[Bioc-devel] Memory usage for bplapply

Lulu Chen luluchen @ending from vt@edu
Sat Jan 5 20:50:33 CET 2019

Hi Martin,

Thanks for your explanation which make me understand BiocParallel
much better.

I compare memory usage in my code before packaged (using doSNOW) and after
packaged (using BiocParallel) and find the increased memory is caused by
the attached packages, especially 'SummarizedExperiment'.
As required to support common Bioconductor class, I used
importFrom(SummarizedExperiment,assay). After deleting this, the memory for
each thread save nearly 200Mb. I open a new R session and find
> pryr::mem_used()
38.5 MB
> library(SummarizedExperiment)
> pryr::mem_used()
314 MB
 (I am still using R 3.5.2, not sure any update in develop version). I
think it should be a issue. A lot of packages are importing
SummarizedExperiment just for a support and never know it can cause such a

My package still imports other packages, e.g limma, fdrtool. Checked by
pryr::mem_used() as above, only 1~2 Mb increase for each. I also check
my_package in a new session, which is around 5Mb. However,  each thread in
parallel computation still increases much larger than 5 Mb. I did a
simulation: In my old code with doSNOW, I just inserted
"require('my_package')" into foreach loop and keep other code as the same.
I used 20 cores and 1000 jobs. Each thread still increases 20~30 Mb. I
don't know if there are any other thing that cause extra cost to each
thread. Thanks!


On Fri, Jan 4, 2019 at 2:38 PM Martin Morgan <mtmorgan.bioc using gmail.com>

> Memory use can be complicated to understand.
>     library(BiocParallel)
>     v <- replicate(100, rnorm(10000), simplify=FALSE)
>     bplapply(v, sum)
> by default, bplapply splits 100 jobs (each element of the list) equally
> between the number of cores available, and sends just the necessary data to
> the cores. Again by default, the jobs are sent 'en masse' to the cores, so
> if there were 10 cores (and hence 10 tasks), the first core would receive
> the first 10 jobs and 10 x 10000 elements, and so on. The memory used to
> store v on the workers would be approximately the size of v, # of workers *
> jobs /per worker  * job size = 10 * 10 * 10000.
> If memory were particularly tight, or if computation time for each job was
> highly variable, it might be advantageous to sends jobs one at a time, by
> setting the number of tasks equal to the number of jobs SnowParam(workers =
> 10, tasks = length(v)). Then the amount of memory used to store v would
> only be # of workers * 1  * 10000; this is generally slower, because there
> is much more communication between the manager and the workers.
>     m <- matrix(rnorm(100 * 10000), 100, 10000)
>     bplapply(seq_len(nrow(m)), function(i, m) sum(m[i]), m)
> Here bplapply doesn't know how to send just some rows to the workers, so
> each worker gets a complete copy of m. This would be expensive.
>     f <- function(x) sum(x)
>     g <- function() {
>         v <- replicate(100, rnorm(10000), simplify=FALSE)
>         bplapply(v, f)
>     }
> this has the same memory consequences as above, the function `f()` is
> defined in the .GlobalEnv, so only the function definition (small) is sent
> to the workers.
>     h <- function() {
>         f <- function(x) sum(x)
>         v <- replicate(100, rnorm(10000), simplify=FALSE)
>         bplapply(v, f)
>     }
>  This is expensive. The function `f()` is defined in the body of the
> function `h()`. So the workers receive both the function f and the
> environment in which it defined. The environment includes v, so each worker
> receives a slice of v (for f() to operate on) AND an entire copy of v
> (because it is in the body of the environment where `f()` was defined. A
> similar cost would be paid in a package, if the package defined large data
> objects at load time.
> For more guidance, it might be helpful to provide a simplified example of
> what you did with doSNOW, and what you do with BiocParallel.
> Hope that helps,
> Martin
> On 1/3/19, 11:52 PM, "Bioc-devel on behalf of Lulu Chen" <
> bioc-devel-bounces using r-project.org on behalf of luluchen using vt.edu> wrote:
>     Dear all,
>     I met a memory issue for bplapply with SnowParam(). I need to calculate
>     something from a large matrix many many times. But from the
> discussions in
>     https://support.bioconductor.org/p/92587, I learned that bplapply
> copied
>     the current and parent environment to each worker thread. Then means
> the
>     large matrix in my package will be copied so many times. Do you have
> better
>     suggestions in windows platform?
>     Before I tried to package my code, I used doSNOW package with foreach
>     %dopar%. It seems to consume less memory in each core (almost the size
> of
>     the matrix the task needs). But bplapply seems to copy more then
> objects in
>     current environment and the above one level environment. I am very
>     confused.and just guess it was copying everything.
>     Thanks for any help!
>     Best,
>     Lulu
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