Apptainer []

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===== Apptainer =====

[[https://apptainer.org|Apptainer]]

Apptainer is already available on the HPC cluster.

Users are encouraged to use it on their system.

==== Install a binary package ====

These instructions are intended for users who wish to install Apptainer on their Linux system.

On a **RedHat Enterpise Linux** system Apptainer can be installed by the administrator with the following command:

<code>
yum install https://github.com/apptainer/apptainer/releases/download/v1.1.8/apptainer-1.1.8-1.x86_64.rpm
</code>

On a **Debian/Ubuntu** system Apptainer can be installed by the administrator with the following command:

<code>
wget -qc https://github.com/apptainer/apptainer/releases/download/v1.1.8/apptainer_1.1.8_amd64.deb
sudo dpkg -i apptainer_1.1.8_amd64.deb
</code>

==== Extract NVIDIA driver ====

The following commands

<code>
bash /hpc/share/tools/nvidia/driver/extract_nvidia_driver.sh 510.47.03 /opt/hpc/system/nvidia/driver-510.47.03
ln -sfn driver-510.47.03 /opt/hpc/system/nvidia/driver
</code>

were executed on worker nodes with GPU by the administrator in a directory that contains the [[https://www.nvidia.it/Download/index.aspx|NVIDIA driver]] setup executable (for example ''NVIDIA-Linux-x86_64-510.47.03.run'').

Users who want to install Apptainer on their Linux system will be able to change the NVIDIA driver version and the installation path:

<code>
bash extract_nvidia_driver.sh <driver_version> </path/to/nvidia/driver_version>
ln -sfn <driver_version> </path/to/nvidia/driver>
</code>

==== Apptainer on a worker node with CPU ====

On the login node of the HPC cluster run the following command:

<code>
srun --nodes=1 --ntasks-per-node=2 --partition=cpu --pty bash
</code>

On the worker node run the following commands:

<code bash>
module load apptainer/1.0

container='/hpc/share/applications/amber/20/amber-20-cpu'

bind="${GROUP:+$GROUP,}${ARCHIVE:+$ARCHIVE,}${SCRATCH:+$SCRATCH,}$(test -d /node && echo /node)"

export APPTAINERENV_PS1='(\[\e[93;40m\]$APPTAINER_NAME\[\e[0m\])[\u@\h \W]\$ '

apptainer shell ${bind:+--bind $bind} "$container.sif"
</code>

Inside the Apptainer container:

<code>
(amber-20-cpu.sif)[user@wn01 ~]$ which pmemd.MPI
/usr/local/amber/bin/pmemd.MPI
</code>

Users who want to try Apptainer on their system will have to copy the Apptainer image

<code>
/hpc/share/applications/amber/20/amber-20-cpu.sif
</code>

from the HPC cluster to their system and appropriately modify the value of the ''container'' and ''bind'' variables.

Users who have installed a binary package do not have to load the ''apptainer'' module.

=== Apptainer on a worker node with GPU ===

On the login node of the HPC cluster run the following command:

<code>
srun --nodes=1 --ntasks-per-node=2 --partition=gpu --gres=gpu:1 --pty bash
</code>

On the worker node run the following commands:

<code bash>
module load apptainer/1.0

container='/hpc/share/applications/amber/20/amber-20-gpu'

bind="${GROUP:+$GROUP,}${ARCHIVE:+$ARCHIVE,}${SCRATCH:+$SCRATCH,}$(test -d /node && echo /node)"
bind="${bind:+$bind,}/opt/hpc/system/nvidia/driver:/usr/local/nvidia/lib,/opt/hpc/system/nvidia/driver:/usr/local/nvidia/bin"

export APPTAINERENV_PS1='(\[\e[92;40m\]$APPTAINER_NAME\[\e[0m\])[\u@\h \W]\$ '

apptainer shell ${bind:+--bind $bind} "$container.sif"
</code>

Inside the Apptainer container:

<code>
(amber-20-gpu.sif)[user@wn41 ~]$ which pmemd.cuda
/usr/local/amber/bin/pmemd.cuda
(amber-20-gpu.sif)[user@wn41 ~]$ nvidia-smi -L
GPU 0: Tesla P100-PCIE-12GB (UUID: GPU-72c0a29f-52d9-dd84-6ebd-dddff9150862)
GPU 1: Tesla P100-PCIE-12GB (UUID: GPU-712c408a-aea1-bedc-0017-e8b596a19813)
GPU 2: Tesla P100-PCIE-12GB (UUID: GPU-28abb0c0-4b8e-4dc1-c900-363178a9fdab)
GPU 3: Tesla P100-PCIE-12GB (UUID: GPU-9bdb3f49-0a09-ffd8-34b2-f6bec452c96c)
GPU 4: Tesla P100-PCIE-12GB (UUID: GPU-7f865f50-b609-1530-4473-a350cd4cd020)
GPU 5: Tesla P100-PCIE-12GB (UUID: GPU-ac67e6d2-f6c2-5c20-34f8-61542b33b030)
GPU 6: Tesla P100-PCIE-12GB (UUID: GPU-199d33ff-3754-7d4a-bda7-f26dbc536ed1)
</code>

Users who want to try Apptainer on their system will have to copy the Apptainer image

<code>
/hpc/share/applications/amber/20/amber-20-gpu.sif
</code>

from the HPC cluster to their system and appropriately modify the value of the ''container'' and ''bind'' variables.

Users who have installed a binary package do not have to load the ''apptainer'' module.

===== Apptainer containers =====

==== Bacterial Genomics software collection ====

''slurm-bactgen.sh'' script to get list of packages present in ''bactgen'' environment and help from ''tormes'' on 1 node (1 task, 4 CPUs per task):

<code bash slurm-bactgen.sh>
#!/bin/bash
#SBATCH --job-name=bactgen
#SBATCH --output=%x.o%j
#SBATCH --error=%x.e%j
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=4
#SBATCH --time=0-01:00:00
#SBATCH --mem=8G
#SBATCH --partition=cpu
#SBATCH --qos=cpu
#SBATCH --account=<account>

module load apptainer
module load bactgen

apptainer run "$CONTAINER" micromamba list
echo '─────────────────────────────────────────────────────────────────────────────────────────'
apptainer run "$CONTAINER" tormes --help
echo '─────────────────────────────────────────────────────────────────────────────────────────'
</code>

Edit the ''slurm-bactgen.sh'' script and submit it with the following command:

<code bash>
sbatch slurm-bactgen.sh
</code>
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