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setpostprocess_locked.py
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244 lines (202 loc) · 9.74 KB
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import numpy as np
import os, sys
import netCDF4 as nc
from batch_system import SUB, BATCHSCRIPT
from identity import USER, SCRATCH
from crawldefs import Job
#This is really a minimal working example. The user has no choice in which fields to provide.
#Any missed fields, and the script will crash. It is however unusual in that the 'workdir' is
#not a folder called jobXX within the postprocess tree, and is probably instead in some *other*
#code's tree--in a way, a little parasitic.
def prep(job):
workdir = job.parameters["workdir"]
gtype = job.parameters["type"]
gcm = job.parameters["gcm"]
cwd = os.getcwd()
homedir = cwd+"/postprocess_locked/job"+str(job.home)
notify = 'ae'
os.system("cp postprocess_locked/clean/* "+workdir+'/')
os.system("cp release.py "+workdir+'/')
os.system("cp crawldefs.py "+workdir+"/")
os.system("cp identity.py "+workdir+"/")
if gtype=="plasim":
data = nc.Dataset("hopper/"+gcm,"r")
lats = data.variables['lat'][:]
lons = data.variables['lon'][:]
if gtype=="lmdz":
data = np.load("hopper/"+gcm).item()
#Or do we need to use rlatv,rlonu? latitude and longitude give us edges I think. But the
#grid seems to be discretized that way too?
lats = data['latitude'][1:-1] #Get rid of poles
lons = data['longitude'][:-1] #Get rid of redundant longitude
np.save(workdir+"/latitudes.npy",lats)
np.save(workdir+"/longitudes.npy",lons)
if "times" in job.parameters:
times = job.parameters["times"]
else:
times="0"
if "angles" in job.parameters:
angles = job.parameters["angles"]
else:
angles="Z"
if "NCORES" in job.parameters:
ncpu = job.parameters["NCORES"]
else:
ncpu = '1'
if "QUEUE" in job.parameters:
queue = job.parameters["QUEUE"]
else:
queue = "workq"
if "notify" in job.parameters:
notify = job.parameters['notify']
part2 = False
if "part2" in job.parameters:
if job.parameters["part2"]=="0":
part2=False
else:
part2=True
color=False
if "color" in job.parameters:
if job.parameters["color"]=="True":
color=True
else:
color=False
makemap=False
if "map" in job.parameters:
if job.parameters["map"]=="True":
makemap=True
else:
makemap=False
tag = ''
if color:
tag+="color "
if makemap:
tag+="map "
if not part2:
jobscript =(BATCHSCRIPT(job,notify)+
"module load gcc/4.9.1 \n"+
"module load python/2.7.9 \n"+
"cd "+workdir+" \n"+
"cp "+cwd+"/postprocess_locked/job"+str(job.home)+"/job.npy ./ \n"+
"mkdir "+SCRATCH+"/postprocess_locked/ \n"+
"mkdir "+SCRATCH+"/postprocess_locked/job"+str(job.home)+"/ \n"+
"cp -a * "+SCRATCH+"/postprocess_locked/job"+str(job.home)+"/ \n"+
"cd "+SCRATCH+"/postprocess_locked/job"+str(job.home)+"/ \n"+
"python -B postprocess_locked.py "+times+" "+angles+" "+tag+" \n"+
"cp -a "+SCRATCH+"/postprocess_locked/job"+str(job.home)+"/* "+workdir+"/ \n"+
"rm -rf * \n"+
"cd "+workdir+" \n"+
"cp spectra.nc "+cwd+"/postprocess_locked/output/"+job.name+"_spectra.nc \n"+
"cp phases.nc "+cwd+"/postprocess_locked/output/"+job.name+"_phases.nc \n"+
"python -B release.py \n")
else:
tag+="phases "
jobscript =(BATCHSCRIPT(job,notify)+
"module load gcc/4.9.1 \n"+
"module load python/2.7.9 \n"+
"cd "+workdir+" \n"+
"cp "+cwd+"/postprocess_locked/job"+str(job.home)+"/job.npy ./ \n"+
"mkdir "+SCRATCH+"/postprocess_locked/ \n"+
"mkdir "+SCRATCH+"/postprocess_locked/job"+str(job.home)+"/ \n"+
"cp -a * "+SCRATCH+"/postprocess_locked/job"+str(job.home)+"/ \n"+
"cd "+SCRATCH+"/postprocess_locked/job"+str(job.home)+"/ \n"+
"python -B postprocess_locked.py "+times+" "+angles+" "+tag+" \n"+
"cp -a "+SCRATCH+"/postprocess_locked/job"+str(job.home)+"/* "+workdir+"/ \n"+
"rm -rf * \n"+
"cd "+workdir+" \n"+
"cp phases.nc "+cwd+"/postprocess_locked/output/"+job.name+"_phases.nc \n"+
"python -B release.py \n")
rs = open(homedir+"/runpostprocess_locked","w")
rs.write(jobscript)
rs.close()
def submit(job):
workdir = job.parameters["workdir"]
cwd = os.getcwd()
homedir = cwd+"/postprocess_locked/job"+str(job.home)
if "DEPENDENCIES" in job.parameters:
dlist = job.parameters["DEPENDENCIES"].split(',')
priorjobs = []
for d in dlist:
with open(d+".id","r") as f:
priorjobs.append(f.read().split('\n')[0].split()[0])
os.system("echo %s >> "%job.pid+d+".id") #indicate that we depend on this job
os.system("cd "+homedir+" && "+HOLD(priorjobs)+" runpostprocess_locked > %s/%s.id && cd ../../"%(job.top,job.pid))
else:
os.system("cd "+homedir+" && "+SUB+" runpostprocess_locked > %s/%s.id && cd ../../"%(job.top,job.pid))
def _prep(job):
workdir = job[0]
cwd = os.getcwd()
top = cwd
gtype = "plasim" #job.parameters["type"]
jobname = job[1]
gcm = top + "/plasim/output/"+jobname+"_snapshot.nc"
homedir = cwd+"/postprocess_locked/"+jobname
notify = 'ae'
os.system("cp postprocess_locked/clean/* "+workdir+'/')
os.system("cp release.py "+workdir+'/')
os.system("cp crawldefs.py "+workdir+"/")
os.system("cp identity.py "+workdir+"/")
data = nc.Dataset(gcm,"r")
lats = data.variables['lat'][:]
lons = data.variables['lon'][:]
np.save(workdir+"/latitudes.npy",lats)
np.save(workdir+"/longitudes.npy",lons)
times = job[2]
angles = job[3]
ncpu = '1'
queue = job[4]
notify = 'ae'
color = True
makemap = True
tag = ''
if color:
tag+="color "
if makemap:
tag+="map "
dummyjob = Job("# PID MODEL JOBNAME STATE NCORES QUEUE","%d pipeline ppc_%s 0 1 %s"%(-9999,jobname,queue),-1)
jobscript =(BATCHSCRIPT(dummyjob,notify)+
"module load gcc/4.9.1 \n"+
"module load python/2.7.9 \n"+
"cd "+workdir+" \n"+
#"cp "+cwd+"/postprocess_locked/job"+str(job.home)+"/job.npy ./ \n"+
"mkdir "+SCRATCH+"/postprocess_locked/ \n"+
"mkdir "+SCRATCH+"/postprocess_locked/"+jobname+"/ \n"+
"tar cvzf stuff.tar.gz * \n"+
"rsync -avzhur stuff.tar.gz "+SCRATCH+"/postprocess_locked/"+jobname+"/ \n"+
"rm -rf stuff.tar.gz \n"+
"cd "+SCRATCH+"/postprocess_locked/"+jobname+"/ \n"+
"tar xvzf stuff.tar.gz \n"+
"rm -rf stuff.tar.gz \n"+
"python -B postprocess_locked.py "+times+" "+angles+" "+tag+" \n"+
"tar cvzf stuff.tar.gz * \n"+
"rsync -avzhur stuff.tar.gz "+workdir+"/ \n"+
"rm -rf * \n"+
"cd "+workdir+" \n"+
"tar xvzf stuff.tar.gz \n"+
"rm stuff.tar.gz \n"+
"cp spectra.nc "+cwd+"/postprocess_locked/output/"+jobname+"_spectra.nc \n"+
"cp phases.nc "+cwd+"/postprocess_locked/output/"+jobname+"_phases.nc \n\n"+
"cd "+cwd+"/postprocess_locked/output/ \n"+
"python -B orthoprojection.py "+jobname+"_phases.nc %s \n"%times+
"mv "+jobname+"*/*.png . \n"+
"for p in $(ls "+jobname+"*.png) \n"+
"do \n"
" mogrify -trim +repage $p \n"+
" mogrify -shave 1x1 +repage $p \n"+
"done \n"+
"rm -rf "+jobname+"*/ \n"+
"cp "+top+"/plasim/output/"+jobname+".nc . \n"+
"cd "+workdir+" \n"+
"python -B release.py \n")
rs = open(workdir+"/runpostprocess_locked","w")
rs.write(jobscript)
rs.close()
def _submit(job):
workdir = job[0]
cwd = os.getcwd()
homedir = cwd+"/postprocess_locked/"+job[1]
os.system("cd "+workdir+" && "+SUB+" runpostprocess_locked && cd ../../")
if __name__=="__main__":
job = sys.argv[1:]
_prep(job)
_submit(job)