alchem0x2A

Add objects to scene in Blender 2.80

Blender 2.80 introduces a new feature of collections, which (in my opinion) is a very important for various purposes like grouping objects, selectively enable / disable in view port, etc.

Accordingly, the codes also needs to be updated in 2.80 for adding an object to the active scene. From the documentation (https://wiki.blender.org/wiki/Reference/Release_Notes/2.80/Python_API/Scene_and_Object_API),

alchem0x2A

Render Blender files on cluster

This is a easy workaround to enable Blender rendering on a super-computing cluster. The samples shown here are based on the Euler cluster of ETH Zürich (IBM LSF batch system).

Step 1: install Blender binary on cluster

alchem0x2A

Install external python packages + virtualenv with Blender

Requirements: Blender 2.80+ (2.79 should also work with pip method, not tested thoroughly)

Step 1: Install virtualenv on the system

In order not to mix the packages installed for Blender (such as scipy, matplotlib) with those system-wide packages, we need to create a virtual environment for the Blender alone.

Best practice is to use a single virtualenv for each version of

alchem0x2A

Math fonts that worth noting

Solutions taken from ftp://tug.ctan.org/pub/tex-archive/info/Free_Math_Font_Survey/survey.html in TUG.

Times-resemble math font

Use either txfonts or mathptmx for Times font support. I personally prefer txfonts since its mathcal symbols look more natural to me.

To use: include \usepackage{txfonts} or \usepackage{mathptmx} in

alchem0x2A

#!/bin/sh

# Provide a wrapper of emacsclient that automatically opens up Emacs or server

function ec_wrapper {
    GREEN='\033[0;32m'
    NC='\033[0m'
    buffers=$@
    cmd="emacsclient -nqc"
    # Excecute command

alchem0x2A

import os, os.path
import subprocess

def convert(in_name, out_name, delete=True):
    prog = "ffmpeg"
    params = ["-i", "{}".format(in_name),
              "-pix_fmt", "yuv420p",
              "-vcodec", "libx264",
              "{}".format(out_name)]
    res = subprocess.call([prog, *params])

alchem0x2A

Preparation

• Compiler: intel/15.0, open_mpi/1.10.0, libxc/3.0.0, fftw/3.3.4, scalapack
• tar for numpy scipy matplotlib

Compile python with intel

Download the python tarball, untar and cd into the root directory.

./configure --prefix="abs/path/to/build" --with-icc CC=icc CXX=icpc

alchem0x2A

# Next time you need to install something with python setup.py -- which should be never but things happen. 

python setup.py install --record files.txt

# This will cause all the installed files to be printed to that directory.
# Then when you want to uninstall it simply run; be careful with the 'sudo'

cat files.txt | xargs sudo rm -rf

alchem0x2A

Preparation

• Compiler: python/3.1.1 (shipped) gcc-6.3.0, open_mpi/3.0.0, libxc/4.3.0, fftw/3.3.3, openblas/0.2.13_seq, scalapack
• tar for numpy scipy matplotlib

Working on virtualenv

python -m venv gpaw
source ~/.virtualenv/gpaw/bin/activate

Alternatively, if you want to use the shipped =numpy= and =scipy= versions,

alchem0x2A

#Generic script for submitting comsol job
#usage: sub_job.sh [COMSOL_IN_NAME] [optional:MEM]
INFILE=$1
OUTFILE=$(echo $INFILE | cut -f 1 -d ".")
OUTFILE+="_out.mph"

#Memory alloc
MEM=4096
if [ $# -ge 2 ]; then
        MEM=$2