From f402736c6885542baec7517c23281157b443ae9e Mon Sep 17 00:00:00 2001 From: mturilli Date: Tue, 20 Aug 2019 23:37:52 -0400 Subject: [PATCH] Reorganize repo and prepare analysis --- analysis/bin/bin/notebook_utils.py | 324 ++++++++++++++++++ analysis/bin/bin/prrte_profiler.py | 59 ++++ .../bin/bin/prrte_profiler_multi_session.py | 93 +++++ .../bin/bin/radical.analytics.log | 0 .../bin/bin/radical.saga.log | 0 .../re.session.summit.20nodes.9hours.tar.gz | Bin .../.re.session.two.jdakka.017806.0004.txt | 0 .../binaries/hyperspaces.py | 0 .../binaries/optimization.py | 0 .../7_hyp_ss_fac_4_run_1/debug.log | 0 .../7_hyp_ss_fac_4_run_1/null-supermic-ss.py | 0 .../7_hyp_ss_fac_4_run_1/null-supermic.py | 0 .../radical.entk.appmanager.0000.prof | 0 .../radical.entk.resource_manager.0000.prof | 0 .../radical.entk.task_manager.0000-obj.prof | 0 .../radical.entk.task_manager.0000-proc.prof | 0 .../radical.entk.wfprocessor.0000-obj.prof | 0 .../radical.entk.wfprocessor.0000-proc.prof | 0 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+import radical.analytics as ra +import matplotlib.pyplot as plt +import matplotlib.pyplot as plt + +from cycler import cycler +from radical.utils.profile import * +from radical.pilot.states import * +from IPython.core.display import display, HTML + +pd.set_option('expand_frame_repr', False) +pd.set_option('display.max_rows', 50) + + +# ---------------------------------------------------------------------------- +# Global configurations +# ---------------------------------------------------------------------------- + +# Expand the notebook to the width of the browser +display(HTML("")) + +# Matplotlib style +plt.style.use('seaborn-ticks') + +# Use LaTeX and its body font for the diagrams' text. +mpl.rcParams['text.usetex'] = True +mpl.rcParams['text.latex.unicode'] = True +mpl.rcParams['font.serif'] = ['Nimbus Roman Becker No9L'] +mpl.rcParams['font.family'] = 'serif' + +# Font sizes +SIZE = 24 +plt.rc('font' , size = SIZE ) # controls default text sizes +plt.rc('axes' , titlesize = SIZE ) # fontsize of the axes title +plt.rc('axes' , labelsize = SIZE ) # fontsize of the x any y labels +plt.rc('xtick' , labelsize = SIZE ) # fontsize of the tick labels +plt.rc('ytick' , labelsize = SIZE ) # fontsize of the tick labels +plt.rc('legend', fontsize = SIZE-2) # legend fontsize +plt.rc('figure', titlesize = SIZE ) # size of the figure title + +# Use thinner lines for axes to avoid distractions. +mpl.rcParams['axes.linewidth'] = 0.75 +mpl.rcParams['xtick.major.width'] = 0.75 +mpl.rcParams['xtick.minor.width'] = 0.75 +mpl.rcParams['ytick.major.width'] = 0.75 +mpl.rcParams['ytick.minor.width'] = 0.75 +mpl.rcParams['lines.linewidth'] = 2 + +# Do not use a box for the legend to avoid distractions. +mpl.rcParams['legend.frameon'] = False + +# Restore part of matplotlib 1.5 behavior +mpl.rcParams['patch.force_edgecolor'] = True +mpl.rcParams['patch.edgecolor'] = 'black' +mpl.rcParams['errorbar.capsize'] = 3 + +# Use coordinated colors. These are the "Tableau 20" colors as +# RGB. Each pair is strong/light. For a theory of color +tableau20 = [(31 , 119, 180), (174, 199, 232), # blue [ 0,1 ] + (255, 127, 14 ), (255, 187, 120), # orange [ 2,3 ] + (44 , 160, 44 ), (152, 223, 138), # green [ 4,5 ] + (214, 39 , 40 ), (255, 152, 150), # red [ 6,7 ] + (148, 103, 189), (197, 176, 213), # purple [ 8,9 ] + (140, 86 , 75 ), (196, 156, 148), # brown [10,11] + (227, 119, 194), (247, 182, 210), # pink [12,13] + (188, 189, 34 ), (219, 219, 141), # yellow [14,15] + (23 , 190, 207), (158, 218, 229), # cyan [16,17] + (65 , 68 , 81 ), (96 , 99 , 106), # gray [18,19] + (127, 127, 127), (143, 135, 130), # gray [20,21] + (165, 172, 175), (199, 199, 199), # gray [22,23] + (207, 207, 207)] # gray [24] + +# Scale the RGB values to the [0, 1] range, which is the format +# matplotlib accepts. +for i in range(len(tableau20)): + r, g, b = tableau20[i] + tableau20[i] = (round(r/255.,1), round(g/255.,1), round(b/255.,1)) + +# ---------------------------------------------------------------------------- +# RCT Configurations +# ---------------------------------------------------------------------------- + +# List of events of RP +event_list = [ + {ru.STATE: 'NEW' , ru.EVENT: 'state' }, + {ru.STATE: 'UMGR_SCHEDULING_PENDING' , ru.EVENT: 'state' }, + {ru.STATE: 'UMGR_SCHEDULING' , ru.EVENT: 'state' }, + {ru.STATE: 'UMGR_STAGING_INPUT_PENDING' , ru.EVENT: 'state' }, + {ru.STATE: 'UMGR_STAGING_INPUT' , ru.EVENT: 'state' }, + {ru.STATE: 'AGENT_STAGING_INPUT_PENDING' , ru.EVENT: 'state' }, + {ru.COMP : 'agent_0' , ru.EVENT: 'get' }, + {ru.STATE: 'AGENT_STAGING_INPUT' , ru.EVENT: 'state' }, + {ru.STATE: 'AGENT_SCHEDULING_PENDING' , ru.EVENT: 'state' }, + {ru.STATE: None , ru.EVENT: 'schedule_try' }, # Scheduling start + # {ru.STATE: 'AGENT_SCHEDULING' , ru.EVENT: 'state' }, + {ru.STATE: None , ru.EVENT: 'schedule_ok' }, # Scheduling stop + {ru.STATE: 'AGENT_EXECUTING_PENDING' , ru.EVENT: 'state' }, # Queuing Execution start + {ru.STATE: 'AGENT_EXECUTING' , ru.EVENT: 'state' }, # Queuing Execution stop | Preparing Execution start + {ru.STATE: None , ru.EVENT: 'exec_mkdir' }, # Agent Executing Component + {ru.STATE: None , ru.EVENT: 'exec_mkdir_done' }, # Agent Executing Component + {ru.STATE: None , ru.EVENT: 'exec_start' }, # Agent Executing Component + {ru.STATE: None , ru.EVENT: 'exec_ok' }, # System OS + {ru.STATE: None , ru.EVENT: 'cu_start' }, # System OS + {ru.STATE: None , ru.EVENT: 'cu_cd_done' }, # CU script + {ru.STATE: None , ru.EVENT: 'cu_pre_start' }, # CU script + {ru.STATE: None , ru.EVENT: 'cu_pre_stop' }, # CU script + {ru.STATE: None , ru.EVENT: 'cu_exec_start' }, # CU script [orterun spawner] + {ru.STATE: None , ru.EVENT: 'app_start' }, # Synapse + {ru.STATE: None , ru.EVENT: 'app_stop' }, # Synapse, orterun [orterun spawner] + {ru.STATE: None , ru.EVENT: 'cu_exec_stop' }, # CU script + {ru.STATE: None , ru.EVENT: 'cu_post_start' }, # CU script + {ru.STATE: None , ru.EVENT: 'cu_post_stop' }, # CU script + {ru.STATE: None , ru.EVENT: 'exec_stop' }, # Agent Executing Component + {ru.STATE: None , ru.EVENT: 'unschedule_start'}, # Agent Scheduling Component + {ru.STATE: None , ru.EVENT: 'unschedule_stop' }, # Agent Scheduling Component # {ru.STATE: 'AGENT_STAGING_OUTPUT_PENDING' , ru.EVENT: 'state' }, + # {ru.STATE: 'UMGR_STAGING_OUTPUT_PENDING' , ru.EVENT: 'state' }, + # {ru.STATE: 'UMGR_STAGING_OUTPUT' , ru.EVENT: 'state' }, + # {ru.STATE: 'AGENT_STAGING_OUTPUT' , ru.EVENT: 'state' }, + # {ru.STATE: 'DONE' , ru.EVENT: 'state' }, +] + +# Durations for events concurrency and scatter plots +event_durations = { + 'Scheduling' : [{ru.STATE: None, ru.EVENT: 'schedule_try'} , {ru.STATE: None, ru.EVENT: 'schedule_ok'}], + 'Queuing Execution' : [{ru.STATE: 'AGENT_EXECUTING_PENDING', ru.EVENT: 'state'}, {ru.STATE: 'AGENT_EXECUTING', ru.EVENT: 'state'}], + 'Preparing Execution': [{ru.STATE: 'AGENT_EXECUTING', ru.EVENT: 'state'} , {ru.STATE: None, ru.EVENT: 'exec_start'}], + 'Making directory' : [{ru.STATE: None, ru.EVENT: 'exec_mkdir'} , {ru.STATE: None, ru.EVENT: 'exec_mkdir_done'}], + 'Spawning' : [{ru.STATE: None, ru.EVENT: 'exec_start'} , {ru.STATE: None, ru.EVENT: 'exec_ok'}], + 'Executing' : [{ru.STATE: None, ru.EVENT: 'exec_ok'} , {ru.STATE: None, ru.EVENT: 'exec_stop'}], + 'Unscheduling' : [{ru.STATE: None, ru.EVENT: 'unschedule_start'} , {ru.STATE: None, ru.EVENT: 'unschedule_stop'}] +} + + +# Unit durations for Tx distribution plots +UNIT_DURATIONS = { + 'exec-tot' : [{STATE: AGENT_EXECUTING, EVENT: 'state' }, + {STATE: AGENT_STAGING_OUTPUT_PENDING, EVENT: 'state' }], + 'exec-rp' : [{STATE: None, EVENT: 'exec_start' }, + {STATE: None, EVENT: 'exec_stop' }], + 'exec-cu' : [{STATE: None, EVENT: 'cu_start' }, + {STATE: None, EVENT: 'cu_exec_stop' }], + 'exec-orte': [{STATE: None, EVENT: 'cu_exec_start'}, + {STATE: None, EVENT: 'cu_exec_stop' }], + 'exec-app' : [{STATE: None, EVENT: 'app_start' }, + {STATE: None, EVENT: 'app_stop' }]} + + + +# ---------------------------------------------------------------------------- +# Utils +# ---------------------------------------------------------------------------- + +# Return a single plot without right and top axes, spanning one column text. +def fig_setup(figsize=None): + if not figsize: + figsize = (13,7) + fig = plt.figure(figsize=figsize) + ax = fig.add_subplot(111) + ax.spines["top"].set_visible(False) + ax.spines["right"].set_visible(False) + ax.get_xaxis().tick_bottom() + ax.get_yaxis().tick_left() + + return fig, ax + + +# Return a single plot without right and top axes, spanning two columns text. +def fig_hdouble_setup(): + fig = plt.figure(figsize=(26,7)) + ax = fig.add_subplot(111) + ax.spines["top"].set_visible(False) + ax.spines["right"].set_visible(False) + ax.get_xaxis().tick_bottom() + ax.get_yaxis().tick_left() + + return fig, ax + + +# load ra session objects. +def load_sessions_units(sdir, sessions, snunits): + # number of units in the sessions + # snunits = sorted(sessions.nunit.unique().tolist()) + + # load the RA session objects + sras = {} + for snunit in snunits: + sras[snunit] = [] + s = sessions[(sessions.nunit == snunit)] + for sid in s.sid.tolist(): + exp = s.loc[sid]['experiment'] + src = '%s/%s/%s' % (sdir, exp, sid) + sras[snunit].append(ra.Session(src, 'radical.pilot')) + + return sras + +# load ra session objects. +def load_sessions_cores(sdir, sessions, sncores): + # number of units in the sessions + # snunits = sorted(sessions.nunit.unique().tolist()) + + # load the RA session objects + sras = {} + for sncore in sncores: + sras[sncore] = [] + s = sessions[(sessions.ncore == sncore)] + for sid in s.sid.tolist(): + exp = s.loc[sid]['experiment'] + src = '%s/%s/%s' % (sdir, exp, sid) + sras[sncore].append(ra.Session(src, 'radical.pilot')) + + return sras + + +# Collect timestamps of all the event specified in event_list for every unit +def get_df_unit_events(session): + s = session + s.filter(etype='unit', inplace=True) + data = dict() + for thing in s.get(): + + tstamps = dict() + for event in event_list: + eid = event[1] + if eid == 'state': + eid = event[5] + times = thing.timestamps(event=event) + if times: + tstamps[eid] = times[0] + else: + tstamps[eid] = None + + data[thing.uid] = tstamps + + # We sort the entities by the timestamp of the first event + df = pd.DataFrame.from_dict(data) +# df = df.sort_values(by=list(df.columns)) + df = df.transpose() + df = df.reset_index() + + # Rename events to make them intellegible + df.rename( # Components + {'index' :'uid' , + 'get' :'DB Bridge Pulls' , # Agent Component + 'schedule_try' :'Scheduler Starts Schedule' , # Agent Scheduling Component + 'schedule_ok' :'Scheduler Stops Schedule' , # Agent Scheduling Component + 'AGENT_EXECUTING_PENDING' :'Scheduler Queues CU' , # Agent Scheduling Component + 'AGENT_EXECUTING' :'Executor Starts' , # Agent Executing Component + 'exec_mkdir' :'Executor Starts Mkdir' , # Agent Executing Component + 'exec_mkdir_done' :'Executor Stops Mkdir' , # Agent Executing Component + 'exec_start' :'Executor Spawns CU' , # Agent Executing Component + 'exec_ok' :'OS Accepts Spawned CU' , # System OS + 'cu_start' :'OS Spawns CU' , # System OS + 'cu_cd_done' :'CU Changes Dir' , # CU script + 'cu_pre_start' :'CU Starts Pre-execute' , # CU script + 'cu_pre_stop' :'CU Stops Pre-execute' , # CU script + 'cu_exec_start' :'CU Spawns Executable' , # CU script [orterun spawner] + 'app_start' :'Executable Starts' , # Synapse + 'app_stop' :'Executable Stops' , # Synapse [orterun spawner] + 'cu_exec_stop' :'CU Spawn Returns' , # CU script (call it process) + 'cu_post_start' :'CU Starts Post-execute' , # CU script + 'cu_post_stop' :'CU Stops Post-execute' , # CU script + 'exec_stop' :'Executor Stops' , # Agent Executing Component + 'unschedule_start' :'Scheduler Starts Unschedule', # Agent Scheduling Component + 'unschedule_stop' :'Scheduler Stops Unschedule'}, # Agent Scheduling Component + axis='columns', inplace=True) + + # Durations sub-component level + df['Scheduler Scheduling'] = df['Scheduler Stops Schedule'] - df['Scheduler Starts Schedule'] + df['Scheduler Queuing CU'] = df['Executor Starts'] - df['Scheduler Queues CU'] + df['Executor Starting'] = df['Executor Starts Mkdir'] - df['Executor Starts'] + df['Executor Making Dir'] = df['Executor Stops Mkdir'] - df['Executor Starts Mkdir'] + df['Executor Spawning CU'] = df['OS Accepts Spawned CU'] - df['Executor Spawns CU'] + df['OS Spawning CU'] = df['OS Spawns CU'] - df['OS Accepts Spawned CU'] + df['CU Changing Dir'] = df['CU Changes Dir'] - df['OS Spawns CU'] + df['CU Pre-executing'] = df['CU Stops Pre-execute'] - df['CU Starts Pre-execute'] + df['CU Spawning Executable'] = df['Executable Starts'] - df['CU Spawns Executable'] + df['Executable Executing'] = df['Executable Stops'] - df['Executable Starts'] + df['CU Post-executing'] = df['CU Stops Post-execute'] - df['CU Starts Post-execute'] + df['Executor Stopping'] = df['Executor Stops'] - df['CU Stops Post-execute'] + df['Scheduler Unscheduling'] = df['Scheduler Stops Unschedule'] - df['Scheduler Starts Unschedule'] + + # Durations component level + + # Durations chunk level + + return df + + +def get_unit_durations(data, sources): + for dname in UNIT_DURATIONS: + data[dname] = list() + + # get the numbers we actually want to plot + fout = open('outliers.dat', 'w') + ucnt = 0 + ocnt = 0 + + for src in sources: + # always point to the tarballs + if src[-4:] != '.tbz': + src += '.tbz' + + session = ra.Session(src, 'radical.pilot') + units = session.filter(etype='unit', inplace=True) + sid = session.uid + + for unit in units.get(): + for dname in UNIT_DURATIONS: + dur = unit.duration(event=UNIT_DURATIONS[dname]) + if dur > 1000.0: + ocnt += 1 + fout.write('%10.1f %s\n' % (dur, src)) + fout.flush() + else: + ucnt += 1 + data[dname].append(dur) + sys.stdout.flush() + return data diff --git a/analysis/bin/bin/prrte_profiler.py b/analysis/bin/bin/prrte_profiler.py new file mode 100755 index 0000000..d41f0b2 --- /dev/null +++ b/analysis/bin/bin/prrte_profiler.py @@ -0,0 +1,59 @@ +#!/usr/bin/env python + +import sys +import radical.utils as ru +import radical.pilot as rp +import radical.analytics as ra + + +# ------------------------------------------------------------------------------ +# +if __name__ == '__main__': + if len(sys.argv) < 2: + print "\n\tusage: %s \n" % sys.argv[0] + sys.exit(1) + + src = sys.argv[1] + stype = 'radical.pilot' + + session = ra.Session(src, stype) + units = session.filter(etype='unit', inplace=False) + unit_0 = units.get()[0] + + print + print 'session: %s' % session.uid + print 'units: %d' % len(units.get()) + + # collect all events for some unit which relate to prte + nevents = list() + for e in unit_0.events: + if 'prte' in e[1]: + nevents.append(e) + + # for that sample unit, print the events and timestamps (ordered) + print + print 'PRTE events for unit %s' % unit_0.uid + for e in nevents: + if 'prte' in e[1]: + print '%14.7f : %s' % (e[0], e[1]) + + # for all event pairs (neighbors), compute the duration for (a) the sample + # unit, and (b) the full session + print + print 'PRTE durations for unit %s and session' % unit_0.uid + idx = 0 + while idx < len(nevents) - 1: + + this = nevents[idx ][1] + that = nevents[idx + 1][1] + duru = unit_0.duration( + event=[{ru.STATE:rp.AGENT_EXECUTING, ru.EVENT:this}, + {ru.STATE:rp.AGENT_EXECUTING, ru.EVENT:that}]) + durs = units.duration( + event=[{ru.STATE:rp.AGENT_EXECUTING, ru.EVENT:this}, + {ru.STATE:rp.AGENT_EXECUTING, ru.EVENT:that}]) + print '%3d: %-30s to %-30s = %14.7f [%14.7f]' \ + % (idx, this, that, duru, durs) + idx += 1 + + print diff --git a/analysis/bin/bin/prrte_profiler_multi_session.py b/analysis/bin/bin/prrte_profiler_multi_session.py new file mode 100755 index 0000000..798d7b2 --- /dev/null +++ b/analysis/bin/bin/prrte_profiler_multi_session.py @@ -0,0 +1,93 @@ +#!/usr/bin/env python + +import sys + +import radical.utils as ru +import radical.pilot as rp +import radical.analytics as ra + + +# ------------------------------------------------------------------------------ +# +if __name__ == '__main__': + + if len(sys.argv) < 2: + print "\n\tusage: %s [...]\n" % sys.argv[0] + sys.exit(1) + + session_csv = open('sessions_prte.csv', 'w') + unit_csv = open('units_prte.csv', 'w') + + prte_events = list() + + for src in sys.argv[1:]: + + stype = 'radical.pilot' + session = ra.Session(src, stype) + units = session.filter(etype='unit', inplace=False) + unit_0 = units.get()[0] + + print + print 'session: %s' % session.uid + print 'units: %d' % len(units.get()) + + # collect all events for some unit which relate to prte - if we don't + # have them yet + if not prte_events: + for e in unit_0.events: + if 'prte' in e[1]: + prte_events.append(e[1]) + idx = 0 + s_row = ['sid'] + u_row = ['uid', 'sid'] + while idx < len(prte_events) - 1: + + this = prte_events[idx] + that = prte_events[idx + 1] + u_row.append('%s_to_%s' % (this, that)) + s_row.append('%s_to_%s' % (this, that)) + idx += 1 + unit_csv.write('%s\n' % ','.join(u_row)) + session_csv.write('%s\n' % ','.join(s_row)) + + # for all event pairs (neighbors), compute the duration for (a) the + # sample unit, and (b) the full session + print + idx = 0 + s_row = [session.uid] + while idx < len(prte_events) - 1: + + this = prte_events[idx] + that = prte_events[idx + 1] + duru = unit_0.duration( + event=[{ru.STATE: rp.AGENT_EXECUTING, ru.EVENT: this}, + {ru.STATE: rp.AGENT_EXECUTING, ru.EVENT: that}]) + dur = units.duration( + event=[{ru.STATE: rp.AGENT_EXECUTING, ru.EVENT: this}, + {ru.STATE: rp.AGENT_EXECUTING, ru.EVENT: that}]) + + s_row.append('%.5f' % dur) + idx += 1 + print '%3d: %-30s to %-30s = %14.7f [%14.7f]' \ + % (idx, this, that, duru, dur) + + session_csv.write('%s\n' % ','.join(s_row)) + + for unit in units.get(): + u_row = [unit.uid, session.uid] + idx = 0 + s_row = [session.uid] + while idx < len(prte_events) - 1: + + this = prte_events[idx] + that = prte_events[idx + 1] + dur = unit_0.duration( + event=[{ru.STATE: rp.AGENT_EXECUTING, ru.EVENT: this}, + {ru.STATE: rp.AGENT_EXECUTING, ru.EVENT: that}]) + u_row.append('%.5f' % dur) + idx += 1 + + unit_csv.write('%s\n' % ','.join(u_row)) + + session_csv.close() + unit_csv.close() diff --git a/stress-ng-12000-supermic-ss/ss-dur-12000/7_hyp_ss_fac_4_run_1/rp.session.two.jdakka.017806.0005/control.pubsub.bridge.0000.child.log b/analysis/bin/bin/radical.analytics.log similarity index 100% rename from stress-ng-12000-supermic-ss/ss-dur-12000/7_hyp_ss_fac_4_run_1/rp.session.two.jdakka.017806.0005/control.pubsub.bridge.0000.child.log rename to analysis/bin/bin/radical.analytics.log diff --git a/stress-ng-12000-supermic-ss/ss-dur-12000/7_hyp_ss_fac_4_run_1/rp.session.two.jdakka.017806.0005/control.pubsub.bridge.0000.log b/analysis/bin/bin/radical.saga.log similarity index 100% rename from stress-ng-12000-supermic-ss/ss-dur-12000/7_hyp_ss_fac_4_run_1/rp.session.two.jdakka.017806.0005/control.pubsub.bridge.0000.log rename to 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