1. Install environment

1) Get depad-utils and configure environment

Login and navigate to your home folder

cd ${HOME}

download and unzip these files (There are hidden files/directories)

Note: Make sure that the etc/skel/.bashrc from the zip file was already deployed as root and that /etc/skel/.bashrc was copied to your home dir when it was created( cp /etc/skel/.bashrc ~ ). If your .bashrc does not have the stuff from the template, you can add it manually and notify an admin to deploy the template in /etc/skel/.

create folder where the modules will be

mkdir /apps/modules/

###copy all files in the folder /apps/modules/ from the zip to the server (if /apps/modules is not possible, NB the copying of these files should go somewhere else)

cp -r depad-utils/apps/modules/* depad-utils/.lmod/ /apps/modules/

NB: Lmod must already have been deployed as root using your Linux distro's package manager. NB2: if apps modules is not possible then ~/.bashrc should also be changed

If lmod is not installed, please do the following (admins-only) in our case for CentOS use

$root>: yum install lmod

To verify /apps/modules/modules.bashrc gets sourced: logout + login. When ${HPC_ENV_PREFIX} is set your are good to continue to the next step.

echo ${HPC_ENV_PREFIX}

2) Create main folders for our HPC environment.

mkdir -m 2775 ${HPC_ENV_PREFIX}/data/
mkdir -m 2775 ${HPC_ENV_PREFIX}/software/
mkdir -m 2775 ${HPC_ENV_PREFIX}/sources/
mkdir -m 2770 ${HPC_ENV_PREFIX}/.tmp/

3) Download EasyBuild bootstrap script

export EASYBUILD_VERSION=2.8.1
mkdir -p /${HPC_ENV_PREFIX}/sources/EasyBuild/
cd /${HPC_ENV_PREFIX}/sources/EasyBuild
curl -O https://raw.githubusercontent.com/hpcugent/easybuild-framework/develop/easybuild/scripts/bootstrap_eb.py
mv bootstrap_eb.py bootstrap_eb_${EASYBUILD_VERSION}.py

4) Bootstrap EasyBuild in apps dir.

python /${HPC_ENV_PREFIX}/sources/EasyBuild/bootstrap_eb_${EASYBUILD_VERSION}.py ${HPC_ENV_PREFIX}

5) Sanity check

logout and login again

module load EasyBuild
module list
eb --version

6) Install toolchain

eb foss-2015b.eb -–robot

Note: some sources should be downloaded manually (see below)

scp gcc-4.9.3.tar.bz2 /${HPC_ENV_PREFIX}/sources/g/GCC/
scp gmp-6.0.0a.tar.bz2 /${HPC_ENV_PREFIX}/sources/g/GCC/
scp mpc-1.0.2.tar.gz /${HPC_ENV_PREFIX}/sources/g/GCC/
scp mpfr-3.1.2.tar.gz /${HPC_ENV_PREFIX}/sources/g/GCC/

7) Installing additional packages

The following packages should be on the cluster/VM (this can only done with root access:

yum install libibverbs-devel
yum install openssl-devel
yum install unzip
yum install libX11-devel
yum install libXrender-devel
yum install libXext-devel
yum install mesa-libGL-devel
yum install mesa-libGLU-devel

8a) Get molgenis-easybuild repo

Now that easybuild is installed we have to have the molgenis easybuild configs because it contains a lot of custom easyconfigs that are (sometimes were at the moment we began with this) not in the original easybuild repo from Ghent University: https://github.com/molgenis/easybuild-easyconfigs

There are 2 options:

  • Fork this repo to your own repo and then do a git clone (on the cluster, then you can skip 8b)
  • Download the latest zip or tar.gz at

https://github.com/molgenis/easybuild-easyconfigs/releases/ (proceed to 8b)

8b) Put the new repo on the cluster/VM

scp -r easybuild-easyconfigs yourusername@yourcluster.nl:${root}/${pathToMYeasybuildconfigs}

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