def create_node(self, parent, tags=None): import Pegasus.DAX3 as dax if tags is None: tags = [] node = Node(self) # Set input / output options node.add_opt('--trig-file', '%s' % parent.storage_path) #node._dax_node.uses(parent, link=dax.Link.INPUT, register=False, # transfer=False) #node._inputs += [parent] node.add_opt('--output-dir', self.out_dir) node.add_profile('condor', 'request_cpus', self.num_threads) # Adding output files as pycbc.workflow.core.File objects out_file = File(self.ifos, 'INSPIRAL', parent.segment, directory=self.out_dir, extension='xml.gz', tags=[parent.tag_str, 'CLUSTERED'], store_file=self.retain_files) out_file.PFN(out_file.cache_entry.path, site="local") #node._dax_node.uses(out_file, link=dax.Link.OUTPUT, register=False, # transfer=False) #node._outputs += [out_file] out_file.node = node #node._add_output(out_file) return node, FileList([out_file])
def create_node(self, trig_files=None, segment_dir=None, out_tags=[], tags=[]): node = Node(self) if not trig_files: raise ValueError("%s must be supplied with trigger files" % self.name) # Data options pad_data = self.cp.get('inspiral', 'pad-data') if pad_data is None: raise ValueError("The option pad-data is a required option of " "%s. Please check the ini file." % self.name) num_trials = int(self.cp.get("trig_combiner", "num-trials")) trig_name = self.cp.get('workflow', 'trigger-name') node.add_opt('--grb-name', trig_name) node.add_opt('--pad-data', pad_data) node.add_opt('--segment-length', self.cp.get('inspiral', 'segment-duration')) node.add_opt('--ifo-tag', self.ifos) node.add_opt('--user-tag', 'INSPIRAL') # Set input / output options node.add_input_list_opt('--input-files', trig_files) node.add_opt('--segment-dir', segment_dir) node.add_opt('--output-dir', self.out_dir) out_files = FileList([]) for out_tag in out_tags: out_file = File(self.ifos, 'INSPIRAL', trig_files[0].segment, directory=self.out_dir, extension='xml.gz', tags=["GRB%s" % trig_name, out_tag], store_file=self.retain_files) #out_file.PFN(out_file.cache_entry.path, site="local") out_files.append(out_file) for trial in range(1, num_trials + 1): out_file = File(self.ifos, 'INSPIRAL', trig_files[0].segment, directory=self.out_dir, extension='xml.gz', tags=["GRB%s" % trig_name, "OFFTRIAL_%d" % trial], store_file=self.retain_files) #out_file.PFN(out_file.cache_entry.path, site="local") out_files.append(out_file) node.add_profile('condor', 'request_cpus', self.num_threads) return node, out_files
def create_node(self, trig_files, bank_file): node = Node(self) node.add_input_opt('--bank-file', bank_file) node.add_input_list_opt('--trigger-files', trig_files) node.new_output_file_opt(trig_files[0].segment, '.hdf', '--output-file', use_tmp_subdirs=True) return node
def create_node(self, trig_files, bank_file, stat_files, veto_file, veto_name, template_str, pivot_ifo, fixed_ifo, tags=None): if tags is None: tags = [] segs = trig_files.get_times_covered_by_files() seg = segments.segment(segs[0][0], segs[-1][1]) node = Node(self) node.add_input_opt('--template-bank', bank_file) node.add_input_list_opt('--trigger-files', trig_files) if len(stat_files) > 0: node.add_input_list_opt('--statistic-files', stat_files) if veto_file is not None: node.add_input_opt('--veto-files', veto_file) node.add_opt('--segment-name', veto_name) node.add_opt('--pivot-ifo', pivot_ifo) node.add_opt('--fixed-ifo', fixed_ifo) node.add_opt('--template-fraction-range', template_str) node.new_output_file_opt(seg, '.hdf', '--output-file', tags=tags) return node
def create_node(self, trig_files, inj_files, seg_dir, tags=[]): node = Node(self) # Set input / output options node.add_input_list_opt('--input-files', trig_files) node.add_input_list_opt('--inj-files', inj_files) node.add_opt('--ifo-tag', self.ifos) node.add_opt('--exclude-segments', '%s/bufferSeg.txt' % seg_dir) node.add_opt('--output-dir', self.out_dir) # Create output files as File objects name_string = inj_files[0].description seg = trig_files[0].segment f_file = File(self.ifos, name_string, seg, extension="xml", directory=self.out_dir, store_file=self.retain_files, tags=[inj_files[0].tag_str.replace("split0", "FOUND")]) m_file = File(self.ifos, name_string, seg, extension="xml", directory=self.out_dir, store_file=self.retain_files, tags=[inj_files[0].tag_str.replace("split0", "MISSED")]) return node, FileList([f_file, m_file])
def create_node(self, zerolag, full_data, injfull, fullinj, ifos, tags=None): if tags is None: tags = [] segs = zerolag.get_times_covered_by_files() seg = segments.segment(segs[0][0], segs[-1][1]) node = Node(self) node.add_input_list_opt('--zero-lag-coincs', zerolag) if isinstance(full_data, list): node.add_input_list_opt('--full-data-background', full_data) else: node.add_input_opt('--full-data-background', full_data) node.add_input_list_opt('--mixed-coincs-inj-full', injfull) node.add_input_list_opt('--mixed-coincs-full-inj', fullinj) node.add_opt('--ifos', ifos) node.new_output_file_opt(seg, '.hdf', '--output-file', tags=tags) return node
def create_node(self, parent, inj_trigs, inj_string, max_inc, segment): node = Node(self) trig_name = self.cp.get('workflow', 'trigger-name') node.add_opt('--inj-string', inj_string) node.add_opt('--max-inclination', max_inc) node.add_opt('--inj-cache', '%s' % parent.storage_path) out_files = FileList([]) for inj_trig in inj_trigs: out_file_tag = [ inj_string, "FILTERED", max_inc, inj_trig.tag_str.rsplit('_', 1)[-1] ] out_file = File(self.ifos, inj_trig.description, inj_trig.segment, extension="xml", directory=self.out_dir, tags=out_file_tag) out_file.PFN(out_file.cache_entry.path, site="local") out_files.append(out_file) node.add_opt('--output-dir', self.out_dir) return node, out_files
def create_node(self, parent=None, seg_dir=None, inj_file=None, tags=[]): node = Node(self) if not parent: raise ValueError("%s must be supplied with trigger files" % self.name) if isinstance(parent, str) and tags[1] == "_unclustered": node.add_opt('--trig-file', '%s' % parent.storage_path) tags[1] = "" else: node.add_opt('--trig-file', '%s' % parent.storage_path) node.add_opt('--grb-name', self.cp.get('workflow', 'trigger-name')) # Set input / output options node.add_opt('--veto-directory', seg_dir) node.add_opt('--segment-dir', seg_dir) out_dir = "%s/output/%s/plots%s" % (self.out_dir, tags[0], tags[1]) node.add_opt('--output-path', out_dir) if inj_file is not None: node.add_opt('--inj-file', inj_file.storage_path) node.add_profile('condor', 'request_cpus', self.num_threads) return node
def create_node(self, parent=None, c_file=None, open_box=False, tuning_tags=None, exclusion_tags=None, html_dir=None, tags=[]): node = Node(self) node.add_opt('--grb-name', self.cp.get('workflow', 'trigger-name')) node.add_opt('--start-time', self.cp.get('workflow', 'trigger-time')) node.add_opt('--ra', self.cp.get('workflow', 'ra')) node.add_opt('--dec', self.cp.get('workflow', 'dec')) node.add_opt('--ifo-tag', self.ifos) if tuning_tags is not None: node.add_opt('--tuning-injections', ','.join(tuning_tags)) if exclusion_tags is not None: node.add_opt('--exclusion-injections', ','.join(exclusion_tags)) if open_box: node.add_opt('--open-box') if html_dir is not None: node.add_opt('--html-path', html_dir) # Set input / output options node.add_opt('--config-file', '%s' % c_file.storage_path) node.add_opt('--output-path', "%s/output" % self.output_dir) node.add_profile('condor', 'request_cpus', self.num_threads) return node
def create_node(self, workflow, inj_file, precalc_psd_files, group_str): node = Node(self) node.add_input_opt('--input-file', inj_file) node.add_opt('--injection-fraction-range', group_str) node.add_input_list_opt('--time-varying-psds', precalc_psd_files) node.new_output_file_opt(workflow.analysis_time, '.xml', '--output-file') return node
def create_node(self, stat_files, tags=[]): node = Node(self) node.add_input_list_opt('--statmap-files', stat_files) node.new_output_file_opt(stat_files[0].segment, '.hdf', '--output-file', tags=tags) return node
def create_node(self, data_seg, valid_seg, parent=None, inj_file=None, dfParents=None, bankVetoBank=None, tags=[]): node = Node(self) if not dfParents: raise ValueError("%s must be supplied with frame files" % self.name) pad_data = self.get_opt('pad-data') if pad_data is None: raise ValueError("The option pad-data is a required option of " "%s. Please check the ini file." % self.name) # Feed in bank_veto_bank.xml if self.cp.has_option('inspiral', 'do-bank-veto'): if not bankVetoBank: raise ValueError("%s must be given a bank veto file if the" "argument 'do-bank-veto' is given" % self.name) node.add_input_opt('--bank-veto-templates', bankVetoBank) node.add_opt('--gps-start-time', data_seg[0] + int(pad_data)) node.add_opt('--gps-end-time', data_seg[1] - int(pad_data)) node.add_opt('--trig-start-time', valid_seg[0]) node.add_opt('--trig-end-time', valid_seg[1]) node.add_profile('condor', 'request_cpus', self.num_threads) # Set the input and output files node.new_output_file_opt(data_seg, '.xml.gz', '--output-file', tags=tags, store_file=self.retain_files) node.add_input_opt( '--non-spin-bank', parent, ) for frameCache in dfParents: node.add_input_opt('--%s-frame-cache' % frameCache.ifo.lower(), frameCache) node.add_arg('--%s-data' % frameCache.ifo.lower()) node.add_opt( '--%s-channel-name' % frameCache.ifo.lower(), self.cp.get('workflow', '%s-channel-name' % frameCache.ifo.lower())) if inj_file is not None: node.add_input_opt('--injection-file', inj_file) return node
def create_node(self, coinc_files, tags=[]): segs = coinc_files.get_times_covered_by_files() seg = segments.segment(segs[0][0], segs[-1][1]) node = Node(self) node.set_memory(5000) node.add_input_list_opt('--coinc-files', coinc_files) node.new_output_file_opt(seg, '.hdf', '--output-file', tags=tags) return node
def create_node(self, parent=None, offsource_file=None, seg_dir=None, found_file=None, missed_file=None, tags=None): if tags is None: tags = [] node = Node(self) if not parent: raise ValueError("%s must be supplied with trigger files" % self.name) # Set input / output options node.add_opt('--onsource-file', '%s' % parent.storage_path) node.add_opt('--offsource-file', '%s' % offsource_file.storage_path) node.add_opt('--veto-directory', seg_dir) node.add_opt('--segment-dir', seg_dir) if found_file and missed_file: node.add_opt('--found-file', '%s' % found_file.storage_path) node.add_opt('--missed-file', '%s' % missed_file.storage_path) out_dir = "%s/output/%s/efficiency_%s" % (self.out_dir, tags[1], tags[0]) if self.cp.has_option_tag('injections', 'min-distance', tags[-1]): lower_dist = float( self.cp.get_opt_tag('injections', 'min-distance', tags[-1])) #Convert distance from kpc to Mpc then add as option lower_dist /= 1e3 node.add_opt('--lower-inj-dist', lower_dist) if self.cp.has_option_tag('injections', 'max-distance', tags[-1]): upper_dist = float( self.cp.get_opt_tag('injections', 'max-distance', tags[-1])) #Convert distance from kpc to Mpc then add as option upper_dist /= 1e3 node.add_opt('--upper-inj-dist', upper_dist) elif found_file or missed_file: if found_file: present = found_file else: present = missed_file raise ValueError("Must either be supplied with no injection files " "or both missed and found injection files. " "Received only %s" % present.name) else: out_dir = "%s/output/%s/efficiency" % (self.out_dir, tags[0]) node.add_opt('--output-path', out_dir) node.add_profile('condor', 'request_cpus', self.num_threads) return node
def create_node(self, statmap_files, cluster_window, tags=None): if tags is None: tags = [] node = Node(self) node.add_input_list_opt('--statmap-files', statmap_files) node.new_output_file_opt(statmap_files[0].segment, '.hdf', '--output-file', tags=tags) node.add_opt('--cluster-window', cluster_window) return node
def create_node(self, trig_files=None, segment_dir=None, analysis_seg=None, out_tags=[], tags=[]): node = Node(self) if not trig_files: raise ValueError("%s must be supplied with trigger files" % self.name) # Data options num_trials = int(self.cp.get("trig_combiner", "num-trials")) trig_name = self.cp.get('workflow', 'trigger-name') if all("COHERENT_NO_INJECTIONS" in t.name for t in trig_files) and \ self.cp.has_option_tag('inspiral', 'do-short-slides', 'coherent_no_injections'): node.add_opt('--short-slides') node.add_opt('--grb-name', trig_name) node.add_opt('--trig-start-time', analysis_seg[0]) node.add_opt('--ifo-tag', self.ifos) node.add_opt('--user-tag', 'INSPIRAL') # Set input / output options node.add_input_list_opt('--input-files', trig_files) node.add_opt('--segment-dir', segment_dir) node.add_opt('--output-dir', self.out_dir) out_files = FileList([]) for out_tag in out_tags: out_file = File(self.ifos, 'INSPIRAL', trig_files[0].segment, directory=self.out_dir, extension='xml.gz', tags=["GRB%s" % trig_name, out_tag], store_file=self.retain_files) out_files.append(out_file) for trial in range(1, num_trials + 1): out_file = File(self.ifos, 'INSPIRAL', trig_files[0].segment, directory=self.out_dir, extension='xml.gz', tags=["GRB%s" % trig_name, "OFFTRIAL_%d" % trial], store_file=self.retain_files) out_files.append(out_file) node.add_profile('condor', 'request_cpus', self.num_threads) return node, out_files
def create_node(self, data_seg, valid_seg, parent=None, inj_file=None, dfParents=None, bankVetoBank=None, tags=[]): node = Node(self) if not dfParents: raise ValueError("%s must be supplied with frame files" % self.name) # If doing single IFO search, make sure slides are disabled if len(self.ifo_list) < 2 and \ ('--do-short-slides' in node._options or \ '--short-slide-offset' in node._options): raise ValueError("Cannot run with time slides in a single IFO " "configuration! Please edit your configuration " "file accordingly.") pad_data = self.get_opt('pad-data') if pad_data is None: raise ValueError("The option pad-data is a required option of " "%s. Please check the ini file." % self.name) # Feed in bank_veto_bank.xml if self.cp.has_option('inspiral', 'do-bank-veto'): if not bankVetoBank: raise ValueError("%s must be given a bank veto file if the " "argument 'do-bank-veto' is given" % self.name) node.add_input_opt('--bank-veto-templates', bankVetoBank) # Set time options node.add_opt('--gps-start-time', data_seg[0] + int(pad_data)) node.add_opt('--gps-end-time', data_seg[1] - int(pad_data)) node.add_opt('--trig-start-time', valid_seg[0]) node.add_opt('--trig-end-time', valid_seg[1]) node.add_profile('condor', 'request_cpus', self.num_threads) # Set the input and output files node.new_output_file_opt(data_seg, '.xml.gz', '--output-file', tags=tags, store_file=self.retain_files) node.add_input_opt('--non-spin-bank', parent, ) for frameCache in dfParents: node.add_input_opt('--%s-frame-cache' % frameCache.ifo.lower(), frameCache) node.add_arg('--%s-data' % frameCache.ifo.lower()) if inj_file is not None: if ('--do-short-slides' in node._options or \ '--short-slide-offset' in node._options): raise ValueError("Cannot run with short slides in an " "injection job. Please edit your " "configuration file accordingly.") node.add_input_opt('--injection-file', inj_file) return node
def create_node(self, trig_file, bank_file, veto_file, veto_name): node = Node(self) # Executable objects are initialized with ifo information node.add_opt('--ifo', self.ifo_string) node.add_input_opt('--trigger-file', trig_file) node.add_input_opt('--bank-file', bank_file) node.add_input_opt('--veto-file', veto_file) node.add_opt('--veto-segment-name', veto_name) node.new_output_file_opt(trig_file.segment, '.hdf', '--output') return node
def create_node(self, statmap_file, other_statmap_files, tags=None): if tags is None: tags = [] node = Node(self) node.add_input_opt('--statmap-file', statmap_file) node.add_input_list_opt('--other-statmap-files', other_statmap_files) node.new_output_file_opt(statmap_file.segment, '.hdf', '--output-file', tags=None) return node
def create_node(self, coinc_files, ifos, tags=None): if tags is None: tags = [] segs = coinc_files.get_times_covered_by_files() seg = segments.segment(segs[0][0], segs[-1][1]) node = Node(self) node.add_input_list_opt('--coinc-files', coinc_files) node.add_opt('--ifos', ifos) node.new_output_file_opt(seg, '.hdf', '--output-file', tags=tags) return node
def create_node(self, statmap_files, background_files, tags=None): if tags is None: tags = [] node = Node(self) node.add_input_list_opt('--statmap-files', statmap_files) if 'injections' in tags: node.add_input_list_opt('--background-files', background_files) node.new_output_file_opt(statmap_files[0].segment, '.hdf', '--output-file', tags=tags) return node
def create_node(self, inj_coinc_file, inj_xml_file, veto_file, veto_name, tags=None): if tags is None: tags = [] node = Node(self) node.add_input_list_opt('--trigger-file', inj_coinc_file) node.add_input_list_opt('--injection-file', inj_xml_file) if veto_name is not None: node.add_input_opt('--veto-file', veto_file) node.add_opt('--segment-name', veto_name) node.new_output_file_opt(inj_xml_file[0].segment, '.hdf', '--output-file', tags=tags) return node
def create_node(self, zerolag, full_data, injfull, fullinj, tags=[]): segs = zerolag.get_times_covered_by_files() seg = segments.segment(segs[0][0], segs[-1][1]) node = Node(self) node.set_memory(5000) node.add_input_list_opt('--zero-lag-coincs', zerolag) node.add_input_list_opt('--full-data-background', full_data) node.add_input_list_opt('--mixed-coincs-inj-full', injfull) node.add_input_list_opt('--mixed-coincs-full-inj', fullinj) node.new_output_file_opt(seg, '.hdf', '--output-file', tags=tags) return node
def create_node(self, bank): """ Set up a CondorDagmanNode class to run lalapps_splitbank code Parameters ---------- bank : pycbc.workflow.core.File The OutFile containing the template bank to be split Returns -------- node : pycbc.workflow.core.Node The node to run the job """ node = Node(self) # FIXME: This is a hack because SplitBank fails if given an input file # whose path contains the character '-' or if the input file is not in # the same directory as the output. Therefore we just set the path to # be the local path fullPath = bank.cache_entry.path bank.cache_entry.path = os.path.basename(fullPath) node.add_input_opt('--bank-file', bank) # FIXME: Set the path back to what it was. This is part of the hack # above and should be removed if possible. bank.cache_entry.path = fullPath # Get the output (taken from inspiral.py) url_list = [] x = bank.filename.split('-') if len(x) != 4: errMsg = "Input file name is not compatible with splitbank. Name " errMsg += "must follow the lal cache standard, for example " errMsg += "H1-TMPLTBANK-900000000-1000.xml. " errMsg += "Got %s." % (bank.filename, ) raise ValueError(errMsg) for i in range(0, self.num_banks): out_file = "%s-%s_%2.2d-%s-%s" % (x[0], x[1], i, x[2], x[3]) out_url = urlparse.urlunparse([ 'file', 'localhost', os.path.join(self.out_dir, out_file), None, None, None ]) url_list.append(out_url) job_tag = bank.description + "_" + self.name.upper() out_file = File(bank.ifo, job_tag, bank.segment, file_url=out_url, tags=bank.tags, store_file=self.retain_files) node._add_output(out_file) return node
def create_node(self, coinc_files, tags=None): if tags is None: tags = [] segs = coinc_files.get_times_covered_by_files() seg = segments.segment(segs[0][0], segs[-1][1]) node = Node(self) node.set_memory(5000) if isinstance(coinc_files, list): node.add_input_list_opt('--coinc-files', coinc_files) else: node.add_input_opt('--coinc-files', coinc_files) node.new_output_file_opt(seg, '.hdf', '--output-file', tags=tags) return node
def create_node(self, parent, tags=[]): node = Node(self) # Set input / output options node.add_opt('--trig-file', '%s' % parent.storage_path) node.add_opt('--output-dir', self.out_dir) node.add_profile('condor', 'request_cpus', self.num_threads) # Adding output files as pycbc.workflow.core.File objects out_file = File(self.ifos, 'INSPIRAL', parent.segment, directory=self.out_dir, extension='xml.gz', tags=[parent.tag_str, 'CLUSTERED'], store_file=self.retain_files) #out_file.PFN(out_file.cache_entry.path, site="local") return node, FileList([out_file])
def create_node(self, trig_files, bank_file, veto_file, veto_name, template_str, tags=[]): segs = trig_files.get_times_covered_by_files() seg = segments.segment(segs[0][0], segs[-1][1]) node = Node(self) node.set_memory(10000) node.add_input_opt('--template-bank', bank_file) node.add_input_list_opt('--trigger-files', trig_files) if veto_file is not None: node.add_input_opt('--veto-files', veto_file) node.add_opt('--segment-name', veto_name) node.add_opt('--template-fraction-range', template_str) node.new_output_file_opt(seg, '.hdf', '--output-file', tags=tags) return node
def create_node(self, coinc_files, bank_file, background_bins, tags=[]): node = Node(self) node.add_input_list_opt('--coinc-files', coinc_files) node.add_input_opt('--bank-file', bank_file) node.add_opt('--background-bins', ' '.join(background_bins)) names = [b.split(':')[0] for b in background_bins] output_files = [ File(coinc_files[0].ifo_list, self.name, coinc_files[0].segment, directory=self.out_dir, tags=tags + ['mbin-%s' % i], extension='.hdf') for i in range(len(background_bins)) ] node.add_output_list_opt('--output-files', output_files) node.names = names return node
def create_node(self, bank_file): node = Node(self) node.add_input_opt('--bank-file', bank_file) node.new_output_file_opt(bank_file.segment, '.hdf', '--output-file') return node
def create_node(self, raw_fit_file, bank_file): node = Node(self) node.add_input_opt('--template-fit-file', raw_fit_file) node.add_input_opt('--bank-file', bank_file) node.new_output_file_opt(raw_fit_file.segment, '.hdf', '--output') return node