Differenze

Queste sono le differenze tra la revisione selezionata e la versione attuale della pagina.

--- calcoloscientifico:userguide:apptainer [20/02/2023 18:33] – fabio.spataro
+++ calcoloscientifico:userguide:apptainer [14/01/2025 13:00] (versione attuale) – [Apptainer] fabio.spataro
@@ Linea 1: / Linea 1: @@
-==== Apptainer ====
+===== Apptainer =====
-[[https://apptainer.org|Apptainer]]
+  * [[https://apptainer.org|Apptainer]]
+  * [[https://github.com/apptainer/apptainer|Apptainer on GitHub]]
 Apptainer is already available on the HPC cluster.
@@ Linea 7: / Linea 8: @@
 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.
@@ Linea 14: / Linea 15: @@
 <code>
-yum install https://github.com/apptainer/apptainer/releases/download/v1.0.1/apptainer-1.0.1-1.x86_64.rpm
+yum install https://github.com/apptainer/apptainer/releases/download/v1.1.8/apptainer-1.1.8-1.x86_64.rpm
 </code>
@@ Linea 20: / Linea 21: @@
 <code>
-sudo apt install https://github.com/apptainer/apptainer/releases/download/v1.0.1/apptainer_1.0.1_amd64.deb
+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 ===
+==== Extract NVIDIA driver ====
 The following commands
@@ Linea 41: / Linea 43: @@
 </code>
-=== 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:
@@ Linea 127: / Linea 129: @@
 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>