hpc:applications_and_libraries
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hpc:applications_and_libraries [2024/03/13 17:05] Adrien Albert [Intro] |
hpc:applications_and_libraries [2024/03/25 16:52] (current) Adrien Albert [Pull an existing image] |
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| ==== Intro ==== | ==== Intro ==== | ||
| - | Apptainer is a Docker like for HPC. It is available directly on the OS, not through module. | + | Apptainer is a Docker like for HPC. It is available directly on the OS, not through module. |
| - | + | As you don't have root access on Baobab, you cannot build recipe file on Baobab. If you need to do this, you may want to build the image on your own machine and transfer the image to Baobab.\\ | |
| - | As you don't have root access on Baobab, you cannot build recipe file on Baobab. If you need to do this, you may want to build the image on your own machine and transfer the image to Baobab. | + | You can download existing images from shub (singularity hub) or from docker (docker public or private registry).\\ |
| - | + | The image will be converted to a read-only squashfs on Baobab disk. It's not possible to have writable images as user. Instead you should build the image as sandbox.\\ | |
| - | You can download existing images from shub (singularity hub) or from docker (docker public or private registry). | + | |
| - | + | ||
| - | The image will be converted to a read-only squashfs on Baobab disk. It's not possible to have writable images as user. Instead you should build the image as sandbox. | + | |
| Apptainer images are immutable, but it is possible to append an overlay, see below. | Apptainer images are immutable, but it is possible to append an overlay, see below. | ||
| === Pull an existing image === | === Pull an existing image === | ||
| - | <note warning> Do not run this command | + | <WRAP round alert 50%> |
| + | Do not run the following commands | ||
| + | </WRAP> | ||
| Exemple with Rstudio: | Exemple with Rstudio: | ||
| Line 1073: | Line 1072: | ||
| (baobab)-[alberta@login2 ~]$ cd !$ | (baobab)-[alberta@login2 ~]$ cd !$ | ||
| (baobab)-[alberta@login2 rocker]$ salloc --partition=shared-cpu --time=00: | (baobab)-[alberta@login2 rocker]$ salloc --partition=shared-cpu --time=00: | ||
| - | (baobab)-[alberta@login2 | + | (baobab)-[alberta@cpu300 |
| - | (baobab)-[alberta@login2 | + | (baobab)-[alberta@cpu300 |
| rstudio_4.2.sif | rstudio_4.2.sif | ||
| - | And Voila; I get my sif image | + | |
| + | And Voila; I get my sif image rstudio_4.2.sif | ||
| ==== Convert a Docker image ==== | ==== Convert a Docker image ==== | ||
hpc/applications_and_libraries.1710345922.txt.gz · Last modified: 2024/03/13 17:05 by Adrien Albert
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