Map Operation for Batch Systems

A parallel and asynchronous Map/mapply for batch systems. Note that this function only defines the computational jobs. The actual computation is started with submitJobs. Results and partial results can be collected with reduceResultsList, reduceResults or loadResult.

For a synchronous Map-like execution, see btmapply.

Usage

batchMap(
  fun,
  ...,
  args = list(),
  more.args = list(),
  reg = getDefaultRegistry()
)

Arguments

fun

[function]
Function to map over arguments provided via .... Parameters given via args or ... are passed as-is, in the respective order and possibly named. If the function has the named formal argument “.job”, the Job is passed to the function on the slave.

...

[ANY]
Arguments to vectorize over (list or vector). Shorter vectors will be recycled (possibly with a warning any length is not a multiple of the longest length). Mutually exclusive with args. Note that although it is possible to iterate over large objects (e.g., lists of data frames or matrices), this usually hurts the overall performance and thus is discouraged.

args

[list | data.frame]
Arguments to vectorize over as (named) list or data frame. Shorter vectors will be recycled (possibly with a warning any length is not a multiple of the longest length). Mutually exclusive with ....

more.args

[list]
A list of further arguments passed to fun. Default is an empty list.

reg

[Registry]
Registry. If not explicitly passed, uses the default registry (see setDefaultRegistry).

Value

[data.table] with ids of added jobs stored in column “job.id”.

See also

batchReduce

Examples

# example using "..." and more.args
tmp = makeRegistry(file.dir = NA, make.default = FALSE)
#> No readable configuration file found
#> Created registry in '/tmp/batchtools-example/reg1' using cluster functions 'Interactive'
f = function(x, y) x^2 + y
ids = batchMap(f, x = 1:10, more.args = list(y = 100), reg = tmp)
#> Adding 10 jobs ...
getJobPars(reg = tmp)
#> Key: <job.id>
#>     job.id  job.pars
#>      <int>    <list>
#>  1:      1 <list[1]>
#>  2:      2 <list[1]>
#>  3:      3 <list[1]>
#>  4:      4 <list[1]>
#>  5:      5 <list[1]>
#>  6:      6 <list[1]>
#>  7:      7 <list[1]>
#>  8:      8 <list[1]>
#>  9:      9 <list[1]>
#> 10:     10 <list[1]>
testJob(6, reg = tmp) # 100 + 6^2 = 136
#> ### [bt]: Setting seed to 23542 ...
#> [1] 136

# vector recycling
tmp = makeRegistry(file.dir = NA, make.default = FALSE)
#> No readable configuration file found
#> Created registry in '/tmp/batchtools-example/reg2' using cluster functions 'Interactive'
f = function(...) list(...)
ids = batchMap(f, x = 1:3, y = 1:6, reg = tmp)
#> Adding 6 jobs ...
getJobPars(reg = tmp)
#> Key: <job.id>
#>    job.id  job.pars
#>     <int>    <list>
#> 1:      1 <list[2]>
#> 2:      2 <list[2]>
#> 3:      3 <list[2]>
#> 4:      4 <list[2]>
#> 5:      5 <list[2]>
#> 6:      6 <list[2]>

# example for an expand.grid()-like operation on parameters
tmp = makeRegistry(file.dir = NA, make.default = FALSE)
#> No readable configuration file found
#> Created registry in '/tmp/batchtools-example/reg3' using cluster functions 'Interactive'
ids = batchMap(paste, args = data.table::CJ(x = letters[1:3], y = 1:3), reg = tmp)
#> Adding 9 jobs ...
getJobPars(reg = tmp)
#> Key: <job.id>
#>    job.id  job.pars
#>     <int>    <list>
#> 1:      1 <list[2]>
#> 2:      2 <list[2]>
#> 3:      3 <list[2]>
#> 4:      4 <list[2]>
#> 5:      5 <list[2]>
#> 6:      6 <list[2]>
#> 7:      7 <list[2]>
#> 8:      8 <list[2]>
#> 9:      9 <list[2]>
testJob(6, reg = tmp)
#> ### [bt]: Setting seed to 13241 ...
#> [1] "b 3"