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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

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

scp -r easybuild-easyconfigs [email protected]:${root}/${pathToMYeasybuildconfigs}
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Outline
1) Get depad-utils and configure environment
2) Create main folders for our HPC environment.
3) Download EasyBuild bootstrap script
4) Bootstrap EasyBuild in apps dir.
5) Sanity check
6) Install toolchain
7) Installing additional packages
8a) Get molgenis-easybuild repo
8b) Put the new repo on the cluster/VM