Hi Martin,
Unfortunately, the error is coming on the data set that I have right now. I
was successfully able to display any field in the matrix and even the whole
matrix when I tried the example code provided by you. However, it is failing
on the dataset I am working on.I can share the file with you if that helps.
Kindly let me know.
Also, please find the sessioninfo() output below:
> sessionInfo()
R version 2.9.2 (2009-08-24)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Matrix_0.999375-30 lattice_0.17-25
loaded via a namespace (and not attached):
[1] grid_2.9.2
>
Thanks
Pallavi
On Wed, Oct 28, 2009 at 7:22 PM, Martin Maechler <maech...@stat.math.ethz.ch
> wrote:
> >>>>> "PP" == Pallavi P <pallavip...@gmail.com>
> >>>>> on Wed, 28 Oct 2009 16:30:25 +0530 writes:
>
> PP> Hi Martin,
> PP> I followed your example on my set of data. Which has non zero
> values in
> PP> 300k positions in 22638 X 80914 sparse matrix. I am able to load
> data into a
> PP> field and was able to do some operations (essentially t(m) %*% m).
> However,
> PP> when I tried to display the value in the resulted matrix. I am
> getting below
> PP> error
> PP> *
> PP> Error in asMethod(object) :
> PP> Cholmod error 'out of memory' at file:../Core/cholmod_memory.c, line
> 148*
>
> PP> The sequence of commands I used are:
>
> >>
> uac=read.table('C:\\personal\\code\\data\\user_album_count.csv',sep=',' ,
> PP> header=T)
> >> library(Matrix)
> >> m<-sparseMatrix(i=uac[,"user"],j=uac[,"item"],x=uac[,"count"])
> >> cm<-t(m) %*% m
>
> The above is less efficient than
>
> cm <- crossprod(m)
>
> please use the latter {not just for sparse matrices; for all
> matrices in R !}
>
> PP> upto this point, I was able to run, however when I tried to display
> cm[1,1],
> PP> I got above error. Kindly let me know if there is anything wrong
> going on
> PP> here.
>
> Interestingly, we had a recent thread on R-devel,
> which also made a point about excessive memory usage when
> accessing elements of a sparse matrix.
>
> I'd really like to investigate further;
> but can you ***PLEASE*** use reproducible code, i.e.,
> similar to the one I used, rather than reading data from one of
> your files.
>
> Note that your matrix is still fine and should be able to work
> with it, even thoug it seems the operation
>
> a <- cm[1,1]
>
> is currently implemented very sub-optimally.
>
> I'm busy for the rest of today with other duties,
> but am looking forward to receive **reproducible** code from
> you, by tonight.
> Also, please do not forget to also show the result of
> sessionInfo() !
>
> Martin Maechler,
>
> PP> Thanks
> PP> Pallavi
>
> PP> On Tue, Oct 27, 2009 at 8:34 PM, Martin Maechler <
> maech...@stat.math.ethz.ch
> >> wrote:
>
> >> >>>>> "PP" == Pallavi P <pallavip...@gmail.com>
> >> >>>>> on Tue, 27 Oct 2009 18:13:22 +0530 writes:
> >>
> PP> Hi Martin,
> PP> Thanks for the help. Just to make sure I understand correctly.
> >>
> PP> The below steps are for creating an example table similar to the one
> >> that I
> PP> read from file.
> >>
> >> yes, exactly
> >>
> >> n <- 22638
> >> m <- 80914
> >> nnz <- 300000 # no idea if this is realistic for you
> >>
> >> set.seed(101)
> >> ex <- cbind(i = sample(n,nnz, replace=TRUE),
> >> j = sample(m,nnz, replace=TRUE),
> >> x = round(100 * rnorm(nnz)))
> >>
> >>
> PP> and I can understand the way sparseMatrix is initialized right now
> >> as
> >> M <- sparseMatrix(i = ex[,"i"],
> >> j = ex[,"j"],
> >> x = ex[,"x"])
> >>
> PP> How ever, I couldn't understand the use of below commands.
> >>
> >> MM. <- tcrossprod(M) # == MM' := M %*% t(M)
> >> M.1 <- M %*% rep(1, ncol(M))
> >> stopifnot(identical(drop(M.1), rowSums(M)))
> >>
> >> They were just for illustrative purposes,
> >> to show how and that you can work with the created sparse matrix
> >> 'M'.
> >>
> >> Regards,
> >> Martin Maechler, ETH Zurich
> >>
> PP> Kindly let me know if I missed something.
> >>
> PP> Thanks
> PP> Pallavi
> >>
> >>
> PP> Hi Martin,<br><br>I followed your example on my set of data. Which
> has non zero values in 300k positions in 22638 X 80914 sparse matrix. I am
> able to load data into a field and was able to do some operations
> (essentially t(m) %*% m). However, when I tried to display the value in the
> resulted matrix. I am getting below error<br>
> PP> <b><br>Error in asMethod(object) : <br> Cholmod error 'out of
> memory' at file:../Core/cholmod_memory.c, line 148</b><br><br>The
> sequence of commands I used
> are:<br><br>>uac=read.table('C:\\personal\\code\\data\\user_album_count.csv',sep=','
> , header=T)<br>
> PP>
> >library(Matrix)<br>>m<-sparseMatrix(i=uac[,"user"],j=uac[,"item"],x=uac[,"count"])<br>>cm<-t(m)
> %*% m<br>upto this point, I was able to run, however when I tried to display
> cm[1,1], I got above error. Kindly let me know if there is anything wrong
> going on here.<br>
> PP> <br>Thanks<br>Pallavi<br><br><div class="gmail_quote">On Tue, Oct
> 27, 2009 at 8:34 PM, Martin Maechler <span dir="ltr"><<a href="mailto:
> maech...@stat.math.ethz.ch">maech...@stat.math.ethz.ch</a>></span>
> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid
> rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
> PP> >>>>> "PP" == Pallavi P <<a
> href="mailto:pallavip...@gmail.com";>pallavip...@gmail.com</a>><br>
> PP> >>>>> on Tue, 27 Oct 2009 18:13:22 +0530
> writes:<br>
> PP> <br>
> PP> PP> Hi Martin,<br>
> PP> PP> Thanks for the help. Just to make sure I understand
> correctly.<br>
> PP> <br>
> PP> PP> The below steps are for creating an example table similar
> to the one that I<br>
> PP> PP> read from file.<br>
> PP> <br>
> PP> yes, exactly<br>
> PP> <div class="im"><br>
> PP> n <- 22638<br>
> PP> m <- 80914<br>
> PP> nnz <- 300000 # no idea if this is realistic for you<br>
> PP> <br>
> PP> set.seed(101)<br>
> PP> ex <- cbind(i = sample(n,nnz, replace=TRUE),<br>
> PP> j = sample(m,nnz, replace=TRUE),<br>
> PP> x = round(100 * rnorm(nnz)))<br>
> PP> <br>
> PP> <br>
> PP> </div> PP> and I can understand the way sparseMatrix is
> initialized right now as<br>
> PP> <div class="im"> M <- sparseMatrix(i = ex[,"i"],<br>
> PP> j = ex[,"j"],<br>
> PP> x = ex[,"x"])<br>
> PP> <br>
> PP> </div> PP> How ever, I couldn't understand the use of
> below commands.<br>
> PP> <div class="im"><br>
> PP> MM. <- tcrossprod(M) # == MM' := M %*% t(M)<br>
> PP> M.1 <- M %*% rep(1, ncol(M))<br>
> PP> stopifnot(identical(drop(M.1), rowSums(M)))<br>
> PP> <br>
> PP> </div>They were just for illustrative purposes,<br>
> PP> to show how and that you can work with the created sparse matrix<br>
> PP> 'M'.<br>
> PP> <br>
> PP> Regards,<br>
> PP> Martin Maechler, ETH Zurich<br>
> PP> <br>
> PP> PP> Kindly let me know if I missed something.<br>
> PP> <br>
> PP> PP> Thanks<br>
> PP> PP> Pallavi<br>
> PP> <br></blockquote></div><br>
>
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