Hi,
First, thanks in advance. Some useful info:
>version
platform x86_64-unknown-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
version.string R version 2.15.1 (2012-06-22)
I'm trying to use the table() function on a 2 column matrix that has 711
million rows (see below). However, it freezes. If I subset the matrix to be
less than or equal to 2^29 (500+ million) then the table() function
finishes in minutes. As soon as I go larger than that--beginning with
2^29+1--it gets stuck, ie. nothing happens even after hours of running. I
assume it has something to do with memory since I believe that's the 32 bit
limit but I'm running on a 64 bit machine.
Here's the matrix:
>head(DRI.mtx)
POSITION BP
38076904 C
38076905 C
38076906 A
38076907 T
38076908 C
38076909 C
The result from table (if the matrix has less than 2^29 rows) is
>head(table(DRI.mtx))
BP
POSITION A C G N T
115247036 17 0 0 0 0
115247037 31 0 0 0 0
115247038 46 0 0 0 0
115247039 0 0 54 0 0
115247040 0 0 1 0 66
115247041 0 0 0 0 78
I've tracked the problem down to the C-file, "unique.c". table() calls
factor() which calls unique() which I believe calls "unique.c". Browsing
through the C file I found an if statement that checks if the size of the
vector is larger than 2^30-1. If TRUE it gives the error message "too large
for hashing". I do not get any error message when I run table() on the full
matrix but I wonder if maybe I should be and if the limit of 2^30 is too
high and should be lowered. Maybe it's just my set up or maybe it has
nothing to do with unique.c. I don't know.
Here's the part of unique.c I was referring to:
/*
Choose M to be the smallest power of 2
not less than 2*n and set K = log2(M).
Need K >= 1 and hence M >= 2, and 2^M <= 2^31 -1, hence n <= 2^30.
Dec 2004: modified from 4*n to 2*n, since in the worst case we have
a 50% full table, and that is still rather efficient -- see
R. Sedgewick (1998) Algorithms in C++ 3rd edition p.606.
*/
static void MKsetup(int n, HashData *d)
{
int n2 = 2 * n;
if(n < 0 || n > 1073741824) /* protect against overflow to -ve */
error(_("length %d is too large for hashing"), n);
d->M = 2;
d->K = 1;
while (d->M < n2) {
d->M *= 2;
d->K += 1;
}
}
"n" I presume is the number of rows of the matrix so I don't see why this
wouldn't run properly though I'm not sure what is causing the problem in
the unique.c file and I have no idea how to troubleshoot.
I have a work around that reads in chunks at a time, but I'm very
interested in why there appears to be a limit at 2^29 when according to the
unique.c file it should be twice that.
Thanks for the help.
-Sean
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