In oder to get the environment running we try to modify the scripts.

We load Tensorflow by module load and we removed h5py.
And I removed the --installed flag.

env_setup/create_env.sh

@@ -20,7 +20,7 @@ source ${ENV_SETUP_DIR}/modules.sh
 # Install additional Python packages.
 python3 -m venv $ENV_DIR
 source ${ENV_DIR}/bin/activate
-pip3 install --ignore-installed -r requirements.txt
+pip3 install -r requirements.txt
 #pip3 install --user netCDF4
 #pip3 install --user numpy
 

env_setup/modules.sh

@@ -7,6 +7,6 @@ module load MVAPICH2/.2.3.1-GDR
 module load GCCcore/.8.3.0
 module load mpi4py/3.0.1-Python-3.6.8
 module load h5py/2.9.0-serial-Python-3.6.8
-#module load TensorFlow/1.13.1-GPU-Python-3.6.8
+module load TensorFlow/1.13.1-GPU-Python-3.6.8
 module load cuDNN/7.5.1.10-CUDA-10.1.105
 

env_setup/requirements.txt

-tensorflow-gpu>=1.9.0
 opencv-python
 scipy
 scikit-image
-h5py
 pandas
 netCDF4

requirements.txt

-absl-py==0.8.0
-astor==0.8.0
-atomicwrites==1.3.0
-attrs==19.1.0
-certifi==2019.3.9
-cffi==1.12.3
-cftime==1.0.3.4
-chardet==3.0.4
-cloudpickle==1.2.2
-coverage==4.5.2
-cycler==0.10.0
-decorator==4.4.1
-dill==0.3.0
-gast==0.3.2
-google-pasta==0.1.7
-graphviz==0.8.4
-grpcio==1.23.0
-h5py==2.9.0
-horovod==0.18.1
-idna==2.8
-imageio==2.6.1
-imbalanced-learn==0.5.0
-imblearn==0.0
-joblib==0.13.2
-Keras-Applications==1.0.8
-Keras-Preprocessing==1.1.0
-kiwisolver==1.1.0
-Markdown==3.1.1
-matplotlib==3.1.2
-mnist==0.2.2
-more-itertools==6.0.0
-mxnet==1.5.0
-netCDF4==1.5.1.2
-networkx==2.4
-nose==1.3.7
-numpy==1.16.2
-opencv-python==4.1.2.30
-pandas==0.24.1
-patsy==0.5.1
-Pillow==6.1.0
-pluggy==0.9.0
-protobuf==3.9.1
-psutil==5.6.1
-py==1.8.0
-pycparser==2.19
-pymongo==3.10.1
-pyparsing==2.4.5
-pytest==4.3.0
-pytest-cov==2.6.1
-python-dateutil==2.8.0
-pytz==2018.9
-PyWavelets==1.1.1
-PyYAML==5.1.2
-requests==2.21.0
-scikit-image==0.16.2
-scikit-learn==0.21.3
-scipy==1.3.1
-six==1.12.0
-sklearn==0.0
-statsmodels==0.9.0
-tensorboard==1.14.0
-tensorflow==1.14.0
-tensorflow-estimator==1.14.0
-termcolor==1.1.0
-tflearn==0.3.2
-torch==1.2.0
-torchvision==0.4.0
-tornado==6.0.1
-tqdm==4.36.1
-urllib3==1.24.1
-Werkzeug==0.15.6
-wrapt==1.11.2