On Aug 9, 2012, at 7:29 PM, Sean Ruddy <srudd...@gmail.com> wrote:
> 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.
>
I believe Prof Ripley has touched this code in R-Devel recently, but I can't
remember if he changed the size of the hash table. See if one the nightly
builds can help you out.
Also, possibly see if Simon Urbanek's fastmatch package can help.
Sorry for the lack of concrete pointers but I'm working from my phone, which
isn't svn equipped ;-)
Michael
> Thanks for the help.
>
> -Sean
>
> [[alternative HTML version deleted]]
>
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