RedisParam provides a BiocParallel ‘back-end’ for parallel
computation. RedisParam uses a Redis server to manage
communication between manager and workers. This offers a number
possibilities not available to other back-ends. For instance,
workers can be launched independently of the manager, including
part way through a parallel evaluation job. RedisParam is well-suited to
kubernetes and other cloud-based scenarios, in part because no special
network configuration is required for manager and worker communication.
RedisParam supports all BiocParallel features, including bplapply(),
bpiterate(), reproducible random number streams, and flexible job
scheduling.
RedisParam 1.6.0
RedisParam implements a BiocParallel backend using redis, rather
than sockets, for communication. It requires a redis server; see
?RedisParam for host and port specification. redis is a good
solution for cloud-based environments using a standard docker image. A
particular feature is that the number of workers can be scaled during
computation, for instance in response to kubernetes auto-scaling.
Ensure that a redis server is running, e.g., from the command line
$ redis-serverOn a single computer, in R, load and use the RedisParam package in the same way as other BiocParallel backends, e.g.,
library(RedisParam)
p <- RedisParam(workers = 5)
result <- bplapply(1:7, function(i) Sys.getpid(), BPPARAM = p)
table(unlist(result))For independently managed workers, start workers in separate processes, e.g.,
Sys.getpid()
library(RedisParam)
p <- RedisParam(jobname = "demo", is.worker = TRUE)
bpstart(p)Start and use the manager in a separate process. Be sure to use the
same jobname =.
Sys.getpid() # e.g., 8563
library(RedisParam)
p <- RedisParam(jobname = 'demo', is.worker = FALSE)
result <- bplapply(1:7, function(i) Sys.getpid(), BPPARAM = p)
unique(unlist(result)) # e.g., 9677Independently started workers can be terminated from the manager
rpstopall(p)This version of the vignette was built on 2024-05-01 with the following software package versions: