poped - unstable R sessions when using analytical solutions

[TheoPapath]

Not sure if this is an issue or not, but I have seen that for most (all?) problems that are based on analytical solutions, the R session is crashing. I cannot always replicate this from my end.

[mattfidler]

Unless it can be replicated, I cannot fix it 😦

[mattfidler]

If you have code that I can look at where this is occurring, then I can try to fix this.

[TheoPapath]

yes, please see the code example here: https://github.com/nlmixr2/babelmixr2/blob/poped-examples-tp/inst/poped/ex.11.PK.prior.babelmixr2.R

[mattfidler]

Thread 1 "R" received signal SIGSEGV, Segmentation fault.
rx_811c6d6fa0c165eef32ef80e785e6f99__calc_lhs (_cSub=0, __t=1, __zzStateVar__=<optimized out>, _lhs=0x7fffffff13f0) at rx_811c6d6fa0c165eef32ef80e785e6f99_.c:695
695   _update_par_ptr(__t, _cSub, _solveData, _idx);
(gdb) bt
#0  rx_811c6d6fa0c165eef32ef80e785e6f99__calc_lhs (_cSub=0, __t=1, __zzStateVar__=<optimized out>, _lhs=0x7fffffff13f0)
    at rx_811c6d6fa0c165eef32ef80e785e6f99_.c:695
#1  0x00007fffed3b2382 in Rcpp::Vector<10, Rcpp::PreserveStorage>::~Vector (this=0x555560a72440, __in_chrg=<optimized out>)
    at /usr/lib/R/site-library/Rcpp/include/Rcpp/vector/Vector.h:28

[mattfidler]

These models calculate the lhs correctly:

> babel.db$babelmixr2$modelMT
rxode2 NA model named rx_9039cf95c5540149d4bcde9607d1ce7e model (✔ ready).
$params: rx__tV, rx__tKa, rx__tCl, rx__eta.v, rx__eta.ka, rx__eta.cl, TAU, DOSE, rxXt_1, rxXt_2, rxXt_3, rxXt_4, rxXt_5
$lhs: rx_pred_, rx_r_
> summary(babel.db$babelmixr2$modelMT)
rxode2 NA model named rx_9039cf95c5540149d4bcde9607d1ce7e model (✔ ready).
DLL: /tmp/RtmpHOcu8A/rxode2/rx_9039cf95c5540149d4bcde9607d1ce7e__.rxd/rx_9039cf95c5540149d4bcde9607d1ce7e_.so
NULL

Calculated Variables:
[1] "rx_pred_" "rx_r_"
── rxode2 Model Syntax ──
rxode2({
    param(rx__tV, rx__tKa, rx__tCl, rx__eta.v, rx__eta.ka, rx__eta.cl,
        TAU, DOSE, rxXt_1, rxXt_2, rxXt_3, rxXt_4, rxXt_5)
    V ~ rx__tV * exp(rx__eta.v)
    KA ~ rx__tKa * exp(rx__eta.ka)
    CL ~ rx__tCl * exp(rx__eta.cl)
    Favail ~ 0.9
    N ~ floor(t/TAU) + 1
    y ~ (DOSE * Favail/V) * (KA/(KA - CL/V)) * (exp(-CL/V * (t -
        (N - 1) * TAU)) * (1 - exp(-N * CL/V * TAU))/(1 - exp(-CL/V *
        TAU)) - exp(-KA * (t - (N - 1) * TAU)) * (1 - exp(-N *
        KA * TAU))/(1 - exp(-KA * TAU)))
    rx_yj_ ~ 2
    rx_lambda_ ~ 1
    rx_low_ ~ 0
    rx_hi_ ~ 1
    rx_pred_f_ ~ y
    rx_pred_ = rx_pred_f_
    rx_r_ = (0.00223606797749979)^2 + (rx_pred_f_)^2 * (0.2)^2
    mtime(rxXt_1_v) ~ rxXt_1
    mtime(rxXt_2_v) ~ rxXt_2
    mtime(rxXt_3_v) ~ rxXt_3
    mtime(rxXt_4_v) ~ rxXt_4
    mtime(rxXt_5_v) ~ rxXt_5
})
> summary(babel.db$babelmixr2$modelF)
rxode2 NA model named rx_4726b1274f5b3a8bea20f8e946050017 model (✔ ready).
DLL: /tmp/RtmpHOcu8A/rxode2/rx_4726b1274f5b3a8bea20f8e946050017__.rxd/rx_4726b1274f5b3a8bea20f8e946050017_.so
NULL

Calculated Variables:
[1] "rx_pred_" "rx_r_"
── rxode2 Model Syntax ──
rxode2({
    param(rx__tV, rx__tKa, rx__tCl, rx__eta.v, rx__eta.ka, rx__eta.cl,
        TAU, DOSE)
    V ~ rx__tV * exp(rx__eta.v)
    KA ~ rx__tKa * exp(rx__eta.ka)
    CL ~ rx__tCl * exp(rx__eta.cl)
    Favail ~ 0.9
    N ~ floor(t/TAU) + 1
    y ~ (DOSE * Favail/V) * (KA/(KA - CL/V)) * (exp(-CL/V * (t -
        (N - 1) * TAU)) * (1 - exp(-N * CL/V * TAU))/(1 - exp(-CL/V *
        TAU)) - exp(-KA * (t - (N - 1) * TAU)) * (1 - exp(-N *
        KA * TAU))/(1 - exp(-KA * TAU)))
    rx_yj_ ~ 2
    rx_lambda_ ~ 1
    rx_low_ ~ 0
    rx_hi_ ~ 1
    rx_pred_f_ ~ y
    rx_pred_ = rx_pred_f_
    rx_r_ = (0.00223606797749979)^2 + (rx_pred_f_)^2 * (0.2)^2
})
>

[mattfidler]

I haven't seen this before, I may be out of my depth here:

vex amd64->IR: unhandled instruction bytes: 0x7 0x0 0x0 0x0 0x0 0x58 0x80 0x72 0x1E 0x0
vex amd64->IR:   REX=0 REX.W=0 REX.R=0 REX.X=0 REX.B=0
vex amd64->IR:   VEX=0 VEX.L=0 VEX.nVVVV=0x0 ESC=NONE
vex amd64->IR:   PFX.66=0 PFX.F2=0 PFX.F3=0
==14801== Invalid read of size 1
==14801==    at 0x1E7280E8: ???
==14801==    by 0x1C938ED0: popedSolveIdME2(Rcpp::Vector<14, Rcpp::PreserveStorage>&, Rcpp::Vector<14, Rcpp::PreserveStorage>&, Rcpp::Vector<14, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, int, int, int) (poped.cpp:624)
==14801==    by 0x1C91E605: _babelmixr2_popedSolveIdME2 (RcppExports.cpp:139)
==14801==    by 0x4958237: ??? (in /usr/lib/R/lib/libR.so)
==14801==    by 0x495888C: ??? (in /usr/lib/R/lib/libR.so)
==14801==    by 0x49AFB97: Rf_eval (in /usr/lib/R/lib/libR.so)
==14801==    by 0x49B3237: ??? (in /usr/lib/R/lib/libR.so)
==14801==    by 0x49AF935: Rf_eval (in /usr/lib/R/lib/libR.so)
==14801==    by 0x49B16DE: ??? (in /usr/lib/R/lib/libR.so)
==14801==    by 0x49B24C6: ??? (in /usr/lib/R/lib/libR.so)
==14801==    by 0x49AF63B: Rf_eval (in /usr/lib/R/lib/libR.so)
==14801==    by 0x49B4751: ??? (in /usr/lib/R/lib/libR.so)
==14801==  Address 0x0 is not stack'd, malloc'd or (recently) free'd
==14801==

 *** caught segfault ***
address (nil), cause 'memory not mapped'

[mattfidler]

It isn't the analytical solutions; its the switching between 2 poped databases. This should be fixed by #133