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message("Testing SnowParam")
test_SnowParam_construction <- function()
{
checkException(SnowParam(logdir = tempdir()))
p <- MulticoreParam(jobname = 'test')
checkIdentical(bpjobname(p), 'test')
}
test_SnowParam_SOCK <- function()
{
if (!requireNamespace("snow", quietly=TRUE))
DEACTIVATED("'snow' package did not load")
param <- SnowParam(2, "SOCK", tasks=2)
checkIdentical(FALSE, bpisup(param))
exp <- bplapply(1:2, function(i) Sys.getpid(), BPPARAM=param)
checkIdentical(2L, length(unique(unlist(exp))))
checkIdentical(FALSE, bpisup(param))
}
test_SnowParam_SOCK_character <- function()
{
bpstop(bpstart(SnowParam("localhost")))
}
test_SnowParam_MPI <- function()
{
if (.Platform$OS.type == "windows")
DEACTIVATED("MPI tests not run on Windows")
DEACTIVATED("MPI tests not run")
param <- SnowParam(2, "MPI", tasks=2)
checkIdentical(FALSE, bpisup(param))
exp <- bplapply(1:2, function(i) mpi.comm.rank(), BPPARAM=param)
checkIdentical(c(1L, 2L), sort(unlist(exp)))
checkIdentical(FALSE, bpisup(param))
}
test_SnowParam_coerce_from_SOCK <- function()
{
if (!requireNamespace("snow", quietly=TRUE))
DEACTIVATED("'snow' package did not load")
cl <- parallel::makeCluster(2L, "SOCK")
p <- as(cl, "SnowParam")
checkTrue(validObject(p))
obs <- tryCatch(bpstart(p), error=conditionMessage)
exp <- "'bpstart' not available; instance from outside BiocParallel?"
checkIdentical(exp, obs)
obs <- tryCatch(bpstop(p), warning=conditionMessage)
exp <- "'bpstop' not available; instance from outside BiocParallel?"
checkIdentical(exp, obs)
exp <- bplapply(1:2, function(i) Sys.getpid(), BPPARAM=p)
checkIdentical(2L, length(unique(unlist(exp))))
checkIdentical(TRUE, bpisup(p))
parallel::stopCluster(cl)
}
test_SnowParam_coerce_from_MPI <- function()
{
if (.Platform$OS.type == "windows")
DEACTIVATED("MPI tests not run on Windows")
if (!requireNamespace("snow", quietly=TRUE) ||
!requireNamespace("Rmpi", quietly=TRUE))
DEACTIVATED("'snow' and/or 'Rmpi' package did not load")
DEACTIVATED("MPI tests not run")
cl <- parallel::makeCluster(2L, "MPI")
p <- as(cl, "SnowParam")
checkTrue(validObject(p))
obs <- tryCatch(bpstart(p), error=conditionMessage)
exp <- "'bpstart' not available; instance from outside BiocParallel?"
checkIdentical(exp, obs)
obs <- tryCatch(bpstop(p), error=conditionMessage)
exp <- "'bpstop' not available; instance from outside BiocParallel?"
checkIdentical(exp, obs)
exp <- bplapply(1:2, function(i) mpi.comm.rank(), BPPARAM=p)
checkIdentical(c(1L, 2L), sort(unlist(exp)))
checkIdentical(TRUE, bpisup(p))
parallel::stopCluster(cl)
}
test_SnowParam_workers <- function()
{
if (.Platform$OS.type == "windows")
return()
if (!requireNamespace("snow", quietly=TRUE) ||
!requireNamespace("Rmpi", quietly=TRUE))
DEACTIVATED("'snow' and/or 'Rmpi' package did not load")
checkException(SnowParam("host", "MPI"), silent=TRUE)
checkException(SnowParam("host", "FORK"), silent=TRUE)
}
test_SnowParam_progressbar <- function()
{
checkIdentical(bptasks(SnowParam()), 0L)
checkIdentical(bptasks(SnowParam(tasks = 0L, progressbar = TRUE)), 0L)
checkIdentical(
bptasks(SnowParam(progressbar = TRUE)),
BiocParallel:::TASKS_MAXIMUM
)
}
test_SnowParam_bpforceGC <- function() {
checkIdentical(FALSE, bpforceGC(SnowParam()))
checkIdentical(FALSE, bpforceGC(SnowParam(force.GC = FALSE)))
checkIdentical(TRUE, bpforceGC(SnowParam(force.GC = TRUE)))
checkException(SnowParam(force.GC = NA), silent = TRUE)
checkException(SnowParam(force.GC = 1:2), silent = TRUE)
}
.test_cache <- function(msg) {
## No initial cache
msg1 <- BiocParallel:::.load_task_static(msg)
checkIdentical(msg, msg1)
## Extract the dynamic part of the task
msg2 <- BiocParallel:::.task_dynamic(msg)
checkTrue(!xor(msg2$static.fun, isTRUE(msg2$data$fun)))
if (length(msg2$static.args))
checkTrue(!any(msg2$static.args %in% names(msg2$data$args)))
else
checkTrue(all(msg2$static.args %in% names(msg2$data$args)))
## rebuild the EXEC
msg3 <- BiocParallel:::.load_task_static(msg2)
checkIdentical(msg, msg3)
## create another different msg
msg4 <- BiocParallel:::.EXEC("test", function(x)x,
args = list(a=1,b=1,c=1),
static.fun = TRUE,
static.args = c("a","b")
)
msg5 <- BiocParallel:::.load_task_static(msg4)
checkIdentical(msg5, msg4)
}
test_SnowParam_taskCache <- function() {
msg1 <- BiocParallel:::.EXEC("mytag1", identity,
args = list(a=1,b=2,c=3)
)
.test_cache(msg1)
msg2 <- BiocParallel:::.EXEC("mytag2", identity,
args = list(a=1,b=2,c=3),
static.fun = TRUE
)
.test_cache(msg2)
msg3 <- BiocParallel:::.EXEC("mytag3", identity,
args = list(a=1,b=2,c=3),
static.fun = TRUE,
static.args = c("a","b")
)
.test_cache(msg3)
msg4 <- BiocParallel:::.EXEC("mytag", identity,
args = NULL,
static.fun = TRUE
)
.test_cache(msg4)
}
test_SnowParam_fallback <- function(){
## trigger fallback
p <- SnowParam(1)
res <- bplapply(1, function(x) Sys.getpid(), BPPARAM = p)[[1]]
checkTrue(res == Sys.getpid())
## disable fallback
bpfallback(p) <- FALSE
res <- bplapply(1, function(x) Sys.getpid(), BPPARAM = p)[[1]]
checkTrue(res != Sys.getpid())
## enable fallback again
bpfallback(p) <- TRUE
res <- bplapply(1, function(x) Sys.getpid(), BPPARAM = p)[[1]]
checkTrue(res == Sys.getpid())
## no fallback
p <- SnowParam(2)
res <- bplapply(1, function(x) Sys.getpid(), BPPARAM = p)[[1]]
checkTrue(res != Sys.getpid())
}
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