Thanks for the info.
For the data type, my matrix as of now is indeed a matrix in a perfect
square shape filled in a previous segment of code, but I believe I could
extract one row/column at a time to do some processing. I can also
change that previous part of code to change the data type of it to
something else if that helps.
Saving it to a file for manipulation and reading it back seems to be
quite IO intensive - writing 600G of data and reading 300G back from a
hard drive would make the code extremely heavy as well as wear my disk
quite badly.
For now I'll try the row-by-row method and hope it works...
Sincerely,
S. Zhang
On 2023/04/12 12:39, avi.e.gr...@gmail.com wrote:
The example given does not leave room for even a single copy of your matrix
so, yes, you need alternatives.
Your example was fairly trivial as all you wanted to do is subtract each
value from 100 and replace it. Obviously something like squaring a matrix
has no trivial way to do without multiple copies out there that won't fit.
One technique that might work is a nested loop that changes one cell of the
matrix at a time and in-place. A variant of this might be a singe loop that
changes a single row (or column) at a time and in place.
Another odd concept is to save your matrix in a file with some format you
can read back in such as a line or row at a time, and then do the
subtraction from 100 and write it back to disk in another file. If you need
it again, I assume you can read it in but perhaps you should consider how to
increase some aspects of your "memory".
Is your matrix a real matrix type or something like a list of lists or a
data.frame? You may do better with some data structures that are more
efficient than others.
Some OS allow you to use virtual memory that is mapped in and out from the
disk that allows larger things to be done, albeit often much slower. I also
note that you can remove some things you are not using and hope garbage
collection happens soon enough.
-----Original Message-----
From: R-help <r-help-boun...@r-project.org> On Behalf Of Shunran Zhang
Sent: Tuesday, April 11, 2023 10:21 PM
To: r-help@r-project.org
Subject: [R] Matrix scalar operation that saves memory?
Hi all,
I am currently working with a quite large matrix that takes 300G of
memory. My computer only has 512G of memory. I would need to do a few
arithmetic on it with a scalar value. My current code looks like this:
mat <- 100 - mat
However such code quickly uses up all of the remaining memory and got
the R script killed by OOM killer.
Are there any more memory-efficient way of doing such operation?
Thanks,
S. Zhang
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