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Switch to logging #623

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a2f6d90
Change all print statements to logger statements
lakesare Jul 23, 2021
c40a6ef
Get rid of the sim.cfg.verbose option
lakesare Aug 2, 2021
917a86d
Merge branch 'master' of https://github.com/lakesare/netpyne into swi…
Aug 2, 2021
07a1c33
Merge conflicts
lakesare Aug 2, 2021
8e2b385
Remove all "from __future__ import print_function"
lakesare Aug 2, 2021
42bf86f
Add a comment about pprint
lakesare Aug 2, 2021
3e6d76b
Merge branch 'Neurosim-lab:development' into switch_to_logging
lakesare Aug 2, 2021
435c2e8
Typo fix
lakesare Aug 2, 2021
c89ba61
Stop propagating the netpyne logger
lakesare Aug 3, 2021
b3e6c14
Some necessary logger.info() => logger.timing()
lakesare Aug 3, 2021
cd869f6
How about we always keep track of timing?
lakesare Aug 3, 2021
2541f00
Fix a typo , => +
lakesare Aug 6, 2021
02f6544
Merge
lakesare Oct 20, 2021
dca1cf4
Get rid of logger.timing
lakesare Oct 20, 2021
6e95444
Convert new print()s to logger.info()s
lakesare Oct 20, 2021
94a985b
Fixes after review
lakesare Oct 20, 2021
d17bd3f
Revert "How about we always keep track of timing?"
lakesare Oct 20, 2021
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15 changes: 7 additions & 8 deletions netpyne/analysis/wrapper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -41,14 +41,13 @@ def plotData():
out = func(**kwargs) # call function with user arguments

# Print timings
if sim.cfg.timing:
sim.timing('stop', 'plotTime')
logger.timing(' Done; plotting time = %0.2f s' % sim.timingData['plotTime'])

sim.timing('stop', 'totalTime')
sumTime = sum([t for k,t in sim.timingData.items() if k not in ['totalTime']])
if sim.timingData['totalTime'] <= 1.2*sumTime: # Print total time (only if makes sense)
logger.timing('\nTotal time = %0.2f s' % sim.timingData['totalTime'])
sim.timing('stop', 'plotTime')
logger.timing(' Done; plotting time = %0.2f s' % sim.timingData['plotTime'])

sim.timing('stop', 'totalTime')
sumTime = sum([t for k,t in sim.timingData.items() if k not in ['totalTime']])
if sim.timingData['totalTime'] <= 1.2*sumTime: # Print total time (only if makes sense)
logger.timing('\nTotal time = %0.2f s' % sim.timingData['totalTime'])

try:
logger.info('\nEnd time: ', datetime.now())
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6 changes: 3 additions & 3 deletions netpyne/sim/load.py
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Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,7 @@ def _byteify(data, ignore_dicts = False):
# if it's anything else, return it in its original form
return data

if hasattr(sim, 'cfg') and sim.cfg.timing: sim.timing('start', 'loadFileTime')
if hasattr(sim, 'cfg'): sim.timing('start', 'loadFileTime')
ext = os.path.basename(filename).split('.')[-1]

# load pickle file
Expand Down Expand Up @@ -126,7 +126,7 @@ def _byteify(data, ignore_dicts = False):
logger.warning('Format not recognized for file %s'%(filename))
return

if hasattr(sim, 'rank') and sim.rank == 0 and hasattr(sim, 'cfg') and sim.cfg.timing:
if hasattr(sim, 'rank') and sim.rank == 0 and hasattr(sim, 'cfg'):
sim.timing('stop', 'loadFileTime')
logger.timing(' Done; file loading time = %0.2f s' % sim.timingData['loadFileTime'])

Expand Down Expand Up @@ -339,7 +339,7 @@ def loadNet(filename, data=None, instantiate=True, compactConnFormat=False):
except:
logger.warning('Unable to create NEURON objects...')

if loadNow and sim.cfg.timing: #if sim.rank == 0 and sim.cfg.timing:
if loadNow: #if sim.rank == 0 and sim.cfg.timing:
sim.timing('stop', 'loadNetTime')
logger.timing(' Done; re-instantiate net time = %0.2f s' % sim.timingData['loadNetTime'])
else:
Expand Down
17 changes: 8 additions & 9 deletions netpyne/sim/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -140,18 +140,17 @@ def timing(mode, processName):
sim.timingData = {}

if hasattr(sim.cfg, 'timing'):
if sim.cfg.timing:
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@lakesare lakesare Aug 3, 2021 •
edited
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@salvadord / @joewgraham, from the PR description:

All if sim.cfg.timing: print() are changed to logger.timing().

This change made the code like logger.timing('\nTotal time = %0.2f s' % sim.timingData['totalTime']) fail when we have sim.cfg.timing set to False.

We can either always track time (this is what this commit does, though we'd have to remove hasattr(sim.cfg, 'timing') too and do a couple of other things - I stopped in the middle here to ask for your opinion), or I can revert all timing statements to if sim.cfg.timing: ...log stuff....

However - have we considered using a higher order function, say in this fashion https://stackoverflow.com/a/15136422/3192470?
Then we'd have it all in a single place:

import time

def timeit(f, message):
    def timed(*args, **kw):
        if sim.cfg.timing and sim.rank == 0:
          ts = time.time()
          result = f(*args, **kw)
          te = time.time()

          logger.info(message % (te-ts))
          return result
    return timed

@timeit(message="  Done; cells modification time =")
def modifyCells(self, params, updateMasterAllCells=False):
  ...

(Instead of https://github.com/Neurosim-lab/netpyne/blob/development/netpyne/network/modify.py)

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It's looking impressive, but I think we should discuss details at the dev meeting tomorrow. I've added notes to the agenda.

if hasattr(sim, 'rank'):
if sim.rank == 0:
if mode == 'start':
sim.timingData[processName] = time()
elif mode == 'stop':
sim.timingData[processName] = time() - sim.timingData[processName]
else:
if hasattr(sim, 'rank'):
if sim.rank == 0:
if mode == 'start':
sim.timingData[processName] = time()
elif mode == 'stop':
sim.timingData[processName] = time() - sim.timingData[processName]
sim.timingData[processName] = time() - sim.timingData[processName]
else:
if mode == 'start':
sim.timingData[processName] = time()
elif mode == 'stop':
sim.timingData[processName] = time() - sim.timingData[processName]


#------------------------------------------------------------------------------
Expand Down