tasktools

• Version: 0.2-0
• Status:
• License:BSD 2-Clause
• Author: Drew Schmidt

Tools for task-based parallelism with MPI via pbdMPI. Currently we provide these basic functions:

1. mpi_napply() --- a distributed lapply() that operates on an integer sequence. Supports checkpoint/restart and non-prescheduled workloads.
2. mpi_lapply() --- a fully general, distributed lapply().

These functions are conceptually similar to pbdLapply() from the pbdMPI package, but with some key differences. The pbdMPI functions have more modes of operation, allowing for different kinds of distributions of the inputs for the more general mpi_lapply(). And naturally, the pbdMPI functions do not handle checkpoint/restart.

In addition to these "ply" functions, also offer mpi_progress() to check on the status of running jobs.

Installation

You can install the stable version from the HPCRAN using the usual install.packages():

install.packages("tasktools", repos=c("https://hpcran.org", "https://cran.rstudio.com"))

The development version is maintained on GitHub:

remotes::install_github("RBigData/tasktools")

Examples

Complete source code for all of these examples can be found in the inst/examples directory of the tasktools source tree. Here we'll take a look at them in pieces. Throughout, we'll use a (fake) "expensive" function for our evaluations:

costly=function(x, waittime)
{
Sys.sleep(waittime)
print(paste("iteration:", x))
sqrt(x)
}

We can run a checkpointed lapply() in serial via crlapply() from the crlapply package:

ret=crlapply::crlapply(1:10, costly, FILE="/tmp/cr.rdata", waittime=0.5)
unlist(ret)

If we save this source to the file crlapply.r. We can run it and kill it a few times to show its effectiveness:

$ r crlapply.r [1] "iteration: 1"
[1] "iteration: 2"
[1] "iteration: 3"
^C
$ r crlapply.r [1] "iteration: 4"
[1] "iteration: 5"
[1] "iteration: 6"
[1] "iteration: 7"
^C
$ r crlapply.r [1] "iteration: 8"
[1] "iteration: 9"
[1] "iteration: 10"
[1] 1.000000 1.414214 1.732051 2.000000 2.236068 2.449490 2.645751 2.828427
[9] 3.000000 3.162278

Since we are operating on the integer sequence of values 1 to 10, we can easily parallelize this, even distributing the work across multiple nodes, with mpi_napply():

ret= mpi_napply(10, costly, checkpoint_path="/tmp", waittime=1)
comm.print(unlist(ret))

To see exactly what happens during execution, we modify the printing in the "costly" function to be:

cat(paste("iter", i, "executed on rank", comm.rank(), "\n"))

Let's run this with 3 MPI ranks. We can again run and kill it a few times to demonstrate the checkpointing:

$ mpirun -np 3 r mpi_napply.r iter 4 executed on rank 1 iter 7 executed on rank 2 iter 1 executed on rank 0 ^Citer 2 executed on rank 0 iter 8 executed on rank 2 iter 5 executed on rank 1 $ mpirun -np 3 r mpi_napply.r iter 9 executed on rank 2 iter 3 executed on rank 0 iter 6 executed on rank 1 iter 10 executed on rank 2 [1] 1.000000 1.414214 1.732051 2.000000 2.236068 2.449490 2.645751 2.828427
[9] 3.000000 3.162278

There is also a non-prescheduling variant. This can be useful if there is a lot of variance among function evaluation for the inputs, and you want the values to be executed on a "first come, first serve" basis. All we have to do is set preschedule=FALSE:

ret= mpi_napply(10, costly, preschedule=FALSE, waittime=1)
comm.print(unlist(ret))

Now, it's worth noting that in this case, rank 0 behaves as the manager, doling out work. So it is not used in computation:

iter 1 executed on rank 1 iter 2 executed on rank 2 iter 3 executed on rank 1 iter 4 executed on rank 2 iter 5 executed on rank 1 iter 6 executed on rank 2 iter 7 executed on rank 1 iter 8 executed on rank 2 iter 9 executed on rank 1 iter 10 executed on rank 2 [1] 1.000000 1.414214 1.732051 2.000000 2.236068 2.449490 2.645751 2.828427
[9] 3.000000 3.162278

This too supports checkpointing, but hopefully how that works is clear.

Progress Bar

We also support a kind of progress bar, but it's definitely not what you're thinking. Let's start with an example similar to the one above:

suppressMessages(library(tasktools))
f=function(i) {print(i); Sys.sleep(1); sqrt(i)}
ignore= mpi_napply(20, f, checkpoint_path="/tmp")
finalize()

We can put these into the file slow_sqrt.r and run it for a bit before manually killing it with Ctrl+c:

$ mpirun -np 3 Rscript slow_sqrt.r
[1] 14
[1] 7
[1] 1
[1] 15
^C[1] 16
[1] 8
[1] 2

We can check the progress by invoking mpi_progress():

$ Rscript -e "tasktools::mpi_progress('/tmp')"## [=================---------------------------------] (7/20)

The progress bar works by scanning the checkpoint files, so we don't actually have to kill the tasks to run the progress bar bit (and in fact for a real workflow, you wouldn't want to). But for the sake of demonstration, this is much simpler.

The above example was run with the default preschedule=TRUE, but it will also work if we have preschedule=FALSE. There are some caveats to the progress bar, however. Please carefully check the ?tasktools::mpi_progress documentation.