Revision d44b370e336fd20143c901199f90ab5e2aa19a46 authored by Alex Nitz on 30 April 2017, 15:47:25 UTC, committed by GitHub on 30 April 2017, 15:47:25 UTC
1 parent 29416a2
pycbc_make_faithsim
#! /usr/bin/env python
import os
import logging
import shutil
import ConfigParser
import subprocess
import glob
import tempfile
from optparse import OptionParser
from pycbc_glue.pipeline import CondorDAGJob, CondorDAGNode, CondorDAG, CondorJob
class BaseJob(CondorDAGJob, CondorJob):
def __init__(self, log_dir, executable, cp, section, accounting_group=None):
CondorDAGJob.__init__(self, "vanilla", executable)
# These are all python jobs so need to pull in the env
self.add_condor_cmd('getenv', 'True')
self.add_condor_cmd('+Allow_OGrid', 'True')
log_base = os.path.join(
log_dir, os.path.basename(executable) + '-$(cluster)-$(process)')
self.set_stderr_file(log_base + '.err')
self.set_stdout_file(log_base + '.out')
self.set_sub_file(section + ".sub")
if cp is not None:
self.add_ini_opts(cp, section)
if accounting_group:
self.add_condor_cmd('accounting_group', accounting_group)
class FaithsimNode(CondorDAGNode):
def __init__(self, job, tmplt_file, match_file, inj_per_job=None):
CondorDAGNode.__init__(self, job)
self.add_file_opt("param-file", tmplt_file)
self.add_file_opt("match-file", match_file, file_is_output_file=True)
def get_ini_opts(confs, section):
op_str = ""
for opt in confs.options(section):
val = confs.get(section, opt)
op_str += "--" + opt + " " + val + " \\" + "\n"
return op_str
def mkdir(dir_name):
try :
os.mkdir(dir_name)
except OSError:
pass
def matches_in_list(slist, match):
import re
matches = []
for st in slist:
if st.startswith(match):
matches.append(st)
return matches
parser = OptionParser()
parser.add_option('--config', type=str)
(options, args) = parser.parse_args()
if options.config is None:
raise ValueError("Config file is required")
logging.basicConfig(format='%(asctime)s %(message)s', level=logging.INFO)
confs = ConfigParser.ConfigParser()
confs.read(options.config)
banksim_prog = confs.get("executables", "faithsim")
templates_per_job = confs.get("workflow", "templates-per-job")
try:
log_path = confs.get("workflow", 'log-path')
except:
log_path = './'
tempfile.tempdir = log_path
tempfile.template='faithsim.dag.log.'
logfile = tempfile.mktemp()
try:
accounting_group = confs.get('workflow', 'accounting-group')
except:
accounting_group = None
logging.warn('Warning: accounting-group not specified, LDG clusters may'
' reject this workflow!')
logging.info("Making workspace directories")
mkdir('scripts')
mkdir('match')
mkdir('bank')
mkdir('log')
mkdir('plots')
logging.info("Copying scripts")
shutil.copy(banksim_prog, 'scripts/pycbc_faithsim')
os.chmod('scripts/pycbc_faithsim', 0777)
logging.info("Creating injection file")
inj_str = "lalapps_inspinj " + get_ini_opts(confs, "inspinj") + "--output inj.xml"
os.system(inj_str)
logging.info("Splitting template bank")
subprocess.call(['pycbc_splitbank',
'--templates-per-bank', str(templates_per_job),
'-t', 'inj.xml',
'-o', 'bank/bank'])
num_banks = len(glob.glob("bank/bank*"))
logging.info("Creating DAG")
dag = CondorDAG(logfile)
dag.set_dag_file("faithsim")
dag.set_dax_file("faithsim")
fs_secs = matches_in_list(confs.sections(), 'faithsim')
fsjobs = []
for sec in fs_secs:
fsjobs.append(BaseJob("log", "scripts/pycbc_faithsim", confs, sec,
accounting_group=accounting_group))
rjob = BaseJob("log", "scripts/pycbc_faithsim_collect_results", None,
'collect_results', accounting_group=accounting_group)
rnode = CondorDAGNode(rjob)
pjob = BaseJob("log", "scripts/pycbc_faithsim_plots", None, 'faithsim_plots',
accounting_group=accounting_group)
pnode = CondorDAGNode(pjob)
for inj_num in range(num_banks):
bn = 'bank/bank' + str(inj_num) + '.xml'
for fsjob, sec in zip(fsjobs, fs_secs):
sec_sub = str(sec[len('faithsim'):])
mf = 'match/match' + sec_sub + '-' + str(inj_num) + '.dat'
fsnode = FaithsimNode(fsjob, bn, mf, inj_per_job=templates_per_job)
dag.add_node(fsnode)
rnode.add_parent(fsnode)
dag.add_node(rnode)
pnode.add_parent(rnode)
dag.add_node(pnode)
f = open("scripts/pycbc_faithsim_collect_results", "w")
f.write("""#!/usr/bin/env python
from os.path import isfile
from numpy import *
from pycbc_glue.ligolw import utils, table, lsctables, ligolw
import glob
class ContentHandler(ligolw.LIGOLWContentHandler):
pass
lsctables.use_in(ContentHandler)
fils = glob.glob("match/match*.dat")
mfields = ('match', 'overlap', 'time_offset', 'sigma1', 'sigma2')
bfields = ('match', 'overlap', 'time_offset', 'sigma1', 'sigma2', 'mass1',
'mass2', 'spin1x', 'spin1y', 'spin1z', 'spin2x', 'spin2y',
'spin2z', 'inclination', 'latitude', 'longitude',
'polarization', 'coa_phase')
dtypem={'names': mfields, 'formats': ('f8', 'f8', 'f8', 'f8', 'f8')}
dtypeo={'names': bfields,
'formats': ('f8', 'f8', 'f8', 'f8', 'f8', 'f8', 'f8', 'f8', 'f8',
'f8', 'f8', 'f8', 'f8', 'f8', 'f8', 'f8', 'f8', 'f8')}
if __name__ == "__main__":
fils = glob.glob("match/match*.dat")
tags = []
for fil in fils:
tags.append(fil.split('-')[1])
tags = list(set(tags))
btables = {}
for tag in tags:
parts = glob.glob("match/match-" + tag + "-*.dat")
data = zeros(0, dtype=dtypeo)
for part in parts:
btag = part.split('-')[2].split('.')[0]
bname = "bank/bank" + btag + ".xml"
if bname not in btables:
indoc = utils.load_filename(bname, False, contenthandler=ContentHandler)
btables[bname] = table.get_table(indoc, lsctables.SimInspiralTable.tableName)
bt = btables[bname]
try:
md = loadtxt(part, dtype=dtypem)
if md.size == 0:
continue
except IOError:
continue
pdata = zeros(len(bt), dtype=dtypeo)
for field in mfields:
pdata[field] = md[field]
for field in bfields:
if field not in mfields:
pdata[field] = bt.get_column(field)
data = append(data, pdata)
savetxt('result-' + tag + '.dat', data)
""")
os.chmod('scripts/pycbc_faithsim_collect_results', 0777)
logging.info("Creating submit script")
f = open("submit.sh", 'w')
f.write("""#!/bin/bash
condor_submit_dag faithsim.dag
""")
os.chmod('submit.sh', 0777)
dag.write_sub_files()
dag.write_script()
dag.write_concrete_dag()
f = open('scripts/pycbc_faithsim_plots', "w")
f.write("""#!/usr/bin/env python
import matplotlib
matplotlib.use('Agg')
import matplotlib.cm
import pylab
from os.path import isfile
from numpy import *
from pycbc_glue.ligolw import utils, table, lsctables
from matplotlib.ticker import MultipleLocator, FormatStrFormatter
import glob
from pycbc import pnutils
bfields = ('match', 'overlap', 'time_offset', 'sigma1', 'sigma2', 'mass1',
'mass2', 'spin1x', 'spin1y', 'spin1z', 'spin2x', 'spin2y',
'spin2z', 'inclination', 'latitude', 'longitude',
'polarization', 'coa_phase')
dtypeo={'names': bfields,
'formats': ('f8', 'f8', 'f8', 'f8', 'f8', 'f8', 'f8', 'f8', 'f8',
'f8', 'f8', 'f8', 'f8', 'f8', 'f8', 'f8', 'f8', 'f8')}
def basic_scatter(out_name, xname, yname, title, xval, yval,
cval=None, cname="", vmin=0, vmax=1, xmin=None,
ymin=None, majorL=None, minorL=None):
cmap = matplotlib.cm.jet
cmap.set_under(color='gray')
fig = pylab.figure(num=None, figsize=(10, 5))
pylab.scatter(xval, yval, c=cval, linewidths=0, s=3, vmin=vmin, vmax=vmax, cmap=cmap, alpha=0.7)
if cval is not None:
bar = pylab.colorbar()
bar.set_label(cname)
pylab.xlabel(xname)
pylab.ylabel(yname)
if xmin is None:
xmin = min(xval)
if ymin is None:
ymin = min(yval)
pylab.xlim(xmin, max(xval))
pylab.ylim(ymin, max(yval))
ax = fig.gca()
if majorL:
ax.xaxis.set_major_locator(MultipleLocator(majorL))
ax.yaxis.set_major_locator(MultipleLocator(majorL))
if minorL:
ax.xaxis.set_minor_locator(MultipleLocator(minorL))
ax.yaxis.set_minor_locator(MultipleLocator(minorL))
fol = 'plots/'
pylab.grid()
pylab.title(title)
pylab.savefig(fol + 'THUMB-' + out_name, dpi=50)
pylab.savefig(fol + out_name, dpi=500)
fils = glob.glob("result*.dat")
for fil in fils:
tag = fil.split('-')[1].split('.')[0]
data = loadtxt(fil, dtype=dtypeo)
mmass1 = maximum(data['mass1'], data['mass2'])
mmass2 = minimum(data['mass1'], data['mass2'])
mchirp, eta = pnutils.mass1_mass2_to_mchirp_eta(mmass1, mmass2)
M = data['mass1'] + data['mass2']
q = maximum(data['mass1'] / data['mass2'], data['mass2'] / data['mass1'])
s1 = (data['spin1x']**2 + data['spin1y']**2 + data['spin1z']**2)**0.5
s2 = (data['spin2x']**2 + data['spin2y']**2 + data['spin2z']**2)**0.5
s81 = data['sigma1'] / 8
s82 = data['sigma2'] / 8
pname = tag + '-'
red_data = data[data['match'] > -0.5]
combs = [('mass1', 'mass2', 'match'),
]
for v1, v2, v3 in combs:
name = pname + 'scatter' + v1 + '-' + v2 + '-' + v3
title = tag
basic_scatter(name, v1, v2, title, data[v1], data[v2], data[v3], v3, xmin=0, ymin=0)
v1 = 'mass1'
v2 = 'mass2'
v3 = 'time_offset'
name = pname + 'scatter' + v1 + '-' + v2 + '-' + v3
title = tag
basic_scatter(name, v1, v2, title, red_data[v1], red_data[v2], red_data[v3], v3, vmin=None, vmax=None)
v1 = 'mass ratio'
v1d = q
v2 = 'spin 1 magnitude'
v2d = s1
v3 = 'match'
v3d = data['match']
name = pname + 'scatter' + v1 + '-' + v2 + '-' + v3
basic_scatter(name, v1, v2, tag, v1d, v2d, v3d, v3)
v1 = 'mass ratio'
v1d = q
v2 = 'spin 1 z'
v2d = data['spin1z']
v3 = 'match'
v3d = data['match']
name = pname + 'scatter' + v1 + '-' + v2 + '-' + v3
basic_scatter(name, v1, v2, tag, v1d, v2d, v3d, v3)
v1 = 'mass ratio'
v1d = q
v2 = 'spin 2 magnitude'
v2d = s2
v3 = 'match'
v3d = data['match']
name = pname + 'scatter' + v1 + '-' + v2 + '-' + v3
basic_scatter(name, v1, v2, tag, v1d, v2d, v3d, v3)
v1 = 'mass ratio'
v1d = q
v2 = 'spin 2 z'
v2d = data['spin2z']
v3 = 'match'
v3d = data['match']
name = pname + 'scatter' + v1 + '-' + v2 + '-' + v3
basic_scatter(name, v1, v2, tag, v1d, v2d, v3d, v3)
v1 = 'mass ratio'
v1d = q
v2 = 'total mass'
v2d = M
v3 = 'match'
v3d = data['match']
name = pname + 'scatter' + v1 + '-' + v2 + '-' + v3
basic_scatter(name, v1, v2, tag, v1d, v2d, v3d, v3)
v1 = 'mass 1'
v1d = mmass1
v2 = 'mass 2'
v2d = mmass2
v3 = 'match'
v3d = data['match']
name = pname + 'scatter' + v1 + '-' + v2 + '-' + v3
basic_scatter(name, v1, v2, tag, v1d, v2d, v3d, v3, xmin=0, ymin=0, majorL=5, minorL=1)
v1 = 'Coalescence Phase'
v1d = data['coa_phase']
v2 = 'Match'
v2d = data['match']
v3 = 'Mchirp'
v3d = mchirp
name = pname + 'scatter' + v1 + '-' + v2 + '-' + v3
basic_scatter(name, v1, v2, tag, v1d, v2d, v3d, v3, vmin=None, vmax=None, ymin=0)
v1 = 'Inclination'
v1d = data['inclination']
v2 = 'Match'
v2d = data['match']
v3 = 'Mchirp'
v3d = mchirp
name = pname + 'scatter' + v1 + '-' + v2 + '-' + v3
basic_scatter(name, v1, v2, tag, v1d, v2d, v3d, v3, vmin=None, vmax=None)
v1 = 'Inclination'
v1d = data['inclination']
v2 = 'Sigma2'
v2d = data['sigma2']
v3 = 'Mchirp'
v3d = mchirp
name = pname + 'scatter' + v1 + '-' + v2 + '-' + v3
basic_scatter(name, v1, v2, tag, v1d, v2d, v3d, v3, vmin=None, vmax=None)
v1 = 'Inclination'
v1d = data['inclination']
v2 = 'Sigma1'
v2d = data['sigma1']
v3 = 'Mchirp'
v3d = mchirp
name = pname + 'scatter' + v1 + '-' + v2 + '-' + v3
basic_scatter(name, v1, v2, tag, v1d, v2d, v3d, v3, vmin=None, vmax=None)
""")
os.chmod('scripts/pycbc_faithsim_plots', 0777)
logging.info('Done')
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