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Abnormal memory consumption of Molecule3dViewer #511

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m97 opened this issue Aug 7, 2020 · 1 comment · Fixed by #576
Closed

Abnormal memory consumption of Molecule3dViewer #511

m97 opened this issue Aug 7, 2020 · 1 comment · Fixed by #576

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@m97
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m97 commented Aug 7, 2020

Molecule3dViewer application memory usage increases while rotating molecule. By increase I mean in order of GB, which consumes whole system memory to the point of crash.

To Reproduce:
Operating system - Linux Mint 20
Web Browser - Google Chrome Version 84.0.4147.105 (Official Build) (64-bit)

  1. Open demo (for example https://dash.plotly.com/dash-bio/molecule3dviewer).
  2. Start rotating molecule while monitoring ram consumption.

Expected behavior:
Interacting with displayed molecule should not lead to dramatic increase of ram consumption and system crash.

Screenshots:
Before rotating displayed molecule:
before_rotation

After few seconds of rapid rotation:
after_rotation

Python version: Python 3.8.2

Python enviroment:

apt-clone 0.2.1
apturl 0.5.2
attrs 19.3.0
backcall 0.1.0
beautifulsoup4 4.8.2
biopython 1.77
bleach 3.1.1
blinker 1.4
Brlapi 0.7.0
Brotli 1.0.7
certifi 2019.11.28
chardet 3.0.4
Click 7.0
colorama 0.4.3
colour 0.1.5
command-not-found 0.3
configobj 5.0.6
crudini 0.9.3
cryptography 2.8
cupshelpers 1.0
cycler 0.10.0
dash 1.14.0
dash-bio 0.4.8
dash-bio-utils 0.0.5
dash-bootstrap-components 0.10.3
dash-core-components 1.10.2
dash-html-components 1.0.3
dash-renderer 1.6.0
dash-table 4.9.0
dbus-python 1.2.16
decorator 4.4.2
defer 1.0.6
defusedxml 0.6.0
distro 1.4.0
entrypoints 0.3
Flask 1.1.2
Flask-Compress 1.5.0
forcelayout 1.0.6
future 0.18.2
GEOparse 2.0.1
grpcio 1.16.1
html5lib 1.0.1
httplib2 0.14.0
idna 2.8
ifaddr 0.1.6
importlib-metadata 1.5.0
iniparse 0.4
ipykernel 5.2.0
ipython 7.13.0
ipython-genutils 0.2.0
itsdangerous 1.1.0
jedi 0.15.2
Jinja2 2.10.1
joblib 0.16.0
jsonschema 3.2.0
jupyter-client 6.1.2
jupyter-console 6.0.0
jupyter-core 4.6.3
keyring 18.0.1
kiwisolver 1.2.0
launchpadlib 1.10.13
lazr.restfulclient 0.14.2
lazr.uri 1.0.3
louis 3.12.0
macaroonbakery 1.3.1
Mako 1.1.0
Markdown 3.1.1
MarkupSafe 1.1.0
matplotlib 3.3.0
meson 0.53.2
mistune 0.8.4
more-itertools 4.2.0
nbconvert 5.6.1
nbformat 5.0.4
nemo-emblems 4.6.0
netifaces 0.10.4
networkx 2.4
nose 1.3.7
notebook 6.0.3
numpy 1.17.4
oauthlib 3.1.0
onboard 1.4.1
packaging 20.3
PAM 0.4.2
pandas 1.1.0
pandocfilters 1.4.2
ParmEd 3.2.0
parso 0.5.2
periodictable 1.5.2
pexpect 4.6.0
pickleshare 0.7.5
Pillow 7.0.0
pip 20.0.2
plotly 4.9.0
prometheus-client 0.7.1
prompt-toolkit 2.0.10
protobuf 3.6.1
psutil 5.5.1
PyAudio 0.2.11
pycairo 1.16.2
pycrypto 2.6.1
pycups 1.9.73
pycurl 7.43.0.2
Pygments 2.3.1
PyGObject 3.36.0
PyICU 2.4.2
pyinotify 0.9.6
PyJWT 1.7.1
pymacaroons 0.13.0
pymol 2.3.0
PyNaCl 1.3.0
PyOpenGL 3.1.0
pyparsing 2.4.6
pyparted 3.11.2
PyQt5 5.14.1
PyQtWebEngine 5.14.0
pyRFC3339 1.1
pyrsistent 0.15.5
python-apt 2.0.0+ubuntu0.20.4.1
python-dateutil 2.7.3
python-debian 0.1.36ubuntu1
python-xapp 2.0.1
python-xlib 0.23
pytz 2019.3
pyxattr 0.6.1
pyxdg 0.26
PyYAML 5.3.1
pyzmq 18.1.1
reportlab 3.5.34
requests 2.22.0
requests-unixsocket 0.2.0
retrying 1.3.3
scikit-learn 0.23.2
scipy 1.5.2
SecretStorage 2.3.1
Send2Trash 1.5.0
sessioninstaller 0.0.0
setproctitle 1.1.10
setuptools 45.2.0
simplejson 3.16.0
sip 4.19.21
six 1.14.0
soupsieve 1.9.5
system-service 0.3
systemd-python 234
terminado 0.8.2
testpath 0.4.4
threadpoolctl 2.1.0
tinycss2 1.0.2
tornado 5.1.1
tqdm 4.48.2
traitlets 4.3.3
ubuntu-advantage-tools 20.3
ubuntu-drivers-common 0.0.0
ufw 0.36
Unidecode 1.1.1
urllib3 1.25.8
urwid 2.0.1
wadllib 1.3.3
wcwidth 0.1.8
webencodings 0.5.1
Werkzeug 1.0.1
wheel 0.34.2
xkit 0.0.0
youtube-dl 2020.3.24
zeroconf 0.24.4
zim 0.72.0
zipp 1.0.0

@NatureGeorge
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Also encounter this issue. This seems to be a common issue with plotly's 3d viewer(harmless for small dataset) but serious in Molecule3dViewer.

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