#Virtual and Real Machines for NuGrid Codes
In order to run all of the NuGrid codes and tools your computer must be properly configured. One way to get started is to use a virtual machine that can be deployed independently of host operating system. This is a great way to try out installation, compilation and running. In the following we describe two options:
Make sure you select the upgrade/update option during installation and/or start with
sudo apt-get update sudo apt-get upgrade sudo apt-get autoclean sudo apt-get autoremove
Then start adding things:
sudo apt-get install make gcc dkms sudo apt-get install emacs gfortran
To make the VM work nicely, e.g. adaptive screen resolution install the VBox additions. First attach the virtual optical drive in the VM Devices menue. Then do
sudo sh /media/fherwig/VBOXADDITIONS_5.0.26_108824/VBoxLinuxAdditions.run
At this point you should shut-down the VM.
Before you restart go to Settings and Shared Folders and add a directory from your host home dir, or even the entire home dir as a shared folder. Select Auto-mount and remember the folder name.
Now boot the machine. Then mount the shared folder:
sudo mount -t vboxsf -o uid=1000,gid=1000 fherwig /home/fherwig/fherwig_hostin your local dir your host home dir (or whatever you have specified in your Shared Folder settings, will now appear in the mount point directory. You will have to do the second commen each time you reboot your VM. So you may want to add the mount command as an alias to your
You may also want to add an alias to .bashrc to mount the NuGrid VOspace volume on CANFAR:
alias mnt.vos="mountvofs --readonly --cache_dir=/tmp/vosCache --cache_limit=2000 --mountpoint=/tmp/nugrid --vospace=vos:nugrid"
Don’t forget to make the mount point needed for the mount command:
$ mkdir /tmp/nugrid
Remember that presently (as of Oct 9, 2016) CANFAR VOS does not support Python 3 (see below how switch between Python 2 and 3 using the Anaconda distribution.
Install and configure git:
sudo apt install git git config --global user.name "Falk Herwig" git config --global user.email "email@example.com"
In order to access your git repos on github you need to add your
id_rsa key to your VM. If you have mounted your host home dir (see above) you have access to your ssh key from your host, the public version of it you will probably already have uploaded to github. Make a directory
.ssh in your VM home dir and copy the private ssh key from your host to your VM:
cp ~/fherwig_host/.ssh/id_rsa ~/.ssh
Now you may clone repos to your VM or go to your repo dir in your mounted host filesystem. Start installing some repos:
mkdir Repos cd Repos git clone firstname.lastname@example.org:NuGrid/NuSE.git git clone email@example.com:NuGrid/NuGridPy.git git clone firstname.lastname@example.org:NuGrid/NuPPN.git
As an example, installing openblas from scratch:
git clone https://github.com/xianyi/OpenBLAS cd OpenBLAS/ make FC=gfortran sudo make PREFIX=/usr/local install
Alternatively, for example you may use the package installer:
sudo apt-get install libopenblas-dev
You will need some python. Here we use the Anaconda distribution which has everyting except the future (or futures) package:
conda create -n py27 python=2.7 anaconda
In order to use the NuGrid Paper template install the following packages using the
sudo apt-get install command:
Some of these installation steps appears to take a little longer. You can use the evince program to look at pdf files.
MNRAS requires packages
newtxmath which may require
to install TexLive
2016 which takes a
moment but should be straight forward.
To edit markdown files you can use emacs or whatever your favourite text editor is. For a two-pannel view download the
.deb package of the Remarkable markdown editor. Double-click on the
.deb file in the file manager to install.
Nubuntu16 is a virtual drive created with the intent of making use of NuGrid tools a breeze for new or casual users.