Generic execute command for SGE grids

Character to be used with the cmd() function to launch a parallelised job on SGE.

sge_parallel_execute

sge_parallel_execute2

sge_parallel_execute_batch

Format

An object of class character of length 1.

An object of class character of length 1.

An object of class character of length 1.

Value

A character object.

Details

Requires cores and parafile fields to be set.

sge_parallel_execute2 doubles the amount slots taken by the job (e.g. to avoid hyperthreading).

sge_parallel_execute_batch eliminates pre-processing on master. Job submitted from compute node. This job will occupy one slot for the duration of the NONMEM run. node. Job pre-processed and submitted from a compute node

See also

nm_getsetters().

Examples

# create example object m1 from package demo files
exdir <- system.file("extdata", "examples", "theopp", package = "NMproject")
m1 <- new_nm(run_id = "m1", 
             based_on = file.path(exdir, "Models", "ADVAN2.mod"),
             data_path = file.path(exdir, "SourceData", "THEOPP.csv")) %>%
  cmd(sge_parallel_execute) %>%
  parafile("/opt/NONMEM/nm75/run/mpilinux8.pnm") %>%
  cores(8)
  
cmd(m1)
#> [1] "execute -run_on_sge -parafile=/opt/NONMEM/nm75/run/mpilinux8.pnm -sge_prepend_flags='-pe orte 8 -V' runm1.mod -dir=m1 -nodes=8"

m2 <- m1 %>% child("m2") ## inherits same command as above

sge_parallel_execute ## view the character to see how psn interfaces with SGE
#> [1] "execute -run_on_sge -parafile={parafile} -sge_prepend_flags='-pe orte {cores} -V' {ctl_name} -dir={run_dir} -nodes={cores}"