Gschneider
Reputation: 254
Using R_alloc in C
I've got C code which I'm calling from R:
.C("giveProb",as.double(2),as.double(2),as.double(c(0,1,0,1,1,0,1,0)))
I'd like to call it a bunch (hundreds of thousands or millions) of times (with differing third arguments), and it works fine when I put it in a for loop for around 100 times, but anything above that crashes R.
I've got a feeling that it's a memory problem from using R_alloc. I've got six arrays allocated in C, e.g.:
newCoefArray = (double *)R_alloc(1,curSize * sizeof(double));
But according to the R Manual "Writing R Extensions":
This memory is taken from the heap, and released at the end of the .C, .Call or .External call.
which I took to mean that the memory would be freed during each iteration of the loop. But in the next sentence:
Users can also manage it, by noting the current position with a call to vmaxget and clearing memory allocated subsequently by a call to vmaxset. This is only recommended for experts.
As someone who is nowhere near an expert, I was hoping someone here could help. The C code, in its entirety is below.
#include <R.h>
#include <Rmath.h>
#include <stdio.h>
void giveProb(double *k, double *q,double *order){
double curSize;
double tmpSize;
double *newCoefArray;
double *oldCoefArray;
double *newAArray;
double *oldAArray;
double *newBArray;
double *oldBArray;
int position=0;
long int factorial(int n){
if(n==0||n==1){
return(1);
}
int tmp=1,i=1;
while(i<=n){
tmp=tmp*i;
i++;
}
return(tmp);
}
void expander(double a, double b,double c,double d,double coeff){
double leadingTerm=beta(a,b);
int bb=b;
double index[bb], sumLeaders[bb];
for(int i=0;i<bb;i++){
index[i]=a+i;
sumLeaders[i]=factorial(a+b-1)/(factorial(index[i])*factorial(a+b-1-index[i]));
newCoefArray[i+position]=coeff*leadingTerm*sumLeaders[i];
newAArray[i+position]=index[i]+c+1;
newBArray[i+position]=a+b+d-index[i];
}
position=position+bb;
curSize=position;
}
void separator(double e, double f){
double a, b, coeff;
for(int i=0; i<tmpSize; i++){
coeff=oldCoefArray[i];
a=oldAArray[i];
b=oldBArray[i];
expander(a,b,e,f,coeff);
}
}
void condenser(){
tmpSize=0;
for(int i=1; i<curSize; i++){
for(int j=0; j<i; j++){
if(newAArray[j]==newAArray[i]){
newCoefArray[j]=newCoefArray[j]+newCoefArray[i];
newCoefArray[i]=0;
}
}
}
for(int i=0; i<curSize; i++){
tmpSize=tmpSize+(newCoefArray[i]!=0);
}
oldCoefArray =(double *) R_alloc(1,tmpSize * sizeof(double));
oldAArray = (double *)R_alloc(1,tmpSize * sizeof(double));
oldBArray = (double *)R_alloc(1,tmpSize * sizeof(double));
for(int i=0; i<tmpSize; i++){
oldCoefArray[i]=newCoefArray[i];
oldAArray[i]=newAArray[i];
oldBArray[i]=newBArray[i];
}
curSize=tmpSize;
}
long double coefficient=1;
for(int i=0;i<*k;i++){
coefficient=coefficient*factorial(*k)/(factorial(i)*factorial(*k-i-1));
}
for(int i=0;i<*q;i++){
coefficient=coefficient*factorial(*q)/(factorial(i)*factorial(*q-i-1));
}
double numObs=*k+*q;
double out=0;
curSize=order[1]+1;
newCoefArray = (double *)R_alloc(1,curSize * sizeof(double));
newAArray = (double *)R_alloc(1,curSize * sizeof(double));
newBArray = (double *)R_alloc(1,curSize * sizeof(double));
expander(order[0]+1,order[1]+1,order[2],order[3],coefficient);
oldCoefArray = (double *)R_alloc(1,curSize * sizeof(double));
oldAArray = (double *)R_alloc(1,curSize * sizeof(double));
oldBArray = (double *)R_alloc(1,curSize * sizeof(double));
for(int i=0;i<curSize; i++){
oldCoefArray[i]=newCoefArray[i];
oldAArray[i]=newAArray[i];
oldBArray[i]=newBArray[i];
}
for(int i=4;i<2*numObs;i+=2){
position=0;
tmpSize=curSize;
separator(order[i],order[i+1]);
condenser();
}
position=0;
for(int i=0;i<curSize;i++){
out=out+newCoefArray[i]*beta(newAArray[i],newBArray[i]);
}
*k=out;
}
UPDATE: Using the suggestion in the comment below, I get the following (which sort of confirms what I had previously thought, right?):
R -d valgrind -f test_script.R
==11131== Memcheck, a memory error detector
==11131== Copyright (C) 2002-2010, and GNU GPL'd, by Julian Seward et al.
==11131== Using Valgrind-3.6.0 and LibVEX; rerun with -h for copyright info
==11131== Command: /usr/lib64/R/bin/exec/R -f test_script.R
==11131==
R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-redhat-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
==11131== Conditional jump or move depends on uninitialised value(s)
==11131== at 0x3A6A685F80: __GI___strcasecmp_l (in /lib64/libc-2.12.so)
==11131== by 0x3A6A61FF24: __gconv_open (in /lib64/libc-2.12.so)
==11131== by 0x3A6A62D3B7: _nl_find_msg (in /lib64/libc-2.12.so)
==11131== by 0x3A6A62DB83: __dcigettext (in /lib64/libc-2.12.so)
==11131== by 0x3A6C3BD2DF: ??? (in /usr/lib64/R/lib/libR.so)
==11131== by 0x3A6C313FC8: setup_Rmainloop (in /usr/lib64/R/lib/libR.so)
==11131== by 0x3A6C315278: Rf_mainloop (in /usr/lib64/R/lib/libR.so)
==11131== by 0x40084A: main (in /usr/lib64/R/bin/exec/R)
==11131==
==11131== Use of uninitialised value of size 8
==11131== at 0x3A6A6863A4: __GI___strcasecmp_l (in /lib64/libc-2.12.so)
==11131== by 0x3A6A61FF24: __gconv_open (in /lib64/libc-2.12.so)
==11131== by 0x3A6A62D3B7: _nl_find_msg (in /lib64/libc-2.12.so)
==11131== by 0x3A6A62DB83: __dcigettext (in /lib64/libc-2.12.so)
==11131== by 0x3A6C3BD2DF: ??? (in /usr/lib64/R/lib/libR.so)
==11131== by 0x3A6C313FC8: setup_Rmainloop (in /usr/lib64/R/lib/libR.so)
==11131== by 0x3A6C315278: Rf_mainloop (in /usr/lib64/R/lib/libR.so)
==11131== by 0x40084A: main (in /usr/lib64/R/bin/exec/R)
==11131==
==11131== Use of uninitialised value of size 8
==11131== at 0x3A6A6863A8: __GI___strcasecmp_l (in /lib64/libc-2.12.so)
==11131== by 0x3A6A61FF24: __gconv_open (in /lib64/libc-2.12.so)
==11131== by 0x3A6A62D3B7: _nl_find_msg (in /lib64/libc-2.12.so)
==11131== by 0x3A6A62DB83: __dcigettext (in /lib64/libc-2.12.so)
==11131== by 0x3A6C3BD2DF: ??? (in /usr/lib64/R/lib/libR.so)
==11131== by 0x3A6C313FC8: setup_Rmainloop (in /usr/lib64/R/lib/libR.so)
==11131== by 0x3A6C315278: Rf_mainloop (in /usr/lib64/R/lib/libR.so)
==11131== by 0x40084A: main (in /usr/lib64/R/bin/exec/R)
==11131==
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
[Previously saved workspace restored]
> dyn.load("SchWolfenew.so")
> for(i in 1:1000){
+ .C("giveProb",as.double(2),as.double(2),as.double(c(0,1,0,1,1,0,1,0)))
+ }
==29371== Invalid read of size 1
==29371== at 0x3A6C31A2E9: ??? (in /usr/lib64/R/lib/libR.so)
==29371== by 0x3A6C31CBC9: Rf_cons (in /usr/lib64/R/lib/libR.so)
==29371== by 0x3A6C2D2B74: ??? (in /usr/lib64/R/lib/libR.so)
==29371== by 0x3A6C2DD121: Rf_eval (in /usr/lib64/R/lib/libR.so)
==29371== by 0x3A6C2DF830: Rf_applyClosure (in /usr/lib64/R/lib/libR.so)
==29371== by 0x3A6C32B828: Rf_usemethod (in /usr/lib64/R/lib/libR.so)
==29371== by 0x3A6C32BAE7: ??? (in /usr/lib64/R/lib/libR.so)
==29371== by 0x3A6C2D290B: ??? (in /usr/lib64/R/lib/libR.so)
==29371== by 0x3A6C2DD121: Rf_eval (in /usr/lib64/R/lib/libR.so)
==29371== by 0x3A6C2DF830: Rf_applyClosure (in /usr/lib64/R/lib/libR.so)
==29371== by 0x3A6C2DD3F7: Rf_eval (in /usr/lib64/R/lib/libR.so)
==29371== by 0x3A6C2DEF4F: ??? (in /usr/lib64/R/lib/libR.so)
==29371== Address 0x3ff0000000000003 is not stack'd, malloc'd or (recently) free'd
==29371==
*** caught segfault ***
address (nil), cause 'unknown'
==29371== Invalid read of size 1
==29371== at 0x3A6C31AF0B: ??? (in /usr/lib64/R/lib/libR.so)
==29371== by 0x3A6C31CBC9: Rf_cons (in /usr/lib64/R/lib/libR.so)
==29371== by 0x3A6C31CC71: Rf_allocList (in /usr/lib64/R/lib/libR.so)
==29371== by 0x3A6C2C8CD4: R_GetTraceback (in /usr/lib64/R/lib/libR.so)
==29371== by 0x3A6C313472: ??? (in /usr/lib64/R/lib/libR.so)
==29371== by 0x3A6B20F4FF: ??? (in /lib64/libpthread-2.12.so)
==29371== by 0x3A6C31A2E8: ??? (in /usr/lib64/R/lib/libR.so)
==29371== by 0x3A6C31CBC9: Rf_cons (in /usr/lib64/R/lib/libR.so)
==29371== by 0x3A6C2D2B74: ??? (in /usr/lib64/R/lib/libR.so)
==29371== by 0x3A6C2DD121: Rf_eval (in /usr/lib64/R/lib/libR.so)
==29371== by 0x3A6C2DF830: Rf_applyClosure (in /usr/lib64/R/lib/libR.so)
==29371== by 0x3A6C32B828: Rf_usemethod (in /usr/lib64/R/lib/libR.so)
==29371== Address 0x4020000000000003 is not stack'd, malloc'd or (recently) free'd
==29371==
==29371==
==29371== Process terminating with default action of signal 11 (SIGSEGV)
==29371== General Protection Fault
==29371== at 0x3A6C31AF0B: ??? (in /usr/lib64/R/lib/libR.so)
==29371== by 0x3A6C31CBC9: Rf_cons (in /usr/lib64/R/lib/libR.so)
==29371== by 0x3A6C31CC71: Rf_allocList (in /usr/lib64/R/lib/libR.so)
==29371== by 0x3A6C2C8CD4: R_GetTraceback (in /usr/lib64/R/lib/libR.so)
==29371== by 0x3A6C313472: ??? (in /usr/lib64/R/lib/libR.so)
==29371== by 0x3A6B20F4FF: ??? (in /lib64/libpthread-2.12.so)
==29371== by 0x3A6C31A2E8: ??? (in /usr/lib64/R/lib/libR.so)
==29371== by 0x3A6C31CBC9: Rf_cons (in /usr/lib64/R/lib/libR.so)
==29371== by 0x3A6C2D2B74: ??? (in /usr/lib64/R/lib/libR.so)
==29371== by 0x3A6C2DD121: Rf_eval (in /usr/lib64/R/lib/libR.so)
==29371== by 0x3A6C2DF830: Rf_applyClosure (in /usr/lib64/R/lib/libR.so)
==29371== by 0x3A6C32B828: Rf_usemethod (in /usr/lib64/R/lib/libR.so)
==29371==
==29371== HEAP SUMMARY:
==29371== in use at exit: 29,307,724 bytes in 12,896 blocks
==29371== total heap usage: 28,845 allocs, 15,949 frees, 48,495,252 bytes allocated
==29371==
==29371== LEAK SUMMARY:
==29371== definitely lost: 0 bytes in 0 blocks
==29371== indirectly lost: 0 bytes in 0 blocks
==29371== possibly lost: 0 bytes in 0 blocks
==29371== still reachable: 29,307,724 bytes in 12,896 blocks
==29371== suppressed: 0 bytes in 0 blocks
==29371== Rerun with --leak-check=full to see details of leaked memory
==29371==
==29371== For counts of detected and suppressed errors, rerun with: -v
==29371== Use --track-origins=yes to see where uninitialised values come from
==29371== ERROR SUMMARY: 5 errors from 5 contexts (suppressed: 21 from 9)
Segmentation fault (core dumped)
Upvotes: 12
Views: 2403
Answers (1)
Martin Morgan
Reputation: 46866
I put your C code in a file memory.c, and ran R CMD SHLIB memory.c. Here's my test script
dyn.load("/tmp/memory.so")
set.seed(123L)
while (TRUE)
.C("giveProb",as.double(2),as.double(2), sample(c(0, 1), 8, TRUE))
And R -d valgrind -f test_script.R says
> dyn.load("/tmp/memory.so")
> set.seed(123L)
> while (TRUE)
+ .C("giveProb",as.double(2),as.double(2), sample(c(0, 1), 8, TRUE))
==3461== Invalid write of size 8
==3461== at 0xBF29D78: expander.4631 (memory.c:35)
==3461== by 0xBF29EBB: separator.4643 (memory.c:49)
==3461== by 0xBF29AAB: giveProb (memory.c:108)
==3461== by 0x4EEAF49: do_dotCode (dotcode.c:1689)
==3461== by 0x4F1F4E2: Rf_eval (eval.c:493)
==3461== by 0x4F218F6: do_for (eval.c:1310)
==3461== by 0x4F1F2E8: Rf_eval (eval.c:467)
==3461== by 0x4F6B5FB: Rf_ReplIteration (main.c:256)
==3461== by 0x4F6B7B2: R_ReplConsole (main.c:305)
==3461== by 0x4F6D022: run_Rmainloop (main.c:987)
==3461== by 0x4F6D037: Rf_mainloop (main.c:994)
==3461== by 0x400845: main (Rmain.c:32)
(plus a lot more). memory.c line 35 is
newCoefArray[i+position]=coeff*leadingTerm*sumLeaders[i];
so i + position is larger than the allocated array.
Upvotes: 14
Related Questions
- Rf_allocVector only allocates and does not zero out memory
- How to alloc memory manually
- defining a rudimentary alloc function
- alloc implementation in c programming
- alloca function in C
- emulating `alloca()` in C
- Heap alloc in c
- R Using function Realoc with .C interface
- Is this use of realloc correct?
- How does alloc work in Objective C?