Nothing
###########################
## examples in vignettes ##
###########################
#library(tmplate)
# one line definition
T <- '<:SHELL_CALL:>
<:SLURM_PARTITION:>
<:SLURM_NODES:>
<:SLURM_TASKS:>
<:SLURM_MEMORY:>
<:SLURM_TIME:>
@r if(!any(grepl("^<:MISS:>$","<:SLURM_ARRAY:>"))) paste("<:SLURM_ARRAY:>")
@r # R chunk (only assignation)
@r if(.Platform$OS.type=="unix"){
@r is_mod <- system("mod=$(module --dumpversion 2>&1) || mod=`echo -1`; echo $mod",intern = TRUE)
@r } else {
@r is_mod <- "-1"
@r }
@r # R chunk (printing)
@r ifelse(is_mod=="-1", "# module environment not found", paste("<:MODULES_LOAD:>"))
<:WORKDIR:>
@r if(!any(grepl("^<:MISS:>$","<:SLURM_ARRAY:>"))) c("<:TASK:>","<:PASS_TASK:>") else paste("<:MISS:>")
<:MPI_N:>
<:MPIRUN:>
<:MESSAGE_CLOSE:>
'
# using input file
T <- readLines(system.file("examples/template.txt", package = "tmplate"))
# translate content
TT <- tmplate::translate(
SHELL_CALL='#!/bin/bash',
SLURM_SBATCH=ifelse(.Platform$OS.type=="unix", ifelse(system("clu=$(sinfo --version 2>&1) || clu=`echo -1`; echo $clu",intern = TRUE)=="-1", '<:MISS:>', '#SBATCH '), '<:MISS:>'),
SLURM_PARTITION='<:SLURM_SBATCH:>--partition=defq',
SLURM_ASK_NODES=2,
SLURM_NODES='<:SLURM_SBATCH:>--nodes=<:SLURM_ASK_NODES:>',
SLURM_ASK_TASKS=4,
SLURM_TASKS='<:SLURM_SBATCH:>--ntasks-per-node=<:SLURM_ASK_TASKS:>',
SLURM_MEMORY='<:SLURM_SBATCH:>--memory=2gb',
SLURM_TIME='<:SLURM_SBATCH:>--time=1:00:00',
SLURM_ARRAY="<:MISS:>",
MODULES_LOAD='module load module/for/openmpi module/for/R',
WORKDIR=ifelse('<:SLURM_SBATCH:>'!='#SBATCH','# no slurm machine','cd ${SLURM_SUBMIT_DIR}'),
TASK="<:MISS:>",
PASS_TASK="<:MISS:>",
PASS_TASK_VAR="<:MISS:>",
MPI_N="<:MISS:>",
MPI_ASK_N='<r@ <:SLURM_ASK_NODES:> * <:SLURM_ASK_TASKS:> @>',
R_HOME=R.home("bin"),
R_OPTIONS='--no-save --no-restore',
R_FILE_INPUT='script.R',
R_ARGS='',
R_FILE_OUTPUT='output.Rout',
MPIRUN='mpirun --mca mpi_warn_on_fork 0 -n <:MPI_ASK_N:> <:R_HOME:>/Rscript <:R_OPTIONS:> /
"<:R_FILE_INPUT:>" <r@ ifelse(!any(grepl("^<:NULL:>$","<:SLURM_ARRAY:>")),"<:PASS_TASK_VAR:>","") @> /
<:R_ARGS:> > <:R_FILE_OUTPUT:>',
MESSAGE_CLOSE='echo "Job submitted on $(date +%F) at $(date +%T)."',
drop = TRUE,
default = "MISS",
template = T
)
# display result output
cat(TT, sep="\n")
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