SingularityRecipe

Recipe on how to create a singularity image file.

Requirements

• Linux OS and singularity installed.

Download a base Ubuntu image to customize

Use Ubuntu 18.04 as a base to customize:

sudo singularity build --sandbox ubuntu_remix_vx.y.z/ library://ubuntu:18.04

Note: replace the suffix _vx.y.z to wathever you need.

• Reference: https://www.youtube.com/watch?v=nrgO3Q8-6hQ&t=342s&ab_channel=DanielPersson

Mount the image for customization

sudo singularity exec --writable ubuntu_remix_vx.y.z /bin/bash

System customization

Update the base system, install vim (or nano) to configure the system repository list:

apt update 
apt upgrade
apt install vim

Update system repository

Edit the /etc/apt/sources.list:

vim /etc/apt/sources.list

It should contain:

deb http://archive.ubuntu.com/ubuntu/ bionic main restricted
deb http://archive.ubuntu.com/ubuntu/ bionic-updates main restricted
deb http://archive.ubuntu.com/ubuntu/ bionic universe
deb http://archive.ubuntu.com/ubuntu/ bionic-updates universe
deb http://archive.ubuntu.com/ubuntu/ bionic multiverse
deb http://archive.ubuntu.com/ubuntu/ bionic-updates multiverse
deb http://archive.ubuntu.com/ubuntu/ bionic-backports main restricted universe multiverse
deb http://security.ubuntu.com/ubuntu bionic-security main restricted
deb http://security.ubuntu.com/ubuntu bionic-security universe
deb http://security.ubuntu.com/ubuntu bionic-security multiverse

Perform a system upgrade:

apt update
apt upgrade

Locale configuration

apt install locales locales-all
dpkg-reconfigure locales

Note: choose the locales 378 e 158 (i.e., 378. pt_BR.UTF-8 UTF-8, 158. en_US.UTF-8 UTF-8) Note: default will be 158 or en_US.UTF-8

And run:

locale-gen

• Reference: https://www.linuxquestions.org/questions/linux-newbie-8/bash-warning-setlocale-lc_all-cannot-change-locale-en-us-utf-8-a-4175628657/

Packages instalation

At this point, your requirements may be different. Install everything you need at this point.

apt install vim-gtk
apt install build-essential  
apt install gdb gdb-doc
apt install cgdb
apt install cmake ksh csh tcsh automake autoconf autoconf-archive libtool pkg-config
apt install libssl-dev uuid-dev libgpgme11-dev squashfs-tools
apt install xauth
apt install rsync wget
apt install zip p7zip-full
apt install subversion git
apt install gcc-4.8 g++-4.8 gfortran-4.8
apt install gcc-5 g++-5 gfortran-5
apt install gcc-6 g++-6 gfortran-6
apt install gcc-7 g++-7 gfortran-7
apt install gcc-8 g++-8 gfortran-8
apt install mpich libstdc++-6-dev manpages-dev
apt install libhugetlbfs0 libhugetlbfs-dev libblas3 liblapack3
apt install grads cdo nco ncl-ncarg gnuplot
apt install python3 curl htop ncftp sshfs sshpass
apt install netcdf-bin libnetcdf-c++4 libnetcdf-dev libnetcdf13 libnetcdff6 ncview 
apt install gdal-bin gdal-data 
apt install cdftools hdf5-tools 
apt install glueviz libjpeg8 imagemagick 
apt install pandoc
apt install doxygen
apt install emacs
apt install mpi-default-dev

gmake alias

cd /usr/bin
ln -s make gmake

• Reference: https://www.programmersought.com/article/97402906000/

libmpi.so configuration

Note: only needed if you use MPI.

Create a symlink to the libmpi_mpifh.so:

cd /usr/lib/x86_64-linux-gnu
ln -s libmpi_mpifh.so.20 libmpi_mpifh.so.40

And run:

ldconfig

• Reference: https://stackoverflow.com/questions/14769599/mpi-error-loading-shared-libraries/40817816

locate command

apt install mlocate
updatedb

• Reference: https://askubuntu.com/questions/215503/how-to-install-the-locate-command

gcc, g++ and gfortran versions

update-alternatives --remove-all gcc
update-alternatives --remove-all g++
update-alternatives --remove-all gfortran

update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.8 10
update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-5 20
update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-6 30
update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-7 40
update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-8 50

update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.8 10
update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-5 20
update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-6 30
update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-7 40
update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-8 50

update-alternatives --install /usr/bin/gfortran gfortran /usr/bin/gfortran-4.8 10
update-alternatives --install /usr/bin/gfortran gfortran /usr/bin/gfortran-5 20
update-alternatives --install /usr/bin/gfortran gfortran /usr/bin/gfortran-6 30
update-alternatives --install /usr/bin/gfortran gfortran /usr/bin/gfortran-7 40
update-alternatives --install /usr/bin/gfortran gfortran /usr/bin/gfortran-8 50

update-alternatives --config gcc
update-alternatives --config g++
update-alternatives --config gfortran

• Reference: https://askubuntu.com/questions/26498/how-to-choose-the-default-gcc-and-g-version

JAVA install and configuration

apt install default-jre default-jdk openjdk-8-jdk

update-alternatives --config java

Choose: /usr/lib/jvm/java-11-openjdk-amd64/bin/java

update-alternatives --config javac 

Choose: /usr/lib/jvm/java-11-openjdk-amd64/bin/javac

• Reference: https://www.digitalocean.com/community/tutorials/como-instalar-o-java-com-apt-no-ubuntu-18-04-pt

System cleanup

Perform a system cleanup before the image creation:

apt update
apt upgrade
apt autoremove
apt autoclean
apt clean

Exit the singularity shell

exit

Create the SIF - Singularity Image File

This is the part where the singularity container image is created. At this point, you've exited the singularity shell and are at your local machine.

sudo singularity build ubuntu_remix_vx.y.z.sif ubuntu_remix_vx.y.z

• Reference: https://www.youtube.com/watch?v=nrgO3Q8-6hQ&t=342s&ab_channel=DanielPersson

If you just want to use the container, you may stop here.

Sign the image

If you don't have a singularity key and follow the screen instructions (it will require a sylabs account - you can use you GitHub or Google account):

singularity keys newpair

Note: take a look at https://sylabs.io/guides/3.0/user-guide/signNverify.html#signing-and-validating-your-own-containers for more information.

If you already have a singularity key (it will require you to login to yout sylabs account):

singularity remote list
singularity remote login SylabsCloud

Note: Go to https://cloud.sylabs.io/auth/tokens and create a new token, copy and paste at the prompt.

singularity keys list
singularity key push <your_key>
singularity sign ubuntu_remix_vx.y.z.sif

Push the created container to the cloud

singularity push ubuntu_remix_vx.y.z.sif library://your_user_name/default/ubuntu_remix

To pull the container

Note: check your containers at https://cloud.sylabs.io/library/your_user_name to see the correct pull command.

Mine is:

singularity pull library://your_user_name/default/ubuntu_remix:latest

To verify the image

singularity verify ubuntu_remix_vx.y.z.sif

• Reference: https://sylabs.io/guides/3.0/user-guide/signNverify.html

To use the created SIF

singularity shell -e image_file.sif