signalling_t *gs, const t_commrec *cr,
+ const t_inputrec *ir, int repl_ex_nst)
+{
+ int i;
+
+ if (MULTISIM(cr))
+ {
+ gs->nstms = multisim_nstsimsync(cr, ir, repl_ex_nst);
+ if (debug)
+ {
+ fprintf(debug, "Syncing simulations for checkpointing and termination every %d steps\n", gs->nstms);
+ }
+ }
+ else
+ {
+ gs->nstms = 1;
+ }
+
+ for (i = 0; i < eglsNR; i++)
+ {
+ gs->sig[i] = 0;
+ gs->set[i] = 0;
+ }
+}
+
+gmx::ArrayRef<real>
+prepareSignalBuffer(struct gmx_signalling_t *gs)
+{
+ if (gs)
+ {
+ gmx::ArrayRef<int> signal(gs->sig);
+ gmx::ArrayRef<real> temp(gs->mpiBuffer);
+
+ std::copy(signal.begin(), signal.end(), temp.begin());
+ return temp;
+ }
+ else
+ {
+ return gmx::EmptyArrayRef();
+ }
+}
+
+void
+handleSignals(struct gmx_signalling_t *gs,
+ const t_commrec *cr,
+ bool bInterSimGS)
+{
+ /* Is the signal in one simulation independent of other simulations? */
+ bool bIsSignalLocal[eglsNR] = { false, false, true };
+
+ if (!gs)
+ {
+ return;
+ }
+
+ if (MULTISIM(cr) && bInterSimGS)
+ {
+ if (MASTER(cr))
+ {
+ /* Communicate the signals between the simulations */
+ gmx_sum_sim(eglsNR, gs->mpiBuffer, cr->ms);
+ }
+ /* Communicate the signals from the master to the others */
+ gmx_bcast(eglsNR*sizeof(gs->mpiBuffer), gs->mpiBuffer, cr);
+ }
+ for (int i = 0; i < eglsNR; i++)
+ {
+ if (bInterSimGS || bIsSignalLocal[i])
+ {
+ /* Set the communicated signal only when it is non-zero,
+ * since signals might not be processed at each MD step.
+ */
+ int gsi = (gs->mpiBuffer[i] >= 0.0 ?
+ (int)(gs->mpiBuffer[i] + 0.5) :
+ (int)(gs->mpiBuffer[i] - 0.5));
+ if (gsi != 0)
+ {
+ gs->set[i] = gsi;
+ }
+ /* Turn off the local signal */
+ gs->sig[i] = 0;
+ }
+ }
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2011,2014,2015, 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ *
+ * \brief This file declares functions for inter-rank signalling by mdrun
+ *
+ * This handles details of responding to termination conditions,
+ * coordinating checkpoints, and coordinating multi-simulations.
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \inlibraryapi
+ * \ingroup module_mdlib
+ */
+#ifndef GMX_MDLIB_MDRUN_SIGNALLING_H
+#define GMX_MDLIB_MDRUN_SIGNALLING_H
+
+#include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/utility/real.h"
+
+struct t_commrec;
+
+namespace gmx
+{
+
+template <typename T>
+class ArrayRef;
+
+}
+
+/*! \brief Simulation conditions to transmit.
+ *
+ * Keep in mind that they are transmitted to other ranks through an
+ * MPI_Reduce after casting them to a real (so the signals can be sent
+ * together with other data). This means that the only meaningful
+ * values are positive, negative or zero. */
+enum {
+ eglsCHKPT, eglsSTOPCOND, eglsRESETCOUNTERS, eglsNR
+};
+
+/*! \internal \brief Object used by mdrun ranks to signal to each other */
+struct gmx_signalling_t {
+ int nstms; /**< The frequency for inter-simulation communication */
+ int sig[eglsNR]; /**< The signal set by this rank in do_md */
+ int set[eglsNR]; /**< The communicated signal, equal for all ranks once communication has occurred */
+ real mpiBuffer[eglsNR]; /**< Buffer for communication */
+};
+
+/*! \brief Construct a struct gmx_signalling_t */
+void init_global_signals(struct gmx_signalling_t *gs,
+ const t_commrec *cr,
+ const t_inputrec *ir,
+ int repl_ex_nst);
+
+/*! \brief Fill the array of reals in which inter- and
+ * intra-simulation signals will be communicated
+ * with the signal values to be sent. */
+gmx::ArrayRef<real>
+prepareSignalBuffer(struct gmx_signalling_t *gs);
+
+/*! \brief Handle intra- and inter-simulation signals recieved
+ *
+ * If a multi-simulation signal should be handled, communicate between
+ * simulation-master ranks, then propagate from the masters to the
+ * rest of the ranks for each simulation.
+ *
+ * Then, set the flags that mdrun will use to respond to the signals
+ * received. */
+void
+handleSignals(struct gmx_signalling_t *gs,
+ const t_commrec *cr,
+ bool bInterSimGS);
+
+#endif
#include "gromacs/legacyheaders/types/fcdata.h"
#include "gromacs/legacyheaders/types/force_flags.h"
#include "gromacs/legacyheaders/types/forcerec.h"
-#include "gromacs/legacyheaders/types/globsig.h"
#include "gromacs/legacyheaders/types/group.h"
#include "gromacs/legacyheaders/types/inputrec.h"
#include "gromacs/legacyheaders/types/interaction_const.h"
#include "gromacs/math/vec.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/mdlib/compute_io.h"
+#include "gromacs/mdlib/mdrun_signalling.h"
#include "gromacs/mdlib/nb_verlet.h"
#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h"
#include "gromacs/pbcutil/mshift.h"
gmx_global_stat_t gstat;
gmx_update_t upd = NULL;
t_graph *graph = NULL;
- globsig_t gs;
+ gmx_signalling_t gs;
gmx_groups_t *groups;
gmx_ekindata_t *ekind, *ekind_save;
gmx_shellfc_t shellfc;
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff