Differenze

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

--- calcoloscientifico:userguide:apptainer [20/02/2023 19:59] – fabio.spataro
+++ calcoloscientifico:userguide:apptainer [14/01/2025 13:00] (versione attuale) – [Apptainer] fabio.spataro
@@ Linea 1: / Linea 1: @@
 ===== 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 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>
@@ Linea 80: / Linea 82: @@
 Users who have installed a binary package do not have to load the ''apptainer'' module.
-==== Apptainer on a worker node with GPU ====
+=== Apptainer on a worker node with GPU ===
 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 ====
-Script ''slurm-bactgen.sh'' to run some commands for demonstration purposes on 1 node (1 task, 4 CPUs per task):
+''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>
@@ Linea 149: / Linea 153: @@
 module load bactgen
-apptainer run "$CONTAINER" dRep
+apptainer run "$CONTAINER" micromamba list
-apptainer run "$CONTAINER" tormes --version
+echo '─────────────────────────────────────────────────────────────────────────────────────────'
-apptainer run "$CONTAINER" lissero --version
+apptainer run "$CONTAINER" tormes --help
-apptainer run "$CONTAINER" roary -h
+echo '─────────────────────────────────────────────────────────────────────────────────────────'
-apptainer run "$CONTAINER" roary -w
-apptainer run "$CONTAINER" scoary -h
-apptainer run "$CONTAINER" scoary --version
-apptainer run "$CONTAINER" prokka --version
-apptainer run "$CONTAINER" staramr -V
 </code>
-Edit the ''slurm-bactgen.sh'' script and submit it with the following command
+Edit the ''slurm-bactgen.sh'' script and submit it with the following command:
 <code bash>