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Commit 5e9d9c78 authored by snuverink_j's avatar snuverink_j
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remove runoptpilot script: optimiser integrated in OPAL, fixes #4

parent dc3c5e59
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runOPAL/runOPAL.py
View file @ 5e9d9c78
......@@ -12,7 +12,6 @@ Script that launches OPAL simulations
import sys,os,shutil,glob
import subprocess
from simulation import Simulation
from runoptpilot import Runoptpilot
from opaldict import OpalDict
def getNearestRestartStep(restart_pos,fn):
......@@ -57,7 +56,6 @@ def printUsage():
print("--test does everything but submitting the job")
print("--keep if same simulation has been run before, keep old data and abort")
print("--nobatch run opal locally not using the batch system and waits until the job is done")
print("--optPilot run optPilot (at the moment with default MOGA settings on host merlinl01.psi.ch)")
print("--info=<num> steers the std-output of OPAL. The range is 0 < num < 6 (default), from minimal to maximum output")
print("--queue=<qname> defines in which queue the job goes. Overwrites QUEUE (deprecated SGE_QUEUE)")
print("--hypert=<num> defines the number of Hyper-Threads used. Default 0")
......@@ -102,7 +100,6 @@ def main(argv):
doTest = False
doKeep = False
doNobatch = False
doOptPilot = False
restart_step = -99
restart_file = ""
queue = ""
......@@ -126,8 +123,6 @@ def main(argv):
doKeep = True
elif arg.startswith("--nobatch"):
doNobatch = True
elif arg.startswith("--optPilot"):
doOptPilot = True
elif arg.startswith("--info"):
info = arg.split("=")[1]
elif arg.startswith("--queue"):
......@@ -178,14 +173,7 @@ def main(argv):
opaldict.addUserValues(argv)
opaldict.scale()
if doOptPilot:
opt = Runoptpilot(opaldict)
qid = opt.run(N, baseFileName, restart_step, inputfilePath, tmplFile, oinpFile, restart_file, doTest, doKeep, doNobatch)
if doNobatch:
print("... finished!\n")
else:
print("SGE-ID= {}\n".format(qid))
elif not opaldict.hasRanges():
if not opaldict.hasRanges():
sim = Simulation(opaldict)
qid = sim.run(N, baseFileName, restart_step, inputfilePath, tmplFile, oinpFile, restart_file, doTest, doKeep, doNobatch, info, queue, hypert, quiet)
if doNobatch:
......
runOPAL/runoptpilot.py deleted 100644 → 0
View file @ dc3c5e59
"""
Runoptpilot class handles sge job related things
@author: Andreas Adelmann <andreas.adelmann@psi.ch>
@author: Yves Ineichen <yves.ineichen@psi.ch>
@version: 0.1
"""
import sys,re,os,string,fileinput,shutil,glob,subprocess #,commands
import time
class Runoptpilot:
def __init__(self, opaldict):
self.opaldict = opaldict
self.dirname = ""
def isOldMpiVersion(self):
mpistr = os.environ.get('OPENMPI')
mpiver = mpistr.partition("-")[2].partition('-')[0]
mpiv = mpiver.split(".")
if mpiv[0] == "1" and mpiv[1] >= "4":
return False
else:
return True
def createDirectory(self, dirname, doKeep):
# If there's already an file remove it...
if os.path.isdir(self.dirname):
if doKeep:
print( 'KEEP existing directory ', self.dirname)
return False
else:
print( 'REMOVE existing directory ', self.dirname)
shutil.rmtree(self.dirname)
# create directory
os.mkdir(self.dirname)
return True
def run(self,N, baseFileName, restart_step, inputfilePath, tmplFile, oinpFile, restart_file, doTest, doKeep, doNobatch):
CORES = int(self.opaldict['CORES'])
if CORES == 0:
CORES = 1
#hostname = commands.getoutput("hostname")
p = subprocess.Popen(['hostname'], stdout=subprocess.PIPE)
hostname, err = p.communicate()
time = os.getenv("SGE_TIME", "s_rt=11:59:00,h_rt=12:00:00")
ram = os.getenv("SGE_RAM", "4")
optpilotexepath = os.getenv("OPT_PILOT_EXE_PATH")
queue = os.getenv("SGE_QUEUE", "prime_bd.q")
resultDir = os.getenv("RESULTDIR", "results");
maxGenerations = os.getenv("MAXGENERATIONS", "100");
initialPopulation = os.getenv("INITIALPOPULATION", "62");
#independentGens = os.getenv("INDEPENDENTGENS", "62");
numCoworkers = os.getenv("NUMCOWORKERS","1")
numMasters = os.getenv("NUMMASTERS","1")
dumpDat = os.getenv("DUMPDAT","1")
solSynch = os.getenv("SOLSYNCH","1")
tmpDir = os.getenv("SIMTMPDIR",".tmp")
mutProb = os.getenv("MUTATIONPROB","0.5")
if (hostname.startswith("merlin")):
print( 'Done with setup of the optPilot simulation and executing the job on ' + str(CORES) + ' cores...\n')
self.WriteSGEOrteMerlin(optpilotexepath, baseFileName, CORES, time, ram, maxGenerations,
initialPopulation, numCoworkers, numMasters, dumpDat,
solSynch, resultDir, tmpDir, mutProb)
if not doTest:
qid = commands.getoutput('qsub -V -q ' + queue + ' -pe openmpi '+str(CORES)+' runopt.sge | awk \'{print $3}\' ')
print( 'Done with setup of the optPilot simulation and submitting the job to ',queue, 'with ',CORES,'cores \n')
else:
print( 'Done with setup of the optPilot simulation but no batch sumbmission \n')
elif not doNobatch:
print( "optPilot is running only on Merlin for now\n")
def WriteSGEOrteMerlin(self, optpilotexepath, oinpFile, cores, time, ram, maxGenerations, initialPopulation, numCoworkers, numMasters, dumpDat, solSynch, resultDir, tmpDir, mutProb):
title=oinpFile.partition(".")[0]
myfile = open('runopt.sge','w')
s1 = "#!/bin/bash \n"
s1 += "#$ -cwd \n"
s1 += "#$ -j y \n"
s1 += "#$ -N " + title + "\n"
s1 += "#$ -pe openmpi " + str(cores) + " \n"
s1 += "#$ -q prime_bd.q \n"
s1 += "#$ -v LD_LIBRARY_PATH,OPT_PILOT_HOME,OPT_PILOT_DIR,OPT_PILOT_EXE_PATH,OPENMPI,OPENMPI_DIR \n"
s1 += "#$ -l " + time + ",ram=" + ram + "G\n"
s1 += "# Set the environment variables:\n"
s1 += "if [ -n \"$OPENMPI\" ]; then \n"
s1 += " MPIEXEC=$OPENMPI/bin/mpiexec\n"
s1 += "elif [ -n \"$OPENMPI_DIR\" ]; then \n"
s1 += " MPIEXEC=$OPENMPI_DIR/bin/mpiexec \n"
s1 += "fi \n"
s1 += "export OMP_NUM_THREADS=1\n"
s1 += "export OMPI_MCA_btl='self,sm,openib' \n"
s1 += "#################################################### \n"
s1 += "# BEGIN DEBUG \n"
s1 += "# Print the SGE environment on master host: \n"
s1 += "####################################################\n"
s1 += "echo \"=== SGE job JOB_NAME=$JOB_NAME JOB_ID=$JOB_ID\" \n"
s1 += "####################################################\n"
s1 += "echo DATE=`date`\n"
s1 += "echo HOSTNAME=`hostname` \n"
s1 += "echo PWD=`pwd`\n"
s1 += "echo NSLOTS=$NSLOTS \n"
s1 += "echo PE_HOSTFILE=$PE_HOSTFILE \n"
s1 += "cat $PE_HOSTFILE \n"
s1 += "# END DEBUG \n"
s1 += "#################################################### \n"
s1 += "THEEXE=" + optpilotexepath + "/pisa-opal.exe \n"
s1 += "#################################################### \n"
s1 += "# START SIMULATION \n"
s1 += "# \n"
s1 += "rm -f *_results.dat *.0 \n"
s1 += "rm -f *.trace \n"
s1 += "rm -rf " + tmpDir + "\n"
s1 += "# \n"
s1 += "export FIELDMAPS=" + os.getenv('FIELDMAPS') + " \n"
s1 += "export DISTRIBUTIONS=" + os.getenv('DISTRIBUTIONS') + " \n"
s1 += "export TEMPLATES=" + os.getenv('TEMPLATES') + " \n"
s1 += "export SIMTMPDIR=`pwd`/tmp \n"
s1 += "export FNBASE="+oinpFile+"\n"
s1 += "rm -rf $SIMTMPDIR && mkdir $SIMTMPDIR \n"
s1 += "# \n"
s1 += "export CMD=\"$THEEXE --inputfile=$TEMPLATES/" + oinpFile + ".tmpl --outdir=$PWD/" + resultDir + " --outfile=" + oinpFile +".dat"
s1 += " --maxGenerations=" + maxGenerations + " --initialPopulation=" + initialPopulation + " --sol-synch=" + solSynch + " --num-coworkers=" + numCoworkers
s1 += " --num-masters=" + numMasters + " --dump-dat=" + dumpDat + " --gene-mutation-probability=" + mutProb + " \" \n"
s1 += "MPICMD=\"$MPIEXEC --prefix $OPENMPI_DIR -x LD_LIBRARY_PATH -x OMP_NUM_THREADS -x OMPI_MCA_btl -np $NSLOTS -machinefile $TMPDIR/machines $CMD\" \n"
s1 += "echo \"Command to run:\" \n"
s1 += "echo $MPICMD \n"
s1 += "# \n"
s1 += "$MPICMD \n"
myfile.write(s1)
myfile.close()
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