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Apptainer: Difference between revisions
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→Important Command Line Options
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Not using any of these options will have the convenience of file systems being mounted and shell variables existing inside your container but be aware such can be the source of issues/errors when running software inside your container. | Not using any of these options will have the convenience of file systems being mounted and shell variables existing inside your container but be aware such can be the source of issues/errors when running software inside your container. | ||
Additionally there is another option, <code>-W</code> or <code>--workdir</code>, one should consider using. On our clusters (and on most Linux systems), the <code>/tmp</code> and similar filesystems use RAM --not disk space-- and jobs are run on our clusters typically with limited RAM requests. This can result in jobs getting killed because they consume too much RAM (relative to what was requested). A suitable work-around for this is to tell Apptainer to use a "workdir" for such filesystems, <code>$HOME</code> (if <code>-c</code> is also used), etc. This is done by passing the <code>-W</code> option followed by a path to a disk space location where Apptainer can read/write temporary files, etc. | |||
====Using GPUs==== | ====Using GPUs==== | ||