# AnVIL Office Hours 16JUN2022 @ 11 AM ET

**URL:** <https://help.anvilproject.org/t/anvil-office-hours-16jun2022-11-am-et/125>\
**Category:** AnVIL Demos\
**Created:** [May 27, 2022, 4:00pm UTC](https://help.anvilproject.org/t/anvil-office-hours-16jun2022-11-am-et/125 "2022-05-27T16:00:32Z")\
**Posts on this page:** 1\
**Showing post:** 8

<div class="post-metadata">

**Author:** ![Martin\_Morgan](https://yyz1.discourse-cdn.com/flex027/user_avatar/help.anvilproject.org/martin_morgan/32/104_2.png) [@Martin\_Morgan](https://help.anvilproject.org/u/Martin_Morgan)\
**Post date:** [June 16, 2022, 6:32pm UTC](https://help.anvilproject.org/t/anvil-office-hours-16jun2022-11-am-et/125/8 "2022-06-16T18:32:52Z")

</div>

Suppose you have a for loop that accumulates results in a vector `result`

```auto
result <- numeric(10)
for (i in 1:10) {
    ## do a lot of work, represented by...
    Sys.sleep(5)
    ## after the calculation add a value to the result
    result[i] <- sqrt(i)
}

```

Convert the body of the loop into a function that returns a value

```auto
my_fun <- function(i) {
    ## do a lot of work, represented by...
    Sys.sleep(5)
    ## return the result
    sqrt(i)
}

```

and instead of using a `for` loop, use `lapply()`

```auto
result <- lapply(1:10, my_fun)

```

So far so good, but it still takes 5 seconds x 10 tasks = 50 seconds

```auto
system.time(result <- lapply(1:10, my_fun))

```

Now use BiocParallel to do the computation in parallel; if you have 10 cores, then this will take just 5 seconds

```auto
library(BiocParallel)
system.time(bpresult <- bplapply(1:20, my_fun))
identical(result, bpresult)

```

Currently the easiest way to get a performance improvement is to simply request a machine with more ‘cores’. Also, the amount of memory needs to be enough to support all cores working simultaneously, so if one iteration of `my_fun()` takes 4 Gb, and you request a machine with 16 cores, you would need 16 x 4 = 64 Gb. Performing parallel computations like this on a single machine is much easier than mastering spark or workflows, although in the long run these might be ‘better’ solutions.

One ‘lesson learned’ is that R code, like any computer code, can be written in such a way that is very inefficient, e.g., try this

```auto
x <- integer(); for (i in 1:1000) x <- c(x, i)
x <- integer(); for (i in 1:100000) x <- c(x, i)

```

This is just making a sequence 1, 2, …; the second one takes phenomenally long! But check out

```auto
x <- integer(); for (i in 1:100000) x[i] <- i

```

This executes almost instantly! So if you have code that takes a long time, and sort-of intuitively it seems like a modern computer should be doing much better than that, then perhaps it would pay to speak with an R ‘expert’ to see if there are obvious inefficiencies.

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