/notes

my notes, my scripts, my unamed things

Primary LanguageJupyter NotebookOtherNOASSERTION

this folder has all the things that I don't know where to keep.

Note for me (and for others too?) so I don't need to remember or google.

See [issues] (https://github.com/hainm/bag_of_tips/issues)

coding

* font:  Liberation Mono, 12
* builtin-in scheme: black on light yellow
* Text color: black
* bg color: light yellow
* Pallette: Linux console

pyspark

  • Use notebook remotely

    • PYSPARK_DRIVER_PYTHON=ipython
      PYSPARK_DRIVER_PYTHON_OPTS="notebook --no-browser --port=8889" ./bin/pyspark

GCC

Install gcc5.3

Common Error

  • libgmp.so.10: cannot open shared object file

    • locate libgmp.so.10
    • export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/libgmp/

How to use IPython, conda, ... in PHENIX

  • Upgrade pip: phenix.python -m pip install pip --upgrade
  • Install readline: phenix.python -m pip install readline
  • Install Ipython: phenix.python -m pip install IPython. Alternate way is to use conda
  • Run: phenix.python -c 'from IPython import start_ipython;start_ipython()
  • conda: phenix.python -m pip install conda
  • install via conda: phenix.python -m conda install package
  • update numpy >= 1.9.0: phenix.python -m conda install numpy
  • To use jupyter notebook, create py2 env with anaconda or miniconda distribution. (man, too much work)
  • Check source_phenix_2376

Install pytraj with PHENIX

  • cd $AMBERHOME/AmberTools/src/pytraj && phenix.python setup.py clean && phenix.python setup.py install

Notes: does not work with pytraj in $AMBERHOME/lib due to wrong Python version. (although two Pythons are 2.7, ack)

Crystal

Install coot

conda install coot -c mw
# update boots >= 1.59
conda install boost=1.59.0 -c omnia

npm
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- 401 error: ?