Fix memory leaks

[richfitz]

valgrind is reporting leaks

[richfitz]

The code

  gen <- odin({
    initial(y[, ]) <- 1
    deriv(y[, ]) <- y[i, j] * r[i, j]
    dim(y) <- c(2, 3)
    dim(r) <- c(2, 3)
    r[, ] <- user()
  })

generates the code:

SEXP odin_create(SEXP user) {
  odin_internal *internal = (odin_internal*) Calloc(1, odin_internal);
  internal->initial_y = NULL;
  internal->r = NULL;
  internal->dim_r_1 = 2;
  internal->dim_r_2 = 3;
  internal->dim_y_1 = 2;
  internal->dim_y_2 = 3;
  internal->dim_r = internal->dim_r_1 * internal->dim_r_2;
  internal->dim_y = internal->dim_y_1 * internal->dim_y_2;
  Free(internal->initial_y);
  internal->initial_y = (double*) Calloc(internal->dim_y, double);
  Free(internal->r);
  internal->r = (double*) Calloc(internal->dim_r, double);
  for (int i = 1; i <= internal->dim_y_1; ++i) {
    for (int j = 1; j <= internal->dim_y_2; ++j) {
      internal->initial_y[i - 1 + internal->dim_y_1 * (j - 1)] = 1;
    }
  }
  internal->r = NULL;
  SEXP ptr = PROTECT(R_MakeExternalPtr(internal, R_NilValue, R_NilValue));
  R_RegisterCFinalizer(ptr, odin_finalise);
  UNPROTECT(1);
  return ptr;
}

We don't want to add the lines

  Free(internal->r);
  internal->r = (double*) Calloc(internal->dim_r, double);

[richfitz]

This model

  gen <- odin({
    ylag <- delay(y, 3, 2)
    initial(y) <- 0.5
    deriv(y) <- 0.2 * ylag * 1 / (1 + ylag^10) - 0.1 * y
    output(ylag) <- ylag
    config(base) <- "delay3"
  })

generates a finalise/create pair that look like

void delay3_finalise(SEXP internal_p) {
  delay3_internal *internal = delay3_get_internal(internal_p, 0);
  if (internal_p) {
    Free(internal);
    R_ClearExternalPtr(internal_p);
  }
}
SEXP delay3_create(SEXP user) {
  delay3_internal *internal = (delay3_internal*) Calloc(1, delay3_internal);
  internal->delay_index_ylag = NULL;
  internal->delay_state_ylag = NULL;
  internal->dim_delay_ylag = 1;
  internal->initial_y = 0.5;
  Free(internal->delay_index_ylag);
  internal->delay_index_ylag = Calloc(internal->dim_delay_ylag, int);
  Free(internal->delay_state_ylag);
  internal->delay_state_ylag = Calloc(internal->dim_delay_ylag, double);
  internal->delay_index_ylag[0] = 0;
  SEXP ptr = PROTECT(R_MakeExternalPtr(internal, R_NilValue, R_NilValue));
  R_RegisterCFinalizer(ptr, delay3_finalise);
  UNPROTECT(1);
  return ptr;
}

with the Free statement missing for delay_index_ylag and delay_state_ylag

[richfitz]

The only one I see now is clearly from R itself:

==28409== 48 (40 direct, 8 indirect) bytes in 1 blocks are definitely lost in loss record 40 of 3,072
==28409==    at 0x4C2FB55: calloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==28409==    by 0x150FF921: value_alloc (yajl_tree.c:69)
==28409==    by 0x150FFBCC: handle_string (yajl_tree.c:282)
==28409==    by 0x150FF5C0: yajl_do_parse (yajl_parser.c:243)
==28409==    by 0x150FFFFE: yajl_tree_parse (yajl_tree.c:441)
==28409==    by 0x150FAA5D: R_parse (parse.c:34)
==28409==    by 0x4F61E50: ??? (in /usr/lib/R/lib/libR.so)
==28409==    by 0x4F6B7AF: Rf_eval (in /usr/lib/R/lib/libR.so)
==28409==    by 0x4F6D110: ??? (in /usr/lib/R/lib/libR.so)
==28409==    by 0x4F62E46: ??? (in /usr/lib/R/lib/libR.so)
==28409==    by 0x4F6B7AF: Rf_eval (in /usr/lib/R/lib/libR.so)
==28409==    by 0x4F6D110: ??? (in /usr/lib/R/lib/libR.so)