Comments (5)
corneliusroemer
commented on September 26, 2024
Interestingly, when running with nextstrain managed conda environment it doesn't crash:
nextstrain build --conda . --configfile config/config.yaml --config data_provenances=gisaid variant_classification=nextstrain_clades geo_resolutions=global
These are the env details for the managed conda:
Managed conda env pip list
Package Version
----------------------------- ----------
absl-py 1.4.0
aiobotocore 2.5.0
aioeasywebdav 2.4.0
aiohttp 3.8.4
aioitertools 0.11.0
aiosignal 1.3.1
amply 0.1.5
appdirs 1.4.4
async-timeout 4.0.2
attmap 0.13.2
attrs 22.2.0
awscli 1.27.76
backports.functools-lru-cache 1.6.4
backrefs 5.2
bcbio-gff 0.6.9
bcrypt 3.2.2
biopython 1.80
blackjax 0.9.6
boto3 1.26.76
botocore 1.29.76
bracex 2.2.1
brotlipy 0.7.0
bx-python 0.9.0
cachetools 5.3.0
certifi 2022.12.7
cffi 1.15.1
chardet 4.0.0
charset-normalizer 2.1.1
colorama 0.4.4
ConfigArgParse 1.5.3
connection-pool 0.0.3
contourpy 1.0.7
crc32c 2.3.post0
cryptography 40.0.2
cvxopt 1.3.0
cycler 0.11.0
datrie 0.8.2
decorator 5.1.1
defusedxml 0.7.1
DendroPy 4.5.2
docutils 0.15.2
dpath 2.1.5
dropbox 11.36.0
epiweeks 2.1.4
evofr 0.1.18
exceptiongroup 1.1.1
fasteners 0.17.3
fastjsonschema 2.16.3
fastprogress 1.0.3
filechunkio 1.8
filelock 3.11.0
fonttools 4.39.3
frozenlist 1.3.3
fsspec 2023.4.0
ftputil 5.0.4
gitdb 4.0.10
GitPython 3.1.31
google-api-core 2.11.0
google-api-python-client 2.85.0
google-auth 2.17.3
google-auth-httplib2 0.1.0
google-cloud-core 2.3.2
google-cloud-storage 2.8.0
google-crc32c 1.1.2
google-resumable-media 2.4.1
googleapis-common-protos 1.57.1
grpcio 1.52.1
httplib2 0.22.0
humanfriendly 10.0
idna 3.4
importlib-metadata 6.4.1
importlib-resources 5.12.0
iniconfig 2.0.0
isal 1.1.0
isodate 0.6.1
jax 0.4.8
jaxlib 0.4.7
jaxopt 0.5.5
Jinja2 3.1.2
jmespath 1.0.1
jsonschema 3.2.0
jupyter_core 5.3.0
kiwisolver 1.4.4
logmuse 0.2.6
markdown-it-py 2.2.0
MarkupSafe 2.1.2
matplotlib 3.7.1
mdurl 0.1.0
ml-dtypes 0.1.0
multidict 6.0.4
multipledispatch 0.6.0
munkres 1.1.4
nbformat 5.8.0
networkx 2.8.8
nextstrain-augur 21.1.0
nextstrain-cli 6.2.1
numpy 1.24.2
numpyro 0.11.0
oauth2client 4.1.3
opt-einsum 3.3.0
packaging 23.1
pandas 1.5.3
pangoLEARN 2022-03-22
paramiko 3.1.0
peppy 0.35.5
phylo-treetime 0.9.6
Pillow 9.5.0
pip 23.1
plac 1.3.5
platformdirs 3.2.0
pluggy 1.0.0
ply 3.11
pooch 1.7.0
prettytable 3.7.0
protobuf 4.21.12
psutil 5.9.4
PuLP 2.7.0
pyasn1 0.4.8
pyasn1-modules 0.2.7
pycparser 2.21
pyfastx 0.8.4
Pygments 2.15.0
PyJWT 2.6.0
PyNaCl 1.5.0
pyOpenSSL 23.1.1
pyparsing 3.0.9
pyrsistent 0.19.3
pysftp 0.2.9
PySocks 1.7.1
pytest 7.3.1
python-dateutil 2.8.2
python-irodsclient 1.1.6
python-lzo 1.14
pytools 2020.1
pytz 2023.3
pyu2f 0.1.5
PyYAML 5.4.1
ratelimiter 1.2.0
requests 2.28.2
reretry 0.11.8
rich 13.3.4
rsa 4.7.2
s3fs 2023.4.0
s3transfer 0.6.0
scipy 1.10.1
setuptools 67.6.1
setuptools-scm 7.1.0
six 1.16.0
slacker 0.14.0
smart-open 6.3.0
smmap 3.0.5
snakemake 7.25.0
stone 3.3.1
stopit 1.1.2
tabulate 0.9.0
throttler 1.2.1
tomli 2.0.1
toposort 1.10
tqdm 4.65.0
traitlets 5.9.0
typing_extensions 4.5.0
ubiquerg 0.6.2
unicodedata2 15.0.0
uritemplate 4.1.1
urllib3 1.26.15
veracitools 0.1.3
wcmatch 8.3
wcwidth 0.2.6
wheel 0.40.0
wrapt 1.15.0
xopen 1.7.0
yarl 1.8.2
yte 1.5.1
zipp 3.15.0
zstandard 0.19.0
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corneliusroemer
commented on September 26, 2024
Could it be due to differences in version of jax(lib)? Left working, right not working.
jax 0.4.8 | jax 0.4.1
jaxlib 0.4.7 | jaxlib 0.3.22
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corneliusroemer
commented on September 26, 2024
Can't upgrade in my env because of some grpc-cpp and libgrpc clash. Some packages require grpc-cpp but the conda-forge recipe for that is behind libgrpc - yet libgrpc constrains grpc-cpp.
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corneliusroemer
commented on September 26, 2024
This seems to be the problem, usher requires libprotobuf >=3.20.2,<3.21.0a0 which means one can use at most grpc-cpp 1.47.1 but that limits the jax version one can use. I guess I can uninstall usher, but heads up to @AngieHinrichs that this could be worth bumping.
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corneliusroemer
commented on September 26, 2024
So now that I've uninstalled usher and updated jax to 0.4.8 it also runs with my ambient environment.
Lesson could be that evofr requires more stringent minimal version constraints for jax @marlinfiggins
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Related Issues (20)
- Forecase Automation: Provision counts files HOT 6
- Add QC for clade sequence counts
- ingest: Update vendored scripts
- Model workflow failing HOT 4
- Failure in genbank/clade-counts HOT 1
- Requested viz updates
- Broader viz suggestions HOT 1
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- Document which `geo_resolution`'s are available
- Allow force include of Pango lineages that might not meet threshold
- Flag potential lineages for new Nextstrain clades HOT 1
- Send Slack notifications for clades without definition
- Add new Nextstrain clade definitions HOT 1
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- Reduce disk write of 20+GB metadata file by filtering on the fly HOT 2
- viz: Add growth advantage scatterplots
- Revisit sequence data inclusion thresholds HOT 2
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