diff --git a/patches/gromacs-4.6.5.diff/src/kernel/CMakeLists.txt b/patches/gromacs-4.6.6.diff/src/kernel/CMakeLists.txt
similarity index 98%
rename from patches/gromacs-4.6.5.diff/src/kernel/CMakeLists.txt
rename to patches/gromacs-4.6.6.diff/src/kernel/CMakeLists.txt
index 3ed862a7cab99b767626ee93d3b2fdf298f0abf4..8e108b361e4e81da6bda32e85095a23533b89bf1 100644
--- a/patches/gromacs-4.6.5.diff/src/kernel/CMakeLists.txt
+++ b/patches/gromacs-4.6.6.diff/src/kernel/CMakeLists.txt
@@ -78,7 +78,7 @@ set(MDRUN_SOURCES
add_library(gmxpreprocess ${GMXPREPROCESS_SOURCES})
target_link_libraries(gmxpreprocess md)
-set_target_properties(gmxpreprocess PROPERTIES OUTPUT_NAME "gmxpreprocess${GMX_LIBS_SUFFIX}" SOVERSION ${SOVERSION} INSTALL_NAME_DIR "${LIB_INSTALL_DIR}"
+set_target_properties(gmxpreprocess PROPERTIES OUTPUT_NAME "gmxpreprocess${GMX_LIBS_SUFFIX}" SOVERSION ${SOVERSION}
COMPILE_FLAGS "${OpenMP_C_FLAGS}")
diff --git a/patches/gromacs-4.6.5.diff/src/kernel/CMakeLists.txt.preplumed b/patches/gromacs-4.6.6.diff/src/kernel/CMakeLists.txt.preplumed
similarity index 98%
rename from patches/gromacs-4.6.5.diff/src/kernel/CMakeLists.txt.preplumed
rename to patches/gromacs-4.6.6.diff/src/kernel/CMakeLists.txt.preplumed
index e2125333387440d266eb0e6e77f23e8adb635511..fea8282ef4fade62c8a764455b21dae78f277236 100644
--- a/patches/gromacs-4.6.5.diff/src/kernel/CMakeLists.txt.preplumed
+++ b/patches/gromacs-4.6.6.diff/src/kernel/CMakeLists.txt.preplumed
@@ -76,7 +76,7 @@ set(MDRUN_SOURCES
add_library(gmxpreprocess ${GMXPREPROCESS_SOURCES})
target_link_libraries(gmxpreprocess md)
-set_target_properties(gmxpreprocess PROPERTIES OUTPUT_NAME "gmxpreprocess${GMX_LIBS_SUFFIX}" SOVERSION ${SOVERSION} INSTALL_NAME_DIR "${LIB_INSTALL_DIR}"
+set_target_properties(gmxpreprocess PROPERTIES OUTPUT_NAME "gmxpreprocess${GMX_LIBS_SUFFIX}" SOVERSION ${SOVERSION}
COMPILE_FLAGS "${OpenMP_C_FLAGS}")
diff --git a/patches/gromacs-4.6.5.diff/src/kernel/md.c b/patches/gromacs-4.6.6.diff/src/kernel/md.c
similarity index 97%
rename from patches/gromacs-4.6.5.diff/src/kernel/md.c
rename to patches/gromacs-4.6.6.diff/src/kernel/md.c
index a96f3bcd40e5f62081515b9a7980411be94a632c..741986ee9998d46db3024f82590f55cdebd0d8cb 100644
--- a/patches/gromacs-4.6.5.diff/src/kernel/md.c
+++ b/patches/gromacs-4.6.6.diff/src/kernel/md.c
@@ -358,6 +358,25 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
(ir->bContinuation ||
(DOMAINDECOMP(cr) && !MASTER(cr))) ?
NULL : state_global->x);
+ if (shellfc && ir->nstcalcenergy != 1)
+ {
+ gmx_fatal(FARGS, "You have nstcalcenergy set to a value (%d) that is different from 1.\nThis is not supported in combinations with shell particles.\nPlease make a new tpr file.", ir->nstcalcenergy);
+ }
+ if (shellfc && DOMAINDECOMP(cr))
+ {
+ gmx_fatal(FARGS, "In order to run parallel simulations with shells you need to use the -pd flag to mdrun.");
+ }
+ if (shellfc && ir->eI == eiNM)
+ {
+ /* Currently shells don't work with Normal Modes */
+ gmx_fatal(FARGS, "Normal Mode analysis is not supported with shells.\nIf you'd like to help with adding support, we have an open discussion at http://redmine.gromacs.org/issues/879\n");
+ }
+
+ if (vsite && ir->eI == eiNM)
+ {
+ /* Currently virtual sites don't work with Normal Modes */
+ gmx_fatal(FARGS, "Normal Mode analysis is not supported with virtual sites.\nIf you'd like to help with adding support, we have an open discussion at http://redmine.gromacs.org/issues/879\n");
+ }
if (DEFORM(*ir))
{
@@ -726,10 +745,10 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
/* PLUMED */
if(plumedswitch){
-/* detect plumed API version */
+ /* detect plumed API version */
int pversion=0;
plumed_cmd(plumedmain,"getApiVersion",&pversion);
-/* setting kbT is only implemented with api>1) */
+ /* setting kbT is only implemented with api>1) */
real kbT=ir->opts.ref_t[0]*BOLTZ;
if(pversion>1) plumed_cmd(plumedmain,"setKbT",&kbT);
@@ -771,14 +790,9 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
}
/* END PLUMED */
- /* Set and write start time */
+ print_start(fplog, cr, runtime, "mdrun");
runtime_start(runtime);
- print_date_and_time(fplog, cr->nodeid, "Started mdrun", runtime);
wallcycle_start(wcycle, ewcRUN);
- if (fplog)
- {
- fprintf(fplog, "\n");
- }
/* safest point to do file checkpointing is here. More general point would be immediately before integrator call */
#ifdef GMX_FAHCORE
@@ -1314,11 +1328,15 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
* step to combine the long-range forces on these steps.
* For nstcalclr=1 this is not done, since the forces would have been added
* directly to the short-range forces already.
+ *
+ * TODO Remove various aspects of VV+twin-range in master
+ * branch, because VV integrators did not ever support
+ * twin-range multiple time stepping with constraints.
*/
bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC,
- f, bUpdateDoLR, fr->f_twin, fcd,
+ f, bUpdateDoLR, fr->f_twin, bCalcVir ? &fr->vir_twin_constr : NULL, fcd,
ekind, M, wcycle, upd, bInitStep, etrtVELOCITY1,
cr, nrnb, constr, &top->idef);
@@ -1369,6 +1387,12 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
cr, nrnb, wcycle, upd, constr,
bInitStep, TRUE, bCalcVir, vetanew);
+ if (bCalcVir && bUpdateDoLR && ir->nstcalclr > 1)
+ {
+ /* Correct the virial for multiple time stepping */
+ m_sub(shake_vir, fr->vir_twin_constr, shake_vir);
+ }
+
if (!bOK && !bFFscan)
{
gmx_fatal(FARGS, "Constraint error: Shake, Lincs or Settle could not solve the constrains");
@@ -1553,6 +1577,10 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
fcReportProgress( ir->nsteps, step );
}
+#if defined(__native_client__)
+ fcCheckin(MASTER(cr));
+#endif
+
/* sync bCPT and fc record-keeping */
if (bCPT && MASTER(cr))
{
@@ -1731,7 +1759,7 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
if (ETC_ANDERSEN(ir->etc)) /* keep this outside of update_tcouple because of the extra info required to pass */
{
gmx_bool bIfRandomize;
- bIfRandomize = update_randomize_velocities(ir, step, mdatoms, state, upd, &top->idef, constr);
+ bIfRandomize = update_randomize_velocities(ir, step, mdatoms, state, upd, &top->idef, constr, DOMAINDECOMP(cr));
/* if we have constraints, we have to remove the kinetic energy parallel to the bonds */
if (constr && bIfRandomize)
{
@@ -1816,7 +1844,7 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
/* velocity half-step update */
update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC, f,
- bUpdateDoLR, fr->f_twin, fcd,
+ bUpdateDoLR, fr->f_twin, bCalcVir ? &fr->vir_twin_constr : NULL, fcd,
ekind, M, wcycle, upd, FALSE, etrtVELOCITY2,
cr, nrnb, constr, &top->idef);
}
@@ -1833,7 +1861,7 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC, f,
- bUpdateDoLR, fr->f_twin, fcd,
+ bUpdateDoLR, fr->f_twin, bCalcVir ? &fr->vir_twin_constr : NULL, fcd,
ekind, M, wcycle, upd, bInitStep, etrtPOSITION, cr, nrnb, constr, &top->idef);
wallcycle_stop(wcycle, ewcUPDATE);
@@ -1843,6 +1871,12 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
cr, nrnb, wcycle, upd, constr,
bInitStep, FALSE, bCalcVir, state->veta);
+ if (bCalcVir && bUpdateDoLR && ir->nstcalclr > 1)
+ {
+ /* Correct the virial for multiple time stepping */
+ m_sub(shake_vir, fr->vir_twin_constr, shake_vir);
+ }
+
if (ir->eI == eiVVAK)
{
/* erase F_EKIN and F_TEMP here? */
@@ -1861,7 +1895,7 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC, f,
- bUpdateDoLR, fr->f_twin, fcd,
+ bUpdateDoLR, fr->f_twin, bCalcVir ? &fr->vir_twin_constr : NULL, fcd,
ekind, M, wcycle, upd, bInitStep, etrtPOSITION, cr, nrnb, constr, &top->idef);
wallcycle_stop(wcycle, ewcUPDATE);
diff --git a/patches/gromacs-4.6.5.diff/src/kernel/md.c.preplumed b/patches/gromacs-4.6.6.diff/src/kernel/md.c.preplumed
similarity index 97%
rename from patches/gromacs-4.6.5.diff/src/kernel/md.c.preplumed
rename to patches/gromacs-4.6.6.diff/src/kernel/md.c.preplumed
index 81fca912a8746a7b6f297836762a0e5912f7ad86..4c4a88c174dbd8b47337a13fed1d23c3dadf4c76 100644
--- a/patches/gromacs-4.6.5.diff/src/kernel/md.c.preplumed
+++ b/patches/gromacs-4.6.6.diff/src/kernel/md.c.preplumed
@@ -347,6 +347,25 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
(ir->bContinuation ||
(DOMAINDECOMP(cr) && !MASTER(cr))) ?
NULL : state_global->x);
+ if (shellfc && ir->nstcalcenergy != 1)
+ {
+ gmx_fatal(FARGS, "You have nstcalcenergy set to a value (%d) that is different from 1.\nThis is not supported in combinations with shell particles.\nPlease make a new tpr file.", ir->nstcalcenergy);
+ }
+ if (shellfc && DOMAINDECOMP(cr))
+ {
+ gmx_fatal(FARGS, "In order to run parallel simulations with shells you need to use the -pd flag to mdrun.");
+ }
+ if (shellfc && ir->eI == eiNM)
+ {
+ /* Currently shells don't work with Normal Modes */
+ gmx_fatal(FARGS, "Normal Mode analysis is not supported with shells.\nIf you'd like to help with adding support, we have an open discussion at http://redmine.gromacs.org/issues/879\n");
+ }
+
+ if (vsite && ir->eI == eiNM)
+ {
+ /* Currently virtual sites don't work with Normal Modes */
+ gmx_fatal(FARGS, "Normal Mode analysis is not supported with virtual sites.\nIf you'd like to help with adding support, we have an open discussion at http://redmine.gromacs.org/issues/879\n");
+ }
if (DEFORM(*ir))
{
@@ -713,14 +732,9 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
fprintf(fplog, "\n");
}
- /* Set and write start time */
+ print_start(fplog, cr, runtime, "mdrun");
runtime_start(runtime);
- print_date_and_time(fplog, cr->nodeid, "Started mdrun", runtime);
wallcycle_start(wcycle, ewcRUN);
- if (fplog)
- {
- fprintf(fplog, "\n");
- }
/* safest point to do file checkpointing is here. More general point would be immediately before integrator call */
#ifdef GMX_FAHCORE
@@ -1222,11 +1236,15 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
* step to combine the long-range forces on these steps.
* For nstcalclr=1 this is not done, since the forces would have been added
* directly to the short-range forces already.
+ *
+ * TODO Remove various aspects of VV+twin-range in master
+ * branch, because VV integrators did not ever support
+ * twin-range multiple time stepping with constraints.
*/
bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC,
- f, bUpdateDoLR, fr->f_twin, fcd,
+ f, bUpdateDoLR, fr->f_twin, bCalcVir ? &fr->vir_twin_constr : NULL, fcd,
ekind, M, wcycle, upd, bInitStep, etrtVELOCITY1,
cr, nrnb, constr, &top->idef);
@@ -1277,6 +1295,12 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
cr, nrnb, wcycle, upd, constr,
bInitStep, TRUE, bCalcVir, vetanew);
+ if (bCalcVir && bUpdateDoLR && ir->nstcalclr > 1)
+ {
+ /* Correct the virial for multiple time stepping */
+ m_sub(shake_vir, fr->vir_twin_constr, shake_vir);
+ }
+
if (!bOK && !bFFscan)
{
gmx_fatal(FARGS, "Constraint error: Shake, Lincs or Settle could not solve the constrains");
@@ -1461,6 +1485,10 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
fcReportProgress( ir->nsteps, step );
}
+#if defined(__native_client__)
+ fcCheckin(MASTER(cr));
+#endif
+
/* sync bCPT and fc record-keeping */
if (bCPT && MASTER(cr))
{
@@ -1639,7 +1667,7 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
if (ETC_ANDERSEN(ir->etc)) /* keep this outside of update_tcouple because of the extra info required to pass */
{
gmx_bool bIfRandomize;
- bIfRandomize = update_randomize_velocities(ir, step, mdatoms, state, upd, &top->idef, constr);
+ bIfRandomize = update_randomize_velocities(ir, step, mdatoms, state, upd, &top->idef, constr, DOMAINDECOMP(cr));
/* if we have constraints, we have to remove the kinetic energy parallel to the bonds */
if (constr && bIfRandomize)
{
@@ -1724,7 +1752,7 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
/* velocity half-step update */
update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC, f,
- bUpdateDoLR, fr->f_twin, fcd,
+ bUpdateDoLR, fr->f_twin, bCalcVir ? &fr->vir_twin_constr : NULL, fcd,
ekind, M, wcycle, upd, FALSE, etrtVELOCITY2,
cr, nrnb, constr, &top->idef);
}
@@ -1741,7 +1769,7 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC, f,
- bUpdateDoLR, fr->f_twin, fcd,
+ bUpdateDoLR, fr->f_twin, bCalcVir ? &fr->vir_twin_constr : NULL, fcd,
ekind, M, wcycle, upd, bInitStep, etrtPOSITION, cr, nrnb, constr, &top->idef);
wallcycle_stop(wcycle, ewcUPDATE);
@@ -1751,6 +1779,12 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
cr, nrnb, wcycle, upd, constr,
bInitStep, FALSE, bCalcVir, state->veta);
+ if (bCalcVir && bUpdateDoLR && ir->nstcalclr > 1)
+ {
+ /* Correct the virial for multiple time stepping */
+ m_sub(shake_vir, fr->vir_twin_constr, shake_vir);
+ }
+
if (ir->eI == eiVVAK)
{
/* erase F_EKIN and F_TEMP here? */
@@ -1769,7 +1803,7 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC, f,
- bUpdateDoLR, fr->f_twin, fcd,
+ bUpdateDoLR, fr->f_twin, bCalcVir ? &fr->vir_twin_constr : NULL, fcd,
ekind, M, wcycle, upd, bInitStep, etrtPOSITION, cr, nrnb, constr, &top->idef);
wallcycle_stop(wcycle, ewcUPDATE);
diff --git a/patches/gromacs-4.6.5.diff/src/kernel/mdrun.c b/patches/gromacs-4.6.6.diff/src/kernel/mdrun.c
similarity index 97%
rename from patches/gromacs-4.6.5.diff/src/kernel/mdrun.c
rename to patches/gromacs-4.6.6.diff/src/kernel/mdrun.c
index e57c646b6155a6cdfb11317d3d4a806658b1980a..ca3b6574d221018a65ba557f97c1d4d2116a7c5f 100644
--- a/patches/gromacs-4.6.5.diff/src/kernel/mdrun.c
+++ b/patches/gromacs-4.6.6.diff/src/kernel/mdrun.c
@@ -106,10 +106,16 @@ int cmain(int argc, char *argv[])
"With thread-MPI there are additional options [TT]-nt[tt], which sets",
"the total number of threads, and [TT]-ntmpi[tt], which sets the number",
"of thread-MPI threads.",
- "Note that using combined MPI+OpenMP parallelization is almost always",
- "slower than single parallelization, except at the scaling limit, where",
- "especially OpenMP parallelization of PME reduces the communication cost.",
- "OpenMP-only parallelization is much faster than MPI-only parallelization",
+ "The number of OpenMP threads used by [TT]mdrun[tt] can also be set with",
+ "the standard environment variable, [TT]OMP_NUM_THREADS[tt].",
+ "The [TT]GMX_PME_NUM_THREADS[tt] environment variable can be used to specify",
+ "the number of threads used by the PME-only processes.[PAR]",
+ "Note that combined MPI+OpenMP parallelization is in many cases",
+ "slower than either on its own. However, at high parallelization, using the",
+ "combination is often beneficial as it reduces the number of domains and/or",
+ "the number of MPI ranks. (Less and larger domains can improve scaling,",
+ "with separate PME processes fewer MPI ranks reduces communication cost.)",
+ "OpenMP-only parallelization is typically faster than MPI-only parallelization",
"on a single CPU(-die). Since we currently don't have proper hardware",
"topology detection, [TT]mdrun[tt] compiled with thread-MPI will only",
"automatically use OpenMP-only parallelization when you use up to 4",
@@ -199,13 +205,16 @@ int cmain(int argc, char *argv[])
"[PAR]",
"When PME is used with domain decomposition, separate nodes can",
"be assigned to do only the PME mesh calculation;",
- "this is computationally more efficient starting at about 12 nodes.",
+ "this is computationally more efficient starting at about 12 nodes",
+ "or even fewer when OpenMP parallelization is used.",
"The number of PME nodes is set with option [TT]-npme[tt],",
"this can not be more than half of the nodes.",
"By default [TT]mdrun[tt] makes a guess for the number of PME",
- "nodes when the number of nodes is larger than 11 or performance wise",
- "not compatible with the PME grid x dimension.",
- "But the user should optimize npme. Performance statistics on this issue",
+ "nodes when the number of nodes is larger than 16. With GPUs,",
+ "PME nodes are not selected automatically, since the optimal setup",
+ "depends very much on the details of the hardware.",
+ "In all cases you might gain performance by optimizing [TT]-npme[tt].",
+ "Performance statistics on this issue",
"are written at the end of the log file.",
"For good load balancing at high parallelization, the PME grid x and y",
"dimensions should be divisible by the number of PME nodes",
diff --git a/patches/gromacs-4.6.5.diff/src/kernel/mdrun.c.preplumed b/patches/gromacs-4.6.6.diff/src/kernel/mdrun.c.preplumed
similarity index 97%
rename from patches/gromacs-4.6.5.diff/src/kernel/mdrun.c.preplumed
rename to patches/gromacs-4.6.6.diff/src/kernel/mdrun.c.preplumed
index 2ccc6f67469c0aab5263ec48636818785073f661..eb30fc99c6c6c360231f0b321772261f79b386c0 100644
--- a/patches/gromacs-4.6.5.diff/src/kernel/mdrun.c.preplumed
+++ b/patches/gromacs-4.6.6.diff/src/kernel/mdrun.c.preplumed
@@ -100,10 +100,16 @@ int cmain(int argc, char *argv[])
"With thread-MPI there are additional options [TT]-nt[tt], which sets",
"the total number of threads, and [TT]-ntmpi[tt], which sets the number",
"of thread-MPI threads.",
- "Note that using combined MPI+OpenMP parallelization is almost always",
- "slower than single parallelization, except at the scaling limit, where",
- "especially OpenMP parallelization of PME reduces the communication cost.",
- "OpenMP-only parallelization is much faster than MPI-only parallelization",
+ "The number of OpenMP threads used by [TT]mdrun[tt] can also be set with",
+ "the standard environment variable, [TT]OMP_NUM_THREADS[tt].",
+ "The [TT]GMX_PME_NUM_THREADS[tt] environment variable can be used to specify",
+ "the number of threads used by the PME-only processes.[PAR]",
+ "Note that combined MPI+OpenMP parallelization is in many cases",
+ "slower than either on its own. However, at high parallelization, using the",
+ "combination is often beneficial as it reduces the number of domains and/or",
+ "the number of MPI ranks. (Less and larger domains can improve scaling,",
+ "with separate PME processes fewer MPI ranks reduces communication cost.)",
+ "OpenMP-only parallelization is typically faster than MPI-only parallelization",
"on a single CPU(-die). Since we currently don't have proper hardware",
"topology detection, [TT]mdrun[tt] compiled with thread-MPI will only",
"automatically use OpenMP-only parallelization when you use up to 4",
@@ -193,13 +199,16 @@ int cmain(int argc, char *argv[])
"[PAR]",
"When PME is used with domain decomposition, separate nodes can",
"be assigned to do only the PME mesh calculation;",
- "this is computationally more efficient starting at about 12 nodes.",
+ "this is computationally more efficient starting at about 12 nodes",
+ "or even fewer when OpenMP parallelization is used.",
"The number of PME nodes is set with option [TT]-npme[tt],",
"this can not be more than half of the nodes.",
"By default [TT]mdrun[tt] makes a guess for the number of PME",
- "nodes when the number of nodes is larger than 11 or performance wise",
- "not compatible with the PME grid x dimension.",
- "But the user should optimize npme. Performance statistics on this issue",
+ "nodes when the number of nodes is larger than 16. With GPUs,",
+ "PME nodes are not selected automatically, since the optimal setup",
+ "depends very much on the details of the hardware.",
+ "In all cases you might gain performance by optimizing [TT]-npme[tt].",
+ "Performance statistics on this issue",
"are written at the end of the log file.",
"For good load balancing at high parallelization, the PME grid x and y",
"dimensions should be divisible by the number of PME nodes",
diff --git a/patches/gromacs-4.6.5.diff/src/kernel/repl_ex.c b/patches/gromacs-4.6.6.diff/src/kernel/repl_ex.c
similarity index 97%
rename from patches/gromacs-4.6.5.diff/src/kernel/repl_ex.c
rename to patches/gromacs-4.6.6.diff/src/kernel/repl_ex.c
index 9fa6dc5cea8a4847f536dbe99c4e19fee97f75c8..7f27136acd73ef02c830fd8fa6dab6712bb27071 100644
--- a/patches/gromacs-4.6.5.diff/src/kernel/repl_ex.c
+++ b/patches/gromacs-4.6.6.diff/src/kernel/repl_ex.c
@@ -278,6 +278,12 @@ gmx_repl_ex_t init_replica_exchange(FILE *fplog,
{
if (re->q[re->type][re->ind[j]] < re->q[re->type][re->ind[i]])
{
+ gmx_fatal(FARGS, "Replicas with indices %d < %d have %ss %g > %g, please order your replicas on increasing %s",
+ i, j,
+ erename[re->type],
+ re->q[re->type][i], re->q[re->type][j],
+ erename[re->type]);
+
k = re->ind[i];
re->ind[i] = re->ind[j];
re->ind[j] = k;
@@ -891,7 +897,7 @@ static real calc_delta(FILE *fplog, gmx_bool bPrint, struct gmx_repl_ex *re, int
dpV = (beta[ap]*re->pres[ap]-beta[bp]*re->pres[bp])*(Vol[b]-Vol[a])/PRESFAC;
if (bPrint)
{
- fprintf(fplog, " dpV = %10.3e d = %10.3e\nb", dpV, delta + dpV);
+ fprintf(fplog, " dpV = %10.3e d = %10.3e\n", dpV, delta + dpV);
}
delta += dpV;
}
@@ -918,7 +924,7 @@ test_for_replica_exchange(FILE *fplog,
gmx_bool bVol = FALSE;
bMultiEx = (re->nex > 1); /* multiple exchanges at each state */
- fprintf(fplog, "Replica exchange at step " gmx_large_int_pfmt " time %g\n", step, time);
+ fprintf(fplog, "Replica exchange at step " gmx_large_int_pfmt " time %.5f\n", step, time);
if (re->bNPT)
{
@@ -1313,13 +1319,9 @@ compute_exchange_order(FILE *fplog,
static void
prepare_to_do_exchange(FILE *fplog,
- const int *destinations,
+ struct gmx_repl_ex *re,
const int replica_id,
- const int nrepl,
int *maxswap,
- int **order,
- int **cyclic,
- int *incycle,
gmx_bool *bThisReplicaExchanged)
{
int i, j;
@@ -1328,9 +1330,9 @@ prepare_to_do_exchange(FILE *fplog,
gmx_bool bAnyReplicaExchanged = FALSE;
*bThisReplicaExchanged = FALSE;
- for (i = 0; i < nrepl; i++)
+ for (i = 0; i < re->nrepl; i++)
{
- if (destinations[i] != i)
+ if (re->destinations[i] != re->ind[i])
{
/* only mark as exchanged if the index has been shuffled */
bAnyReplicaExchanged = TRUE;
@@ -1340,27 +1342,27 @@ prepare_to_do_exchange(FILE *fplog,
if (bAnyReplicaExchanged)
{
/* reinitialize the placeholder arrays */
- for (i = 0; i < nrepl; i++)
+ for (i = 0; i < re->nrepl; i++)
{
- for (j = 0; j < nrepl; j++)
+ for (j = 0; j < re->nrepl; j++)
{
- cyclic[i][j] = -1;
- order[i][j] = -1;
+ re->cyclic[i][j] = -1;
+ re->order[i][j] = -1;
}
}
/* Identify the cyclic decomposition of the permutation (very
* fast if neighbor replica exchange). */
- cyclic_decomposition(fplog, destinations, cyclic, incycle, nrepl, maxswap);
+ cyclic_decomposition(fplog, re->destinations, re->cyclic, re->incycle, re->nrepl, maxswap);
/* Now translate the decomposition into a replica exchange
* order at each step. */
- compute_exchange_order(fplog, cyclic, order, nrepl, *maxswap);
+ compute_exchange_order(fplog, re->cyclic, re->order, re->nrepl, *maxswap);
/* Did this replica do any exchange at any point? */
for (j = 0; j < *maxswap; j++)
{
- if (replica_id != order[replica_id][j])
+ if (replica_id != re->order[replica_id][j])
{
*bThisReplicaExchanged = TRUE;
break;
@@ -1391,8 +1393,7 @@ gmx_bool replica_exchange(FILE *fplog, const t_commrec *cr, struct gmx_repl_ex *
{
replica_id = re->repl;
test_for_replica_exchange(fplog, cr->ms, re, enerd, det(state_local->box), step, time);
- prepare_to_do_exchange(fplog, re->destinations, replica_id, re->nrepl, &maxswap,
- re->order, re->cyclic, re->incycle, &bThisReplicaExchanged);
+ prepare_to_do_exchange(fplog, re, replica_id, &maxswap, &bThisReplicaExchanged);
}
/* Do intra-simulation broadcast so all processors belonging to
* each simulation know whether they need to participate in
@@ -1440,10 +1441,10 @@ gmx_bool replica_exchange(FILE *fplog, const t_commrec *cr, struct gmx_repl_ex *
if (exchange_partner != replica_id)
{
/* Exchange the global states between the master nodes */
- //if (debug)
- //{
- fprintf(fplog, "Exchanging %d with %d\n", replica_id, exchange_partner);
- //}
+ if (debug)
+ {
+ fprintf(debug, "Exchanging %d with %d\n", replica_id, exchange_partner);
+ }
exchange_state(cr->ms, exchange_partner, state);
}
}
diff --git a/patches/gromacs-4.6.5.diff/src/kernel/repl_ex.c.preplumed b/patches/gromacs-4.6.6.diff/src/kernel/repl_ex.c.preplumed
similarity index 97%
rename from patches/gromacs-4.6.5.diff/src/kernel/repl_ex.c.preplumed
rename to patches/gromacs-4.6.6.diff/src/kernel/repl_ex.c.preplumed
index 3bbb3f94ef4b0304e48cc62c7960ac130487625a..0f094d4e267aa65df321b1da7e12e548db2e96c2 100644
--- a/patches/gromacs-4.6.5.diff/src/kernel/repl_ex.c.preplumed
+++ b/patches/gromacs-4.6.6.diff/src/kernel/repl_ex.c.preplumed
@@ -266,6 +266,16 @@ gmx_repl_ex_t init_replica_exchange(FILE *fplog,
{
if (re->q[re->type][re->ind[j]] < re->q[re->type][re->ind[i]])
{
+ /* Unordered replicas are supposed to work, but there
+ * is still an issues somewhere.
+ * Note that at this point still re->ind[i]=i.
+ */
+ gmx_fatal(FARGS, "Replicas with indices %d < %d have %ss %g > %g, please order your replicas on increasing %s",
+ i, j,
+ erename[re->type],
+ re->q[re->type][i], re->q[re->type][j],
+ erename[re->type]);
+
k = re->ind[i];
re->ind[i] = re->ind[j];
re->ind[j] = k;
@@ -877,7 +887,7 @@ static real calc_delta(FILE *fplog, gmx_bool bPrint, struct gmx_repl_ex *re, int
dpV = (beta[ap]*re->pres[ap]-beta[bp]*re->pres[bp])*(Vol[b]-Vol[a])/PRESFAC;
if (bPrint)
{
- fprintf(fplog, " dpV = %10.3e d = %10.3e\nb", dpV, delta + dpV);
+ fprintf(fplog, " dpV = %10.3e d = %10.3e\n", dpV, delta + dpV);
}
delta += dpV;
}
@@ -904,7 +914,7 @@ test_for_replica_exchange(FILE *fplog,
gmx_bool bVol = FALSE;
bMultiEx = (re->nex > 1); /* multiple exchanges at each state */
- fprintf(fplog, "Replica exchange at step " gmx_large_int_pfmt " time %g\n", step, time);
+ fprintf(fplog, "Replica exchange at step " gmx_large_int_pfmt " time %.5f\n", step, time);
if (re->bNPT)
{
@@ -1238,13 +1248,9 @@ compute_exchange_order(FILE *fplog,
static void
prepare_to_do_exchange(FILE *fplog,
- const int *destinations,
+ struct gmx_repl_ex *re,
const int replica_id,
- const int nrepl,
int *maxswap,
- int **order,
- int **cyclic,
- int *incycle,
gmx_bool *bThisReplicaExchanged)
{
int i, j;
@@ -1253,9 +1259,9 @@ prepare_to_do_exchange(FILE *fplog,
gmx_bool bAnyReplicaExchanged = FALSE;
*bThisReplicaExchanged = FALSE;
- for (i = 0; i < nrepl; i++)
+ for (i = 0; i < re->nrepl; i++)
{
- if (destinations[i] != i)
+ if (re->destinations[i] != re->ind[i])
{
/* only mark as exchanged if the index has been shuffled */
bAnyReplicaExchanged = TRUE;
@@ -1265,27 +1271,27 @@ prepare_to_do_exchange(FILE *fplog,
if (bAnyReplicaExchanged)
{
/* reinitialize the placeholder arrays */
- for (i = 0; i < nrepl; i++)
+ for (i = 0; i < re->nrepl; i++)
{
- for (j = 0; j < nrepl; j++)
+ for (j = 0; j < re->nrepl; j++)
{
- cyclic[i][j] = -1;
- order[i][j] = -1;
+ re->cyclic[i][j] = -1;
+ re->order[i][j] = -1;
}
}
/* Identify the cyclic decomposition of the permutation (very
* fast if neighbor replica exchange). */
- cyclic_decomposition(fplog, destinations, cyclic, incycle, nrepl, maxswap);
+ cyclic_decomposition(fplog, re->destinations, re->cyclic, re->incycle, re->nrepl, maxswap);
/* Now translate the decomposition into a replica exchange
* order at each step. */
- compute_exchange_order(fplog, cyclic, order, nrepl, *maxswap);
+ compute_exchange_order(fplog, re->cyclic, re->order, re->nrepl, *maxswap);
/* Did this replica do any exchange at any point? */
for (j = 0; j < *maxswap; j++)
{
- if (replica_id != order[replica_id][j])
+ if (replica_id != re->order[replica_id][j])
{
*bThisReplicaExchanged = TRUE;
break;
@@ -1312,8 +1318,7 @@ gmx_bool replica_exchange(FILE *fplog, const t_commrec *cr, struct gmx_repl_ex *
{
replica_id = re->repl;
test_for_replica_exchange(fplog, cr->ms, re, enerd, det(state_local->box), step, time);
- prepare_to_do_exchange(fplog, re->destinations, replica_id, re->nrepl, &maxswap,
- re->order, re->cyclic, re->incycle, &bThisReplicaExchanged);
+ prepare_to_do_exchange(fplog, re, replica_id, &maxswap, &bThisReplicaExchanged);
}
/* Do intra-simulation broadcast so all processors belonging to
* each simulation know whether they need to participate in
diff --git a/patches/gromacs-4.6.5.diff/src/mdlib/force.c b/patches/gromacs-4.6.6.diff/src/mdlib/force.c
similarity index 100%
rename from patches/gromacs-4.6.5.diff/src/mdlib/force.c
rename to patches/gromacs-4.6.6.diff/src/mdlib/force.c
diff --git a/patches/gromacs-4.6.5.diff/src/mdlib/force.c.preplumed b/patches/gromacs-4.6.6.diff/src/mdlib/force.c.preplumed
similarity index 100%
rename from patches/gromacs-4.6.5.diff/src/mdlib/force.c.preplumed
rename to patches/gromacs-4.6.6.diff/src/mdlib/force.c.preplumed
diff --git a/patches/gromacs-4.6.5.diff/src/mdlib/minimize.c b/patches/gromacs-4.6.6.diff/src/mdlib/minimize.c
similarity index 99%
rename from patches/gromacs-4.6.5.diff/src/mdlib/minimize.c
rename to patches/gromacs-4.6.6.diff/src/mdlib/minimize.c
index 79f002127165bbd84e3c7dc6e9073f06ff6db335..f800e6225704db6ab644f108bac0ebab94e19380 100644
--- a/patches/gromacs-4.6.5.diff/src/mdlib/minimize.c
+++ b/patches/gromacs-4.6.6.diff/src/mdlib/minimize.c
@@ -67,6 +67,7 @@
#include "force.h"
#include "mdrun.h"
#include "md_support.h"
+#include "sim_util.h"
#include "domdec.h"
#include "partdec.h"
#include "trnio.h"
@@ -114,15 +115,11 @@ static void print_em_start(FILE *fplog, t_commrec *cr, gmx_runtime_t *runtime,
gmx_wallcycle_t wcycle,
const char *name)
{
- char buf[STRLEN];
-
runtime_start(runtime);
-
- sprintf(buf, "Started %s", name);
- print_date_and_time(fplog, cr->nodeid, buf, NULL);
-
wallcycle_start(wcycle, ewcRUN);
+ print_start(fplog, cr, runtime, name);
}
+
static void em_time_end(FILE *fplog, t_commrec *cr, gmx_runtime_t *runtime,
gmx_wallcycle_t wcycle)
{
diff --git a/patches/gromacs-4.6.5.diff/src/mdlib/minimize.c.preplumed b/patches/gromacs-4.6.6.diff/src/mdlib/minimize.c.preplumed
similarity index 99%
rename from patches/gromacs-4.6.5.diff/src/mdlib/minimize.c.preplumed
rename to patches/gromacs-4.6.6.diff/src/mdlib/minimize.c.preplumed
index 5df3936cfbef96b8583e01a95ddd9e0b27c8efb0..8afe436f44640703d2c7c6a93bc90861ae5cd038 100644
--- a/patches/gromacs-4.6.5.diff/src/mdlib/minimize.c.preplumed
+++ b/patches/gromacs-4.6.6.diff/src/mdlib/minimize.c.preplumed
@@ -67,6 +67,7 @@
#include "force.h"
#include "mdrun.h"
#include "md_support.h"
+#include "sim_util.h"
#include "domdec.h"
#include "partdec.h"
#include "trnio.h"
@@ -108,15 +109,11 @@ static void print_em_start(FILE *fplog, t_commrec *cr, gmx_runtime_t *runtime,
gmx_wallcycle_t wcycle,
const char *name)
{
- char buf[STRLEN];
-
runtime_start(runtime);
-
- sprintf(buf, "Started %s", name);
- print_date_and_time(fplog, cr->nodeid, buf, NULL);
-
wallcycle_start(wcycle, ewcRUN);
+ print_start(fplog, cr, runtime, name);
}
+
static void em_time_end(FILE *fplog, t_commrec *cr, gmx_runtime_t *runtime,
gmx_wallcycle_t wcycle)
{