Chunk size support has been added in R-devel 74353. Please let me know if you find any problem.


Thanks,
Tomas

On 03/01/2018 09:19 AM, Christian Krause wrote:
Dear Tomas,

Thanks for your commitment to fix this issue and also to add the chunk size as 
an argument. If you want our input, let us know ;)

Best Regards

On 02/26/2018 04:01 PM, Tomas Kalibera wrote:
Dear Christian and Henrik,

thank you for spotting the problem and suggestions for a fix. We'll probably 
add a chunk.size argument to parLapplyLB and parLapply to follow OpenMP 
terminology, which has already been an inspiration for the present code 
(parLapply already implements static scheduling via internal function 
staticClusterApply, yet with a fixed chunk size; parLapplyLB already implements 
dynamic scheduling via internal function dynamicClusterApply, but with a fixed 
chunk size set to an unlucky value so that it behaves like static scheduling). 
The default chunk size for parallelLapplyLB will be set so that there is some 
dynamism in the schedule even by default. I am now testing a patch with these 
changes.

Best
Tomas


On 02/20/2018 11:45 AM, Christian Krause wrote:
Dear Henrik,

The rationale is just that it is within these extremes and that it is really 
simple to calculate, without making any assumptions and knowing that it won't 
be perfect.

The extremes A and B you are mentioning are special cases based on assumptions. 
Case A is based on the assumption that the function has a long runtime or 
varying runtime, then you are likely to get the best load balancing with really 
small chunks. Case B is based on the assumption that the function runtime is 
the same for each list element, i.e. where you don't actually need load 
balancing, i.e. just use `parLapply` without load balancing.

This new default is **not the best one**. It's just a better one than we had 
before. There is no best one we can use as default because **we don't know the 
function runtime and how it varies**. The user needs to decide that because 
he/she knows the function. As mentioned before, I will write a patch that makes 
the chunk size an optional argument, so the user can decide because only he/she 
has all the information to choose the best chunk size, just like you did with 
the `future.scheduling` parameter.

Best Regards

On February 19, 2018 10:11:04 PM GMT+01:00, Henrik Bengtsson 
<henrik.bengts...@gmail.com> wrote:
Hi, I'm trying to understand the rationale for your proposed amount of
splitting and more precisely why that one is THE one.

If I put labels on your example numbers in one of your previous post:

nbrOfElements <- 97
nbrOfWorkers <- 5

With these, there are two extremes in how you can split up the
processing in chunks such that all workers are utilized:

(A) Each worker, called multiple times, processes one element each
time:

nbrOfElements <- 97
nbrOfWorkers <- 5
nbrOfChunks <- nbrOfElements
sapply(parallel:::splitList(1:nbrOfElements, nbrOfChunks), length)
[1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
[30] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
[59] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
[88] 1 1 1 1 1 1 1 1 1 1


(B) Each worker, called once, processes multiple element:

nbrOfElements <- 97
nbrOfWorkers <- 5
nbrOfChunks <- nbrOfWorkers
sapply(parallel:::splitList(1:nbrOfElements, nbrOfChunks), length)
[1] 20 19 19 19 20

I understand that neither of these two extremes may be the best when
it comes to orchestration overhead and load balancing. Instead, the
best might be somewhere in-between, e.g.

(C) Each worker, called multiple times, processing multiple elements:

nbrOfElements <- 97
nbrOfWorkers <- 5
nbrOfChunks <- nbrOfElements / nbrOfWorkers
sapply(parallel:::splitList(1:nbrOfElements, nbrOfChunks), length)
[1] 5 5 5 5 4 5 5 5 5 5 4 5 5 5 5 4 5 5 5 5

However, there are multiple alternatives between the two extremes, e.g.

nbrOfChunks <- scale * nbrOfElements / nbrOfWorkers
So, is there a reason why you argue for scale = 1.0 to be the optimal?

FYI, In future.apply::future_lapply(X, FUN, ...) there is a
'future.scheduling' scale factor(*) argument where default
future.scheduling = 1 corresponds to (B) and future.scheduling = +Inf
to (A).  Using future.scheduling = 4 achieves the amount of
load-balancing you propose in (C).   (*) Different definition from the
above 'scale'. (Disclaimer: I'm the author)

/Henrik

On Mon, Feb 19, 2018 at 10:21 AM, Christian Krause
<christian.kra...@idiv.de> wrote:
Dear R-Devel List,

I have installed R 3.4.3 with the patch applied on our cluster and
ran a *real-world* job of one of our users to confirm that the patch
works to my satisfaction. Here are the results.
The original was a series of jobs, all essentially doing the same
stuff using bootstrapped data, so for the original there is more data
and I show the arithmetic mean with standard deviation. The
confirmation with the patched R was only a single instance of that
series of jobs.
## Job Efficiency

The job efficiency is defined as (this is what the `qacct-efficiency`
tool below does):
```
efficiency = cputime / cores / wallclocktime * 100%
```

In simpler words: how well did the job utilize its CPU cores. It
shows the percentage of time the job was actually doing stuff, as
opposed to the difference:
```
wasted = 100% - efficiency
```

... which, essentially, tells us how much of the resources were
wasted, i.e. CPU cores just idling, without being used by anyone. We
care a lot about that because, for our scientific computing cluster,
wasted resources is like burning money.
### original

This is the entire series from our job accounting database, filteres
the successful jobs, calculates efficiency and then shows the average
and standard deviation of the efficiency:
```
$ qacct -j 4433299 | qacct-success | qacct-efficiency | meansd
n=945 ∅ 61.7276 ± 7.78719
```

This is the entire series from our job accounting database, filteres
the successful jobs, calculates efficiency and does sort of a
histogram-like binning before calculation of mean and standard
deviation (to get a more detailed impression of the distribution when
standard deviation of the previous command is comparatively high):
```
$ qacct -j 4433299 | qacct-success | qacct-efficiency | meansd-bin -w
10 | sort -gk1 | column -t
10  -  20  ->  n=3    ∅  19.21666666666667   ±  0.9112811494447459
20  -  30  ->  n=6    ∅  26.418333333333333  ±  2.665996374091058
30  -  40  ->  n=12   ∅  35.11583333333334   ±  2.8575783082671196
40  -  50  ->  n=14   ∅  45.35285714285715   ±  2.98623361591005
50  -  60  ->  n=344  ∅  57.114593023255814  ±  2.1922005551774415
60  -  70  ->  n=453  ∅  64.29536423841049   ±  2.8334788433963856
70  -  80  ->  n=108  ∅  72.95592592592598   ±  2.5219474143639276
80  -  90  ->  n=5    ∅  81.526              ±  1.2802265424525452
```

I have attached an example graph from our monitoring system of a
single instance in my previous mail. There you can see that the load
balancing does not actually work, i.e. same as `parLapply`. This
reflects in the job efficiency.
### patch applied

This is the single instance I used to confirm that the patch works:

```
$ qacct -j 4562202 | qacct-efficiency
97.36
```

The graph from our monitoring system is attached. As you can see, the
load balancing works to a satisfying degree and the efficiency is well
above 90% which was what I had hoped for :-)
## Additional Notes

The list used in this jobs `parLapplyLB` is 5812 elements long. With
the `splitList`-chunking from the patch, you'll get 208 lists of about
28 elements (208 chunks of size 28). The job ran on 28 CPU cores and
had a wallclock time of 120351.590 seconds, i.e. 33.43 hours. Thus, the
function we apply to our list takes about 580 seconds per list element,
i.e. about 10 minutes. I suppose, for that runtime, we would get even
better load balancing if we would reduce the chunk size even further,
maybe even down to 1, thus getting our efficiency even closer to 100%.
Of course, for really short-running functions, a higher chunk size
may be more efficient because of the overhead. In our case, the
overhead is negligible and that is why the low chunk size works really
well. In contrast, for smallish lists with short-running functions, you
might not even need load balancing and `parLapply` suffices. It only
becomes an issue, when the runtime of the function is high and / or
varying.
In our case, the entire runtime of the entire series of jobs was:

```
$ qacct -j 4433299 | awk '$1 == "wallclock" { sum += $2 } END { print
sum, "seconds" }'
4.72439e+09 seconds
```

Thats about 150 years on a single core or 7.5 years on a 20 core
server! Our user was constantly using about 500 cores, so this took
about 110 days. If you compare this to my 97% efficiency example, the
jobs could have been finished in 75 days instead ;-)
## Upcoming Patch

If this patch gets applied to the R code base (and I hope it will
:-)) my colleague and I will submit another patch that adds the chunk
size as an optional parameter to all off the load balancing functions.
With that parameter, users of these functions *can* decide for
themselves which chunk size they prefer for their code. As mentioned
before, the most efficient chunk size depends on the used functions
runtime, which is the only thing R does not know and users really
should be allowed to specify explicitly. The default of this new
optional parameter would be the one we used here and this would make
that upcoming patch fully source-compatible.
Best Regards

On 02/12/2018 08:08 PM, Christian Krause wrote:
Dear R-Devel List,

**TL;DR:** The function **parLapplyLB** of the parallel package has
[reportedly][1] (see also attached RRD output) not
been doing its job, i.e. not actually balancing the load. My
colleague Dirk Sarpe and I found the cause of the problem
and we also have a patch to fix it (attached). A similar fix has
also been provided [here][2].
[1]:
https://stackoverflow.com/questions/38230831/why-does-parlapplylb-not-actually-balance-load
[2]: https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=16792


## The Call Chain

First, we traced the relevant R function calls through the code,
beginning with `parLapplyLB`:
1.  **parLapplyLB:** clusterApply.R:177, calls **splitList**, then
**clusterApplyLB**
2.  **splitList:** clusterApply.R:157
3.  **clusterApplyLB:** clusterApply.R:87, calls
**dynamicClusterApply**
4.  **dynamicClusterApply:** clusterApply.R:39


## splitList

We used both our whiteboard and an R session to manually *run* a few
examples. We were using lists of 100 elements and 5
workers. First, lets take a look at **splitList**:

```r
sapply(parallel:::splitList(1:100, 5), length)
[1] 20 20 20 20 20

sapply(parallel:::splitList(1:97, 5), length)
[1] 20 19 19 19 20

sapply(parallel:::splitList(1:97, 20), length)
   [1] 5 5 5 5 4 5 5 5 5 5 4 5 5 5 5 4 5 5 5 5
```

As we can see in the examples, the work is distributed as equally as
possible.
## dynamicClusterApply

**dynamicClusterApply** works this way (simplified):

1.  it first gives a chunk to each worker
2.  once a worker comes back with the result, it is given the next
chunk
**This is the important part:** As long as there are **more** chunks
than workers, there will be load balancing. If
there are fewer chunks than workers, each worker will get **at most
one chunk** and there is **no** load balancing.
## parLapplyLB

This is how **parLapplyLB** splits the input list (with a bit of
refactoring, for readability):
```r
parLapplyLB <- function(cl = NULL, X, fun, ...)
{
      cl <- defaultCluster(cl)

      chunks <- splitList(X, length(cl))

      do.call(c,
              clusterApplyLB(cl, x = chunks, fun = lapply, fun, ...),
              quote = TRUE)
}
```

For our examples, the chunks have these sizes:

```r
sapply(parallel:::splitList(1:100, 5), length)
[1] 20 20 20 20 20
```

There we have it: 5 chunks. 5 workers. With this work distribution,
there can't possibly be any load balancing, because
each worker is given a single chunk and then it stops working
because there are no more chunks.
Instead, **parLapplyLB** should look like this (patch is attached):

```r
parLapplyLB <- function(cl = NULL, X, fun, ...)
{
      cl <- defaultCluster(cl)

      chunkSize <- max(length(cl), ceiling(length(X) / length(cl)))

      chunks <- splitList(X, chunkSize)

      do.call(c,
              clusterApplyLB(cl, x = chunks, fun = lapply, fun, ...),
              quote = TRUE)
}
```

Examples with a cluster of 5 workers:

```r
# length(cl) < length(X)
sapply(parallel:::splitList(1:100, ceiling(100 / 5)), length)
   [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5

# length(cl) >= length(X)
sapply(parallel:::splitList(1:4, 4), length)
[1] 1 1 1 1
# one worker idles here, but we can't do better than that
```

With this patch, the number of chunks is larger than the number of
workers, if possible at all, and then load balancing
should work.

Best Regards



______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel

--
Christian Krause

Scientific Computing Administration and Support


------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Email: christian.kra...@idiv.de

Office: BioCity Leipzig 5e, Room 3.201.3

Phone: +49 341 97 33144


------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
German Centre for Integrative Biodiversity Research (iDiv)
Halle-Jena-Leipzig
Deutscher Platz 5e

04103 Leipzig

Germany


------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
iDiv is a research centre of the DFG – Deutsche
Forschungsgemeinschaft
iDiv ist eine zentrale Einrichtung der Universität Leipzig im Sinne
des § 92 Abs. 1 SächsHSFG und wird zusammen mit der
Martin-Luther-Universität Halle-Wittenberg und der
Friedrich-Schiller-Universität Jena betrieben sowie in Kooperation mit
dem Helmholtz-Zentrum für Umweltforschung GmbH – UFZ. Beteiligte
Kooperationspartner sind die folgenden außeruniversitären
Forschungseinrichtungen: das Helmholtz-Zentrum für Umweltforschung GmbH
- UFZ, das Max-Planck-Institut für Biogeochemie (MPI BGC), das
Max-Planck-Institut für chemische Ökologie (MPI CE), das
Max-Planck-Institut für evolutionäre Anthropologie (MPI EVA), das
Leibniz-Institut Deutsche Sammlung von Mikroorganismen und Zellkulturen
(DSMZ), das Leibniz-Institut für Pflanzenbiochemie (IPB), das
Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)
und das Leibniz-Institut Senckenberg Museum für Naturkunde Görlitz
(SMNG). USt-IdNr. DE 141510383
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel



______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel

Reply via email to