netcdf error when running python setup.py build

[eigenstate]

netcdf error when running python setup.py build

[RasmusFonseca]

Have you tried brew install netcdf?

[akma327]

awesome that works!

[RasmusFonseca]

Great, @Eigenstate I'd suggest that the README section on dependencies came before installation instructions and explicitly stated that the easiest way to satisfy those dependencies on mac is to install homebrew and run brew install netcdf; pip install numpy.

[akma327]

On a related note, I'm trying to replicate the brew install on a computing cluster am now facing issues on getting brew downloaded on linux. Any ideas on if it is a permission issue to get around?
"
[akm64@farnam2 MDContactNetworks]$ sh -c "$(curl -fsSL https://raw.githubusercontent.com/Linuxbrew/install/master/install.sh)"

HEAD is now at c85a991 Python.user_site_packages: Check python suceeds [Linux] (#563)
==> Downloading https://homebrew.bintray.com/bottles-portable/portable-ruby-2.3.3.x86_64_linux.bottle.1.tar.gz
######################################################################## 100.0%
==> Pouring portable-ruby-2.3.3.x86_64_linux.bottle.1.tar.gz
==> Tapping homebrew/core
Cloning into '/ysm-gpfs/home/akm64/.linuxbrew/Homebrew/Library/Taps/homebrew/homebrew-core'...
remote: Counting objects: 4748, done.
remote: Compressing objects: 100% (4521/4521), done.
remote: Total 4748 (delta 38), reused 370 (delta 9), pack-reused 0
Receiving objects: 100% (4748/4748), 4.01 MiB | 0 bytes/s, done.
Resolving deltas: 100% (38/38), done.
Tapped 4509 formulae (4,793 files, 12.6MB)
Already up-to-date.
==> Installation successful!

==> Homebrew has enabled anonymous aggregate user behaviour analytics.
Read the analytics documentation (and how to opt-out) here:
http://docs.brew.sh/Analytics.html

==> Next steps:

• Install the Linuxbrew dependencies if you have sudo access:
  Debian, Ubuntu, etc.
  sudo apt-get install build-essential
  Fedora, Red Hat, CentOS, etc.
  sudo yum groupinstall 'Development Tools'
  See http://linuxbrew.sh/#dependencies for more information.
• Add Linuxbrew to your /.profile by running
  echo 'export PATH="/ysm-gpfs/home/akm64/.linuxbrew/bin:$PATH"' >>/.profile
  echo 'export MANPATH="/ysm-gpfs/home/akm64/.linuxbrew/share/man:$MANPATH"' >>/.profile
  echo 'export INFOPATH="/ysm-gpfs/home/akm64/.linuxbrew/share/info:$INFOPATH"' >>/.profile
• Add Linuxbrew to your PATH
  PATH="/ysm-gpfs/home/akm64/.linuxbrew/bin:$PATH"
• We recommend that you install GCC by running:
  brew install gcc
• Run brew help to get started
• Further documentation:
  http://docs.brew.sh
  Warning: /ysm-gpfs/home/akm64/.linuxbrew/bin is not in your PATH.
  [akm64@farnam2 MDContactNetworks]$ brew help
  bash: brew: command not found..."

[RasmusFonseca]

Ah, brew is a mac-only package manager. On linux you'd want whatever package manager the distro uses. For ubuntu I think it's Synaptic (i.e. apt-get install ...)

[Eigenstate]

On linux you can just install the binary, no need to build!
conda install -c rbetz vmd-python

[akma327]

Hmm, I'm on a new cluster right now and get
[akm64@farnam2 vmd-python]$ conda install -c https://conda.anaconda.org/rbetz vmd-python
bash: conda: command not found...
[akm64@farnam2 vmd-python]$ conda --version
bash: conda: command not found...

How should I install conda?

[RasmusFonseca]

https://www.anaconda.com/download

[akma327]

Awesome! 2 for 2! works on local machine and a foreign cluster :D