geoffwoollard
commented
1 week ago (flexutils-tensorflow) (base) [gwoollard@workergpu004 Cryo-EM-Heterogeneity-Challenge-1]$ pip freeze
absl-py==2.1.0
addict==2.4.0
astunparse==1.6.3
attrs==24.2.0
bibtexparser==1.2.0
biopython==1.76
blinker==1.8.2
cachetools==5.5.0
certifi==2024.8.30
charset-normalizer==3.3.2
click==8.1.7
cloudpickle==3.0.0
ConfigArgParse==1.7
contourpy==1.3.0
cycler==0.12.1
dash==2.18.1
dash-core-components==2.0.0
dash-html-components==2.0.0
dash-table==5.0.0
decorator==5.1.1
dill==0.3.9
dm-tree==0.1.8
emfile==0.3.0
emtable==0.0.14
exceptiongroup==1.2.2
fastjsonschema==2.20.0
Flask==3.0.3
flatbuffers==24.3.25
fonttools==4.54.1
future==1.0.0
gast==0.6.0
google-auth==2.35.0
google-auth-oauthlib==1.2.1
google-pasta==0.2.0
grpcio==1.66.2
h5py==3.12.1
idna==3.10
imageio==2.35.1
importlib_metadata==8.5.0
importlib_resources==6.4.5
iniconfig==2.0.0
itsdangerous==2.2.0
Jinja2==3.1.4
joblib==1.4.2
jsonschema==4.23.0
jsonschema-specifications==2023.12.1
jupyter_core==5.7.2
keras==2.15.0
kiwisolver==1.4.7
libclang==18.1.1
Markdown==3.7
MarkupSafe==2.1.5
matplotlib==3.8.2
ml-dtypes==0.3.2
morphsnakes==2.0.1
mrcfile==1.4.3
multiprocess==0.70.17
nbformat==5.10.4
nest-asyncio==1.6.0
networkx==3.2.1
numpy==1.23.5
nvidia-cublas-cu12==12.2.5.6
nvidia-cuda-cupti-cu12==12.2.142
nvidia-cuda-nvcc-cu12==12.2.140
nvidia-cuda-nvrtc-cu12==12.2.140
nvidia-cuda-runtime-cu12==12.2.140
nvidia-cudnn-cu12==8.9.4.25
nvidia-cufft-cu12==11.0.8.103
nvidia-curand-cu12==10.3.3.141
nvidia-cusolver-cu12==11.5.2.141
nvidia-cusparse-cu12==12.1.2.141
nvidia-nccl-cu12==2.16.5
nvidia-nvjitlink-cu12==12.2.140
oauthlib==3.2.2
open3d @ file:///mnt/home/gwoollard/ceph/repos/Open3D/build/lib/python_package/pip_package/open3d-0.18.0%2Bdd0d35956-cp39-cp39-manylinux_2_28_x86_64.whl#sha256=c744177f77b4ea2a3ea1f3f6a627be24dbb14327aec4dceddf9f0d917cc2f711
opt_einsum==3.4.0
packaging==24.1
pandas==2.1.4
pathos==0.3.3
Pillow==10.1.0
platformdirs==4.3.6
plotly==5.24.1
pluggy==1.5.0
pox==0.3.5
ppft==1.7.6.9
ProDy==2.4.1
protobuf==4.23.4
psutil==5.8.0
pyarrow==17.0.0
pyasn1==0.6.1
pyasn1_modules==0.4.1
pyparsing==3.1.4
pyquaternion==0.9.9
pytest==8.3.3
python-dateutil==2.9.0.post0
pytz==2024.2
PyWavelets==1.6.0
PyYAML @ file:///home/conda/feedstock_root/build_artifacts/pyyaml_1695373447169/work
referencing==0.35.1
requests==2.32.3
requests-oauthlib==2.0.0
retrying==1.3.4
rpds-py==0.20.0
rsa==4.9
scikit-image==0.19.3
scikit-learn==1.3.2
scipy==1.11.4
seaborn==0.13.2
six==1.16.0
starfile==0.5.8
tenacity==9.0.0
tensorboard==2.15.2
tensorboard-data-server==0.7.2
tensorflow==2.15.1
tensorflow-addons==0.23.0
tensorflow-estimator==2.15.0
tensorflow-io-gcs-filesystem==0.37.1
tensorflow-probability==0.23.0
-e git+https://github.com/I2PC/Flexutils-Toolkit.git@8f7b695520d5b67e86c39efc6915b81c2b31874e#egg=tensorflow_toolkit
termcolor==2.4.0
tf-siren==0.0.5
threadpoolctl==3.5.0
tifffile==2021.3.5
tkcolorpicker==2.1.3
tomli==2.0.2
tqdm==4.66.5
traitlets==5.14.3
typeguard==2.13.3
typing_extensions==4.12.2
tzdata==2024.2
urllib3==2.2.3
Werkzeug==3.0.4
wrapt==1.14.1
xmipp_metadata @ git+https://github.com/DavidHerreros/xmipp_metadata.git@fb37e4a1386706257d956d4f0bfff426ed35b82d
yapf==0.40.2
yellowbrick==1.5
zipp==3.20.2
DavidHerreros
The file
ref_2_16x16x16.npyis shape (2,16**3).The error seems to be coming from the xmipp ImageHandler,
ih.scaleSplines(data=volume, ...).Probably a version issue.
(flexutils-tensorflow) (base) [gwoollard@workergpu004 Cryo-EM-Heterogeneity-Challenge-1]$ compute_distance_matrix_zernike3deep.py --references_file tmp_zernike/ref_2_16x16x16.npy --targ ets_file tmp_zernike/ref_2_16x16x16.npy --out_path tmp_zernike/ --gpu 0 --thr 20 2024-11-14 14:56:42.032833: I tensorflow/core/util/port.cc:113] oneDNN custom operations are on. You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable
sys.exit(main())
File "/mnt/ceph/users/gwoollard/repos/Flexutils-Toolkit/tensorflow_toolkit/scripts/compute_distance_matrix_zernike3deep.py", line 164, in main
compute_distance_matrix(**inputs)
File "/mnt/ceph/users/gwoollard/repos/Flexutils-Toolkit/tensorflow_toolkit/scripts/compute_distance_matrix_zernike3deep.py", line 61, in compute_distance_matrix
volume = ih.scaleSplines(data=volume, finalDimension=64)
TypeError: scaleSplines() got an unexpected keyword argument 'data'
TF_ENABLE_ONEDNN_OPTS=0. 2024-11-14 14:56:42.071005: E external/local_xla/xla/stream_executor/cuda/cuda_dnn.cc:9261] Unable to register cuDNN factory: Attempting to register factory for plugin cuDNN when one has already been registered 2024-11-14 14:56:42.071033: E external/local_xla/xla/stream_executor/cuda/cuda_fft.cc:607] Unable to register cuFFT factory: Attempting to register factory for plugin cuFFT when one has already been registered 2024-11-14 14:56:42.072179: E external/local_xla/xla/stream_executor/cuda/cuda_blas.cc:1515] Unable to register cuBLAS factory: Attempting to register factory for plugin cuBLAS when one has already been registered 2024-11-14 14:56:42.078630: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations. To enable the following instructions: AVX2 AVX512F AVX512_VNNI FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags. 2024-11-14 14:56:42.853031: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT Projecting volumes: 0%| | 0/2 [00:00<?, ?it/s] Traceback (most recent call last): File "/mnt/home/gwoollard/software/mambaforge/envs/flexutils-tensorflow/bin/compute_distance_matrix_zernike3deep.py", line 8, in