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Tips_and_Tricks.md

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Tips

  • jupyter trick for code dev on hpc
1. Run jupyter notebook on remote (say HPC1) using 
jupyter notebook --no-browser --port=8888
2. Listen to the remote port using ssh
ssh -N -f -L localhost:8888:localhost:8888 $USER@hpc1.engr.ucdavis.edu
If you get an error saying that port 8888 is busy, use the following command to find and kill the process
 lsof -ti:8888 | xargs kill -9

3. Run the jupyter notebook using the local browser by copy pasting the token
  • automate logins to hpc
  • use ase.db
  • automated rsync
  • scripts on hpc to quickly do repetitive tasks
  • code for getting papers off campus
  • folder organization
  • reading papers and organizing lit
  • presentation tips, how to do a lit review
  • use queue wait times for submitting jobs on cori.
  • configuring pycharm: make sure to configure your conda environment with pycharm follow these directions and use the path you obtain by typing which python in your command line as the interpreter.
  • chmod reference
  • chgrp reference:

Sticking points

  • vasp scripts crashing (check header is correct, use debug queue, fix environment variable, make sure modules are loaded)
  • optimization/vibration output is bad, how to fix
  • neb tips (opt fs and use vasprun for is .. )
  • python scripts crashing (start with really simple problem, make sure PATH is set up, break into separate subtestable scripts, print internal variables)
  • python code not running on hpc: make sure utf8 header is there, chmod u+x, in bin folder

HPC1  There seems to be difference between different CPUs. I find that c6-XX (Intel(R) Xeon(R) Silver 4110 CPU @ 2.10GHz) is faster than c5-XX ( Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz). If you find similar behavior with other codes (I tested cp2k), please let me know. 

CP2K  Metadynamics - Be careful about the units being used. CP2K defaults into internal_cp2k while providing output, we usually care about Ang.  Indexing - cp2k counts from index 1 .. N, while ASE/VMD starts from index 0 

Packages not loaded in NERSC: Make sure to download the .bashrc file and .bash.ext file from the repo_shared folder to your account Cannot get Pulse Secure to connect: Sam still has problems with this scipy.optimize.minimize not working: function to optimize must be a function of one argument containing all the parameters you want to optimize python can't call ase: make sure ase has the correct path variable math eqns in python don't work: make sure things are written as 2*x not 2x and x**3 instead of x^3 weird things happen during vasp vibrational calculation: set NSW to 1