From 18840da5f2766cf4686c139db5138bdddcb74c47 Mon Sep 17 00:00:00 2001
From: Carlo Camilloni <carlo.camilloni@gmail.com>
Date: Sun, 7 Aug 2016 11:35:13 +0200
Subject: [PATCH] Gromacs 2016 patch
---
.../src/gromacs/CMakeLists.txt | 5 +
.../src/gromacs/CMakeLists.txt.preplumed | 5 +
.../src/gromacs/mdlib/force.cpp | 0
.../src/gromacs/mdlib/force.cpp.preplumed | 0
.../src/gromacs/mdlib/minimize.cpp | 5 +
.../src/gromacs/mdlib/minimize.cpp.preplumed | 5 +
.../src/programs/mdrun/md.cpp | 203 +++++++++---------
.../src/programs/mdrun/md.cpp.preplumed | 203 +++++++++---------
.../src/programs/mdrun/mdrun.cpp | 24 ++-
.../src/programs/mdrun/mdrun.cpp.preplumed | 24 ++-
.../src/programs/mdrun/repl_ex.cpp | 0
.../src/programs/mdrun/repl_ex.cpp.preplumed | 0
.../src/programs/mdrun/runner.cpp | 25 ++-
.../src/programs/mdrun/runner.cpp.preplumed | 25 ++-
14 files changed, 314 insertions(+), 210 deletions(-)
rename patches/{gromacs-2016-beta2.diff => gromacs-2016.diff}/src/gromacs/CMakeLists.txt (96%)
rename patches/{gromacs-2016-beta2.diff => gromacs-2016.diff}/src/gromacs/CMakeLists.txt.preplumed (96%)
rename patches/{gromacs-2016-beta2.diff => gromacs-2016.diff}/src/gromacs/mdlib/force.cpp (100%)
rename patches/{gromacs-2016-beta2.diff => gromacs-2016.diff}/src/gromacs/mdlib/force.cpp.preplumed (100%)
rename patches/{gromacs-2016-beta2.diff => gromacs-2016.diff}/src/gromacs/mdlib/minimize.cpp (99%)
rename patches/{gromacs-2016-beta2.diff => gromacs-2016.diff}/src/gromacs/mdlib/minimize.cpp.preplumed (99%)
rename patches/{gromacs-2016-beta2.diff => gromacs-2016.diff}/src/programs/mdrun/md.cpp (92%)
rename patches/{gromacs-2016-beta2.diff => gromacs-2016.diff}/src/programs/mdrun/md.cpp.preplumed (92%)
rename patches/{gromacs-2016-beta2.diff => gromacs-2016.diff}/src/programs/mdrun/mdrun.cpp (97%)
rename patches/{gromacs-2016-beta2.diff => gromacs-2016.diff}/src/programs/mdrun/mdrun.cpp.preplumed (96%)
rename patches/{gromacs-2016-beta2.diff => gromacs-2016.diff}/src/programs/mdrun/repl_ex.cpp (100%)
rename patches/{gromacs-2016-beta2.diff => gromacs-2016.diff}/src/programs/mdrun/repl_ex.cpp.preplumed (100%)
rename patches/{gromacs-2016-beta2.diff => gromacs-2016.diff}/src/programs/mdrun/runner.cpp (98%)
rename patches/{gromacs-2016-beta2.diff => gromacs-2016.diff}/src/programs/mdrun/runner.cpp.preplumed (98%)
diff --git a/patches/gromacs-2016-beta2.diff/src/gromacs/CMakeLists.txt b/patches/gromacs-2016.diff/src/gromacs/CMakeLists.txt
similarity index 96%
rename from patches/gromacs-2016-beta2.diff/src/gromacs/CMakeLists.txt
rename to patches/gromacs-2016.diff/src/gromacs/CMakeLists.txt
index a9f3b4fd3..dfb7260df 100644
--- a/patches/gromacs-2016-beta2.diff/src/gromacs/CMakeLists.txt
+++ b/patches/gromacs-2016.diff/src/gromacs/CMakeLists.txt
@@ -126,6 +126,10 @@ list(APPEND LIBGROMACS_SOURCES ${THREAD_MPI_SOURCES})
list(APPEND LIBGROMACS_SOURCES ${TNG_SOURCES})
tng_set_source_properties(WITH_ZLIB ${HAVE_ZLIB})
+get_lmfit_properties(LMFIT_SOURCES LMFIT_LIBRARIES_TO_LINK LMFIT_INCLUDE_DIRECTORY LMFIT_INCLUDE_DIR_ORDER)
+include_directories(${LMFIT_INCLUDE_DIR_ORDER} SYSTEM "${LMFIT_INCLUDE_DIRECTORY}")
+list(APPEND LIBGROMACS_SOURCES ${LMFIT_SOURCES})
+
configure_file(version.h.cmakein version.h)
gmx_install_headers(
analysisdata.h
@@ -183,6 +187,7 @@ target_link_libraries(libgromacs
${TNG_IO_LIBRARIES}
${FFT_LIBRARIES} ${LINEAR_ALGEBRA_LIBRARIES}
${XML_LIBRARIES}
+ ${LMFIT_LIBRARIES_TO_LINK}
${THREAD_LIB} ${GMX_SHARED_LINKER_FLAGS} ${OPENCL_LIBRARIES}
${GMX_STDLIB_LIBRARIES})
set_target_properties(libgromacs PROPERTIES
diff --git a/patches/gromacs-2016-beta2.diff/src/gromacs/CMakeLists.txt.preplumed b/patches/gromacs-2016.diff/src/gromacs/CMakeLists.txt.preplumed
similarity index 96%
rename from patches/gromacs-2016-beta2.diff/src/gromacs/CMakeLists.txt.preplumed
rename to patches/gromacs-2016.diff/src/gromacs/CMakeLists.txt.preplumed
index ab9d64df4..fd321f1e1 100644
--- a/patches/gromacs-2016-beta2.diff/src/gromacs/CMakeLists.txt.preplumed
+++ b/patches/gromacs-2016.diff/src/gromacs/CMakeLists.txt.preplumed
@@ -124,6 +124,10 @@ list(APPEND LIBGROMACS_SOURCES ${THREAD_MPI_SOURCES})
list(APPEND LIBGROMACS_SOURCES ${TNG_SOURCES})
tng_set_source_properties(WITH_ZLIB ${HAVE_ZLIB})
+get_lmfit_properties(LMFIT_SOURCES LMFIT_LIBRARIES_TO_LINK LMFIT_INCLUDE_DIRECTORY LMFIT_INCLUDE_DIR_ORDER)
+include_directories(${LMFIT_INCLUDE_DIR_ORDER} SYSTEM "${LMFIT_INCLUDE_DIRECTORY}")
+list(APPEND LIBGROMACS_SOURCES ${LMFIT_SOURCES})
+
configure_file(version.h.cmakein version.h)
gmx_install_headers(
analysisdata.h
@@ -179,6 +183,7 @@ target_link_libraries(libgromacs
${TNG_IO_LIBRARIES}
${FFT_LIBRARIES} ${LINEAR_ALGEBRA_LIBRARIES}
${XML_LIBRARIES}
+ ${LMFIT_LIBRARIES_TO_LINK}
${THREAD_LIB} ${GMX_SHARED_LINKER_FLAGS} ${OPENCL_LIBRARIES}
${GMX_STDLIB_LIBRARIES})
set_target_properties(libgromacs PROPERTIES
diff --git a/patches/gromacs-2016-beta2.diff/src/gromacs/mdlib/force.cpp b/patches/gromacs-2016.diff/src/gromacs/mdlib/force.cpp
similarity index 100%
rename from patches/gromacs-2016-beta2.diff/src/gromacs/mdlib/force.cpp
rename to patches/gromacs-2016.diff/src/gromacs/mdlib/force.cpp
diff --git a/patches/gromacs-2016-beta2.diff/src/gromacs/mdlib/force.cpp.preplumed b/patches/gromacs-2016.diff/src/gromacs/mdlib/force.cpp.preplumed
similarity index 100%
rename from patches/gromacs-2016-beta2.diff/src/gromacs/mdlib/force.cpp.preplumed
rename to patches/gromacs-2016.diff/src/gromacs/mdlib/force.cpp.preplumed
diff --git a/patches/gromacs-2016-beta2.diff/src/gromacs/mdlib/minimize.cpp b/patches/gromacs-2016.diff/src/gromacs/mdlib/minimize.cpp
similarity index 99%
rename from patches/gromacs-2016-beta2.diff/src/gromacs/mdlib/minimize.cpp
rename to patches/gromacs-2016.diff/src/gromacs/mdlib/minimize.cpp
index b60b80991..6282d144c 100644
--- a/patches/gromacs-2016-beta2.diff/src/gromacs/mdlib/minimize.cpp
+++ b/patches/gromacs-2016.diff/src/gromacs/mdlib/minimize.cpp
@@ -1089,6 +1089,7 @@ namespace gmx
gmx_edsam_t ed,
t_forcerec *fr,
int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
+ gmx_membed_t gmx_unused *membed,
real cpt_period, real max_hours,
int imdport,
unsigned long Flags,
@@ -1108,6 +1109,7 @@ double do_cg(FILE *fplog, t_commrec *cr,
gmx_edsam_t gmx_unused ed,
t_forcerec *fr,
int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
+ gmx_membed_t gmx_unused *membed,
real gmx_unused cpt_period, real gmx_unused max_hours,
int imdport,
unsigned long gmx_unused Flags,
@@ -1754,6 +1756,7 @@ double do_lbfgs(FILE *fplog, t_commrec *cr,
gmx_edsam_t gmx_unused ed,
t_forcerec *fr,
int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
+ gmx_membed_t gmx_unused *membed,
real gmx_unused cpt_period, real gmx_unused max_hours,
int imdport,
unsigned long gmx_unused Flags,
@@ -2581,6 +2584,7 @@ double do_steep(FILE *fplog, t_commrec *cr,
gmx_edsam_t gmx_unused ed,
t_forcerec *fr,
int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
+ gmx_membed_t gmx_unused *membed,
real gmx_unused cpt_period, real gmx_unused max_hours,
int imdport,
unsigned long gmx_unused Flags,
@@ -2848,6 +2852,7 @@ double do_nm(FILE *fplog, t_commrec *cr,
gmx_edsam_t gmx_unused ed,
t_forcerec *fr,
int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
+ gmx_membed_t gmx_unused *membed,
real gmx_unused cpt_period, real gmx_unused max_hours,
int imdport,
unsigned long gmx_unused Flags,
diff --git a/patches/gromacs-2016-beta2.diff/src/gromacs/mdlib/minimize.cpp.preplumed b/patches/gromacs-2016.diff/src/gromacs/mdlib/minimize.cpp.preplumed
similarity index 99%
rename from patches/gromacs-2016-beta2.diff/src/gromacs/mdlib/minimize.cpp.preplumed
rename to patches/gromacs-2016.diff/src/gromacs/mdlib/minimize.cpp.preplumed
index 55200ce0a..3890e24e3 100644
--- a/patches/gromacs-2016-beta2.diff/src/gromacs/mdlib/minimize.cpp.preplumed
+++ b/patches/gromacs-2016.diff/src/gromacs/mdlib/minimize.cpp.preplumed
@@ -1015,6 +1015,7 @@ namespace gmx
gmx_edsam_t ed,
t_forcerec *fr,
int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
+ gmx_membed_t gmx_unused *membed,
real cpt_period, real max_hours,
int imdport,
unsigned long Flags,
@@ -1034,6 +1035,7 @@ double do_cg(FILE *fplog, t_commrec *cr,
gmx_edsam_t gmx_unused ed,
t_forcerec *fr,
int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
+ gmx_membed_t gmx_unused *membed,
real gmx_unused cpt_period, real gmx_unused max_hours,
int imdport,
unsigned long gmx_unused Flags,
@@ -1680,6 +1682,7 @@ double do_lbfgs(FILE *fplog, t_commrec *cr,
gmx_edsam_t gmx_unused ed,
t_forcerec *fr,
int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
+ gmx_membed_t gmx_unused *membed,
real gmx_unused cpt_period, real gmx_unused max_hours,
int imdport,
unsigned long gmx_unused Flags,
@@ -2507,6 +2510,7 @@ double do_steep(FILE *fplog, t_commrec *cr,
gmx_edsam_t gmx_unused ed,
t_forcerec *fr,
int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
+ gmx_membed_t gmx_unused *membed,
real gmx_unused cpt_period, real gmx_unused max_hours,
int imdport,
unsigned long gmx_unused Flags,
@@ -2774,6 +2778,7 @@ double do_nm(FILE *fplog, t_commrec *cr,
gmx_edsam_t gmx_unused ed,
t_forcerec *fr,
int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
+ gmx_membed_t gmx_unused *membed,
real gmx_unused cpt_period, real gmx_unused max_hours,
int imdport,
unsigned long gmx_unused Flags,
diff --git a/patches/gromacs-2016-beta2.diff/src/programs/mdrun/md.cpp b/patches/gromacs-2016.diff/src/programs/mdrun/md.cpp
similarity index 92%
rename from patches/gromacs-2016-beta2.diff/src/programs/mdrun/md.cpp
rename to patches/gromacs-2016.diff/src/programs/mdrun/md.cpp
index 19cea9f69..90633b424 100644
--- a/patches/gromacs-2016-beta2.diff/src/programs/mdrun/md.cpp
+++ b/patches/gromacs-2016.diff/src/programs/mdrun/md.cpp
@@ -77,13 +77,13 @@
#include "gromacs/mdlib/mdebin.h"
#include "gromacs/mdlib/mdoutf.h"
#include "gromacs/mdlib/mdrun.h"
-#include "gromacs/mdlib/mdrun_signalling.h"
#include "gromacs/mdlib/nb_verlet.h"
#include "gromacs/mdlib/nbnxn_gpu_data_mgmt.h"
#include "gromacs/mdlib/ns.h"
#include "gromacs/mdlib/shellfc.h"
#include "gromacs/mdlib/sighandler.h"
#include "gromacs/mdlib/sim_util.h"
+#include "gromacs/mdlib/simulationsignal.h"
#include "gromacs/mdlib/tgroup.h"
#include "gromacs/mdlib/trajectory_writing.h"
#include "gromacs/mdlib/update.h"
@@ -131,6 +131,8 @@ extern plumed plumedmain;
#include "corewrap.h"
#endif
+using gmx::SimulationSignaller;
+
/*! \brief Check whether bonded interactions are missing, if appropriate
*
* \param[in] fplog Log file pointer
@@ -224,6 +226,7 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
gmx_edsam_t ed, t_forcerec *fr,
int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
+ gmx_membed_t *membed,
real cpt_period, real max_hours,
int imdport,
unsigned long Flags,
@@ -236,7 +239,7 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
gmx_bool bGStatEveryStep, bGStat, bCalcVir, bCalcEnerStep, bCalcEner;
gmx_bool bNS, bNStList, bSimAnn, bStopCM, bRerunMD,
bFirstStep, startingFromCheckpoint, bInitStep, bLastStep = FALSE,
- bBornRadii;
+ bBornRadii, bUsingEnsembleRestraints;
gmx_bool bDoDHDL = FALSE, bDoFEP = FALSE, bDoExpanded = FALSE;
gmx_bool do_ene, do_log, do_verbose, bRerunWarnNoV = TRUE,
bForceUpdate = FALSE, bCPT;
@@ -259,7 +262,6 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
gmx_global_stat_t gstat;
gmx_update_t *upd = NULL;
t_graph *graph = NULL;
- gmx_signalling_t gs;
gmx_groups_t *groups;
gmx_ekindata_t *ekind;
gmx_shellfc_t *shellfc;
@@ -280,9 +282,8 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
int **trotter_seq;
char sbuf[STEPSTRSIZE], sbuf2[STEPSTRSIZE];
int handled_stop_condition = gmx_stop_cond_none; /* compare to get_stop_condition*/
- gmx_int64_t multisim_nsteps = -1; /* number of steps to do before first multisim
- simulation stops. If equal to zero, don't
- communicate any more between multisims.*/
+
+
/* PME load balancing data for GPU kernels */
pme_load_balancing_t *pme_loadbal = NULL;
gmx_bool bPMETune = FALSE;
@@ -290,7 +291,6 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
/* Interactive MD */
gmx_bool bIMDstep = FALSE;
- gmx_membed_t *membed = NULL;
/* PLUMED */
int plumedNeedsEnergy=0;
@@ -308,8 +308,13 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
code. So we do that alongside the first global energy reduction
after a new DD is made. These variables handle whether the
check happens, and the result it returns. */
- bool shouldCheckNumberOfBondedInteractions = false;
- int totalNumberOfBondedInteractions = -1;
+ bool shouldCheckNumberOfBondedInteractions = false;
+ int totalNumberOfBondedInteractions = -1;
+
+ SimulationSignals signals;
+ // Most global communnication stages don't propagate mdrun
+ // signals, and will use this object to achieve that.
+ SimulationSignaller nullSignaller(nullptr, nullptr, false, false);
/* Check for special mdrun options */
bRerunMD = (Flags & MD_RERUN);
@@ -348,18 +353,6 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
}
groups = &top_global->groups;
- if (opt2bSet("-membed", nfile, fnm))
- {
- if (MASTER(cr))
- {
- fprintf(stderr, "Initializing membed");
- }
- /* Note that membed cannot work in parallel because mtop is
- * changed here. Fix this if we ever want to make it run with
- * multiple ranks. */
- membed = init_membed(fplog, nfile, fnm, top_global, ir, state_global, cr, &cpt_period);
- }
-
if (ir->eSwapCoords != eswapNO)
{
/* Initialize ion swapping code */
@@ -605,7 +598,7 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
bSumEkinhOld = FALSE;
compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
NULL, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
- constr, NULL, FALSE, state->box,
+ constr, &nullSignaller, state->box,
&totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags
| (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
checkNumberOfBondedInteractions(fplog, cr, totalNumberOfBondedInteractions,
@@ -621,7 +614,7 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
NULL, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
- constr, NULL, FALSE, state->box,
+ constr, &nullSignaller, state->box,
NULL, &bSumEkinhOld,
cglo_flags &~(CGLO_STOPCM | CGLO_PRESSURE));
}
@@ -818,22 +811,46 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
bSumEkinhOld = FALSE;
bExchanged = FALSE;
bNeedRepartition = FALSE;
+ // TODO This implementation of ensemble orientation restraints is nasty because
+ // a user can't just do multi-sim with single-sim orientation restraints.
+ bUsingEnsembleRestraints = (fcd->disres.nsystems > 1) || (cr->ms && fcd->orires.nr);
- init_global_signals(&gs, cr, ir, repl_ex_nst);
+ {
+ // Replica exchange and ensemble restraints need all
+ // simulations to remain synchronized, so they need
+ // checkpoints and stop conditions to act on the same step, so
+ // the propagation of such signals must take place between
+ // simulations, not just within simulations.
+ bool checkpointIsLocal = (repl_ex_nst <= 0) && !bUsingEnsembleRestraints;
+ bool stopConditionIsLocal = (repl_ex_nst <= 0) && !bUsingEnsembleRestraints;
+ bool resetCountersIsLocal = true;
+ signals[eglsCHKPT] = SimulationSignal(checkpointIsLocal);
+ signals[eglsSTOPCOND] = SimulationSignal(stopConditionIsLocal);
+ signals[eglsRESETCOUNTERS] = SimulationSignal(resetCountersIsLocal);
+ }
step = ir->init_step;
step_rel = 0;
- if (MULTISIM(cr) && (repl_ex_nst <= 0 ))
+ // TODO extract this to new multi-simulation module
+ if (MASTER(cr) && MULTISIM(cr) && (repl_ex_nst <= 0 ))
{
- /* check how many steps are left in other sims */
- multisim_nsteps = get_multisim_nsteps(cr, ir->nsteps);
+ if (!multisim_int_all_are_equal(cr->ms, ir->nsteps))
+ {
+ md_print_info(cr, fplog,
+ "Note: The number of steps is not consistent across multi simulations,\n"
+ "but we are proceeding anyway!\n");
+ }
+ if (!multisim_int_all_are_equal(cr->ms, ir->init_step))
+ {
+ md_print_info(cr, fplog,
+ "Note: The initial step is not consistent across multi simulations,\n"
+ "but we are proceeding anyway!\n");
+ }
}
-
/* and stop now if we should */
- bLastStep = (bLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps) ||
- ((multisim_nsteps >= 0) && (step_rel >= multisim_nsteps )));
+ bLastStep = (bLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
while (!bLastStep)
{
@@ -876,6 +893,7 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
t = t0 + step*ir->delta_t;
}
+ // TODO Refactor this, so that nstfep does not need a default value of zero
if (ir->efep != efepNO || ir->bSimTemp)
{
/* find and set the current lambdas. If rerunning, we either read in a state, or a lambda value,
@@ -961,7 +979,6 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
{
/* for rerun MD always do Neighbour Searching */
bNS = (bFirstStep || ir->nstlist != 0);
- bNStList = bNS;
}
else
{
@@ -969,30 +986,9 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
bNS = (bFirstStep || bNStList || bExchanged || bNeedRepartition);
}
- /* check whether we should stop because another simulation has
- stopped. */
- if (MULTISIM(cr))
- {
- if ( (multisim_nsteps >= 0) && (step_rel >= multisim_nsteps) &&
- (multisim_nsteps != ir->nsteps) )
- {
- if (bNS)
- {
- if (MASTER(cr))
- {
- fprintf(stderr,
- "Stopping simulation %d because another one has finished\n",
- cr->ms->sim);
- }
- bLastStep = TRUE;
- gs.sig[eglsCHKPT] = 1;
- }
- }
- }
-
- /* < 0 means stop after this step, > 0 means stop at next NS step */
- if ( (gs.set[eglsSTOPCOND] < 0) ||
- ( (gs.set[eglsSTOPCOND] > 0) && (bNStList || ir->nstlist == 0) ) )
+ /* < 0 means stop at next step, > 0 means stop at next NS step */
+ if ( (signals[eglsSTOPCOND].set < 0) ||
+ ( (signals[eglsSTOPCOND].set > 0 ) && ( bNS || ir->nstlist == 0)))
{
bLastStep = TRUE;
}
@@ -1077,7 +1073,7 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
/* This may not be quite working correctly yet . . . . */
compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
wcycle, enerd, NULL, NULL, NULL, NULL, mu_tot,
- constr, NULL, FALSE, state->box,
+ constr, &nullSignaller, state->box,
&totalNumberOfBondedInteractions, &bSumEkinhOld,
CGLO_GSTAT | CGLO_TEMPERATURE | CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS);
checkNumberOfBondedInteractions(fplog, cr, totalNumberOfBondedInteractions,
@@ -1091,12 +1087,12 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
* or at the last step (but not when we do not want confout),
* but never at the first step or with rerun.
*/
- bCPT = (((gs.set[eglsCHKPT] && (bNS || ir->nstlist == 0)) ||
+ bCPT = (((signals[eglsCHKPT].set && (bNS || ir->nstlist == 0)) ||
(bLastStep && (Flags & MD_CONFOUT))) &&
step > ir->init_step && !bRerunMD);
if (bCPT)
{
- gs.set[eglsCHKPT] = 0;
+ signals[eglsCHKPT].set = 0;
}
/* Determine the energy and pressure:
@@ -1271,7 +1267,7 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
wallcycle_stop(wcycle, ewcUPDATE);
compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
- constr, NULL, FALSE, state->box,
+ constr, &nullSignaller, state->box,
&totalNumberOfBondedInteractions, &bSumEkinhOld,
(bGStat ? CGLO_GSTAT : 0)
| CGLO_ENERGY
@@ -1319,7 +1315,7 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
/* This may not be quite working correctly yet . . . . */
compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
wcycle, enerd, NULL, NULL, NULL, NULL, mu_tot,
- constr, NULL, FALSE, state->box,
+ constr, &nullSignaller, state->box,
NULL, &bSumEkinhOld,
CGLO_GSTAT | CGLO_TEMPERATURE);
wallcycle_start(wcycle, ewcUPDATE);
@@ -1398,18 +1394,18 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
{
int nsteps_stop = -1;
- /* this is just make gs.sig compatible with the hack
- of sending signals around by MPI_Reduce with together with
+ /* this just makes signals[].sig compatible with the hack
+ of sending signals around by MPI_Reduce together with
other floats */
if (gmx_get_stop_condition() == gmx_stop_cond_next_ns)
{
- gs.sig[eglsSTOPCOND] = 1;
- nsteps_stop = std::max(ir->nstlist, 2*nstglobalcomm);
+ signals[eglsSTOPCOND].sig = 1;
+ nsteps_stop = std::max(ir->nstlist, 2*nstglobalcomm);
}
if (gmx_get_stop_condition() == gmx_stop_cond_next)
{
- gs.sig[eglsSTOPCOND] = -1;
- nsteps_stop = nstglobalcomm + 1;
+ signals[eglsSTOPCOND].sig = -1;
+ nsteps_stop = nstglobalcomm + 1;
}
if (fplog)
{
@@ -1426,10 +1422,10 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
}
else if (MASTER(cr) && (bNS || ir->nstlist <= 0) &&
(max_hours > 0 && elapsed_time > max_hours*60.0*60.0*0.99) &&
- gs.sig[eglsSTOPCOND] == 0 && gs.set[eglsSTOPCOND] == 0)
+ signals[eglsSTOPCOND].sig == 0 && signals[eglsSTOPCOND].set == 0)
{
/* Signal to terminate the run */
- gs.sig[eglsSTOPCOND] = 1;
+ signals[eglsSTOPCOND].sig = 1;
if (fplog)
{
fprintf(fplog, "\nStep %s: Run time exceeded %.3f hours, will terminate the run\n", gmx_step_str(step, sbuf), max_hours*0.99);
@@ -1441,7 +1437,7 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
elapsed_time > max_hours*60.0*60.0*0.495)
{
/* Set flag that will communicate the signal to all ranks in the simulation */
- gs.sig[eglsRESETCOUNTERS] = 1;
+ signals[eglsRESETCOUNTERS].sig = 1;
}
/* In parallel we only have to check for checkpointing in steps
@@ -1452,9 +1448,9 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
cpt_period >= 0 &&
(cpt_period == 0 ||
elapsed_time >= nchkpt*cpt_period*60.0)) &&
- gs.set[eglsCHKPT] == 0)
+ signals[eglsCHKPT].set == 0)
{
- gs.sig[eglsCHKPT] = 1;
+ signals[eglsCHKPT].sig = 1;
}
/* ######### START SECOND UPDATE STEP ################# */
@@ -1544,7 +1540,7 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
/* just compute the kinetic energy at the half step to perform a trotter step */
compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
- constr, NULL, FALSE, lastbox,
+ constr, &nullSignaller, lastbox,
NULL, &bSumEkinhOld,
(bGStat ? CGLO_GSTAT : 0) | CGLO_TEMPERATURE
);
@@ -1620,26 +1616,40 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
* non-communication steps, but we need to calculate
* the kinetic energy one step before communication.
*/
- if (bGStat || (!EI_VV(ir->eI) && do_per_step(step+1, nstglobalcomm)))
{
- compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
- wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
- constr, &gs,
- (step_rel % gs.nstms == 0) &&
- (multisim_nsteps < 0 || (step_rel < multisim_nsteps)),
- lastbox,
- &totalNumberOfBondedInteractions, &bSumEkinhOld,
- (bGStat ? CGLO_GSTAT : 0)
- | (!EI_VV(ir->eI) || bRerunMD ? CGLO_ENERGY : 0)
- | (!EI_VV(ir->eI) && bStopCM ? CGLO_STOPCM : 0)
- | (!EI_VV(ir->eI) ? CGLO_TEMPERATURE : 0)
- | (!EI_VV(ir->eI) || bRerunMD ? CGLO_PRESSURE : 0)
- | CGLO_CONSTRAINT
- | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0)
- );
- checkNumberOfBondedInteractions(fplog, cr, totalNumberOfBondedInteractions,
- top_global, top, state,
- &shouldCheckNumberOfBondedInteractions);
+ // Organize to do inter-simulation signalling on steps if
+ // and when algorithms require it.
+ bool doInterSimSignal = (!bFirstStep && bDoReplEx) || bUsingEnsembleRestraints;
+
+ if (bGStat || (!EI_VV(ir->eI) && do_per_step(step+1, nstglobalcomm)) || doInterSimSignal)
+ {
+ // Since we're already communicating at this step, we
+ // can propagate intra-simulation signals. Note that
+ // check_nstglobalcomm has the responsibility for
+ // choosing the value of nstglobalcomm that is one way
+ // bGStat becomes true, so we can't get into a
+ // situation where e.g. checkpointing can't be
+ // signalled.
+ bool doIntraSimSignal = true;
+ SimulationSignaller signaller(&signals, cr, doInterSimSignal, doIntraSimSignal);
+
+ compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
+ wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
+ constr, &signaller,
+ lastbox,
+ &totalNumberOfBondedInteractions, &bSumEkinhOld,
+ (bGStat ? CGLO_GSTAT : 0)
+ | (!EI_VV(ir->eI) || bRerunMD ? CGLO_ENERGY : 0)
+ | (!EI_VV(ir->eI) && bStopCM ? CGLO_STOPCM : 0)
+ | (!EI_VV(ir->eI) ? CGLO_TEMPERATURE : 0)
+ | (!EI_VV(ir->eI) || bRerunMD ? CGLO_PRESSURE : 0)
+ | CGLO_CONSTRAINT
+ | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0)
+ );
+ checkNumberOfBondedInteractions(fplog, cr, totalNumberOfBondedInteractions,
+ top_global, top, state,
+ &shouldCheckNumberOfBondedInteractions);
+ }
}
/* ############# END CALC EKIN AND PRESSURE ################# */
@@ -1843,7 +1853,7 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
/* If it is time to reset counters, set a flag that remains
true until counters actually get reset */
if (step_rel == wcycle_get_reset_counters(wcycle) ||
- gs.set[eglsRESETCOUNTERS] != 0)
+ signals[eglsRESETCOUNTERS].set != 0)
{
if (pme_loadbal_is_active(pme_loadbal))
{
@@ -1872,9 +1882,9 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
/* Correct max_hours for the elapsed time */
max_hours -= elapsed_time/(60.0*60.0);
/* If mdrun -maxh -resethway was active, it can only trigger once */
- bResetCountersHalfMaxH = FALSE; /* TODO move this to where gs.sig[eglsRESETCOUNTERS] is set */
+ bResetCountersHalfMaxH = FALSE; /* TODO move this to where signals[eglsRESETCOUNTERS].sig is set */
/* Reset can only happen once, so clear the triggering flag. */
- gs.set[eglsRESETCOUNTERS] = 0;
+ signals[eglsRESETCOUNTERS].set = 0;
}
/* If bIMD is TRUE, the master updates the IMD energy record and sends positions to VMD client */
@@ -1930,11 +1940,6 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
finish_swapcoords(ir->swap);
}
- if (membed != nullptr)
- {
- free_membed(membed);
- }
-
/* IMD cleanup, if bIMD is TRUE. */
IMD_finalize(ir->bIMD, ir->imd);
diff --git a/patches/gromacs-2016-beta2.diff/src/programs/mdrun/md.cpp.preplumed b/patches/gromacs-2016.diff/src/programs/mdrun/md.cpp.preplumed
similarity index 92%
rename from patches/gromacs-2016-beta2.diff/src/programs/mdrun/md.cpp.preplumed
rename to patches/gromacs-2016.diff/src/programs/mdrun/md.cpp.preplumed
index 92fa911eb..2a49aba4a 100644
--- a/patches/gromacs-2016-beta2.diff/src/programs/mdrun/md.cpp.preplumed
+++ b/patches/gromacs-2016.diff/src/programs/mdrun/md.cpp.preplumed
@@ -76,13 +76,13 @@
#include "gromacs/mdlib/mdebin.h"
#include "gromacs/mdlib/mdoutf.h"
#include "gromacs/mdlib/mdrun.h"
-#include "gromacs/mdlib/mdrun_signalling.h"
#include "gromacs/mdlib/nb_verlet.h"
#include "gromacs/mdlib/nbnxn_gpu_data_mgmt.h"
#include "gromacs/mdlib/ns.h"
#include "gromacs/mdlib/shellfc.h"
#include "gromacs/mdlib/sighandler.h"
#include "gromacs/mdlib/sim_util.h"
+#include "gromacs/mdlib/simulationsignal.h"
#include "gromacs/mdlib/tgroup.h"
#include "gromacs/mdlib/trajectory_writing.h"
#include "gromacs/mdlib/update.h"
@@ -124,6 +124,8 @@
#include "corewrap.h"
#endif
+using gmx::SimulationSignaller;
+
/*! \brief Check whether bonded interactions are missing, if appropriate
*
* \param[in] fplog Log file pointer
@@ -217,6 +219,7 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
gmx_edsam_t ed, t_forcerec *fr,
int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
+ gmx_membed_t *membed,
real cpt_period, real max_hours,
int imdport,
unsigned long Flags,
@@ -229,7 +232,7 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
gmx_bool bGStatEveryStep, bGStat, bCalcVir, bCalcEnerStep, bCalcEner;
gmx_bool bNS, bNStList, bSimAnn, bStopCM, bRerunMD,
bFirstStep, startingFromCheckpoint, bInitStep, bLastStep = FALSE,
- bBornRadii;
+ bBornRadii, bUsingEnsembleRestraints;
gmx_bool bDoDHDL = FALSE, bDoFEP = FALSE, bDoExpanded = FALSE;
gmx_bool do_ene, do_log, do_verbose, bRerunWarnNoV = TRUE,
bForceUpdate = FALSE, bCPT;
@@ -252,7 +255,6 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
gmx_global_stat_t gstat;
gmx_update_t *upd = NULL;
t_graph *graph = NULL;
- gmx_signalling_t gs;
gmx_groups_t *groups;
gmx_ekindata_t *ekind;
gmx_shellfc_t *shellfc;
@@ -273,9 +275,8 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
int **trotter_seq;
char sbuf[STEPSTRSIZE], sbuf2[STEPSTRSIZE];
int handled_stop_condition = gmx_stop_cond_none; /* compare to get_stop_condition*/
- gmx_int64_t multisim_nsteps = -1; /* number of steps to do before first multisim
- simulation stops. If equal to zero, don't
- communicate any more between multisims.*/
+
+
/* PME load balancing data for GPU kernels */
pme_load_balancing_t *pme_loadbal = NULL;
gmx_bool bPMETune = FALSE;
@@ -283,7 +284,6 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
/* Interactive MD */
gmx_bool bIMDstep = FALSE;
- gmx_membed_t *membed = NULL;
#ifdef GMX_FAHCORE
/* Temporary addition for FAHCORE checkpointing */
@@ -295,8 +295,13 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
code. So we do that alongside the first global energy reduction
after a new DD is made. These variables handle whether the
check happens, and the result it returns. */
- bool shouldCheckNumberOfBondedInteractions = false;
- int totalNumberOfBondedInteractions = -1;
+ bool shouldCheckNumberOfBondedInteractions = false;
+ int totalNumberOfBondedInteractions = -1;
+
+ SimulationSignals signals;
+ // Most global communnication stages don't propagate mdrun
+ // signals, and will use this object to achieve that.
+ SimulationSignaller nullSignaller(nullptr, nullptr, false, false);
/* Check for special mdrun options */
bRerunMD = (Flags & MD_RERUN);
@@ -335,18 +340,6 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
}
groups = &top_global->groups;
- if (opt2bSet("-membed", nfile, fnm))
- {
- if (MASTER(cr))
- {
- fprintf(stderr, "Initializing membed");
- }
- /* Note that membed cannot work in parallel because mtop is
- * changed here. Fix this if we ever want to make it run with
- * multiple ranks. */
- membed = init_membed(fplog, nfile, fnm, top_global, ir, state_global, cr, &cpt_period);
- }
-
if (ir->eSwapCoords != eswapNO)
{
/* Initialize ion swapping code */
@@ -592,7 +585,7 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
bSumEkinhOld = FALSE;
compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
NULL, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
- constr, NULL, FALSE, state->box,
+ constr, &nullSignaller, state->box,
&totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags
| (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
checkNumberOfBondedInteractions(fplog, cr, totalNumberOfBondedInteractions,
@@ -608,7 +601,7 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
NULL, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
- constr, NULL, FALSE, state->box,
+ constr, &nullSignaller, state->box,
NULL, &bSumEkinhOld,
cglo_flags &~(CGLO_STOPCM | CGLO_PRESSURE));
}
@@ -759,22 +752,46 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
bSumEkinhOld = FALSE;
bExchanged = FALSE;
bNeedRepartition = FALSE;
+ // TODO This implementation of ensemble orientation restraints is nasty because
+ // a user can't just do multi-sim with single-sim orientation restraints.
+ bUsingEnsembleRestraints = (fcd->disres.nsystems > 1) || (cr->ms && fcd->orires.nr);
- init_global_signals(&gs, cr, ir, repl_ex_nst);
+ {
+ // Replica exchange and ensemble restraints need all
+ // simulations to remain synchronized, so they need
+ // checkpoints and stop conditions to act on the same step, so
+ // the propagation of such signals must take place between
+ // simulations, not just within simulations.
+ bool checkpointIsLocal = (repl_ex_nst <= 0) && !bUsingEnsembleRestraints;
+ bool stopConditionIsLocal = (repl_ex_nst <= 0) && !bUsingEnsembleRestraints;
+ bool resetCountersIsLocal = true;
+ signals[eglsCHKPT] = SimulationSignal(checkpointIsLocal);
+ signals[eglsSTOPCOND] = SimulationSignal(stopConditionIsLocal);
+ signals[eglsRESETCOUNTERS] = SimulationSignal(resetCountersIsLocal);
+ }
step = ir->init_step;
step_rel = 0;
- if (MULTISIM(cr) && (repl_ex_nst <= 0 ))
+ // TODO extract this to new multi-simulation module
+ if (MASTER(cr) && MULTISIM(cr) && (repl_ex_nst <= 0 ))
{
- /* check how many steps are left in other sims */
- multisim_nsteps = get_multisim_nsteps(cr, ir->nsteps);
+ if (!multisim_int_all_are_equal(cr->ms, ir->nsteps))
+ {
+ md_print_info(cr, fplog,
+ "Note: The number of steps is not consistent across multi simulations,\n"
+ "but we are proceeding anyway!\n");
+ }
+ if (!multisim_int_all_are_equal(cr->ms, ir->init_step))
+ {
+ md_print_info(cr, fplog,
+ "Note: The initial step is not consistent across multi simulations,\n"
+ "but we are proceeding anyway!\n");
+ }
}
-
/* and stop now if we should */
- bLastStep = (bLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps) ||
- ((multisim_nsteps >= 0) && (step_rel >= multisim_nsteps )));
+ bLastStep = (bLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
while (!bLastStep)
{
@@ -817,6 +834,7 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
t = t0 + step*ir->delta_t;
}
+ // TODO Refactor this, so that nstfep does not need a default value of zero
if (ir->efep != efepNO || ir->bSimTemp)
{
/* find and set the current lambdas. If rerunning, we either read in a state, or a lambda value,
@@ -902,7 +920,6 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
{
/* for rerun MD always do Neighbour Searching */
bNS = (bFirstStep || ir->nstlist != 0);
- bNStList = bNS;
}
else
{
@@ -910,30 +927,9 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
bNS = (bFirstStep || bNStList || bExchanged || bNeedRepartition);
}
- /* check whether we should stop because another simulation has
- stopped. */
- if (MULTISIM(cr))
- {
- if ( (multisim_nsteps >= 0) && (step_rel >= multisim_nsteps) &&
- (multisim_nsteps != ir->nsteps) )
- {
- if (bNS)
- {
- if (MASTER(cr))
- {
- fprintf(stderr,
- "Stopping simulation %d because another one has finished\n",
- cr->ms->sim);
- }
- bLastStep = TRUE;
- gs.sig[eglsCHKPT] = 1;
- }
- }
- }
-
- /* < 0 means stop after this step, > 0 means stop at next NS step */
- if ( (gs.set[eglsSTOPCOND] < 0) ||
- ( (gs.set[eglsSTOPCOND] > 0) && (bNStList || ir->nstlist == 0) ) )
+ /* < 0 means stop at next step, > 0 means stop at next NS step */
+ if ( (signals[eglsSTOPCOND].set < 0) ||
+ ( (signals[eglsSTOPCOND].set > 0 ) && ( bNS || ir->nstlist == 0)))
{
bLastStep = TRUE;
}
@@ -1011,7 +1007,7 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
/* This may not be quite working correctly yet . . . . */
compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
wcycle, enerd, NULL, NULL, NULL, NULL, mu_tot,
- constr, NULL, FALSE, state->box,
+ constr, &nullSignaller, state->box,
&totalNumberOfBondedInteractions, &bSumEkinhOld,
CGLO_GSTAT | CGLO_TEMPERATURE | CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS);
checkNumberOfBondedInteractions(fplog, cr, totalNumberOfBondedInteractions,
@@ -1025,12 +1021,12 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
* or at the last step (but not when we do not want confout),
* but never at the first step or with rerun.
*/
- bCPT = (((gs.set[eglsCHKPT] && (bNS || ir->nstlist == 0)) ||
+ bCPT = (((signals[eglsCHKPT].set && (bNS || ir->nstlist == 0)) ||
(bLastStep && (Flags & MD_CONFOUT))) &&
step > ir->init_step && !bRerunMD);
if (bCPT)
{
- gs.set[eglsCHKPT] = 0;
+ signals[eglsCHKPT].set = 0;
}
/* Determine the energy and pressure:
@@ -1168,7 +1164,7 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
wallcycle_stop(wcycle, ewcUPDATE);
compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
- constr, NULL, FALSE, state->box,
+ constr, &nullSignaller, state->box,
&totalNumberOfBondedInteractions, &bSumEkinhOld,
(bGStat ? CGLO_GSTAT : 0)
| CGLO_ENERGY
@@ -1216,7 +1212,7 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
/* This may not be quite working correctly yet . . . . */
compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
wcycle, enerd, NULL, NULL, NULL, NULL, mu_tot,
- constr, NULL, FALSE, state->box,
+ constr, &nullSignaller, state->box,
NULL, &bSumEkinhOld,
CGLO_GSTAT | CGLO_TEMPERATURE);
wallcycle_start(wcycle, ewcUPDATE);
@@ -1295,18 +1291,18 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
{
int nsteps_stop = -1;
- /* this is just make gs.sig compatible with the hack
- of sending signals around by MPI_Reduce with together with
+ /* this just makes signals[].sig compatible with the hack
+ of sending signals around by MPI_Reduce together with
other floats */
if (gmx_get_stop_condition() == gmx_stop_cond_next_ns)
{
- gs.sig[eglsSTOPCOND] = 1;
- nsteps_stop = std::max(ir->nstlist, 2*nstglobalcomm);
+ signals[eglsSTOPCOND].sig = 1;
+ nsteps_stop = std::max(ir->nstlist, 2*nstglobalcomm);
}
if (gmx_get_stop_condition() == gmx_stop_cond_next)
{
- gs.sig[eglsSTOPCOND] = -1;
- nsteps_stop = nstglobalcomm + 1;
+ signals[eglsSTOPCOND].sig = -1;
+ nsteps_stop = nstglobalcomm + 1;
}
if (fplog)
{
@@ -1323,10 +1319,10 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
}
else if (MASTER(cr) && (bNS || ir->nstlist <= 0) &&
(max_hours > 0 && elapsed_time > max_hours*60.0*60.0*0.99) &&
- gs.sig[eglsSTOPCOND] == 0 && gs.set[eglsSTOPCOND] == 0)
+ signals[eglsSTOPCOND].sig == 0 && signals[eglsSTOPCOND].set == 0)
{
/* Signal to terminate the run */
- gs.sig[eglsSTOPCOND] = 1;
+ signals[eglsSTOPCOND].sig = 1;
if (fplog)
{
fprintf(fplog, "\nStep %s: Run time exceeded %.3f hours, will terminate the run\n", gmx_step_str(step, sbuf), max_hours*0.99);
@@ -1338,7 +1334,7 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
elapsed_time > max_hours*60.0*60.0*0.495)
{
/* Set flag that will communicate the signal to all ranks in the simulation */
- gs.sig[eglsRESETCOUNTERS] = 1;
+ signals[eglsRESETCOUNTERS].sig = 1;
}
/* In parallel we only have to check for checkpointing in steps
@@ -1349,9 +1345,9 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
cpt_period >= 0 &&
(cpt_period == 0 ||
elapsed_time >= nchkpt*cpt_period*60.0)) &&
- gs.set[eglsCHKPT] == 0)
+ signals[eglsCHKPT].set == 0)
{
- gs.sig[eglsCHKPT] = 1;
+ signals[eglsCHKPT].sig = 1;
}
/* ######### START SECOND UPDATE STEP ################# */
@@ -1441,7 +1437,7 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
/* just compute the kinetic energy at the half step to perform a trotter step */
compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
- constr, NULL, FALSE, lastbox,
+ constr, &nullSignaller, lastbox,
NULL, &bSumEkinhOld,
(bGStat ? CGLO_GSTAT : 0) | CGLO_TEMPERATURE
);
@@ -1517,26 +1513,40 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
* non-communication steps, but we need to calculate
* the kinetic energy one step before communication.
*/
- if (bGStat || (!EI_VV(ir->eI) && do_per_step(step+1, nstglobalcomm)))
{
- compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
- wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
- constr, &gs,
- (step_rel % gs.nstms == 0) &&
- (multisim_nsteps < 0 || (step_rel < multisim_nsteps)),
- lastbox,
- &totalNumberOfBondedInteractions, &bSumEkinhOld,
- (bGStat ? CGLO_GSTAT : 0)
- | (!EI_VV(ir->eI) || bRerunMD ? CGLO_ENERGY : 0)
- | (!EI_VV(ir->eI) && bStopCM ? CGLO_STOPCM : 0)
- | (!EI_VV(ir->eI) ? CGLO_TEMPERATURE : 0)
- | (!EI_VV(ir->eI) || bRerunMD ? CGLO_PRESSURE : 0)
- | CGLO_CONSTRAINT
- | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0)
- );
- checkNumberOfBondedInteractions(fplog, cr, totalNumberOfBondedInteractions,
- top_global, top, state,
- &shouldCheckNumberOfBondedInteractions);
+ // Organize to do inter-simulation signalling on steps if
+ // and when algorithms require it.
+ bool doInterSimSignal = (!bFirstStep && bDoReplEx) || bUsingEnsembleRestraints;
+
+ if (bGStat || (!EI_VV(ir->eI) && do_per_step(step+1, nstglobalcomm)) || doInterSimSignal)
+ {
+ // Since we're already communicating at this step, we
+ // can propagate intra-simulation signals. Note that
+ // check_nstglobalcomm has the responsibility for
+ // choosing the value of nstglobalcomm that is one way
+ // bGStat becomes true, so we can't get into a
+ // situation where e.g. checkpointing can't be
+ // signalled.
+ bool doIntraSimSignal = true;
+ SimulationSignaller signaller(&signals, cr, doInterSimSignal, doIntraSimSignal);
+
+ compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
+ wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
+ constr, &signaller,
+ lastbox,
+ &totalNumberOfBondedInteractions, &bSumEkinhOld,
+ (bGStat ? CGLO_GSTAT : 0)
+ | (!EI_VV(ir->eI) || bRerunMD ? CGLO_ENERGY : 0)
+ | (!EI_VV(ir->eI) && bStopCM ? CGLO_STOPCM : 0)
+ | (!EI_VV(ir->eI) ? CGLO_TEMPERATURE : 0)
+ | (!EI_VV(ir->eI) || bRerunMD ? CGLO_PRESSURE : 0)
+ | CGLO_CONSTRAINT
+ | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0)
+ );
+ checkNumberOfBondedInteractions(fplog, cr, totalNumberOfBondedInteractions,
+ top_global, top, state,
+ &shouldCheckNumberOfBondedInteractions);
+ }
}
/* ############# END CALC EKIN AND PRESSURE ################# */
@@ -1740,7 +1750,7 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
/* If it is time to reset counters, set a flag that remains
true until counters actually get reset */
if (step_rel == wcycle_get_reset_counters(wcycle) ||
- gs.set[eglsRESETCOUNTERS] != 0)
+ signals[eglsRESETCOUNTERS].set != 0)
{
if (pme_loadbal_is_active(pme_loadbal))
{
@@ -1769,9 +1779,9 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
/* Correct max_hours for the elapsed time */
max_hours -= elapsed_time/(60.0*60.0);
/* If mdrun -maxh -resethway was active, it can only trigger once */
- bResetCountersHalfMaxH = FALSE; /* TODO move this to where gs.sig[eglsRESETCOUNTERS] is set */
+ bResetCountersHalfMaxH = FALSE; /* TODO move this to where signals[eglsRESETCOUNTERS].sig is set */
/* Reset can only happen once, so clear the triggering flag. */
- gs.set[eglsRESETCOUNTERS] = 0;
+ signals[eglsRESETCOUNTERS].set = 0;
}
/* If bIMD is TRUE, the master updates the IMD energy record and sends positions to VMD client */
@@ -1827,11 +1837,6 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
finish_swapcoords(ir->swap);
}
- if (membed != nullptr)
- {
- free_membed(membed);
- }
-
/* IMD cleanup, if bIMD is TRUE. */
IMD_finalize(ir->bIMD, ir->imd);
diff --git a/patches/gromacs-2016-beta2.diff/src/programs/mdrun/mdrun.cpp b/patches/gromacs-2016.diff/src/programs/mdrun/mdrun.cpp
similarity index 97%
rename from patches/gromacs-2016-beta2.diff/src/programs/mdrun/mdrun.cpp
rename to patches/gromacs-2016.diff/src/programs/mdrun/mdrun.cpp
index 3efc27c46..2c3906175 100644
--- a/patches/gromacs-2016-beta2.diff/src/programs/mdrun/mdrun.cpp
+++ b/patches/gromacs-2016.diff/src/programs/mdrun/mdrun.cpp
@@ -489,16 +489,30 @@ int gmx_mdrun(int argc, char *argv[])
if (nmultisim >= 1)
{
#if !GMX_THREAD_MPI
- gmx_bool bParFn = (multidir == NULL);
- init_multisystem(cr, nmultisim, multidir, NFILE, fnm, bParFn);
+ init_multisystem(cr, nmultisim, multidir, NFILE, fnm);
#else
gmx_fatal(FARGS, "mdrun -multi or -multidir are not supported with the thread-MPI library. "
"Please compile GROMACS with a proper external MPI library.");
#endif
}
- handleRestart(cr, bTryToAppendFiles, NFILE, fnm,
- &bDoAppendFiles, &bStartFromCpt);
+ if (!opt2bSet("-cpi", NFILE, fnm))
+ {
+ // If we are not starting from a checkpoint we never allow files to be appended
+ // to, since that has caused a ton of strange behaviour and bugs in the past.
+ if (opt2parg_bSet("-append", asize(pa), pa))
+ {
+ // If the user explicitly used the -append option, explain that it is not possible.
+ gmx_fatal(FARGS, "GROMACS can only append to files when restarting from a checkpoint.");
+ }
+ else
+ {
+ // If the user did not say anything explicit, just disable appending.
+ bTryToAppendFiles = FALSE;
+ }
+ }
+
+ handleRestart(cr, bTryToAppendFiles, NFILE, fnm, &bDoAppendFiles, &bStartFromCpt);
Flags = opt2bSet("-rerun", NFILE, fnm) ? MD_RERUN : 0;
Flags = Flags | (bDDBondCheck ? MD_DDBONDCHECK : 0);
@@ -507,7 +521,7 @@ int gmx_mdrun(int argc, char *argv[])
Flags = Flags | (bConfout ? MD_CONFOUT : 0);
Flags = Flags | (bRerunVSite ? MD_RERUN_VSITE : 0);
Flags = Flags | (bReproducible ? MD_REPRODUCIBLE : 0);
- Flags = Flags | (bDoAppendFiles ? MD_APPENDFILES : 0);
+ Flags = Flags | (bDoAppendFiles ? MD_APPENDFILES : 0);
Flags = Flags | (opt2parg_bSet("-append", asize(pa), pa) ? MD_APPENDFILESSET : 0);
Flags = Flags | (bKeepAndNumCPT ? MD_KEEPANDNUMCPT : 0);
Flags = Flags | (bStartFromCpt ? MD_STARTFROMCPT : 0);
diff --git a/patches/gromacs-2016-beta2.diff/src/programs/mdrun/mdrun.cpp.preplumed b/patches/gromacs-2016.diff/src/programs/mdrun/mdrun.cpp.preplumed
similarity index 96%
rename from patches/gromacs-2016-beta2.diff/src/programs/mdrun/mdrun.cpp.preplumed
rename to patches/gromacs-2016.diff/src/programs/mdrun/mdrun.cpp.preplumed
index e56c4a145..7829a823a 100644
--- a/patches/gromacs-2016-beta2.diff/src/programs/mdrun/mdrun.cpp.preplumed
+++ b/patches/gromacs-2016.diff/src/programs/mdrun/mdrun.cpp.preplumed
@@ -481,16 +481,30 @@ int gmx_mdrun(int argc, char *argv[])
if (nmultisim >= 1)
{
#if !GMX_THREAD_MPI
- gmx_bool bParFn = (multidir == NULL);
- init_multisystem(cr, nmultisim, multidir, NFILE, fnm, bParFn);
+ init_multisystem(cr, nmultisim, multidir, NFILE, fnm);
#else
gmx_fatal(FARGS, "mdrun -multi or -multidir are not supported with the thread-MPI library. "
"Please compile GROMACS with a proper external MPI library.");
#endif
}
- handleRestart(cr, bTryToAppendFiles, NFILE, fnm,
- &bDoAppendFiles, &bStartFromCpt);
+ if (!opt2bSet("-cpi", NFILE, fnm))
+ {
+ // If we are not starting from a checkpoint we never allow files to be appended
+ // to, since that has caused a ton of strange behaviour and bugs in the past.
+ if (opt2parg_bSet("-append", asize(pa), pa))
+ {
+ // If the user explicitly used the -append option, explain that it is not possible.
+ gmx_fatal(FARGS, "GROMACS can only append to files when restarting from a checkpoint.");
+ }
+ else
+ {
+ // If the user did not say anything explicit, just disable appending.
+ bTryToAppendFiles = FALSE;
+ }
+ }
+
+ handleRestart(cr, bTryToAppendFiles, NFILE, fnm, &bDoAppendFiles, &bStartFromCpt);
Flags = opt2bSet("-rerun", NFILE, fnm) ? MD_RERUN : 0;
Flags = Flags | (bDDBondCheck ? MD_DDBONDCHECK : 0);
@@ -499,7 +513,7 @@ int gmx_mdrun(int argc, char *argv[])
Flags = Flags | (bConfout ? MD_CONFOUT : 0);
Flags = Flags | (bRerunVSite ? MD_RERUN_VSITE : 0);
Flags = Flags | (bReproducible ? MD_REPRODUCIBLE : 0);
- Flags = Flags | (bDoAppendFiles ? MD_APPENDFILES : 0);
+ Flags = Flags | (bDoAppendFiles ? MD_APPENDFILES : 0);
Flags = Flags | (opt2parg_bSet("-append", asize(pa), pa) ? MD_APPENDFILESSET : 0);
Flags = Flags | (bKeepAndNumCPT ? MD_KEEPANDNUMCPT : 0);
Flags = Flags | (bStartFromCpt ? MD_STARTFROMCPT : 0);
diff --git a/patches/gromacs-2016-beta2.diff/src/programs/mdrun/repl_ex.cpp b/patches/gromacs-2016.diff/src/programs/mdrun/repl_ex.cpp
similarity index 100%
rename from patches/gromacs-2016-beta2.diff/src/programs/mdrun/repl_ex.cpp
rename to patches/gromacs-2016.diff/src/programs/mdrun/repl_ex.cpp
diff --git a/patches/gromacs-2016-beta2.diff/src/programs/mdrun/repl_ex.cpp.preplumed b/patches/gromacs-2016.diff/src/programs/mdrun/repl_ex.cpp.preplumed
similarity index 100%
rename from patches/gromacs-2016-beta2.diff/src/programs/mdrun/repl_ex.cpp.preplumed
rename to patches/gromacs-2016.diff/src/programs/mdrun/repl_ex.cpp.preplumed
diff --git a/patches/gromacs-2016-beta2.diff/src/programs/mdrun/runner.cpp b/patches/gromacs-2016.diff/src/programs/mdrun/runner.cpp
similarity index 98%
rename from patches/gromacs-2016-beta2.diff/src/programs/mdrun/runner.cpp
rename to patches/gromacs-2016.diff/src/programs/mdrun/runner.cpp
index b8550c39e..f3e0e4ece 100644
--- a/patches/gromacs-2016-beta2.diff/src/programs/mdrun/runner.cpp
+++ b/patches/gromacs-2016.diff/src/programs/mdrun/runner.cpp
@@ -110,6 +110,7 @@
#include "deform.h"
#include "md.h"
+#include "membed.h"
#include "repl_ex.h"
#include "resource-division.h"
@@ -715,6 +716,7 @@ int mdrunner(gmx_hw_opt_t *hw_opt,
gmx_int64_t reset_counters;
gmx_edsam_t ed = NULL;
int nthreads_pme = 1;
+ gmx_membed_t * membed = NULL;
gmx_hw_info_t *hwinfo = NULL;
/* The master rank decides early on bUseGPU and broadcasts this later */
gmx_bool bUseGPU = FALSE;
@@ -729,6 +731,7 @@ int mdrunner(gmx_hw_opt_t *hw_opt,
fplog = NULL;
}
+ bool doMembed = opt2bSet("-membed", nfile, fnm);
bRerunMD = (Flags & MD_RERUN);
bForceUseGPU = (strncmp(nbpu_opt, "gpu", 3) == 0);
bTryUseGPU = (strncmp(nbpu_opt, "auto", 4) == 0) || bForceUseGPU;
@@ -836,7 +839,8 @@ int mdrunner(gmx_hw_opt_t *hw_opt,
hw_opt->nthreads_tmpi = get_nthreads_mpi(hwinfo,
hw_opt,
inputrec, mtop,
- cr, fplog, bUseGPU);
+ cr, fplog, bUseGPU,
+ doMembed);
if (hw_opt->nthreads_tmpi > 1)
{
@@ -1148,6 +1152,19 @@ int mdrunner(gmx_hw_opt_t *hw_opt,
wcycle_set_reset_counters(wcycle, reset_counters);
}
+ // Membrane embedding must be initialized before we call init_forcerec()
+ if (doMembed)
+ {
+ if (MASTER(cr))
+ {
+ fprintf(stderr, "Initializing membed");
+ }
+ /* Note that membed cannot work in parallel because mtop is
+ * changed here. Fix this if we ever want to make it run with
+ * multiple ranks. */
+ membed = init_membed(fplog, nfile, fnm, mtop, inputrec, state, cr, &cpt_period);
+ }
+
snew(nrnb, 1);
if (cr->duty & DUTY_PP)
{
@@ -1323,6 +1340,7 @@ int mdrunner(gmx_hw_opt_t *hw_opt,
fcd, state,
mdatoms, nrnb, wcycle, ed, fr,
repl_ex_nst, repl_ex_nex, repl_ex_seed,
+ membed,
cpt_period, max_hours,
imdport,
Flags,
@@ -1361,6 +1379,11 @@ int mdrunner(gmx_hw_opt_t *hw_opt,
/* Free GPU memory and context */
free_gpu_resources(fr, cr, &hwinfo->gpu_info, fr ? fr->gpu_opt : NULL);
+ if (doMembed)
+ {
+ free_membed(membed);
+ }
+
gmx_hardware_info_free(hwinfo);
/* Does what it says */
diff --git a/patches/gromacs-2016-beta2.diff/src/programs/mdrun/runner.cpp.preplumed b/patches/gromacs-2016.diff/src/programs/mdrun/runner.cpp.preplumed
similarity index 98%
rename from patches/gromacs-2016-beta2.diff/src/programs/mdrun/runner.cpp.preplumed
rename to patches/gromacs-2016.diff/src/programs/mdrun/runner.cpp.preplumed
index ddc5895c9..560b923ba 100644
--- a/patches/gromacs-2016-beta2.diff/src/programs/mdrun/runner.cpp.preplumed
+++ b/patches/gromacs-2016.diff/src/programs/mdrun/runner.cpp.preplumed
@@ -110,6 +110,7 @@
#include "deform.h"
#include "md.h"
+#include "membed.h"
#include "repl_ex.h"
#include "resource-division.h"
@@ -709,6 +710,7 @@ int mdrunner(gmx_hw_opt_t *hw_opt,
gmx_int64_t reset_counters;
gmx_edsam_t ed = NULL;
int nthreads_pme = 1;
+ gmx_membed_t * membed = NULL;
gmx_hw_info_t *hwinfo = NULL;
/* The master rank decides early on bUseGPU and broadcasts this later */
gmx_bool bUseGPU = FALSE;
@@ -723,6 +725,7 @@ int mdrunner(gmx_hw_opt_t *hw_opt,
fplog = NULL;
}
+ bool doMembed = opt2bSet("-membed", nfile, fnm);
bRerunMD = (Flags & MD_RERUN);
bForceUseGPU = (strncmp(nbpu_opt, "gpu", 3) == 0);
bTryUseGPU = (strncmp(nbpu_opt, "auto", 4) == 0) || bForceUseGPU;
@@ -830,7 +833,8 @@ int mdrunner(gmx_hw_opt_t *hw_opt,
hw_opt->nthreads_tmpi = get_nthreads_mpi(hwinfo,
hw_opt,
inputrec, mtop,
- cr, fplog, bUseGPU);
+ cr, fplog, bUseGPU,
+ doMembed);
if (hw_opt->nthreads_tmpi > 1)
{
@@ -1142,6 +1146,19 @@ int mdrunner(gmx_hw_opt_t *hw_opt,
wcycle_set_reset_counters(wcycle, reset_counters);
}
+ // Membrane embedding must be initialized before we call init_forcerec()
+ if (doMembed)
+ {
+ if (MASTER(cr))
+ {
+ fprintf(stderr, "Initializing membed");
+ }
+ /* Note that membed cannot work in parallel because mtop is
+ * changed here. Fix this if we ever want to make it run with
+ * multiple ranks. */
+ membed = init_membed(fplog, nfile, fnm, mtop, inputrec, state, cr, &cpt_period);
+ }
+
snew(nrnb, 1);
if (cr->duty & DUTY_PP)
{
@@ -1317,6 +1334,7 @@ int mdrunner(gmx_hw_opt_t *hw_opt,
fcd, state,
mdatoms, nrnb, wcycle, ed, fr,
repl_ex_nst, repl_ex_nex, repl_ex_seed,
+ membed,
cpt_period, max_hours,
imdport,
Flags,
@@ -1355,6 +1373,11 @@ int mdrunner(gmx_hw_opt_t *hw_opt,
/* Free GPU memory and context */
free_gpu_resources(fr, cr, &hwinfo->gpu_info, fr ? fr->gpu_opt : NULL);
+ if (doMembed)
+ {
+ free_membed(membed);
+ }
+
gmx_hardware_info_free(hwinfo);
/* Does what it says */
--
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