Why was my R process killed spontaneously?

I tried to use gpuCor function in the gputools package of R to calcuate
the
pairwise correlations of a matrix of 40,000 columns.

Becuase there would be memory issues if I use the whole matrix at a
time, I
splitted the matrix into submatrix of 10,000 columns and then calculate
the
pairwise correlation of different submatrices. There are altogether 4
submatrices, so I need to calculate the pearson correlation of sub
matrix 1
with sub matrix 1,2,3,4, and sub matrix 2 with submatrix 1,2,3,4, etc.

The program runs well at first, but at the last step, which is
calculating
the correlation between submatrix 4 with itself, the program was killed
and
gave no error messages.

Have anybody else encountered this before?

Actually it doesn't have to be related with gpuCor. Just generally
speaking, in what circumstances would a R program be killed
spontaneously
without any error messages?

Thanks.

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Thanks for your reply.

Does what you said by resources mean memory or something else? Inside
my
loop, I removed the objects that are created but not used by the next
loop
and did garbage collection as well. Do you have any idea how I should
modify my code such that the system won't kill it? Thanks.





On Thu, Aug 23, 2012 at 5:06 PM, Jeff Newmiller
<jdnewmil at dcn.davis.ca.us>wrote:

Yes. Operating systems kill processes that consume excessive

resources.

That excess may arise from one large computation or from a small one

on top

of many other allocations... the "straw that broke the camel's back"
problem.

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flora flora <floraflora196 at gmail.com> wrote:

I tried to use gpuCor function in the gputools package of R to

calcuate

the
pairwise correlations of a matrix of 40,000 columns.

Becuase there would be memory issues if I use the whole matrix at a
time, I
splitted the matrix into submatrix of 10,000 columns and then

calculate

the
pairwise correlation of different submatrices. There are altogether

4

submatrices, so I need to calculate the pearson correlation of sub
matrix 1
with sub matrix 1,2,3,4, and sub matrix 2 with submatrix 1,2,3,4,

etc.

The program runs well at first, but at the last step, which is
calculating
the correlation between submatrix 4 with itself, the program was

killed

and
gave no error messages.

Have anybody else encountered this before?

Actually it doesn't have to be related with gpuCor. Just generally
speaking, in what circumstances would a R program be killed
spontaneously
without any error messages?

Thanks.

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