R/NMgenPNM.R

In NMsim: Seamless 'Nonmem' Simulation Platform

##' Generate PNM file for sge clusters
##'
##' @param nc number of cores wanted
##' @param file The file path to write the result to
##' @return The file path (character string)
##' @keywords internal

NMgenPNM <- function(nc,file){

    if(missing(file)) file <- tempfile()
    
    text <- sprintf("$GENERAL
NODES=%s PARSE_TYPE=2 TIMEOUTI=100 TIMEOUT=10 PARAPRINT=0 TRANSFER_TYPE=1
;SINGLE node: NODES=1
;MULTI node: NODES>1
;WORKER node: NODES=0
; parse_num=number of subjects to give to each node
; parse_type=0, give each node parse_num subjects
; parse_type=1, evenly distribute numbers of subjects among available nodes
; parse_type=2, load balance among nodes
; parse_type=3, assign subjects to nodes based on idranges
; parse_type=4, load balance among nodes, taking into account loading time.  Will assess ideal number of nodes.
; If loading time too costly, will eventually revert to single CPU mode.
; timeouti=seconds to wait for node to start.  if not started in time, deassign node, and give its load to next worker, until next iteration
; timeout=minutes to wait for node to compelte.  if not completed by then, deassign node, and have manager complete it.
; paraprint=1  print to console the parallel computing process.  Can be modified at runt-time with ctrl-B toggle.
; But parallel.log always records parallelization progress.
; transfer_type=0 for file transfer, 1 for mpi

;THE EXCLUDE/INCLUDE may be used to selectively use certain nodes, out of a large list.
;$EXCLUDE 5-7 ; exclude nodes 5-7
;$EXCLUDE ALL 
;$INCLUDE 1,4-6

$COMMANDS ;each node gets a command line, used to launch the node session
1: /usr/local/mpich3/bin/mpiexec -wdir \"$PWD\" -n 1 ./nonmem $*
2:-wdir \"$PWD\" -n %s ./nonmem -wnf

$DIRECTORIES
1:NONE ; FIRST DIRECTORY IS THE COMMON DIRECTORY
2-[nodes]:worker{#-1} ; NEXT SET ARE THE WORKER directories

$IDRANGES ; USED IF PARSE_TYPE=3
1:1,50
2:51,100",as.character(nc),as.character(nc-1))

    ## con.newfile <- file(file, "wb")
    ## writeLines(text, con = con.newfile)
    ## close(con.newfile)
    writeTextFile(lines=text,file=file)
    
    return(file)
    
}