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Install environment

1) Get depad-utils and configure environment

Login and navigate to your home folder
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cd ${HOME}
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download and unzip these files (There are hidden files/directories)
Note: Make sure that the etc/skel/.bashrc from the zip file was already deployed as root and that /etc/skel/.bashrc was copied to your home dir when it was created( cp /etc/skel/.bashrc ~ ). If your .bashrc does not have the stuff from the template, you can add it manually and notify an admin to deploy the template in /etc/skel/.
create folder where the modules will be
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mkdir /apps/modules/
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###copy all files in the folder /apps/modules/ from the zip to the server (if /apps/modules is not possible, NB the copying of these files should go somewhere else)
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cp -r depad-utils/apps/modules/* depad-utils/.lmod/ /apps/modules/
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NB: Lmod must already have been deployed as root using your Linux distro's package manager. NB2: if apps modules is not possible then ~/.bashrc should also be changed
If lmod is not installed, please do the following (admins-only) in our case for CentOS use
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$root>: yum install lmod
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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.
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echo ${HPC_ENV_PREFIX}
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2) Create main folders for our HPC environment.

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mkdir -m 2775 ${HPC_ENV_PREFIX}/data/
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mkdir -m 2775 ${HPC_ENV_PREFIX}/software/
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mkdir -m 2775 ${HPC_ENV_PREFIX}/sources/
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mkdir -m 2770 ${HPC_ENV_PREFIX}/.tmp/
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3) Download EasyBuild bootstrap script

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

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python /${HPC_ENV_PREFIX}/sources/EasyBuild/bootstrap_eb_${EASYBUILD_VERSION}.py ${HPC_ENV_PREFIX}
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5) Sanity check

logout and login again
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module load EasyBuild
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module list
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eb --version
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6) Install toolchain

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eb foss-2015b.eb -–robot
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Note: some sources should be downloaded manually (see below)
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scp gcc-4.9.3.tar.bz2 /${HPC_ENV_PREFIX}/sources/g/GCC/
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scp gmp-6.0.0a.tar.bz2 /${HPC_ENV_PREFIX}/sources/g/GCC/
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scp mpc-1.0.2.tar.gz /${HPC_ENV_PREFIX}/sources/g/GCC/
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scp mpfr-3.1.2.tar.gz /${HPC_ENV_PREFIX}/sources/g/GCC/
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7) Installing additional packages

The following packages should be on the cluster/VM (this can only done with root access:
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yum install libibverbs-devel
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yum install openssl-devel
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yum install unzip
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yum install libX11-devel
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yum install libXrender-devel
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yum install libXext-devel
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yum install mesa-libGL-devel
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yum install mesa-libGLU-devel
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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

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scp -r easybuild-easyconfigs [email protected]:${root}/${pathToMYeasybuildconfigs}
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Last modified 3yr ago