def read_mainlog_ewc(self):
"""
Read errors, warnings and comments from the main output and the log file.
:return: Two namedtuple instances: main, log.
The lists of strings with the corresponding messages are
available in main.errors, main.warnings, main.comments, log.errors etc.
"""
from pymatgen.io.abinitio.events import EventsParser
parser = EventsParser()
main_events = parser.parse(self.last_output())
log_events = parser.parse(self.log_name)
return main_events, log_events
def read_mainlog_ewc(self):
"""
Read errors, warnings and comments from the main output and the log file.
:return: Two namedtuple instances: main, log.
The lists of strings with the corresponding messages are
available in main.errors, main.warnings, main.comments, log.errors etc.
"""
from pymatgen.io.abinitio.events import EventsParser
parser = EventsParser()
main_events = parser.parse(self.last_output())
log_events = parser.parse(self.log_name)
return main_events, log_events
def __init__(self, parent, filepath, **kwargs):
super(AbinitEventsPanel, self).__init__(parent, -1, **kwargs)
self.filepath = os.path.abspath(filepath)
parser = EventsParser()
self.events = events = parser.parse(self.filepath)
main_sizer = wx.BoxSizer(wx.VERTICAL)
vbox = wx.BoxSizer(wx.VERTICAL)
panel1 = awx.Panel(self, -1)
panel2 = awx.Panel(self, -1)
self.tree = tree = wx.TreeCtrl(panel1, 1, wx.DefaultPosition, (-1, -1), wx.TR_HIDE_ROOT | wx.TR_HAS_BUTTONS)
root = self.tree.AddRoot('Events')
err_tree = tree.AppendItem(root, "%d Errors" % events.num_errors)
warn_tree = tree.AppendItem(root, "%d Warnings" % events.num_warnings)
com_tree = tree.AppendItem(root, "%d Comments" % events.num_comments)
for e in self.events.errors:
tree.AppendItem(err_tree, "line: " + str(e.lineno), data=wx.TreeItemData(e.message))
for w in self.events.warnings:
tree.AppendItem(warn_tree, "line: " + str(w.lineno), data=wx.TreeItemData(w.message))
for c in self.events.comments:
tree.AppendItem(com_tree, "line: " + str(c.lineno), data=wx.TreeItemData(c.message))
tree.Bind(wx.EVT_TREE_SEL_CHANGED, self.OnSelChanged, id=1)
self.display = wx.StaticText(panel2, -1, '', (10, 10), style=wx.ALIGN_LEFT)
vbox.Add(self.tree, 1, wx.EXPAND)
main_sizer.Add(panel1, 1, wx.EXPAND)
main_sizer.Add(panel2, 1, wx.EXPAND)
panel1.SetSizerAndFit(vbox)
self.SetSizerAndFit(main_sizer)
self.Centre()
def main():
parser = argparse.ArgumentParser(epilog=str_examples(), formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('filepath', nargs="?", help="File to inspect (output file or log file)")
# Create the parsers for the sub-commands
subparsers = parser.add_subparsers(dest='command', help='sub-command help', description="Valid subcommands")
# Subparser for status command.
p_status = subparsers.add_parser('status', help="Check the status of the run (errors, warning, completion)")
#p_status.add_argument('format', nargs="?", default="cif", type=str, help="Format of the output file (ciff, POSCAR, json).")
# Subparser for plot command.
p_plot = subparsers.add_parser('plot', help="Plot data")
#p_plot.add_argument('visualizer', nargs="?", default="xcrysden", type=str, help="Visualizer.")
p_timer = subparsers.add_parser('timer', help="Show timing data.")
# Parse command line.
try:
options = parser.parse_args()
except:
show_examples_and_exit(error_code=1)
if options.command == "status":
# Parse the Abinit Events in filepath.
parser = EventsParser()
report = parser.parse(options.filepath)
print(report)
elif options.command == "plot":
# TODO: At present only GS runs are supported by plottable_from_outfile
obj = plottable_from_outfile(options.filepath)
if obj is not None:
obj.plot()
else:
raise ValueError("Don't know how to extract plottable data from %s" % options.filepath)
elif options.command == "timer":
parser = AbinitTimerParser()
parser.parse(options.filepath)
parser.show_pie(key="wall_time", minfract=0.05)
else:
raise ValueError("Unsupported command %s" % options.command)
return 0
def events(self):
"""List of ABINIT events reported in the file."""
return EventsParser().parse(self.filepath)
def main():
def str_examples():
examples = """
Usage example:\n
abiinsp.py OUTFILE status ==> Report the list of Warning, Commments, Errors
abiinsp.py OUTFILE plot ==> Plot results of the GS Scf cycle, Phonon Scf cycle...
abiinsp.py OUTFILE timer ==> Visualize timing data with matplotlib.
"""
return examples
def show_examples_and_exit(err_msg=None, error_code=1):
"""Display the usage of the script."""
sys.stderr.write(str_examples())
if err_msg: sys.stderr.write("Fatal Error\n" + err_msg + "\n")
sys.exit(error_code)
parser = argparse.ArgumentParser(epilog=str_examples(), formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('filepath', nargs="?", help="File to inspect (output file or log file)")
# Create the parsers for the sub-commands
subparsers = parser.add_subparsers(dest='command', help='sub-command help', description="Valid subcommands")
# Subparser for status command.
p_status = subparsers.add_parser('status', help="Check the status of the run (errors, warning, completion)")
#p_status.add_argument('format', nargs="?", default="cif", type=str, help="Format of the output file (ciff, POSCAR, json).")
# Subparser for plot command.
p_plot = subparsers.add_parser('plot', help="Plot data")
#p_plot.add_argument('visualizer', nargs="?", default="xcrysden", type=str, help="Visualizer.")
subparsers.add_parser('timer', help="Show timing data.")
subparsers.add_parser('pseudo', help="Show info on pseudopotential file.")
# Parse command line.
try:
options = parser.parse_args()
except:
show_examples_and_exit(error_code=1)
if options.command == "status":
# Parse the Abinit Events in filepath.
parser = EventsParser()
report = parser.parse(options.filepath)
print(report)
elif options.command == "plot":
# TODO: At present only GS runs are supported by plottable_from_outfile
obj = plottable_from_outfile(options.filepath)
if obj is not None:
obj.plot()
else:
raise ValueError("Don't know how to extract plottable data from %s" % options.filepath)
elif options.command == "timer":
parser = AbinitTimerParser()
parser.parse(options.filepath)
#parser.show_pie(key="wall_time", minfract=0.05)
#parser.show_efficiency),
#parser.show_stacked_hist),
elif options.command == "pseudo":
from pymatgen.io.abinitio.pseudos import PseudoParser
pseudo = PseudoParser().parse(options.filepath)
print(pseudo)
else:
raise ValueError("Unsupported command %s" % options.command)
return 0
def main():
def str_examples():
examples = """\
Usage example:\n
abirun.py [FLOWDIR] rapid => Keep repeating, stop when no task can be executed.
abirun.py [FLOWDIR] scheduler => Execute flow with the scheduler
abirun.py [FLOWDIR] events => Print ABINIT events (Warning/Error/Comment)
abirun.py [FLOWDIR] history => Print Task history.
abirun.py [FLOWDIR] gui => Open the GUI.
abirun.py [FLOWDIR] manager slurm => Document the TaskManager options availabe for Slurm.
abirun.py [FLOWDIR] manager script => Show the job script that will be produced.
nohup abirun.py [FLOWDIR] sheduler -s 30 & => Start the scheduler to schedule task submission.
If FLOWDIR is not given, abirun.py automatically selects the database located within
the working directory. An Exception is raised if multiple databases are found.
Options for developers:
abirun.py prof ABIRUN_ARGS => to profile abirun.py
abirun.py tracemalloc ABIRUN_ARGS => to trace memory blocks allocated by Python
"""
return examples
def show_examples_and_exit(err_msg=None, error_code=1):
"""Display the usage of the script."""
sys.stderr.write(str_examples())
if err_msg: sys.stderr.write("Fatal Error\n" + err_msg + "\n")
sys.exit(error_code)
def parse_nids(s):
"""parse nids argument"""
if s is None: return s
try:
if "," in s:
return [int(t) for t in s.split(",")]
else:
# Convert string to slice and return list.
s = as_slice(s)
if s.stop is None: raise argparse.ArgumentTypeError("stop must be specified")
return list(range(s.start, s.stop, s.step))
except:
raise argparse.ArgumentTypeError("Invalid nids string %s\n Expecting None or int or comma-separated integers or slice sintax" % s)
def parse_wslice(s):
s = as_slice(s)
if s is None: return s
if s.stop is None: raise argparse.ArgumentTypeError("stop must be specified")
return s
# Parent parser for commands that need to know on which subset of tasks/workflows we have to operate.
# wslide and nids are mutually exclusive.
flow_selector_parser = argparse.ArgumentParser(add_help=False)
group = flow_selector_parser.add_mutually_exclusive_group()
group.add_argument("-n", '--nids', default=None, type=parse_nids, help=(
"Node identifier(s) used to select the task. Integer or comma-separated list of integers. Use `status` command to get the node ids."
"Examples: --nids=12 --nids=12,13,16 --nids=10:12 to select 10 and 11, --nids=2:5:2 to select 2,4"
))
group.add_argument("-w", '--wslice', default=None, type=parse_wslice,
help=("Select the list of works to analyze (python syntax for slices):"
"Examples: --wslice=1 to select the second workflow, --wslice=:3 for 0,1,2,"
"--wslice=-1 for the last workflow, --wslice::2 for even indices"))
group.add_argument("-S", '--task-status', default=None, type=Status.as_status,
help="Select only the tasks with the given status. Default: None i.e. ignored. Possible values: %s" %
Status.all_status_strings())
#group.add_argument("-p", "--task-pos", default=None, type=parse_wslice, help="List of tuples with the position of the tasl in the flow.")
# Parent parse for common options.
copts_parser = argparse.ArgumentParser(add_help=False)
copts_parser.add_argument('-v', '--verbose', default=0, action='count', # -vv --> verbose=2
help='verbose, can be supplied multiple times to increase verbosity')
copts_parser.add_argument('--remove-lock', default=False, type=bool, help="Remove the lock file of the pickle file storing the flow.")
copts_parser.add_argument('--no-colors', default=False, help='Disable ASCII colors')
copts_parser.add_argument('--loglevel', default="ERROR", type=str,
help="set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG")
# Build the main parser.
parser = argparse.ArgumentParser(epilog=str_examples(), formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('flowdir', nargs="?", help=("File or directory containing the ABINIT flow"
"If not given, the first flow in the current workdir is selected"))
# Create the parsers for the sub-commands
subparsers = parser.add_subparsers(dest='command', help='sub-command help', description="Valid subcommands")
subparsers.add_parser('version', parents=[copts_parser], help='Show version number and exit')
# Subparser for single command.
p_single = subparsers.add_parser('single', parents=[copts_parser], help="Run single task.")
# Subparser for rapidfire command.
p_rapid = subparsers.add_parser('rapid', parents=[copts_parser], help="Run all tasks in rapidfire mode")
# Subparser for scheduler command.
p_scheduler = subparsers.add_parser('scheduler', parents=[copts_parser], help="Run all tasks with a Python scheduler.")
p_scheduler.add_argument('-w', '--weeks', default=0, type=int, help="number of weeks to wait")
p_scheduler.add_argument('-d', '--days', default=0, type=int, help="number of days to wait")
p_scheduler.add_argument('-hs', '--hours', default=0, type=int, help="number of hours to wait")
p_scheduler.add_argument('-m', '--minutes', default=0, type=int, help="number of minutes to wait")
p_scheduler.add_argument('-s', '--seconds', default=0, type=int, help="number of seconds to wait")
# Subparser for batch command.
p_batch = subparsers.add_parser('batch', parents=[copts_parser], help="Run scheduler in batch script.")
p_batch.add_argument("-t", '--timelimit', default=None, help=("Time limit for batch script. "
"Accept int with seconds or string with time given in the slurm convention: "
"`days-hours:minutes:seconds`. If timelimit is None, the default value specified"
" in the `batch_adapter` entry of `manager.yml` is used."))
# Subparser for status command.
p_status = subparsers.add_parser('status', parents=[copts_parser, flow_selector_parser], help="Show task status.")
p_status.add_argument('-d', '--delay', default=0, type=int, help=("If 0, exit after the first analysis.\n" +
"If > 0, enter an infinite loop and delay execution for the given number of seconds."))
p_status.add_argument('-s', '--summary', default=False, action="store_true", help="Print short version with status counters.")
# Subparser for set_status command.
p_set_status = subparsers.add_parser('set_status', parents=[copts_parser, flow_selector_parser],
help="Change the status of the task. WARNING: Option for developers!")
p_set_status.add_argument('new_status', help="New value of status. Possible values: %s" % Status.all_status_strings())
# Subparser for cancel command.
p_cancel = subparsers.add_parser('cancel', parents=[copts_parser, flow_selector_parser], help="Cancel the tasks in the queue.")
p_cancel.add_argument("-r", "--rmtree", action="store_true", default=False, help="Remove flow directory.")
# Subparser for restart command.
p_restart = subparsers.add_parser('restart', parents=[copts_parser, flow_selector_parser],
help="Restart the tasks of the flow. By default, only the task with status==Unconverged are restarted."
"Use -S `status` and/or -n node_ids to select particular tasks.")
# Subparser for reset command.
p_reset = subparsers.add_parser('reset', parents=[copts_parser, flow_selector_parser],
help="Reset the tasks of the flow with the specified status.")
# Subparser for move command.
p_move = subparsers.add_parser('move', parents=[copts_parser], help="Move the flow to a new directory and change the absolute paths")
p_move.add_argument('dest', nargs=1)
# Subparser for open command.
p_open = subparsers.add_parser('open', parents=[copts_parser, flow_selector_parser],
help="Open files in $EDITOR, type `abirun.py FLOWDIR open --help` for help)")
p_open.add_argument('what', nargs="?", default="o",
help="""\
Specify the files to open. Possible choices:
i ==> input_file
o ==> output_file
f ==> files_file
j ==> job_file
l ==> log_file
e ==> stderr_file
q ==> qout_file
all ==> all files.
""")
p_ncopen = subparsers.add_parser('ncopen', parents=[copts_parser, flow_selector_parser],
help="Open netcdf files in ipython. Use --help` for more info")
p_ncopen.add_argument('ncext', nargs="?", default="GSR", help="Select the type of file to open")
# Subparser for gui command.
p_gui = subparsers.add_parser('gui', help="Open the GUI (requires wxPython).")
p_gui.add_argument("--chroot", default="", type=str, help=("Use chroot as new directory of the flow." +
"Mainly used for opening a flow located on a remote filesystem mounted with sshfs." +
"In this case chroot is the absolute path to the flow on the **localhost**",
"Note that it is not possible to change the flow from remote when chroot is used."))
p_new_manager = subparsers.add_parser('new_manager', parents=[copts_parser, flow_selector_parser], help="Change the TaskManager.")
p_new_manager.add_argument("manager_file", default="", type=str, help="YAML file with the new manager")
p_tail = subparsers.add_parser('tail', parents=[copts_parser, flow_selector_parser], help="Use tail to follow the main output files of the flow.")
p_tail.add_argument('what_tail', nargs="?", type=str, default="o", help="What to follow: o for output (default), l for logfile, e for stderr")
p_qstat = subparsers.add_parser('qstat', parents=[copts_parser], help="Show additional info on the jobs in the queue.")
p_deps = subparsers.add_parser('deps', parents=[copts_parser], help="Show dependencies.")
p_robot = subparsers.add_parser('robot', parents=[copts_parser, flow_selector_parser],
help="Use a robot to analyze the results of multiple tasks (requires ipython)")
p_robot.add_argument('robot_ext', nargs="?", type=str, default="GSR", help="The file extension of the netcdf file")
p_plot = subparsers.add_parser('plot', parents=[copts_parser, flow_selector_parser], help="Plot data. Use --help for more info.")
p_plot.add_argument("what", nargs="?", type=str, default="ebands", help="Object to plot")
p_inspect = subparsers.add_parser('inspect', parents=[copts_parser, flow_selector_parser], help="Inspect the tasks")
p_inputs= subparsers.add_parser('inputs', parents=[copts_parser, flow_selector_parser], help="Show the input files of the tasks")
p_manager = subparsers.add_parser('manager', parents=[copts_parser], help="Document the TaskManager options")
p_manager.add_argument("qtype", nargs="?", default=None, help=("Write job script to terminal if qtype='script' else"
" document the qparams for the given QueueAdapter qtype e.g. slurm"))
p_events = subparsers.add_parser('events', parents=[copts_parser, flow_selector_parser],
help="Show ABINIT events (error messages, warnings, comments)")
#p_events.add_argument("-t", "event-type", default=)
p_corrections = subparsers.add_parser('corrections', parents=[copts_parser, flow_selector_parser], help="Show abipy corrections")
p_history = subparsers.add_parser('history', parents=[copts_parser, flow_selector_parser], help="Show Node history.")
p_history.add_argument("-m", "--metadata", action="store_true", default=False, help="Print history metadata")
#p_history.add_argument("-t", "--task-history", action="store_true", default=True, help=)
p_handlers = subparsers.add_parser('handlers', parents=[copts_parser], help="Show event handlers installed in the flow")
p_handlers.add_argument("-d", "--doc", action="store_true", default=False,
help="Show documentation about all the handlers that can be installed.")
p_notebook = subparsers.add_parser('notebook', parents=[copts_parser], help="Create and open an ipython notebook to interact with the flow.")
p_ipython = subparsers.add_parser('ipython', parents=[copts_parser], help="Embed IPython. Useful for advanced operations or debugging purposes.")
p_ipython.add_argument('--argv', nargs="?", default="", type=shlex.split,
help="Command-line options passed to ipython. Must be enclosed by quotes. "
"Example: --argv='--matplotlib=wx'")
p_tar = subparsers.add_parser('tar', parents=[copts_parser], help="Create tarball file.")
p_tar.add_argument("-s", "--max-filesize", default=None,
help="Exclude file whose size > max-filesize bytes. Accept integer or string e.g `1Mb`.")
def parse_strings(s): return s.split(",") if s is not None else s
p_tar.add_argument("-e", "--exclude-exts", default=None, type=parse_strings,
help="Exclude file extensions. Accept string or comma-separated strings. Ex: -eWFK or --exclude-exts=WFK,GSR")
p_tar.add_argument("-d", "--exclude-dirs", default=None, type=parse_strings,
help="Exclude directories. Accept string or comma-separated strings. Ex: --exlude-dirs=indir,outdir")
p_tar.add_argument("-l", "--light", default=False, action="store_true",
help="Create light-weight version of the tarball for debugging purposes. Other options are ignored.")
p_debug = subparsers.add_parser('debug', parents=[copts_parser, flow_selector_parser],
help="Scan error files and log files for possible error messages.")
p_group = subparsers.add_parser('group', parents=[copts_parser, flow_selector_parser],
help="Group tasks according to property.")
p_diff = subparsers.add_parser('diff', parents=[copts_parser, flow_selector_parser],
help="Compare files produced by two or three nodes.")
p_diff.add_argument('what_diff', nargs="?", type=str, default="i",
help="What to diff: i for input (default), o for output, l for logfile, e for stderr")
p_networkx = subparsers.add_parser('networkx', parents=[copts_parser], #, flow_selector_parser],
help="Draw flow and node dependecies with networkx package.")
p_networkx.add_argument('--nxmode', default="status",
help="Type of network plot. Possible values: `status`, `network`")
p_networkx.add_argument('--edge-labels', action="store_true", default=False, help="Show edge labels")
p_listext = subparsers.add_parser('listext', parents=[copts_parser],
help="List all the output files with the given extension that have been produced by the nodes of the flow.")
p_listext.add_argument('listexts', nargs="+", help="List of Abinit file extensions. e.g DDB, GSR, WFK etc")
# Parse command line.
try:
options = parser.parse_args()
except Exception as exc:
show_examples_and_exit(error_code=1)
# loglevel is bound to the string value obtained from the command line argument.
# Convert to upper case to allow the user to specify --loglevel=DEBUG or --loglevel=debug
import logging
numeric_level = getattr(logging, options.loglevel.upper(), None)
if not isinstance(numeric_level, int):
raise ValueError('Invalid log level: %s' % options.loglevel)
logging.basicConfig(level=numeric_level)
if options.command == "version":
from abipy.core.release import version
print(version)
return 0
if options.no_colors:
# Disable colors
termcolor.enable(False)
if options.command == "manager":
# Document TaskManager options and qparams.
qtype = options.qtype
if qtype == "script":
manager = abilab.TaskManager.from_user_config()
script = manager.qadapter.get_script_str(
job_name="job_name",
launch_dir="workdir",
executable="executable",
qout_path="qout_file.path",
qerr_path="qerr_file.path",
stdin="stdin",
stdout="stdout",
stderr="stderr",
)
print(script)
else:
print(abilab.TaskManager.autodoc())
from pymatgen.io.abinitio.qadapters import show_qparams, all_qtypes
print("qtype supported: %s" % all_qtypes())
print("Use `abirun.py . manager slurm` to have the list of qparams for slurm.\n")
if qtype is not None:
print("QPARAMS for %s" % qtype)
show_qparams(qtype)
sys.exit(0)
# Read the flow from the pickle database.
if options.flowdir is None:
# Will try to figure out the location of the Flow.
options.flowdir = os.getcwd()
flow = abilab.Flow.pickle_load(options.flowdir, remove_lock=options.remove_lock)
#flow.set_spectator_mode(False)
retcode = 0
if options.command == "gui":
if options.chroot:
# Change the workdir of flow.
print("Will chroot to %s..." % options.chroot)
flow.chroot(options.chroot)
from abipy.gui.flowviewer import wxapp_flow_viewer
wxapp_flow_viewer(flow).MainLoop()
elif options.command == "new_manager":
# Read the new manager from file.
new_manager = abilab.TaskManager.from_file(options.manager_file)
# Default status for reset is QCritical
if options.task_status: options.task_status = Status.as_status("QCritical")
# Change the manager of the errored tasks.
print("Resetting tasks with status: %s" % options.task_status)
for task in flow.iflat_tasks(status=options.task_status, nids=selected_nids(flow, options)):
task.reset()
task.set_manager(new_manager)
# Update the database.
return flow.build_and_pickle_dump()
elif options.command == "events":
nrows, ncols = get_terminal_size()
for task in flow.iflat_tasks(status=options.task_status, nids=selected_nids(flow, options)):
report = task.get_event_report()
print(make_banner(str(task), width=ncols, mark="="))
#report = report.filter_types()
print(report)
elif options.command == "corrections":
nrows, ncols = get_terminal_size()
count = 0
for task in flow.iflat_tasks(status=options.task_status, nids=selected_nids(flow, options)):
if task.num_corrections == 0: continue
count += 1
print(make_banner(str(task), width=ncols, mark="="))
for corr in task.corrections:
pprint(corr)
if not count:
print("No correction found.")
elif options.command == "history":
nrows, ncols = get_terminal_size()
works_done = []
# Loop on the tasks and show the history of the work is not in works_done
for task in flow.iflat_tasks(status=options.task_status, nids=selected_nids(flow, options)):
work = task.work
if work not in works_done:
works_done.append(work)
print(make_banner(str(work), width=ncols, mark="="))
print(work.history.to_string(metadata=options.metadata))
print(make_banner(str(task), width=ncols, mark="="))
print(task.history.to_string(metadata=options.metadata))
# Print the history of the flow.
print(make_banner(str(flow), width=ncols, mark="="))
print(flow.history.to_string(metadata=options.metadata))
elif options.command == "handlers":
if options.doc:
autodoc_event_handlers()
else:
flow.show_event_handlers()
elif options.command == "single":
nlaunch = flow.single_shot()
print("Number of tasks launched: %d" % nlaunch)
if nlaunch: flow.show_status()
elif options.command == "rapid":
nlaunch = flow.rapidfire()
print("Number of tasks launched: %d" % nlaunch)
if nlaunch: flow.show_status()
elif options.command == "scheduler":
# Check that the env on the local machine is properly configured before starting the scheduler.
abilab.abicheck()
sched_options = {oname: getattr(options, oname) for oname in
("weeks", "days", "hours", "minutes", "seconds")}
if all(v == 0 for v in sched_options.values()):
sched = flow.make_scheduler()
else:
sched = flow.make_scheduler(**sched_options)
print(sched)
return sched.start()
elif options.command == "batch":
return flow.batch(timelimit=options.timelimit)
elif options.command == "status":
# Select the method to call.
show_func = flow.show_status if not options.summary else flow.show_summary
if options.delay:
cprint("Entering infinite loop. Press CTRL+C to exit", color="magenta", end="", flush=True)
try:
while True:
print(2*"\n" + time.asctime() + "\n")
flow.check_status()
show_func(verbose=options.verbose, nids=selected_nids(flow, options))
if flow.all_ok: break
time.sleep(options.delay)
except KeyboardInterrupt:
pass
else:
show_func(verbose=options.verbose, nids=selected_nids(flow, options))
if options.verbose and flow.manager.has_queue:
print("Total number of jobs in queue: %s" % flow.manager.get_njobs_in_queue())
elif options.command == "set_status":
# Default status for reset is QCritical
if options.task_status is None: options.task_status = Status.as_status("QCritical")
new_status = Status.as_status(options.new_status)
print("Will set all tasks with status: ", options.task_status, " to new_status", new_status)
count = 0
for task in flow.iflat_tasks(status=options.task_status, nids=selected_nids(flow, options)):
task.set_status(new_status, msg="Changed by abirun from %s to %s" % (task.status, new_status))
count += 1
print("Number of tasks modified: %s" % count)
if count:
# update database
flow.pickle_dump()
elif options.command == "open":
flow.open_files(what=options.what, status=None, op="==", nids=selected_nids(flow, options))
elif options.command == "ncopen":
# The name of the method associated to this netcdf file.
methname = "open_" + options.ncext.lower()
# List of netcdf file objects.
ncfiles = [getattr(task, methname)() for task in flow.select_tasks(nids=options.nids, wslice=options.wslice)
if hasattr(task, methname)]
if ncfiles:
# Start ipython shell with namespace
import IPython
if len(ncfiles) == 1:
IPython.start_ipython(argv=[], user_ns={"ncfile": ncfiles[0]})
else:
IPython.start_ipython(argv=[], user_ns={"ncfiles": ncfiles})
else:
cprint("Cannot find any netcdf file with extension %s" % options.ncext, color="magenta")
elif options.command == "cancel":
print("Number of jobs cancelled %d" % flow.cancel(nids=selected_nids(flow, options)))
# Remove directory
if options.rmtree: flow.rmtree()
elif options.command == "restart":
# Default status for reset is Unconverged if no option is provided by the user.
if options.task_status is None and options.nids is None:
options.task_status = Status.as_status("Unconverged")
nlaunch, excs = 0, []
for task in flow.iflat_tasks(status=options.task_status, nids=selected_nids(flow, options)):
if options.verbose:
print("Will try to restart %s, with status %s" % (task, task.status))
try:
fired = task.restart()
if fired: nlaunch += 1
except Exception:
excs.append(straceback())
cprint("Number of jobs restarted %d" % nlaunch, "blue")
if nlaunch:
# update database
flow.pickle_dump()
if excs:
print("Exceptions raised\n")
pprint(excs)
elif options.command == "reset":
# Default status for reset is QCritical
if options.task_status: options.task_status = Status.as_status("QCritical")
print("Will reset tasks with status: %s" % options.task_status)
count = 0
for task in flow.iflat_tasks(status=options.task_status, nids=selected_nids(flow, options)):
print("Resetting task %s" % task)
failed = task.reset()
if failed:
print("Task %s couldn't be reset" % task)
else:
count += 1
cprint("%d tasks have been reset" % count, "blue")
nlaunch = flow.rapidfire()
flow.show_status()
print("Number of tasks launched: %d" % nlaunch)
if nlaunch == 0:
g = flow.find_deadlocks()
#print("deadlocked:", gdeadlocked)
#print("runnables:", grunnables)
#print("running:", g.running)
if g.deadlocked and not (g.runnables or g.running):
print("*** Flow is deadlocked ***")
flow.pickle_dump()
elif options.command == "move":
print("Will move flow to %s..." % options.dest)
flow.chroot(options.dest)
flow.move(options.dest)
elif options.command == "tail":
def get_path(task):
"""Helper function used to select the files of a task."""
choices = {
"o": task.output_file,
"l": task.log_file,
"e": task.stderr_file,
}
return getattr(choices[options.what_tail], "path")
# Default status for tail is Running
if options.status is None: status = Status.as_status("Running")
paths = [get_path(task) for task in flow.iflat_tasks(status=options.task_status, nids=selected_nids(flow, options))]
if not paths:
cprint("No job is running. Exiting!", "red")
else:
cprint("Press CTRL+C to interrupt. Number of output files %d" % len(paths), color="magenta", end="", flush=True)
try:
os.system("tail -f %s" % " ".join(paths))
except KeyboardInterrupt:
pass
elif options.command == "qstat":
#for task in flow.select_tasks(nids=options.nids, wslice=options.wslice):
for task in flow.iflat_tasks():
if not task.qjob: continue
print("qjob", task.qjob)
print("info", task.qjob.get_info())
print("e start-time", task.qjob.estimated_start_time())
print("qstats", task.qjob.get_stats())
elif options.command == "deps":
flow.check_status()
flow.show_dependencies()
elif options.command == "robot":
import IPython
with abilab.abirobot(flow, options.robot_ext, nids=selected_nids(flow, options)) as robot:
#IPython.embed(header=str(robot) + "\nType `robot` in the terminal and use <TAB> to list its methods", robot=robot)
IPython.start_ipython(argv=[], user_ns={"robot": robot})
elif options.command == "plot":
fext = dict(
ebands="gsr",
)[options.what]
open_method = "open_" + fext
plot_method = "plot_" + options.what
for task in flow.select_tasks(nids=options.nids, wslice=options.wslice):
try:
with getattr(task, open_method)() as ncfile:
getattr(ncfile, plot_method)()
except Exception as exc:
print(exc)
elif options.command == "inspect":
tasks = flow.select_tasks(nids=options.nids, wslice=options.wslice)
# Use different thread to inspect the task so that master can catch KeyboardInterrupt and exit.
# One could use matplotlib non-blocking interface with show(block=False) but this one seems to work well.
from multiprocessing import Process
def plot_graphs():
for task in tasks:
if hasattr(task, "inspect"):
try:
task.inspect()
except Exception as exc:
cprint("%s: inspect method raised %s " % (task, exc), color="blue")
else:
cprint("Task %s does not provide an inspect method" % task, color="blue")
plot_graphs()
# This works with py3k but not with py2
#p = Process(target=plot_graphs)
#p.start()
#num_tasks = len(tasks)
#if num_tasks == 1:
# p.join()
#else:
# cprint("Will produce %d matplotlib plots. Press CTRL+C to interrupt..." % num_tasks, color="magenta", end="", flush=True)
# try:
# p.join()
# except KeyboardInterrupt:
# print("\nTerminating thread...")
# p.terminate()
elif options.command == "inputs":
flow.show_inputs(nids=selected_nids(flow, options))
elif options.command == "notebook":
write_notebook(flow, options)
elif options.command == "ipython":
import IPython
#IPython.embed(header="")
#print("options:", options.argv)
IPython.start_ipython(argv=options.argv, user_ns={"flow": flow})# , header="flow.show_status()")
elif options.command == "tar":
if not options.light:
tarfile = flow.make_tarfile(name=None,
max_filesize=options.max_filesize,
exclude_exts=options.exclude_exts,
exclude_dirs=options.exclude_dirs,
verbose=options.verbose)
print("Created tarball file %s" % tarfile)
else:
tarfile = flow.make_light_tarfile()
print("Created light tarball file %s" % tarfile)
elif options.command == "debug":
nrows, ncols = get_terminal_size()
# Test for scheduler exceptions first.
sched_excfile = os.path.join(flow.workdir, "_exceptions")
if os.path.exists(sched_excfile):
with open(sched_excfile, "r") as fh:
cprint(fh.read(), color="red")
return 0
if options.task_status is not None:
tasks = list(flow.iflat_tasks(status=options.task_status, nids=selected_nids(flow, options)))
else:
errors = list(flow.iflat_tasks(status=flow.S_ERROR, nids=selected_nids(flow, options)))
qcriticals = list(flow.iflat_tasks(status=flow.S_QCRITICAL, nids=selected_nids(flow, options)))
abicriticals = list(flow.iflat_tasks(status=flow.S_ABICRITICAL, nids=selected_nids(flow, options)))
tasks = errors + qcriticals + abicriticals
# For each task selected:
#
# 1) Check the error files of the task. If not empty, print the content to stdout and we are done.
# 2) If error files are empty, look at the master log file for possible errors
# 3) If also this check failes, scan all the process log files.
# TODO: This check is not needed if we introduce a new __abinit_error__ file
# that is created by the first MPI process that invokes MPI abort!
#
ntasks = 0
for task in tasks:
print(make_banner(str(task), width=ncols, mark="="))
ntasks += 1
# Start with error files.
for efname in ["qerr_file", "stderr_file",]:
err_file = getattr(task, efname)
if err_file.exists:
s = err_file.read()
if not s: continue
print(make_banner(str(err_file), width=ncols, mark="="))
cprint(s, color="red")
#count += 1
# Check main log file.
try:
report = task.get_event_report()
if report and report.num_errors:
print(make_banner(os.path.basename(report.filename), width=ncols, mark="="))
s = "\n".join(str(e) for e in report.errors)
else:
s = None
except Exception as exc:
s = str(exc)
count = 0 # count > 0 means we found some useful info that could explain the failures.
if s is not None:
cprint(s, color="red")
count += 1
if not count:
# Inspect all log files produced by the other nodes.
log_files = task.tmpdir.list_filepaths(wildcard="*LOG_*")
if not log_files:
cprint("No *LOG_* file in tmpdir. This usually happens if you are running with many CPUs", color="magenta")
for log_file in log_files:
try:
report = EventsParser().parse(log_file)
if report.errors:
print(report)
count += 1
break
except Exception as exc:
cprint(str(exc), color="red")
count += 1
break
if not count:
cprint("Houston, we could not find any error message that can explain the problem", color="magenta")
print("Number of tasks analyzed: %d" % ntasks)
elif options.command == "group":
d = defaultdict(list)
for task in flow.iflat_tasks(status=options.task_status, nids=selected_nids(flow, options)):
key = task.status
d[key].append(task.node_id)
print("Mapping status --> List of node identifiers")
for k, v in d.items():
print(" ",k, " --> ", v)
elif options.command == "diff":
if options.nids is None:
raise ValueError("nids must be specified when using diff command")
tasks = list(flow.iflat_tasks(nids=selected_nids(flow, options)))
if len(tasks) not in (2, 3):
if len(tasks) == 1:
cprint("task == task, returning\n" , color="magenta", end="", flush=True)
return 0
else:
raise ValueError("Don't know how to compare files produced by %d tasks" % len(tasks))
# Build list of lists. Each sub-list contains the files associated to the i-th task.
files_for_task = [None] * len(tasks)
for i, task in enumerate(tasks):
files_for_task[i] = task.select_files(options.what_diff)
for diff_files in zip(*files_for_task):
print("Comparing", ", ".join(os.path.relpath(p) for p in diff_files))
args = " ".join(os.path.relpath(p) for p in diff_files)
# TODO: I should have written a Differ object somewhere!
os.system("vimdiff %s" % args)
elif options.command == "networkx":
flow.plot_networkx(mode=options.nxmode,
with_edge_labels=options.edge_labels)
elif options.command == "listext":
for ext in options.listexts:
flow.listext(ext)
print("")
else:
raise RuntimeError("Don't know what to do with command %s!" % options.command)
return retcode
def main():
def str_examples():
examples = """
Usage example:\n
abiinsp.py OUTFILE status ==> Report the list of Warning, Commments, Errors
abiinsp.py OUTFILE plot ==> Plot results of the GS Scf cycle, Phonon Scf cycle...
abiinsp.py OUTFILE timer ==> Visualize timing data with matplotlib.
"""
return examples
def show_examples_and_exit(err_msg=None, error_code=1):
"""Display the usage of the script."""
sys.stderr.write(str_examples())
if err_msg: sys.stderr.write("Fatal Error\n" + err_msg + "\n")
sys.exit(error_code)
parser = argparse.ArgumentParser(
epilog=str_examples(),
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('filepath',
nargs="?",
help="File to inspect (output file or log file)")
# Create the parsers for the sub-commands
subparsers = parser.add_subparsers(dest='command',
help='sub-command help',
description="Valid subcommands")
# Subparser for status command.
p_status = subparsers.add_parser(
'status',
help="Check the status of the run (errors, warning, completion)")
#p_status.add_argument('format', nargs="?", default="cif", type=str, help="Format of the output file (ciff, POSCAR, json).")
# Subparser for plot command.
p_plot = subparsers.add_parser('plot', help="Plot data")
#p_plot.add_argument('visualizer', nargs="?", default="xcrysden", type=str, help="Visualizer.")
subparsers.add_parser('timer', help="Show timing data.")
subparsers.add_parser('pseudo', help="Show info on pseudopotential file.")
# Parse command line.
try:
options = parser.parse_args()
except:
show_examples_and_exit(error_code=1)
if options.command == "status":
# Parse the Abinit Events in filepath.
parser = EventsParser()
report = parser.parse(options.filepath)
print(report)
elif options.command == "plot":
# TODO: At present only GS runs are supported by plottable_from_outfile
obj = plottable_from_outfile(options.filepath)
if obj is not None:
obj.plot()
else:
raise ValueError(
"Don't know how to extract plottable data from %s" %
options.filepath)
elif options.command == "timer":
parser = AbinitTimerParser()
parser.parse(options.filepath)
#parser.show_pie(key="wall_time", minfract=0.05)
#parser.show_efficiency),
#parser.show_stacked_hist),
elif options.command == "pseudo":
from pymatgen.io.abinitio.pseudos import PseudoParser
pseudo = PseudoParser().parse(options.filepath)
print(pseudo)
else:
raise ValueError("Unsupported command %s" % options.command)
return 0