diff --git a/patches/gromacs-5.1.0.diff/src/gromacs/CMakeLists.txt b/patches/gromacs-5.1.2.diff/src/gromacs/CMakeLists.txt
similarity index 100%
rename from patches/gromacs-5.1.0.diff/src/gromacs/CMakeLists.txt
rename to patches/gromacs-5.1.2.diff/src/gromacs/CMakeLists.txt
diff --git a/patches/gromacs-5.1.0.diff/src/gromacs/CMakeLists.txt.preplumed b/patches/gromacs-5.1.2.diff/src/gromacs/CMakeLists.txt.preplumed
similarity index 100%
rename from patches/gromacs-5.1.0.diff/src/gromacs/CMakeLists.txt.preplumed
rename to patches/gromacs-5.1.2.diff/src/gromacs/CMakeLists.txt.preplumed
diff --git a/patches/gromacs-5.1.0.diff/src/gromacs/mdlib/force.cpp b/patches/gromacs-5.1.2.diff/src/gromacs/mdlib/force.cpp
similarity index 100%
rename from patches/gromacs-5.1.0.diff/src/gromacs/mdlib/force.cpp
rename to patches/gromacs-5.1.2.diff/src/gromacs/mdlib/force.cpp
diff --git a/patches/gromacs-5.1.0.diff/src/gromacs/mdlib/force.cpp.preplumed b/patches/gromacs-5.1.2.diff/src/gromacs/mdlib/force.cpp.preplumed
similarity index 100%
rename from patches/gromacs-5.1.0.diff/src/gromacs/mdlib/force.cpp.preplumed
rename to patches/gromacs-5.1.2.diff/src/gromacs/mdlib/force.cpp.preplumed
diff --git a/patches/gromacs-5.1.0.diff/src/gromacs/mdlib/minimize.cpp b/patches/gromacs-5.1.2.diff/src/gromacs/mdlib/minimize.cpp
similarity index 100%
rename from patches/gromacs-5.1.0.diff/src/gromacs/mdlib/minimize.cpp
rename to patches/gromacs-5.1.2.diff/src/gromacs/mdlib/minimize.cpp
diff --git a/patches/gromacs-5.1.0.diff/src/gromacs/mdlib/minimize.cpp.preplumed b/patches/gromacs-5.1.2.diff/src/gromacs/mdlib/minimize.cpp.preplumed
similarity index 100%
rename from patches/gromacs-5.1.0.diff/src/gromacs/mdlib/minimize.cpp.preplumed
rename to patches/gromacs-5.1.2.diff/src/gromacs/mdlib/minimize.cpp.preplumed
diff --git a/patches/gromacs-5.1.0.diff/src/programs/mdrun/md.cpp b/patches/gromacs-5.1.2.diff/src/programs/mdrun/md.cpp
similarity index 98%
rename from patches/gromacs-5.1.0.diff/src/programs/mdrun/md.cpp
rename to patches/gromacs-5.1.2.diff/src/programs/mdrun/md.cpp
index a914b2d7f14053caf34a72210ccf56e31dac925c..0007817df2c5c9c4f44428e8742ba03a31627d66 100644
--- a/patches/gromacs-5.1.0.diff/src/programs/mdrun/md.cpp
+++ b/patches/gromacs-5.1.2.diff/src/programs/mdrun/md.cpp
@@ -235,7 +235,7 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
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;
+ pme_load_balancing_t *pme_loadbal = NULL;
gmx_bool bPMETune = FALSE;
gmx_bool bPMETunePrinting = FALSE;
@@ -1431,6 +1431,7 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
if (bResetCountersHalfMaxH && MASTER(cr) &&
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;
}
@@ -1845,10 +1846,28 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
step_rel++;
}
+ /* TODO make a counter-reset module */
+ /* 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)
{
- /* Reset all the counters related to performance over the run */
+ if (pme_loadbal_is_active(pme_loadbal))
+ {
+ /* Do not permit counter reset while PME load
+ * balancing is active. The only purpose for resetting
+ * counters is to measure reliable performance data,
+ * and that can't be done before balancing
+ * completes.
+ *
+ * TODO consider fixing this by delaying the reset
+ * until after load balancing completes,
+ * e.g. https://gerrit.gromacs.org/#/c/4964/2 */
+ gmx_fatal(FARGS, "PME tuning was still active when attempting to "
+ "reset mdrun counters at step " GMX_PRId64 ". Try "
+ "resetting counters later in the run, e.g. with gmx "
+ "mdrun -resetstep.", step);
+ }
reset_all_counters(fplog, cr, step, &step_rel, ir, wcycle, nrnb, walltime_accounting,
use_GPU(fr->nbv) ? fr->nbv : NULL);
wcycle_set_reset_counters(wcycle, -1);
@@ -1859,7 +1878,9 @@ double 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);
- bResetCountersHalfMaxH = FALSE;
+ /* If mdrun -maxh -resethway was active, it can only trigger once */
+ bResetCountersHalfMaxH = FALSE; /* TODO move this to where gs.sig[eglsRESETCOUNTERS] is set */
+ /* Reset can only happen once, so clear the triggering flag. */
gs.set[eglsRESETCOUNTERS] = 0;
}
diff --git a/patches/gromacs-5.1.0.diff/src/programs/mdrun/md.cpp.preplumed b/patches/gromacs-5.1.2.diff/src/programs/mdrun/md.cpp.preplumed
similarity index 98%
rename from patches/gromacs-5.1.0.diff/src/programs/mdrun/md.cpp.preplumed
rename to patches/gromacs-5.1.2.diff/src/programs/mdrun/md.cpp.preplumed
index f1372731958a627d77d317fab8fa1976527874a6..4f33d897e950a2793d76d963e8451ed0d6c8dd96 100644
--- a/patches/gromacs-5.1.0.diff/src/programs/mdrun/md.cpp.preplumed
+++ b/patches/gromacs-5.1.2.diff/src/programs/mdrun/md.cpp.preplumed
@@ -229,7 +229,7 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
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;
+ pme_load_balancing_t *pme_loadbal = NULL;
gmx_bool bPMETune = FALSE;
gmx_bool bPMETunePrinting = FALSE;
@@ -1333,6 +1333,7 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
if (bResetCountersHalfMaxH && MASTER(cr) &&
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;
}
@@ -1747,10 +1748,28 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
step_rel++;
}
+ /* TODO make a counter-reset module */
+ /* 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)
{
- /* Reset all the counters related to performance over the run */
+ if (pme_loadbal_is_active(pme_loadbal))
+ {
+ /* Do not permit counter reset while PME load
+ * balancing is active. The only purpose for resetting
+ * counters is to measure reliable performance data,
+ * and that can't be done before balancing
+ * completes.
+ *
+ * TODO consider fixing this by delaying the reset
+ * until after load balancing completes,
+ * e.g. https://gerrit.gromacs.org/#/c/4964/2 */
+ gmx_fatal(FARGS, "PME tuning was still active when attempting to "
+ "reset mdrun counters at step " GMX_PRId64 ". Try "
+ "resetting counters later in the run, e.g. with gmx "
+ "mdrun -resetstep.", step);
+ }
reset_all_counters(fplog, cr, step, &step_rel, ir, wcycle, nrnb, walltime_accounting,
use_GPU(fr->nbv) ? fr->nbv : NULL);
wcycle_set_reset_counters(wcycle, -1);
@@ -1761,7 +1780,9 @@ double 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);
- bResetCountersHalfMaxH = FALSE;
+ /* If mdrun -maxh -resethway was active, it can only trigger once */
+ bResetCountersHalfMaxH = FALSE; /* TODO move this to where gs.sig[eglsRESETCOUNTERS] is set */
+ /* Reset can only happen once, so clear the triggering flag. */
gs.set[eglsRESETCOUNTERS] = 0;
}
diff --git a/patches/gromacs-5.1.0.diff/src/programs/mdrun/mdrun.cpp b/patches/gromacs-5.1.2.diff/src/programs/mdrun/mdrun.cpp
similarity index 100%
rename from patches/gromacs-5.1.0.diff/src/programs/mdrun/mdrun.cpp
rename to patches/gromacs-5.1.2.diff/src/programs/mdrun/mdrun.cpp
diff --git a/patches/gromacs-5.1.0.diff/src/programs/mdrun/mdrun.cpp.preplumed b/patches/gromacs-5.1.2.diff/src/programs/mdrun/mdrun.cpp.preplumed
similarity index 100%
rename from patches/gromacs-5.1.0.diff/src/programs/mdrun/mdrun.cpp.preplumed
rename to patches/gromacs-5.1.2.diff/src/programs/mdrun/mdrun.cpp.preplumed
diff --git a/patches/gromacs-5.1.0.diff/src/programs/mdrun/repl_ex.cpp b/patches/gromacs-5.1.2.diff/src/programs/mdrun/repl_ex.cpp
similarity index 100%
rename from patches/gromacs-5.1.0.diff/src/programs/mdrun/repl_ex.cpp
rename to patches/gromacs-5.1.2.diff/src/programs/mdrun/repl_ex.cpp
diff --git a/patches/gromacs-5.1.0.diff/src/programs/mdrun/repl_ex.cpp.preplumed b/patches/gromacs-5.1.2.diff/src/programs/mdrun/repl_ex.cpp.preplumed
similarity index 100%
rename from patches/gromacs-5.1.0.diff/src/programs/mdrun/repl_ex.cpp.preplumed
rename to patches/gromacs-5.1.2.diff/src/programs/mdrun/repl_ex.cpp.preplumed