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Make rxode2 more thread safe #992

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e645f29
Replace shared op->badSolve reads with per-individual localBadSolve f…
billdenney Mar 2, 2026
dd0035b
Use atomic writes for op->badSolve and op->naTime in parallel regions
billdenney Mar 3, 2026
c46d617
Replace Rf_errorcall in _getDur with NA_REAL return and badSolve flag
billdenney Mar 3, 2026
39d9f44
Mark abort flag as volatile in parallel solve loops
billdenney Mar 3, 2026
caf7498
Fix rx_get_thread off-by-one and fallback to prevent thread collisions
billdenney Mar 3, 2026
dd70fea
Refactor linCmtB to per-thread vector for thread safety
billdenney Mar 3, 2026
4422d42
Refactor DOP853 solver to use context struct for thread safety
billdenney Mar 3, 2026
a7e3241
Merge main into parallel-updates
billdenney Mar 3, 2026
97671af
Fix linCmtB macro collision: use J macro instead of lcb.J
billdenney Mar 3, 2026
0e1db6a
Update src/linCmt.cpp
mattfidler Mar 16, 2026
c58e252
Initial plan
Copilot Mar 16, 2026
59e4356
Initial plan
Copilot Mar 16, 2026
0d4f8a2
Update dop853.h documentation to match thread-safe refactoring
Copilot Mar 16, 2026
512b2fc
Preserve first error's diagnostic code in op->naTime using read-check…
Copilot Mar 16, 2026
48a3212
Merge pull request #994 from nlmixr2/copilot/sub-pr-992
mattfidler Mar 17, 2026
c64cc5a
Merge pull request #995 from nlmixr2/copilot/sub-pr-992-again
mattfidler Mar 17, 2026
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52 changes: 40 additions & 12 deletions inst/include/rxode2parseGetTime.h
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Original file line number Diff line number Diff line change
Expand Up @@ -38,9 +38,16 @@ static inline double getLag(rx_solving_options_ind *ind, int id, int cmt, double
}
double ret = LAG(id, cmt, time);
if (ISNA(ret)) {
op->badSolve=1;
if (op->naTime == 0) {
op->naTime = 1 + 10*cmt;
int newBadSolve = 1;
#pragma omp atomic write
op->badSolve = newBadSolve;
int curNaTime;
#pragma omp atomic read
curNaTime = op->naTime;
if (curNaTime == 0) {
int newNaTime = 1 + 10*cmt;
#pragma omp atomic write
op->naTime = newNaTime;
}
}
return ret;
Expand All @@ -51,9 +58,16 @@ static inline double getRate(rx_solving_options_ind *ind, int id, int cmt, doubl
returnBadTime(t);
double ret = RATE(id, cmt, dose, t);
if (ISNA(ret)){
op->badSolve=1;
if (op->naTime == 0) {
op->naTime = 2 + 10*cmt;
int newBadSolve = 1;
#pragma omp atomic write
op->badSolve = newBadSolve;
int curNaTime;
#pragma omp atomic read
curNaTime = op->naTime;
if (curNaTime == 0) {
int newNaTime = 2 + 10*cmt;
#pragma omp atomic write
op->naTime = newNaTime;
}
}
return ret;
Expand All @@ -65,9 +79,16 @@ static inline double getDur(rx_solving_options_ind *ind, int id, int cmt, double
if (ISNA(t)) return t;
double ret = DUR(id, cmt, dose, t);
if (ISNA(ret)){
op->badSolve=1;
if (op->naTime == 0) {
op->naTime = 3 + 10*cmt;
int newBadSolve = 1;
#pragma omp atomic write
op->badSolve = newBadSolve;
int curNaTime;
#pragma omp atomic read
curNaTime = op->naTime;
if (curNaTime == 0) {
int newNaTime = 3 + 10*cmt;
#pragma omp atomic write
op->naTime = newNaTime;
}
}
return ret;
Expand Down Expand Up @@ -340,9 +361,16 @@ static inline double handleInfusionItem(int idx, rx_solve *rx, rx_solving_option
ind->idx = oIdx;
if (ISNA(f)){
rx_solving_options *op = &op_global;
op->badSolve=1;
if (op->naTime == 0) {
op->naTime = 4 + 10*ind->cmt;
int newBadSolve = 1;
#pragma omp atomic write
op->badSolve = newBadSolve;
int curNaTime;
#pragma omp atomic read
curNaTime = op->naTime;
if (curNaTime == 0) {
int newNaTime = 4 + 10*ind->cmt;
#pragma omp atomic write
op->naTime = newNaTime;
}
}
double durOld = (getAllTimes(ind, ind->idose[infEidx]) -
Expand Down
77 changes: 42 additions & 35 deletions inst/include/rxode2parseHandleEvid.h
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Original file line number Diff line number Diff line change
Expand Up @@ -285,8 +285,17 @@ static inline double getAmt(rx_solving_options_ind *ind, int id, int cmt,
double ret = AMT(id, cmt, dose, t, y);
if (ISNA(ret)){
rx_solving_options *op = &op_global;
op->badSolve=1;
op->naTime = 5 + 10*cmt;
int newBadSolve = 1;
#pragma omp atomic write
op->badSolve = newBadSolve;
int curNaTime;
#pragma omp atomic read
curNaTime = op->naTime;
if (curNaTime == 0) {
int newNaTime = 5 + 10*cmt;
#pragma omp atomic write
op->naTime = newNaTime;
}
}
return ret;
}
Expand All @@ -309,20 +318,22 @@ static inline int pushIgnoredDose(int doseIdx, rx_solving_options_ind *ind) {
}
if (ind->ignoredDosesN[0]+1 >= ind->ignoredDosesAllocN[0]) {
rx_solving_options *op = &op_global;
int allocFailed = 0;
#pragma omp critical
{
int *tmpI = (int*)realloc(ind->ignoredDoses, (ind->ignoredDosesN[0]+1+EVID_EXTRA_SIZE)*sizeof(int));
if (tmpI == NULL) {
op->badSolve = 1;
// return 0;
allocFailed = 1;
} else {
ind->ignoredDoses = tmpI;
ind->ignoredDosesAllocN[0] = (ind->ignoredDosesN[0]+1+EVID_EXTRA_SIZE);
re = 1;
}
}
if (op->badSolve) {
return 0; // don't continue if we have a bad solve.
if (allocFailed) {
#pragma omp atomic write
op->badSolve = 1;
return 0;
}
}
ind->ignoredDoses[ind->ignoredDosesN[0]] = doseIdx;
Expand All @@ -334,19 +345,21 @@ static inline int pushPendingDose(int doseIdx, rx_solving_options_ind *ind) {
int re = 0;
if (ind->pendingDosesN[0]+1 >= ind->pendingDosesAllocN[0]) {
rx_solving_options *op = &op_global;
int allocFailed = 0;
#pragma omp critical
{
int *tmpI = (int*)realloc(ind->pendingDoses, (ind->pendingDosesN[0]+1+EVID_EXTRA_SIZE)*sizeof(int));
if (tmpI == NULL) {
op->badSolve = 1;
//return 0;
allocFailed = 1;
} else {
ind->pendingDoses = tmpI;
ind->pendingDosesAllocN[0] = (ind->pendingDosesN[0]+1+EVID_EXTRA_SIZE);
re = 1;
}
}
if (op->badSolve == 1) {
if (allocFailed) {
#pragma omp atomic write
op->badSolve = 1;
return 0;
}
}
Expand All @@ -361,32 +374,29 @@ static inline int pushDosingEvent(double time, double amt, int evid,
int re = 0;
if (ind->extraDoseN[0]+1 >= ind->extraDoseAllocN[0]) {
rx_solving_options *op = &op_global;
int allocFailed = 0; // 0=ok, 1=partial alloc, -1=first alloc failed
#pragma omp critical
{
int *tmpI = (int*)realloc(ind->extraDoseTimeIdx, (ind->extraDoseN[0]+1+EVID_EXTRA_SIZE)*sizeof(int));
if (tmpI == NULL) {
op->badSolve = -1;
// return 0;
allocFailed = -1;
} else {
ind->extraDoseTimeIdx = tmpI;

tmpI = (int*)realloc(ind->extraDoseEvid, (ind->extraDoseN[0]+1+EVID_EXTRA_SIZE)*sizeof(int));
if (tmpI == NULL) {
op->badSolve = 1;
// return 1;
allocFailed = 1;
} else {
ind->extraDoseEvid = tmpI;
double * tmpD = (double*)realloc(ind->extraDoseTime, (ind->extraDoseN[0]+1+EVID_EXTRA_SIZE)*sizeof(double));
if (tmpD == NULL) {
op->badSolve = 1;
//return 1;
allocFailed = 1;
} else {
ind->extraDoseTime = tmpD;

tmpD = (double*)realloc(ind->extraDoseDose, (ind->extraDoseN[0]+1+EVID_EXTRA_SIZE)*sizeof(double));
if (tmpD == NULL) {
op->badSolve = 1;
//return 1;
allocFailed = 1;
} else {
ind->extraDoseDose = tmpD;

Expand All @@ -397,11 +407,11 @@ static inline int pushDosingEvent(double time, double amt, int evid,
}
}
}
if (op->badSolve == 1) {
return 1;
} else if (op->badSolve == -1) {
op->badSolve = 1; // set to bad solve.
return 0;
if (allocFailed != 0) {
int newBadSolve = 1;
#pragma omp atomic write
op->badSolve = newBadSolve;
return (allocFailed == 1) ? 1 : 0;
}
}
ind->extraDoseTimeIdx[ind->extraDoseN[0]] = ind->extraDoseN[0];
Expand All @@ -419,33 +429,30 @@ static inline int pushUniqueDosingEvent(double time, double amt, int evid,
int re = 0;
if (ind->extraDoseN[0]+1 >= ind->extraDoseAllocN[0]) {
rx_solving_options *op = &op_global;
int allocFailed = 0; // 0=ok, 1=partial alloc, -1=first alloc failed
#pragma omp critical
{
int *tmpI = (int*)realloc(ind->extraDoseTimeIdx, (ind->extraDoseN[0]+1+EVID_EXTRA_SIZE)*sizeof(int));
if (tmpI == NULL) {
op->badSolve = -1;
// return 0;
allocFailed = -1;
} else {
ind->extraDoseTimeIdx = tmpI;

tmpI = (int*)realloc(ind->extraDoseEvid, (ind->extraDoseN[0]+1+EVID_EXTRA_SIZE)*sizeof(int));
if (tmpI == NULL) {
op->badSolve = 1;
// return 1;
allocFailed = 1;
} else {
ind->extraDoseEvid = tmpI;

double * tmpD = (double*)realloc(ind->extraDoseTime, (ind->extraDoseN[0]+1+EVID_EXTRA_SIZE)*sizeof(double));
if (tmpD == NULL) {
op->badSolve = 1;
//return 1;
allocFailed = 1;
} else {
ind->extraDoseTime = tmpD;

tmpD = (double*)realloc(ind->extraDoseDose, (ind->extraDoseN[0]+1+EVID_EXTRA_SIZE)*sizeof(double));
if (tmpD == NULL) {
op->badSolve = 1;
// return 1;
allocFailed = 1;
} else {
ind->extraDoseDose = tmpD;

Expand All @@ -455,11 +462,11 @@ static inline int pushUniqueDosingEvent(double time, double amt, int evid,
}
}
}
if (op->badSolve == 1) {
return 1; // don't continue if we have a bad solve.
} else if (op->badSolve == -1) {
op->badSolve = 1; // set to bad solve.
return 0;
if (allocFailed != 0) {
int newBadSolve = 1;
#pragma omp atomic write
op->badSolve = newBadSolve;
return (allocFailed == 1) ? 1 : 0;
}
re = 1;
}
Expand Down
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