def get_nellip(conf, is2n):
s2n = shapesim.get_s2n(conf, is2n)
s2n_fac = conf['s2n_fac']
nellip = shapesim.get_s2n_nrepeat(s2n, fac=s2n_fac)
if nellip < conf['min_gcount']:
nellip=conf['min_gcount']
return nellip
def main():
options,args = parser.parse_args(sys.argv[1:])
if len(args) < 3:
parser.print_help()
sys.exit(45)
run=args[0]
nodes=int(args[1])
ppn=int(args[2])
np=nodes*ppn
# seconds per ellip ring pair. this is for exp...
seconds_per=get_seconds_per_pair()
c = shapesim.read_config(run)
sim_config = c['sim_config']
mcmc_config = c['mcmc_config']
nsplit = c['nsplit']
s2n_vals = c['s2n_vals']
s2n_fac = c['s2n_fac']
min_npair = c['min_npair']
ns2n = len(s2n_vals)
pbsd = shapesim.get_pbs_dir(run)
logdir=os.path.join(pbsd,'logs')
outd = shapesim.get_output_dir(run, sub='bytrial')
if not os.path.exists(pbsd):
os.makedirs(pbsd)
if not os.path.exists(logdir):
os.makedirs(logdir)
if not os.path.exists(outd):
os.makedirs(outd)
rstr=run
job_name = '-'.join( (rstr.split('-'))[1:] )
script_url=shapesim.get_minions_script_url(run)
script_base=os.path.basename(script_url)
print script_url
with open(script_url,'w') as fobj:
c['version'] = options.version
fobj.write(_script_template % c)
print
pbsf=shapesim.get_minions_url(run,0)
cmdf=shapesim.get_commands_url(run,0)
print cmdf
ntot=0
with open(cmdf,'w') as fobj:
for is2n in xrange(ns2n):
s2n = s2n_vals[is2n]
npair = shapesim.get_s2n_nrepeat(s2n, fac=s2n_fac)
if npair < min_npair:
npair = min_npair
ntot += npair*nsplit
for isplit in xrange(nsplit):
output = shapesim.get_output_url(run, 0, is2n, itrial=isplit)
outbname=os.path.basename(output)
logf=outbname.replace('.rec','.log')
cmd=_cmd_template.format(script_file=script_base,
s2n=s2n,
npair=npair,
output=output,
logfile=logf)
fobj.write(cmd)
fobj.write('\n')
time_seconds = ntot*seconds_per/(np-1)
print pbsf
hours_raw = time_seconds/3600.
hours = int(round(hours_raw)) + 1
print ' raw hours:',hours_raw,'hours used:',hours
if options.version=='hopper':
minions_cmd='minions-hopper'
else:
minions_cmd='minions'
with open(pbsf,'w') as fobj:
cmd_bname=os.path.basename(cmdf)
pbslog=os.path.basename(pbsf)+'.pbslog'
pbs_text=_pbs_template.format(minions_cmd=minions_cmd,
job_name=job_name,
pbslog=pbslog,
nodes=nodes,
ppn=ppn,
np=np,
hours=hours,
commands_file=cmd_bname)
fobj.write(pbs_text)