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How to install HDF5 and h5py supporting MPI on OS X

Works on Mac OS 10.11.6, HDF5 1.8.17

HDF5

0. Download and install dependencies like zlib, openmpi. Use homebrew.
1. Download source tarball from http://www.hdfgroup.org/HDF5/release/obtain5.html
2. Configure Makefile using the following command:

$ CC=/usr/local/bin/mpicc ./configure --with-zlib=/usr/local/opt --disable-fortran --prefix=/usr/local/ --enable-shared --enable-parallel

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How to mount a VirtualBox shared folder when the Guest OS boots

Problem

While using VirtualBox's Guest Additions to mount shared folders provides a seamless way to mount shared folders, there are also disadvantages.

• Shared folders will always mount in /media/sf_(share name) unless specified using through vbox drivers in the guest OS
• Mounting does not happen at boot-time. Applications that require paths at boot will not be able to access the shared folder even after it is mounted - such as Docker.

Solution

Instead of relying on Guest Additions, if you have sudo permissions, shared folders can be mounted at boot-time using fstab. Using this approach allows

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Remove ALL containers

docker rm -f $(docker ps -a -q)

Remove ALL images

docker rmi $(docker images -q)

Remove dangling docker images

docker images -qf dangling=true | xargs docker rmi

Bind docker.sock to access docker commands from inside a container

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Overview

Bayesian phylogentic programs like MrBayes and BEAST work better when the BEAGLE library is installed. BEAGLE provides these programs with an MCMC sampler using CPU-based or GPU-based computation. Therefore, before compiling or using MrBayes and BEAST, BEAGLE and other prerequisites must be set-up and installed first. Unfortunately, setting-up all these software and libraries can become pretty frustrating very quickly.

Here I show how to properly set-up these programs to keep your frustration to a minimum. Broadly speaking, these instructions are applicable for Windows, Mac, and Linux. However, because I am specifically recounting my own experiencing setting-up my Linux machine, the more detailed parts of this guide focuses on installing on Linux.

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GENETIC_CODE = {
      'AAA': 'K',
      'AAC': 'N',
      'AAG': 'K',
      'AAT': 'N',
      'ACA': 'T',
      'ACC': 'T',
      'ACG': 'T',
      'ACT': 'T',
      'AGA': 'R',

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# 1. What will the following code print out?
x = 0
if x > 10:
    print(True)
else:
    print(False)
    
# 2. Refer to the following function
def f(a, b=0):
    if 0 in a:

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def fibo_r(x):
    if x <= 2:
        return 1
    return fibo_r(x-1) + fibo_r(x-2)

def fibo_l(x):
    l = [0, 1, 1]
    if x <= 2:
        return 1
    for i in range(3, x):

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# Add .asoundrc file

Copied from https://gist.github.com/AfzalivE/54214bf437ca1775b5b8e7934cc137db
```
# ps3 eye + 3.5mm speaker Raspberry Pi
## Suggested by http://julius.sourceforge.jp/forum/viewtopic.php?f=9&t=66
## Modified by https://github.com/afzalive
pcm.jack {
  type hw
  card ALSA