Update yt

[xuanweishan]

1. Learn how to update lib yt.
2. Test the update procedure on eureka32
3. Apply update on all nodes.

[hyschive]

@xuanweishan Just a reminder of this. I list some related tasks below:

• Support both python 2 and 3
• Install the latest version of yt

[xuanweishan]

Installation of yt4:

1. Install python3 with source code:
   1. cd /work1/xuanshan/Python-3.9.10
   2. ./configure --enable-optimizations --enable-shared
   3. make altinstall
   4. cp libpython3.9.so.1.0 /usr/lib64/
   5. Check python3.9
   6. Make link python3 to python3.9: rm /usr/bin/python3 ln -s /usr/local/bin/python3.9 /usr/bin/python3
2. Upgrade pip install necessary packages for python3:
   1. Upgrade pip3: pip3 install -U pip
   2. Install necessary packages:

      pip3 install --ignore-installed pyparsing
      pip3 install --upgrade dnspython
      pip3 install --upgrade pyudev
      pip3 install --ignore-installed --upgrade python-ldap
      pip3 install --upgrade ipython
      pip3 install --upgrade numpy
      pip3 install --upgrade cython
      pip3 install --upgrade six
      pip3 install --upgrade urllib3
      pip3 install idna==2.10
      pip3 install --upgrade certifi
      pip3 install chardet==4.0.0
      pip3 install --upgrade jupyter
      export HDF5_DIR=/software/hdf5/default
      pip3 install --no-binary=h5py h5py
      pip3 install --upgrade scipy
      pip3 install --upgrade astropy
      pip3 install --upgrade matplotlib
      pip3 install --upgrade gitpython
      pip3 install --upgrade pandas

3. Install yt in python3 from source code.
   1. cd /work1/xuanshan/yt
   2. pip3 install -e .
   3. Check:
      1. LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/software/gcc/default/lib64
      2. python3 -c "import yt"
4. check yt version and update yt.
   1. python3 -m pip install -U yt
   2. yt version
5. Install other python3 packages

   pip3 install mpi4py
   pip3 install dulwich
   pip3 install girder-client

[xuanweishan]

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[xuanweishan]

Issue

The library is locate at /work1/xuanshan/yt and it supose to be at default path of python3 library.