write_HPC_shell: Make HPCC Shell Files to Run Xdbs

Description Usage Arguments Details Examples

View source: R/write_batch_funs.R

Description

This function makes a shell script to defining experiment runs for MSU's High Performance Computing Cluster (HPCC). This bash script copies the files needed to run SALUS (salus_gnu, gdb, cdb, sdb, xdb, and wdb files) to the current directory. Then the bash script will run SALUS. Then the bash script will remove the SALUS files from the current directories.Then the bash script will copy the SALUS results to your scratch directory. Modified from python writeTorque function by Brian Baer and Lydia Rill.

Usage

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write_HPC_shell(shDir, hpcHomeDir, hpcXdbDir, hpcOutDir, Nflag, xdb, sdb,
  wdbZip, DayVars, SeaVars, walltime, memory, cdb)

Arguments

shDir

Directory in which to save the output shell sh file. the sh filename is pulled from xdb filename

hpcHomeDir

Directory on HPCC in which source files reside for this run (sdb, xdb, zipped weather, etc). Should end in a forward slash

hpcOutDir

Directory on HPCC to write results to, Should end in a forward slash

Nflag

'-w' or '-wn'. -w runs SALUS without considerations of N stress

xdb

filename of the experiment file, without extension. sh name will be pulled from this.

sdb

filename of the soil file (no path, no .sdb.xml extension)

wdbZip

filename of the zipped weather file. Script will unzip on the node

DayVars

CSV string of SALUS daily variables to return

SeaVars

CSV string of SALUS seasonal variables to return

walltime

For HPCC - how long you expect the job to run. Format HH:MM:SS

memory

For HPCC - how much memory the job will need. ie, '2gb' or '2000mb'

cdb

filename of the crop cdb.xml file, without the extension

Details

Recommended to follow this with the 'write_HPCC_bat' function in order to generate the batch bat file that will submit multiple shell files to the HPCC queue.

Examples

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#set variables
shDir <- 'C:/Users/deinesji/Dropbox/1PhdJill/hpa/LEMAs/SALUS/testHPCCrun'
hpcHomeDir <- '/mnt/home/deinesji/Example_SALUS_wheat/'
hpcOutDir <- '/mnt/home/deinesji/Example_SALUS_wheat/results/'
xdb <- 'lema_wheat_continuous'
sdb <- "KS"
wdbZip <- 'testHPCCrun.tar.gz'
DayVars <- 'ExpID,Title,SpeciesID,GWAD,IRRC,CWAD,DRNC,PREC,LAI'
SeaVars <- 'ExpID,Title,SpeciesID,GWAD,IRRC,CWAD,DRNC,PREC'
walltime <- '01:00:00'
memory <- '2000mb'

write_HPC_shell(shDir, hpcHomeDir, hpcOutDir, xdb, sdb, wdbZip, DayVars,
                SeaVars, walltime, memory)

jdeines/salustools documentation built on May 29, 2019, 1:03 a.m.