Allocating many small objects triggers numerous garbage collections as R
grows its memory, seriously degrading performance. The specific use case
is in creating a STRSXP of several 1,000,000's of elements of 60-100
characters each; a simplified illustration understating the effects
(because there is initially little to garbage collect, in contrast to an
R session with several packages loaded) is below.
A simple solution is to provide a mechanism for the C programmer to
request sufficient memory in advance. R_gc_needed might also be re-used
at two other locations in memory.c (2221 and 2361) and could be exposed
at the R level via a new argument, with default 0, to gc().
%> time R --vanilla -e "dyn.load('gc.so'); x = .Call('doit', 1000000,
FALSE)"
> dyn.load('gc.so'); x = .Call('doit', 1000000, FALSE)
real 0m9.865s
user 0m9.697s
sys 0m0.146s
%> time R --vanilla -e "dyn.load('gc.so'); x = .Call('doit', 1000000,
TRUE)"
> dyn.load('gc.so'); x = .Call('doit', 1000000, TRUE)
real 0m6.952s
user 0m6.802s
sys 0m0.132s
This is the test code
#include <stdio.h>
#include "Rdefines.h"
SEXP doit(SEXP len, SEXP needed)
{
int i, n = asInteger(len);
char **s = Calloc(n, char *);
SEXP ans;
for (i = 0; i < n; ++i) {
s[i] = Calloc(80, char);
sprintf(s[i], "%78d", i);
}
if (asLogical(needed))
R_gc_needed(80 * n);
PROTECT(ans = allocVector(STRSXP, n));
for (i = 0; i < n; ++i)
SET_STRING_ELT(ans, i, mkChar(s[i]));
UNPROTECT(1);
return ans;
}
and a patch
Index: src/include/R_ext/Memory.h
===================================================================
--- src/include/R_ext/Memory.h (revision 57169)
+++ src/include/R_ext/Memory.h (working copy)
@@ -36,6 +36,7 @@
void vmaxset(const void *);
void R_gc(void);
+void R_gc_needed(size_t);
char* R_alloc(size_t, int);
char* S_alloc(long, int);
Index: src/main/memory.c
===================================================================
--- src/main/memory.c (revision 57169)
+++ src/main/memory.c (working copy)
@@ -2503,6 +2503,17 @@
R_gc_internal(0);
}
+void R_gc_needed(R_size_t size_needed)
+{
+ if (FORCE_GC || NO_FREE_NODES() || VHEAP_FREE() < size_needed) {
+ R_gc_internal(size_needed);
+ if (NO_FREE_NODES())
+ mem_err_cons();
+ if (VHEAP_FREE() < size_needed)
+ mem_err_heap(0);
+ }
+}
+
static void R_gc_full(R_size_t size_needed)
{
num_old_gens_to_collect = NUM_OLD_GENERATIONS;
--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
Location: M1-B861
Telephone: 206 667-2793
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