calcoloscientifico:userguide:apptainer
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calcoloscientifico:userguide:apptainer [20/02/2023 18:33] fabio.spataro |
calcoloscientifico:userguide:apptainer [01/06/2023 16:15] (versione attuale) fabio.spataro |
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| - | ==== Apptainer ==== | + | ===== Apptainer |
| [[https:// | [[https:// | ||
| Linea 7: | Linea 7: | ||
| Users are encouraged to use it on their system. | Users are encouraged to use it on their system. | ||
| - | === Install a binary package === | + | ==== Install a binary package |
| These instructions are intended for users who wish to install Apptainer on their Linux system. | These instructions are intended for users who wish to install Apptainer on their Linux system. | ||
| Linea 14: | Linea 14: | ||
| < | < | ||
| - | yum install https:// | + | yum install https:// |
| </ | </ | ||
| Linea 20: | Linea 20: | ||
| < | < | ||
| - | sudo apt install | + | wget -qc https:// |
| + | sudo dpkg -i apptainer_1.1.8_amd64.deb | ||
| </ | </ | ||
| - | === Extract NVIDIA driver === | + | ==== Extract NVIDIA driver |
| The following commands | The following commands | ||
| Linea 41: | Linea 42: | ||
| </ | </ | ||
| - | === Apptainer on a worker node with CPU === | + | ==== Apptainer on a worker node with CPU ==== |
| On the login node of the HPC cluster run the following command: | On the login node of the HPC cluster run the following command: | ||
| Linea 127: | Linea 128: | ||
| Users who have installed a binary package do not have to load the '' | Users who have installed a binary package do not have to load the '' | ||
| + | |||
| + | ===== Apptainer containers ===== | ||
| + | |||
| + | ==== Bacterial Genomics software collection ==== | ||
| + | |||
| + | '' | ||
| + | |||
| + | <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: | ||
| + | #SBATCH --mem=8G | ||
| + | #SBATCH --partition=cpu | ||
| + | #SBATCH --qos=cpu | ||
| + | #SBATCH --account=< | ||
| + | |||
| + | module load apptainer | ||
| + | module load bactgen | ||
| + | |||
| + | apptainer run " | ||
| + | echo ' | ||
| + | apptainer run " | ||
| + | echo ' | ||
| + | </ | ||
| + | |||
| + | Edit the '' | ||
| + | |||
| + | <code bash> | ||
| + | sbatch slurm-bactgen.sh | ||
| + | </ | ||
calcoloscientifico/userguide/apptainer.1676914395.txt.gz · Ultima modifica: 20/02/2023 18:33 da fabio.spataro
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