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high memory usage + job taking long time #140

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asnaylor opened this issue Nov 11, 2020 · 0 comments
Open

high memory usage + job taking long time #140

asnaylor opened this issue Nov 11, 2020 · 0 comments

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@asnaylor
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asnaylor commented Nov 11, 2020

In fast_carpenter when trying to multiple/divide variables together I have seen high memory usage and jobs taking a very very long time. I was histogramming two variables in a 2.4 GB file in multiprocessing mode with 8 CPU cores and it took 30 seconds. However when I had the variables in an expression (see yaml config below) where they were divided and multiplied fast_carpenter was running for 4 hours and reached a high memory usage of 30 GB before I decided to kill the program as nothing was seeming to happen. I ran both test on the same machine, with the same file and same number of CPU's and in multiprocessing mode. I also tried using coffea:local on the file but nothing seemed to happen after about 10 mins.

yaml config file:

stages:
  - make_vars: fast_carpenter.Define
  - cuts: fast_carpenter.CutFlow
  - binned_data: fast_carpenter.BinnedDataframe
make_vars:
  variables:
    - single_scatter: (ss.nSingleScatters > 0)
    - s1c: 
       formula: ss.correctedS1Area_phd
    - s2c:
        formula: ss.correctedS2Area_phd
    - log_s2c:
        formula: log10(s2c)
    - E:
        formula: 0.0111*((s1c/0.10) + (s2c/100.00) )
cuts:
  selection:
    All:
      - single_scatter
binned_data:
  binning:
    - in: s1c
      bins:
        low: 0
        high: 1e4
        nbins: 1000
    - in: log_s2c
      bins:
        low: 2
        high: 7
        nbins: 1000
    - in: E
      bins:
        low: 0
        high: 500
        nbins: 500

Versions:
Python 3.8.5

Full `pip freeze` output:
alphatwirl==0.25.5
argon2-cffi==20.1.0
async-generator==1.10
atpbar==1.0.8
atsge==0.2.1
attrs==20.3.0
atuproot==0.1.13
awkward==0.14.0
awkward1==0.4.3
backcall==0.2.0
bleach==3.2.1
cachetools==4.1.1
certifi==2020.6.20
cffi==1.14.3
chardet==3.0.4
cloudpickle==1.6.0
coffea==0.6.42
cycler==0.10.0
decorator==4.4.2
defusedxml==0.6.0
entrypoints==0.3
fast-carpenter==0.19.1
fast-curator==0.7.0
fast-flow==0.6.1
idna==2.10
ipykernel==5.3.4
ipython==7.19.0
ipython-genutils==0.2.0
ipywidgets==7.5.1
jedi==0.17.2
Jinja2==2.11.2
jsonschema==3.2.0
jupyter-client==6.1.7
jupyter-core==4.6.3
jupyterlab-pygments==0.1.2
kiwisolver==1.3.1
llvmlite==0.34.0
lz4==3.1.0
mantichora==0.9.7
MarkupSafe==1.1.1
matplotlib==3.3.2
mistune==0.8.4
mplhep==0.2.8
nbclient==0.5.1
nbconvert==6.0.7
nbformat==5.0.8
nest-asyncio==1.4.2
notebook==6.1.5
numba==0.51.2
numexpr==2.7.1
numpy==1.19.4
packaging==20.4
pandas==1.1.4
pandocfilters==1.4.3
parso==0.7.1
pexpect==4.8.0
pickleshare==0.7.5
Pillow==8.0.1
prometheus-client==0.8.0
prompt-toolkit==3.0.8
ptyprocess==0.6.0
pycparser==2.20
Pygments==2.7.2
pyparsing==2.4.7
pyrsistent==0.17.3
python-dateutil==2.8.1
python3-nersc-customs==0.2.0
python3-nersc-modster==0.2.0
python3-nersc-sitecustomize==0.2.0
python3-nerscjson==0.9
pytz==2020.4
PyYAML==5.3.1
pyzmq==19.0.2
requests==2.24.0
scipy==1.5.4
Send2Trash==1.5.0
six==1.15.0
terminado==0.9.1
testpath==0.4.4
tornado==6.1
tqdm==4.51.0
traitlets==5.0.5
uproot==3.13.0
uproot-methods==0.8.0
urllib3==1.25.11
wcwidth==0.2.5
webencodings==0.5.1
widgetsnbextension==3.5.1
xrootd==5.0.2
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