Skip to content
System Status: All systems are operational • Services are available and operational.
Click for detailed status

Python

Python is a high-level, general-purpose programming language.

Python on Euler

On Euler the following versions are available via modules:

Version Module Command
3.12.8 module load stack/2024-06 python/3.12.8
3.11.6 with CUDA* module load stack/2024-06 python_cuda/3.11.6
3.11.6 module load stack/2024-06 python/3.11.6
3.10.13 module load stack/2024-06 python/3.10.13
3.9.18 module load stack/2024-06 python/3.9.18
3.9.18 with CUDA* module load stack/2024-06 python_cuda/3.9.18

*additionally loads CUDA, NCCL, OpenBlas modules

Packages in Python 3.12.8 absl-py 2.1.0
AccessControl 7.2
Acquisition 6.1
aiohappyeyeballs 2.4.4
aiohttp 3.11.12
aiohttp-cors 0.7.0
aioredis 2.0.1
aiosignal 1.3.2
alabaster 1.0.0
alembic 1.14.1
amply 0.1.6
anndata 0.11.3
annotated-types 0.7.0
anyio 4.8.0
appdirs 1.4.4
argh 0.31.3
argon2 0.1.10
argon2-cffi 23.1.0
argon2-cffi-bindings 21.2.0
argparse-dataclass 2.0.0
array_api_compat 1.10.0
arrow 1.3.0
asn1crypto 1.5.1
astor 0.8.1
asttokens 3.0.0
astunparse 1.6.3
async-generator 1.10
async-lru 2.0.4
async-timeout 5.0.1
atomicwrites 1.4.1
attrs 25.1.0
AuthEncoding 5.0
babel 2.17.0
beautifulsoup4 4.13.3
bids-validator 1.14.7.post0
bidsschematools 1.0.1
bleach 6.2.0
blessings 1.7
blosc2 3.0.0
bokeh 3.6.3
Bottleneck 1.4.2
BTrees 6.1
cachetools 5.5.1
certifi 2025.1.31
certipy 0.2.1
cffi 1.17.1
cftime 1.6.4.post1
Chameleon 4.6.0
chardet 5.2.0
charset-normalizer 3.4.1
clang 17.0.6
click 8.1.8
click-plugins 1.1.1
cligj 0.7.2
cloudpickle 3.1.1
colorama 0.4.6
colorful 0.5.6
colorlog 6.9.0
colorlover 0.3.0
comm 0.2.2
commonmark 0.9.1
conda-inject 1.3.2
ConfigArgParse 1.7
configobj 5.0.9
connection_pool 0.0.3
contourpy 1.3.1
cryptography 44.0.0
cycler 0.12.1
Cython 3.0.11
dask 2025.1.0
DateTime 5.5
datrie 0.8.2
debugpy 1.8.12
decorator 5.1.1
deepdiff 8.2.0
defusedxml 0.7.1
Deprecated 1.2.18
deprecation 2.1.0
distributed 2025.1.0
dm-tree 0.1.9
dnspython 2.7.0
docopt 0.6.2
DocumentTemplate 4.6
docutils 0.21.2
dpath 2.2.0
entrypoints 0.4
et_xmlfile 2.0.0
executing 2.2.0
ExtensionClass 6.0
fastjsonschema 2.21.1
filelock 3.17.0
flexcache 0.3
flexparser 0.4
flit 3.10.1
flit_core 3.10.1
fonttools 4.56.0
fqdn 1.5.1
frozenlist 1.5.0
fsspec 2025.2.0
future 1.0.0
gitdb 4.0.12
gitdb2 4.0.2
GitPython 3.1.44
gprMax 3.1.4
greenlet 3.1.1
grpcio 1.70.0
h11 0.14.0
h5py 3.12.1
HeapDict 1.0.1
hiredis 3.1.0
html5lib 1.1
httpcore 1.0.7
httpx 0.28.1
humanfriendly 10.0
hyperopt 0.2.7
hypothesis 6.125.2
idna 3.10
imageio 2.37.0
imagesize 1.4.1
immutables 0.21
importlib_metadata 8.6.1
importlib_resources 6.5.2
iniconfig 2.0.0
ipykernel 6.29.5
ipython 8.32.0
ipython-genutils 0.2.0
ipywidgets 8.1.5
isodate 0.7.2
isoduration 20.11.0
jedi 0.19.2
Jinja2 3.1.5
joblib 1.4.2
json5 0.10.0
jsonargparse 4.36.0
jsonpickle 4.0.1
jsonpointer 3.0.0
jsonschema 4.23.0
jsonschema-specifications 2024.10.1
jupyter 1.1.1
jupyter_client 8.6.3
jupyter-console 6.6.3
jupyter_contrib_core 0.4.2
jupyter_core 5.7.2
jupyter-events 0.12.0
jupyter-lsp 2.2.5
jupyter_server 2.15.0
jupyter_server_proxy 4.4.0
jupyter_server_terminals 0.5.3
jupyter-telemetry 0.1.0
jupyterhub 5.2.1
jupyterlab 4.3.5
jupyterlab_pygments 0.3.0
jupyterlab_server 2.27.3
jupyterlab_widgets 3.0.13
kiwisolver 1.4.8
lazy_loader 0.4
libclang 18.1.1
llvmlite 0.44.0
locket 1.0.0
lxml 5.3.1
Mako 1.3.9
Markdown 3.7
MarkupSafe 3.0.2
matplotlib 3.10.0
matplotlib-inline 0.1.7
maturin 1.8.2
meson 1.7.0
mistune 3.1.1
mock 5.1.0
more-itertools 10.6.0
mpmath 1.3.0
msgpack 1.1.0
multidict 6.1.0
MultiMapping 5.0
multipart 1.2.1
narwhals 1.25.2
natsort 8.4.0
nbclassic 1.2.0
nbclient 0.10.2
nbconvert 7.16.6
nbformat 5.10.4
nbgitpuller 1.2.2
ndindex 1.9.2
nest-asyncio 1.6.0
networkx 3.4.2
nibabel 5.3.2
ninja 1.11.1.3
nose 1.3.7
notebook 7.3.2
notebook_shim 0.2.4
num2words 0.5.14
numba 0.61.0
numexpr 2.10.2
numpy 2.1.3
oauthlib 3.2.2
opencv-python 4.11.0.86
openpyxl 3.1.5
opt_einsum 3.4.0
ordered-set 4.1.0
orderly-set 5.3.0
overrides 7.7.0
packaging 24.2
pamela 1.2.0
pandas 2.2.3
pandoc 2.4
pandocfilters 1.5.1
parso 0.8.4
partd 1.4.2
PasteDeploy 3.1.0
patchelf 0.17.2.1
patsy 1.0.1
pbr 6.1.1
Persistence 5.1
persistent 6.1
pexpect 4.9.0
pickleshare 0.7.5
pillow 11.1.0
Pint 0.24.4
pip 25.0
plac 1.4.3
platformdirs 4.3.6
plotly 6.0.0
pluggy 1.5.0
plumbum 1.9.0
ply 3.11
pooch 1.8.2
prometheus_client 0.21.1
promise 2.3
prompt_toolkit 3.0.50
propcache 0.2.1
psutil 6.1.1
ptyprocess 0.7.0
PuLP 2.9.0
pure_eval 0.2.3
py 1.11.0
py-cpuinfo 9.0.0
py-spy 0.4.0
py4j 0.10.9.9
pyasn1 0.6.1
pyasn1_modules 0.4.1
pycollada 0.8
pycparser 2.22
pydantic 2.10.6
pydantic_core 2.27.2
pyface 8.0.0
pyglet 2.1.2
Pygments 2.19.1
PyGSP 0.5.1
pymongo 4.11
pyOpenSSL 25.0.0
pyparsing 3.2.1
Pyro4 4.82
pyrsistent 0.20.0
pyshp 2.3.1
PySocks 1.7.1
pytest 8.3.4
python-dateutil 2.9.0.post0
python-gettext 5.0
python-json-logger 3.2.1
pytoml 0.1.21
pytz 2025.1
pyutillib 0.3.0
PyWavelets 1.8.0
PyYAML 6.0.2
pyzmq 26.2.1
qtconsole 5.6.1
QtPy 2.4.2
ratelimiter 1.2.0.post0
rdflib 7.1.3
redis 5.2.1
referencing 0.36.2
requests 2.32.3
requests-oauthlib 2.0.0
reretry 0.11.8
RestrictedPython 8.0
retry 0.9.2
retrying 1.3.4
rfc3339-validator 0.1.4
rfc3986-validator 0.1.1
roman 5.0
rpds-py 0.22.3
ruamel.yaml 0.18.10
ruamel.yaml.clib 0.2.12
scikit-image 0.25.1
scikit-learn 1.6.1
scipy 1.15.1
seaborn 0.13.2
Send2Trash 1.8.3
sentry-sdk 2.20.0
serpent 1.41
setuptools 75.8.0
setuptools-scm 8.1.0
shortuuid 1.0.13
simpervisor 1.0.0
simplegeneric 0.8.1
simplejson 3.19.3
simpy 4.1.1
six 1.17.0
smart-open 7.1.0
smmap 5.0.2
smmap2 3.0.1
snakemake 8.27.1
snakemake-interface-common 1.17.4
snakemake-interface-executor-plugins 9.3.3
snakemake-interface-report-plugins 1.1.0
snakemake-interface-storage-plugins 3.3.0
sniffio 1.3.1
snowballstemmer 2.2.0
sortedcontainers 2.4.0
soupsieve 2.6
Sphinx 8.1.3
sphinxcontrib-applehelp 2.0.0
sphinxcontrib-devhelp 2.0.0
sphinxcontrib-htmlhelp 2.1.0
sphinxcontrib-jsmath 1.0.1
sphinxcontrib-qthelp 2.0.0
sphinxcontrib-serializinghtml 2.0.0
sphinxcontrib-websupport 2.0.0
SQLAlchemy 2.0.38
stack-data 0.6.3
statsmodels 0.14.4
stopit 1.1.2
svg.path 6.3
tables 3.10.2
tabulate 0.9.0
tasklogger 1.2.0
tblib 3.0.0
tenacity 9.0.0
termcolor 2.3.0
terminado 0.18.1
terminaltables 3.1.10
threadpoolctl 3.5.0
throttler 1.2.2
tifffile 2025.1.10
tinycss2 1.4.0
toml 0.10.2
tomli 2.2.1
tomli_w 1.2.0
toolz 1.0.0
toposort 1.10
tornado 6.4.2
tqdm 4.67.1
traitlets 5.14.3
traits 7.0.2
transaction 5.0
trimesh 4.6.1
types-python-dateutil 2.9.0.20241206
typing_extensions 4.12.2
tzdata 2025.1
uri-template 1.3.0
urllib3 2.3.0
waitress 3.0.2
wcwidth 0.2.13
webcolors 24.11.1
webencodings 0.5.1
WebOb 1.8.9
websocket-client 1.8.0
WebTest 3.0.4
wheel 0.45.1
widgetsnbextension 4.0.13
wrapt 1.17.2
WSGIProxy2 0.5.1
xengsort 2.0.8
xlrd 2.0.1
xxhash 3.5.0
xyzservices 2025.1.0
yarl 1.18.3
yaspin 3.1.0
yte 1.5.7
z3c.pt 4.4
zc.lockfile 3.0.post1
ZConfig 4.2
zExceptions 5.0
zict 3.0.0
zipp 3.21.0
ZODB 6.0
zodbpickle 4.1.1
zope.browser 3.0
zope.component 6.0
zope.configuration 6.0
zope.contentprovider 6.0
zope.contenttype 5.1
zope.deferredimport 5.0
zope.deprecation 5.1
zope.event 5.0
zope.exceptions 5.2
zope.hookable 7.0
zope.i18n 5.2
zope.i18nmessageid 7.0
zope.interface 7.2
zope.location 5.1
zope.proxy 6.1
zope.publisher 7.2
zope.schema 7.0.1
zope.security 7.3
zope.sequencesort 5.1
zope.structuredtext 5.0
zope.tales 6.0
zope.testing 5.0.1
zope.traversing 5.0
Packages in Python 3.11.6 absl-py 2.1.0
addict 2.4.0
aiofiles 22.1.0
aiohttp 3.9.5
aiosignal 1.3.1
aiosqlite 0.20.0
alabaster 0.7.16
alembic 1.13.1
annotated-types 0.7.0
anyio 4.4.0
appdirs 1.4.4
argon2-cffi 23.1.0
argon2-cffi-bindings 21.2.0
argparse-dataclass 2.0.0
arrow 1.3.0
asttokens 2.4.1
astunparse 1.6.3
async-lru 2.0.4
attrs 23.2.0
Babel 2.15.0
beautifulsoup4 4.12.3
biopython 1.83
bleach 6.1.0
blinker 1.8.2
blosc2 2.7.0
cachetools 5.3.3
certifi 2024.6.2
certipy 0.1.3
cffi 1.16.0
charset-normalizer 3.3.2
click 8.1.7
coloredlogs 15.0.1
colormath 3.0.0
comm 0.2.2
conda-inject 1.3.2
ConfigArgParse 1.7
connection_pool 0.0.3
contourpy 1.2.1
cryptography 42.0.8
cycler 0.12.1
Cython 3.0.10
dash 2.17.1
dash-core-components 2.0.0
dash-html-components 2.0.0
dash-table 5.0.0
DateTime 5.5
datrie 0.8.2
debugpy 1.8.1
decorator 5.1.1
deepTools 3.5.5
deeptoolsintervals 0.1.9
defusedxml 0.7.1
docker-pycreds 0.4.0
docutils 0.21.2
dpath 2.2.0
emcee 3.1.6
entrypoints 0.4
executing 2.0.1
fastjsonschema 2.20.0
filelock 3.15.3
Flask 3.0.3
flatbuffers 24.3.25
flexcache 0.3
flexparser 0.4
fonttools 4.53.0
fqdn 1.5.1
frozenlist 1.4.1
fsspec 2024.6.0
gast 0.5.4
gitdb 4.0.11
GitPython 3.1.43
google-auth 2.31.0
google-auth-oauthlib 1.2.0
google-pasta 0.2.0
graphviz 0.20.3
greenlet 3.0.3
grpcio 1.64.1
h11 0.14.0
h5py 3.11.0
httpcore 1.0.5
httpx 0.27.0
humanfriendly 10.0
humanize 4.9.0
idna 3.7
imageio 2.34.1
imagesize 1.4.1
immutables 0.20
importlib_metadata 7.2.0
iniconfig 2.0.0
ipykernel 6.29.4
ipython 8.25.0
ipython-genutils 0.2.0
ipywidgets 8.1.3
isodate 0.6.1
isoduration 20.11.0
itsdangerous 2.2.0
jax 0.4.30
jax-cuda12-pjrt 0.4.30
jax-cuda12-plugin 0.4.30
jaxlib 0.4.30
jedi 0.19.1
Jinja2 3.1.4
joblib 1.4.2
json5 0.9.25
jsonpointer 3.0.0
jsonschema 4.22.0
jsonschema-specifications 2023.12.1
jupyter_client 7.4.9
jupyter_core 5.7.2
jupyter-events 0.10.0
jupyter-lsp 2.2.5
jupyter_server 2.14.1
jupyter_server_fileid 0.9.2
jupyter_server_proxy 4.2.0
jupyter_server_terminals 0.5.3
jupyter_server_ydoc 0.8.0
jupyter-ydoc 0.2.5
jupyterhub 5.0.0
jupyterlab 4.2.2
jupyterlab_pygments 0.3.0
jupyterlab_server 2.27.2
jupyterlab_slurm 3.0.1
jupyterlab_widgets 3.0.11
kaleido 0.2.1
keras 2.15.0
Keras-Preprocessing 1.1.2
kiwisolver 1.4.5
lazy_loader 0.4
libclang 18.1.1
lightning 2.3.0
lightning-utilities 0.11.2
llvmlite 0.43.0
Mako 1.3.5
Markdown 3.6
markdown-it-py 3.0.0
MarkupSafe 2.1.5
matplotlib 3.9.0
matplotlib-inline 0.1.7
mdurl 0.1.2
meson 1.4.1
mistune 3.0.2
ml-dtypes 0.2.0
more-itertools 10.3.0
mpmath 1.3.0
msgpack 1.0.8
multidict 6.0.5
multiqc 1.22.3
namex 0.0.8
nbclassic 1.1.0
nbclient 0.10.0
nbconvert 7.16.4
nbformat 5.10.4
nbgitpuller 1.2.1
ndindex 1.8
nest-asyncio 1.6.0
networkx 3.3
ninja 1.11.1.1
nose 1.3.7
notebook 6.5.7
notebook_shim 0.2.4
numba 0.60.0
numexpr 2.10.1
numpy 1.25.2
numpydoc 1.7.0
nvidia-cublas-cu12 12.1.3.1
nvidia-cuda-cupti-cu12 12.1.105
nvidia-cuda-nvrtc-cu12 12.1.105
nvidia-cuda-runtime-cu12 12.1.105
nvidia-cudnn-cu12 8.9.2.26
nvidia-cufft-cu12 11.0.2.54
nvidia-curand-cu12 10.3.2.106
nvidia-cusolver-cu12 11.4.5.107
nvidia-cusparse-cu12 12.1.0.106
nvidia-nccl-cu12 2.20.5
nvidia-nvjitlink-cu12 12.3.101
nvidia-nvtx-cu12 12.1.105
oauthlib 3.2.2
open3d 0.18.0
opencv-contrib-python 4.10.0.84
opencv-python 4.10.0.84
openseespy 3.6.0.2
openseespylinux 3.6.0.2
opt-einsum 3.3.0
optree 0.11.0
overrides 7.7.0
packaging 24.1
pamela 1.1.0
pandas 2.2.2
pandoc 2.3
pandocfilters 1.5.1
parso 0.8.4
patsy 0.5.6
pexpect 4.9.0
pillow 10.3.0
Pint 0.24.4
pip 23.2.1
plac 1.4.3
platformdirs 4.2.2
plotly 5.22.0
pluggy 1.5.0
plumbum 1.8.3
ply 3.11
prometheus_client 0.20.0
prompt_toolkit 3.0.47
protobuf 4.25.3
psutil 6.0.0
ptyprocess 0.7.0
PuLP 2.8.0
pure-eval 0.2.2
py-cpuinfo 9.0.0
py2bit 0.3.0
pyaml-env 1.2.1
pyasn1 0.6.0
pyasn1_modules 0.4.0
pyBigWig 0.3.23
PyBIS 1.36.3
pycparser 2.22
pydantic 2.7.4
pydantic_core 2.18.4
pyg-lib 0.4.0+pt22cu121
Pygments 2.18.0
Pyomo 6.7.3
pyOpenSSL 24.1.0
pyparsing 3.1.2
PyQt5 5.15.10
PyQt5-Qt5 5.15.2
PyQt5-sip 12.13.0
pyquaternion 0.9.9
pysam 0.22.1
pytest 8.2.2
python-dateutil 2.9.0.post0
python-json-logger 2.0.7
pytorch-lightning 2.3.0
pytz 2024.1
PyYAML 6.0.1
pyzmq 26.0.3
QtPy 2.4.1
rdflib 7.0.0
referencing 0.35.1
requests 2.32.3
requests-oauthlib 2.0.0
reretry 0.11.8
retrying 1.3.4
rfc3339-validator 0.1.4
rfc3986-validator 0.1.1
rich 13.7.1
rich-click 1.8.3
rpds-py 0.18.1
rsa 4.9
scikit-image 0.24.0
scikit-learn 1.5.0
scipy 1.13.1
SCons 4.7.0
seaborn 0.13.2
Send2Trash 1.8.3
sentry-sdk 2.6.0
setproctitle 1.3.3
setuptools 65.5.0
shapely 2.0.4
simpervisor 1.0.0
six 1.16.0
smart-open 7.0.4
smmap 5.0.1
snakemake 8.14.0
snakemake-interface-common 1.17.2
snakemake-interface-executor-plugins 9.1.1
snakemake-interface-report-plugins 1.0.0
snakemake-interface-storage-plugins 3.2.2
sniffio 1.3.1
snowballstemmer 2.2.0
soupsieve 2.5
spectra 0.0.11
Sphinx 7.4.3
sphinxcontrib-applehelp 1.0.8
sphinxcontrib-devhelp 1.0.6
sphinxcontrib-htmlhelp 2.0.5
sphinxcontrib-jsmath 1.0.1
sphinxcontrib-qthelp 1.0.7
sphinxcontrib-serializinghtml 1.1.10
SQLAlchemy 2.0.31
stack-data 0.6.3
statsmodels 0.14.2
stopit 1.1.2
sympy 1.12.1
tables 3.9.2
tabulate 0.9.0
tenacity 8.4.1
tensorboard 2.15.2
tensorboard-data-server 0.7.2
tensorboardX 2.6.2.2
tensorflow 2.15.0
tensorflow-estimator 2.15.0
tensorflow-io-gcs-filesystem 0.37.0
tensorrt 10.1.0
tensorrt-cu12 10.1.0
tensorrt-cu12-bindings 10.1.0
tensorrt-cu12-libs 10.1.0
termcolor 2.4.0
terminado 0.18.1
texttable 1.7.0
threadpoolctl 3.5.0
throttler 1.2.2
tifffile 2024.6.18
tinycss2 1.3.0
toposort 1.10
torch 2.3.1
torch_cluster 1.6.3+pt22cu121
torch-fidelity 0.3.0
torch_geometric 2.5.3
torch_scatter 2.1.2+pt22cu121
torch_sparse 0.6.18+pt22cu121
torch_spline_conv 1.2.2+pt22cu121
torchaudio 2.3.1
torchmetrics 1.4.0.post0
torchvision 0.18.1
tornado 6.4.1
tqdm 4.66.4
traitlets 5.14.3
traits 6.4.3
trame 3.6.3
trame-client 3.2.0
trame-jupyter-extension 2.1.2
trame-server 3.0.2
triton 2.3.1
typeguard 4.3.0
types-python-dateutil 2.9.0.20240316
typing_extensions 4.12.2
tzdata 2024.1
uri-template 1.3.0
urllib3 2.2.2
wandb 0.17.2
wcwidth 0.2.13
webcolors 24.6.0
webencodings 0.5.1
websocket-client 1.8.0
Werkzeug 3.0.3
wheel 0.43.0
widgetsnbextension 4.0.11
wrapt 1.14.1
wslink 2.1.1
xgboost 2.1.0
y-py 0.6.2
yarl 1.9.4
ypy-websocket 0.8.4
yte 1.5.4
zipp 3.19.2
zope.interface 6.4.post2
Packages in Python 3.9.18 absl-py 2.1.0
addict 2.4.0
aiofiles 22.1.0
aiohttp 3.9.5
aiosignal 1.3.1
aiosqlite 0.20.0
alembic 1.13.1
annotated-types 0.7.0
anyio 4.4.0
appdirs 1.4.4
argon2-cffi 23.1.0
argon2-cffi-bindings 21.2.0
arrow 1.3.0
asttokens 2.4.1
astunparse 1.6.3
async-generator 1.10
async-lru 2.0.4
async-timeout 4.0.3
attrs 23.2.0
Babel 2.15.0
beautifulsoup4 4.12.3
biopython 1.83
bleach 6.1.0
blinker 1.8.2
blosc2 2.5.1
cachetools 5.3.3
certifi 2024.6.2
certipy 0.1.3
cffi 1.16.0
charset-normalizer 3.3.2
click 8.1.7
coloredlogs 15.0.1
colormath 3.0.0
comm 0.2.2
ConfigArgParse 1.7
connection-pool 0.0.3
contourpy 1.2.1
cryptography 42.0.8
cycler 0.12.1
Cython 3.0.10
dash 2.17.1
dash-core-components 2.0.0
dash-html-components 2.0.0
dash-table 5.0.0
DateTime 5.5
datrie 0.8.2
debugpy 1.8.1
decorator 5.1.1
defusedxml 0.7.1
docker-pycreds 0.4.0
docutils 0.21.2
dpath 2.2.0
emcee 3.1.6
entrypoints 0.4
exceptiongroup 1.2.1
executing 2.0.1
fastjsonschema 2.20.0
filelock 3.15.3
Flask 3.0.3
flatbuffers 24.3.25
fonttools 4.53.0
fqdn 1.5.1
frozenlist 1.4.1
fsspec 2024.6.0
gast 0.5.4
gitdb 4.0.11
GitPython 3.1.43
google-auth 2.31.0
google-auth-oauthlib 1.2.0
google-pasta 0.2.0
greenlet 3.0.3
grpcio 1.64.1
h11 0.14.0
h5py 3.11.0
httpcore 1.0.5
httpx 0.27.0
humanfriendly 10.0
humanize 4.9.0
idna 3.7
imageio 2.34.1
importlib_metadata 7.2.0
importlib_resources 6.4.0
iniconfig 2.0.0
ipykernel 6.29.4
ipython 8.18.1
ipython-genutils 0.2.0
ipywidgets 8.1.3
isodate 0.6.1
isoduration 20.11.0
itsdangerous 2.2.0
jax 0.4.30
jax-cuda12-pjrt 0.4.30
jax-cuda12-plugin 0.4.30
jaxlib 0.4.30
jedi 0.19.1
Jinja2 3.1.4
joblib 1.4.2
json5 0.9.25
jsonpointer 3.0.0
jsonschema 4.22.0
jsonschema-specifications 2023.12.1
jupyter_client 7.4.9
jupyter_core 5.7.2
jupyter-events 0.10.0
jupyter-lsp 2.2.5
jupyter_server 2.14.1
jupyter_server_fileid 0.9.2
jupyter_server_proxy 4.2.0
jupyter_server_terminals 0.5.3
jupyter_server_ydoc 0.8.0
jupyter-ydoc 0.2.5
jupyterhub 5.0.0
jupyterlab 4.2.2
jupyterlab_pygments 0.3.0
jupyterlab_server 2.27.2
jupyterlab_slurm 3.0.1
jupyterlab_widgets 3.0.11
kaleido 0.2.1
keras 2.15.0
Keras-Preprocessing 1.1.2
kiwisolver 1.4.5
lazy_loader 0.4
libclang 18.1.1
lightning 2.3.0
lightning-utilities 0.11.2
llvmlite 0.43.0
Mako 1.3.5
Markdown 3.6
markdown-it-py 3.0.0
MarkupSafe 2.1.5
matplotlib 3.9.0
matplotlib-inline 0.1.7
mdurl 0.1.2
meson 1.4.1
mistune 3.0.2
ml-dtypes 0.2.0
more-itertools 10.3.0
mpmath 1.3.0
msgpack 1.0.8
multidict 6.0.5
multiqc 1.22.3
namex 0.0.8
nbclassic 1.1.0
nbclient 0.10.0
nbconvert 7.16.4
nbformat 5.10.4
nbgitpuller 1.2.1
ndindex 1.8
nest-asyncio 1.6.0
networkx 3.2.1
ninja 1.11.1.1
nose 1.3.7
notebook 6.5.7
notebook_shim 0.2.4
numba 0.60.0
numexpr 2.10.1
numpy 1.25.2
nvidia-cublas-cu12 12.1.3.1
nvidia-cuda-cupti-cu12 12.1.105
nvidia-cuda-nvrtc-cu12 12.1.105
nvidia-cuda-runtime-cu12 12.1.105
nvidia-cudnn-cu12 8.9.2.26
nvidia-cufft-cu12 11.0.2.54
nvidia-curand-cu12 10.3.2.106
nvidia-cusolver-cu12 11.4.5.107
nvidia-cusparse-cu12 12.1.0.106
nvidia-nccl-cu12 2.20.5
nvidia-nvjitlink-cu12 12.3.101
nvidia-nvtx-cu12 12.1.105
oauthlib 3.2.2
open3d 0.18.0
opencv-contrib-python 4.10.0.84
opencv-python 4.10.0.84
openseespy 3.6.0.2
openseespylinux 3.6.0.2
opt-einsum 3.3.0
optree 0.11.0
overrides 7.7.0
packaging 24.1
pamela 1.1.0
pandas 2.2.2
pandoc 2.3
pandocfilters 1.5.1
parso 0.8.4
patsy 0.5.6
pexpect 4.9.0
pillow 10.3.0
pip 23.0.1
plac 1.4.3
platformdirs 4.2.2
plotly 5.22.0
pluggy 1.5.0
plumbum 1.8.3
ply 3.11
prometheus_client 0.20.0
prompt_toolkit 3.0.47
protobuf 4.25.3
psutil 6.0.0
ptyprocess 0.7.0
PuLP 2.8.0
pure-eval 0.2.2
py-cpuinfo 9.0.0
pyaml-env 1.2.1
pyasn1 0.6.0
pyasn1_modules 0.4.0
PyBIS 1.36.3
pycparser 2.22
pydantic 2.7.4
pydantic_core 2.18.4
pyg-lib 0.4.0+pt22cu121
Pygments 2.18.0
Pyomo 6.7.3
pyOpenSSL 24.1.0
pyparsing 3.1.2
PyQt5 5.15.10
PyQt5-Qt5 5.15.2
PyQt5-sip 12.13.0
pyquaternion 0.9.9
pysam 0.22.1
pytest 8.2.2
python-dateutil 2.9.0.post0
python-json-logger 2.0.7
pytorch-lightning 2.3.0
pytz 2024.1
PyYAML 6.0.1
pyzmq 26.0.3
QtPy 2.4.1
rdflib 7.0.0
referencing 0.35.1
requests 2.32.3
requests-oauthlib 2.0.0
reretry 0.11.8
retrying 1.3.4
rfc3339-validator 0.1.4
rfc3986-validator 0.1.1
rich 13.7.1
rich-click 1.8.3
rpds-py 0.18.1
rsa 4.9
scikit-image 0.24.0
scikit-learn 1.5.0
scipy 1.13.1
SCons 4.7.0
seaborn 0.13.2
Send2Trash 1.8.3
sentry-sdk 2.6.0
setproctitle 1.3.3
setuptools 58.1.0
shapely 2.0.4
simpervisor 1.0.0
six 1.16.0
smart-open 7.0.4
smmap 5.0.1
snakemake 7.32.4
sniffio 1.3.1
soupsieve 2.5
spectra 0.0.11
SQLAlchemy 2.0.31
stack-data 0.6.3
statsmodels 0.14.2
stopit 1.1.2
sympy 1.12.1
tables 3.9.2
tabulate 0.9.0
tenacity 8.4.1
tensorboard 2.15.2
tensorboard-data-server 0.7.2
tensorboardX 2.6.2.2
tensorflow 2.15.0
tensorflow-estimator 2.15.0
tensorflow-io-gcs-filesystem 0.37.0
tensorrt 10.1.0
tensorrt-cu12 10.1.0
tensorrt-cu12-bindings 10.1.0
tensorrt-cu12-libs 10.1.0
termcolor 2.4.0
terminado 0.18.1
texttable 1.7.0
threadpoolctl 3.5.0
throttler 1.2.2
tifffile 2024.6.18
tinycss2 1.3.0
tomli 2.0.1
toposort 1.10
torch 2.3.1
torch_cluster 1.6.3+pt22cu121
torch-fidelity 0.3.0
torch_geometric 2.5.3
torch_scatter 2.1.2+pt22cu121
torch_sparse 0.6.18+pt22cu121
torch_spline_conv 1.2.2+pt22cu121
torchaudio 2.3.1
torchmetrics 1.4.0.post0
torchvision 0.18.1
tornado 6.4.1
tqdm 4.66.4
traitlets 5.14.3
traits 6.4.3
trame 3.6.3
trame-client 3.2.0
trame-jupyter-extension 2.1.2
trame-server 3.0.2
triton 2.3.1
typeguard 4.3.0
types-python-dateutil 2.9.0.20240316
typing_extensions 4.12.2
tzdata 2024.1
uri-template 1.3.0
urllib3 2.2.2
wandb 0.17.2
wcwidth 0.2.13
webcolors 24.6.0
webencodings 0.5.1
websocket-client 1.8.0
Werkzeug 3.0.3
wheel 0.43.0
widgetsnbextension 4.0.11
wrapt 1.14.1
wslink 2.1.1
xgboost 2.1.0
y-py 0.6.2
yarl 1.9.4
ypy-websocket 0.8.4
yte 1.5.4
zipp 3.19.2
zope.interface 6.4.post2

Package installation

  • Pip is the package installer for Python. Use pip to install packages from the Python Package Index and other sources.
  • Conda is an open source package and environment manager for installing multiple versions of software packages and their dependencies.
  • uv is a fast Python package and project manager written in Rust.
  • distutils is deprecated.

To install packages locally into $HOME/.local using pip, use --user: 

pip install --user <package>
or, install into a virtual environment for better isolation: 
python -m venv <venv_name>
source <venv_name>/bin/activate
pip install <package>
To give the virtual environment access to system site-packages use --system-site-packages: 
python -m venv --system-site-packages <venv_name>

Interactive session

module load stack/2024-06 python
python
starts an interactive session and you should see 
>>>
Now you can try one of Python's easter eggs by typring import this and then press Enter. To quit the session, type quit() and press Enter.

Example program

Create a file hello.py containing 

print("Hello, World!")
and execute it with 
module load stack/2024-06 python
python hello.py
You should see 
Hello, World!

⚠️ Known issues

ThreadPool in Slurm jobs

This issues applies to Python versions prior to 3.13.

Summary:

  • Use ThreadPool(processes=len(os.sched_getaffinity(0))) to create a thread pool that matches the allocated CPU cores.
  • ThreadPool() without arguments ignores Slurm's CPU limits.

And here is the full explanation:

When using multiprocessing.pool.ThreadPool in a Slurm job, you may encounter surprising effects because in Python versions prior to 3.13, ThreadPool ignores the CPU limits set by Slurm, which internally uses cgroups to limit the number of CPU cores a Slurm job can use. This can lead to performance degradation due to excessive context switching and resource contention.

First let's look at the root cause of the issue. 

srun --ntasks=1 --cpus-per-task=2 python3 -c "from multiprocessing.pool import ThreadPool; print(ThreadPool()._processes)"
This command allocates 2 CPU cores using srun --ntasks=1 --cpus-per-task=2 and then runs a Python one-liner that creates a ThreadPool with the default number of processes and prints the number of processes in the pool.

In Python versions prior to 3.13, this command will output the total number of physical CPU cores on the node, not the 2 cores allocated by Slurm.

In Python 3.13 and later, ThreadPool respects the CPU limits set by cgroups and will output 2.

To work around this issue, you can explicitly set the number of processes in a ThreadPool with ThreadPool(processes=len(os.sched_getaffinity(0))), where os.sched_getaffinity(0) returns the set of CPU cores allocated to the current process by Slurm.