[EMAN2] Conda Installation of 2.99.66

[Renbin Yang]

Hello Steve and eman2 team,

I followed your protocol to install the latest build of EMAN2 2.99.66 on Rocky-linux8 in a cluster environment:

https://blake.bcm.edu/emanwiki/EMAN2/Install/CondaInstall

1. Installed mamba: 

wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh

2. After updating base, created EMAN2 env, biopython won't be automatically installed in our case but is essential for EMAN2. Tensorflow was installed by default as 2.17 but won't work for test_tensorflow.py:

mamba create --yes -n 2.99.66_TF2.16 eman-dev python=3.12 biopython tensorflow=2.16 -c cryoem -c conda-forge

3. Installed EMAN2:

cmake ${appDIR}/git/eman2 -DENABLE_OPTIMIZE_MACHINE=ON
for i in {1..5} ; do make -j${SLURM_CPUS_ON_NODE} ; done
make install
make install-sphire

However, while the tests and applications seems to work, there're annoying warning messages during the running of "python EMAN2/2.99/examples/test_tensorflow.py":

"UserWarning: The value of the smallest subnormal for <class 'numpy.float32'> type is zero."

That warning message is explained well elsewhere: https://moyix.blogspot.com/2022/09/someones-been-messing-with-my-subnormals.html

It seems that some of the dependency packages are not fully compatible. Did you observe the same warning message during your test and do you have a more detailed version list of your essential dependencies? Many thanks for any comment and suggestion.

Best,

Renbin