alchem0x2A

Useful command when Alt+power fails in macbook installation

0. Determine the disk number

# Enter grub cmdline by pressing Right-Shift and c
grub> ls
(proc) (hd0) ...

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#!/bin/bash
# This script runs a bootstrap process to setup gh in google colab and setup the authentication
# It requires GITHUB_TOKEN to be set (e.g. use a cell with `getpass`)
if [ -z "$GITHUB_TOKEN" ] && [ -z "$GH_TOKEN" ] 
then
  echo "Neither GITHUB_TOKEN nor GH_TOKEN not set! Exit"
  exit 1
fi

# Download the gh cli for debian

alchem0x2A

vasp/5.4.4-hsw, all pass
vasp/6.2.1-hsw, all pass
vasp/6.3.2-hsw, all pass
vasp-tpc/5.4.4-hsw, all pass
vasp-tpc/6.2.1-hsw, all pass
vasp-tpc/6.3.2-hsw, all pass
#Last updated: 2022-10-28T19:33:13-0700

alchem0x2A

from finetuna.atomistic_methods import Relaxation
from finetuna.online_learner.online_learner import OnlineLearner
from vasp_interactive import VaspInteractive
from ase.optimize import BFGS
from finetuna.ml_potentials.finetuner_ensemble_calc import FinetunerEnsembleCalc
from ase.io import Trajectory
from finetuna.utils import calculate_surface_k_points

if __name__ == "__main__":

alchem0x2A

Example yaml files to use launchpad in FireWorks

Choose the template for your configuration

• Plaintext password: my_lauchpad_passwd.yaml
• X509 TLS certificate: my_lauchpad_certx509.yaml

Remember to modify the fields marked with <>. The certificate file should be placed in a searchable location (with proper mode)

alchem0x2A

This is a very rough tutorial for myself when setting up the "NAS" on Raspi4. Don't copy all steps if you want RAID on the NAS (for the moment)

Network setting part

1. Burn the image of Raspberry Pi onto the card. Follow this guide
2. Edit the Wifi / SSH / password etc
3. Install mDNS avahi-daemon. Remeber to enable the lines with

publish-workstation=yes

alchem0x2A

$ ffmpeg -i input.mp4 -vcodec h264 -acodec mp2 output.mp4

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This can reduce files to ~15% of their size (2.3M to 345K, in one case) with no obvious degradation of quality.

ghostscript -sDEVICE=pdfwrite -dCompatibilityLevel=1.4 -dPDFSETTINGS=/printer -dNOPAUSE -dQUIET -dBATCH -sOutputFile=output.pdf input.pdf

Other options for PDFSETTINGS:

• /screen selects low-resolution output similar to the Acrobat Distiller "Screen Optimized" setting.
• /ebook selects medium-resolution output similar to the Acrobat Distiller "eBook" setting.
• /printer selects output similar to the Acrobat Distiller "Print Optimized" setting.
• /prepress selects output similar to Acrobat Distiller "Prepress Optimized" setting.

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Problem

Python binding for openbabel might be not trivial to install on HPC cluster. Simple pip install openbabel are very likely to fail. Sample error messages are like:

Error: SWIG failed. Is Open Babel installed?
    You may need to manually specify the location of Open Babel include and library directories. For example:
      python setup.py build_ext -I/usr/local/include/openbabel-2.0 -L/usr/local/lib
      python setup.py install
    ----------------------------------------

alchem0x2A

Install python API for IBM LSF batch system

The short introduction describes how to install the python API for the IBM LSF batch system (like Euler cluster of ETH Zürich).

Find the system-wide LSF configure files

The python API relies on the system environment that is defined inside the file profile.lsf. On Euler cluster it is at: $LSF_ENVDIR/profile.lsf

Load the environmental variables by