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chore: The from and to components of the R representation of an igraph objects use ALTREP to avoid unnecessary materialization #804

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Merged
krlmlr merged 9 commits into from
May 27, 2023
Merged

chore: The from and to components of the R representation of an igraph objects use ALTREP to avoid unnecessary materialization #804

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1d6c6d5
`from` altrep vector
Antonov548 May 21, 2023
041354e
`to` altrep vector
Antonov548 May 21, 2023
ab9ea7f
add `igraph.verbose` option
Antonov548 May 22, 2023
e20b990
fix spaces
Antonov548 May 22, 2023
d650420
Merge remote-tracking branch 'origin/main' into from-to-altrep
Antonov548 May 22, 2023
d02f749
Update src/rinterface_extra.c
Antonov548 May 23, 2023
a8853f6
add external pointer logs
Antonov548 May 25, 2023
79674da
Merge branch 'main' into from-to-altrep
krlmlr May 27, 2023
ec99408
Require R 3.5.0 for ALTREP
krlmlr May 27, 2023
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ URL: https://r.igraph.org/, https://igraph.org/,
BugReports: https://github.com/igraph/rigraph/issues
Depends:
methods,
R (>= 3.0.2)
R (>= 3.5.0)
Imports:
cli,
graphics,
Expand Down
2 changes: 2 additions & 0 deletions src/init.cpp
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Expand Up @@ -3,9 +3,11 @@
#include "igraph.h"

extern "C" void R_igraph_init_handlers(DllInfo* dll);
extern "C" void R_igraph_init_vector_class(DllInfo* dll);

[[cpp11::init]]
void igraph_init(DllInfo* dll)
{
R_igraph_init_handlers(dll);
R_igraph_init_vector_class(dll);
}
77 changes: 65 additions & 12 deletions src/rinterface_extra.c
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Expand Up @@ -34,6 +34,7 @@
#include <Rinternals.h>
#include <Rdefines.h>
#include <R_ext/Visibility.h>
#include <R_ext/Altrep.h>

#include "rinterface.h"
#include "rrandom.h"
Expand Down Expand Up @@ -2547,6 +2548,59 @@ int R_igraph_status_handler(const char *message, void *data) {
return 0;
}

static R_xlen_t R_igraph_altrep_length(SEXP vec) {
SEXP xp=Rf_findVar(Rf_install("igraph"), R_altrep_data1(vec));
igraph_t *g=(igraph_t*)(R_ExternalPtrAddr(xp));
return igraph_ecount(g);
}

static void *R_igraph_altrep_from(SEXP vec, Rboolean writeable) {
SEXP data=R_altrep_data2(vec);
if (data == R_NilValue) {
R_igraph_status_handler("Materializing 'from' vector.\n", NULL);
SEXP xp=Rf_findVar(Rf_install("igraph"), R_altrep_data1(vec));
igraph_t *g=(igraph_t*)(R_ExternalPtrAddr(xp));

long int no_of_edges=igraph_ecount(g);
data=NEW_NUMERIC(no_of_edges);
memcpy(REAL(data), g->from.stor_begin, sizeof(igraph_real_t)*(size_t) no_of_edges);
R_set_altrep_data2(vec, data);
}

return REAL(data);
}

static void *R_igraph_altrep_to(SEXP vec, Rboolean writeable) {
SEXP data=R_altrep_data2(vec);
if (data == R_NilValue) {
R_igraph_status_handler("Materializing 'to' vector.\n", NULL);

SEXP xp=Rf_findVar(Rf_install("igraph"), R_altrep_data1(vec));
igraph_t *g=(igraph_t*)(R_ExternalPtrAddr(xp));

long int no_of_edges=igraph_ecount(g);
data=NEW_NUMERIC(no_of_edges);
memcpy(REAL(data), g->to.stor_begin, sizeof(igraph_real_t)*(size_t) no_of_edges);
R_set_altrep_data2(vec, data);
}

return REAL(data);
}

static R_altrep_class_t R_igraph_altrep_from_class;
static R_altrep_class_t R_igraph_altrep_to_class;

void R_igraph_init_vector_class(DllInfo *dll) {
R_igraph_altrep_from_class=R_make_altreal_class("igraph_from", "base", dll);
R_igraph_altrep_to_class=R_make_altreal_class("igraph_to", "base", dll);

R_set_altrep_Length_method(R_igraph_altrep_from_class, R_igraph_altrep_length);
R_set_altvec_Dataptr_method(R_igraph_altrep_from_class, R_igraph_altrep_from);

R_set_altrep_Length_method(R_igraph_altrep_to_class, R_igraph_altrep_length);
R_set_altvec_Dataptr_method(R_igraph_altrep_to_class, R_igraph_altrep_to);
}

void R_igraph_init_handlers(DllInfo *dll) {
igraph_rng_R_install();

Expand Down Expand Up @@ -2859,6 +2913,7 @@ SEXP R_igraph_graph_env(SEXP graph) {
}

static void free_graph(SEXP xp) {
R_igraph_status_handler("Free graph external pointer.\n", NULL);
igraph_t *graph = (igraph_t*)(R_ExternalPtrAddr(xp));
igraph_vector_destroy(&graph->from);
igraph_vector_destroy(&graph->to);
Expand All @@ -2875,6 +2930,8 @@ void R_igraph_set_pointer(SEXP result, const igraph_t* graph) {
igraph_t *pgraph = IGRAPH_CALLOC(1, igraph_t);
*pgraph = *graph;

R_igraph_status_handler("Make graph external pointer.\n", NULL);

SEXP l1 = PROTECT(Rf_install("igraph")); px++;
SEXP l2 = PROTECT(R_MakeExternalPtr(pgraph, R_NilValue, R_NilValue)); px++;
Rf_defineVar(l1, l2, R_igraph_graph_env(result));
Expand All @@ -2889,6 +2946,8 @@ void R_igraph_restore_pointer(SEXP graph) {
igraph_integer_t n=REAL(VECTOR_ELT(graph, igraph_t_idx_n))[0];
igraph_bool_t directed=LOGICAL(VECTOR_ELT(graph, igraph_t_idx_directed))[0];

R_igraph_status_handler("Restore graph external pointer.\n", NULL);

igraph_vector_t from;
R_SEXP_to_vector(VECTOR_ELT(graph, igraph_t_idx_from), &from);

Expand All @@ -2898,8 +2957,7 @@ void R_igraph_restore_pointer(SEXP graph) {
igraph_integer_t i, s=igraph_vector_size(&from);
igraph_vector_init(&v, s*2);

for (i = 0; i < s; ++i)
{
for (i = 0; i < s; ++i) {
igraph_vector_set(&v, i*2, VECTOR(from)[i]);
igraph_vector_set(&v, i*2+1, VECTOR(to)[i]);
}
Expand Down Expand Up @@ -2952,10 +3010,7 @@ igraph_bool_t R_igraph_get_directed(SEXP graph) {
}

void R_igraph_set_from(SEXP rgraph, const igraph_t *graph) {
long int no_of_edges=igraph_ecount(graph);
SET_VECTOR_ELT(rgraph, igraph_t_idx_from, NEW_NUMERIC(no_of_edges));
memcpy(REAL(VECTOR_ELT(rgraph, igraph_t_idx_from)), graph->from.stor_begin,
sizeof(igraph_real_t)*(size_t) no_of_edges);
SET_VECTOR_ELT(rgraph, igraph_t_idx_from, R_new_altrep(R_igraph_altrep_from_class, R_igraph_graph_env(rgraph), R_NilValue));
}

void R_igraph_get_from(SEXP graph, igraph_vector_t* from) {
Expand All @@ -2964,10 +3019,7 @@ void R_igraph_get_from(SEXP graph, igraph_vector_t* from) {
}

void R_igraph_set_to(SEXP rgraph, const igraph_t *graph) {
long int no_of_edges=igraph_ecount(graph);
SET_VECTOR_ELT(rgraph, igraph_t_idx_to, NEW_NUMERIC(no_of_edges));
memcpy(REAL(VECTOR_ELT(rgraph, igraph_t_idx_to)), graph->to.stor_begin,
sizeof(igraph_real_t)*(size_t) no_of_edges);
SET_VECTOR_ELT(rgraph, igraph_t_idx_to, R_new_altrep(R_igraph_altrep_to_class, R_igraph_graph_env(rgraph), R_NilValue));
}

void R_igraph_get_to(SEXP graph, igraph_vector_t* to) {
Expand Down Expand Up @@ -3004,8 +3056,6 @@ SEXP R_igraph_to_SEXP(const igraph_t *graph) {
PROTECT(result=NEW_LIST(igraph_t_idx_max));
R_igraph_set_n(result, graph);
R_igraph_set_directed(result, graph);
R_igraph_set_from(result, graph);
R_igraph_set_to(result, graph);

SET_CLASS(result, Rf_ScalarString(Rf_mkChar("igraph")));

Expand All @@ -3017,6 +3067,9 @@ SEXP R_igraph_to_SEXP(const igraph_t *graph) {
SET_VECTOR_ELT(result, igraph_t_idx_env, R_NilValue);
R_igraph_add_env(result);
R_igraph_set_pointer(result, graph);
/* Set from and to requires environment */
R_igraph_set_from(result, graph);
R_igraph_set_to(result, graph);

UNPROTECT(1);
return result;
Expand Down