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runtime_tips.md format -l part
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bclaremar authored May 7, 2024
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61 changes: 30 additions & 31 deletions docs/cluster_guides/running_jobs/runtime_tips.md
Original file line number Diff line number Diff line change
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[What do the fields PRIORITY and REASON mean in "jobinfo" output?](jobinfo_reason.md)

???- question "What is causing the sbatch script error 'Unknown shell type `load`'?"
???- question "How do I use the modules in batch jobs?"

???- info "For UPPMAX staff"
- In order to make running installed programs easier you should use the module command.
- The different module that are installed sets the correct environments that are needed for the programs to run, like ``PATH``, ``LD_LIBRARY_PATH`` and ``MANPATH``.
-To see what what modules that are available, type ``module avail``. To see what modules you have loaded, type ``module list``.

TODO: InfoGlue link: `https://www.uppmax.uu.se/support/faq/running-jobs-faq/sbatch-script-error--unknown-shell-type--load--/`
- Note. For the batch system slurm to work with modules you must have

If you're getting the error message
```
#!/bin/bash -l
```

```
init.c(379):ERROR:109: Unknown shell type load
```
in your submit script.

when running your sbatch script, then your script is probably starting with the line
- For more information, read the [module system guide](../modules.md)

```
#!/bin/bash
```
To remedy this you need to make sure that your script starts with
???- question "What is causing the sbatch script error 'Unknown shell type `load`'?"

```
#!/bin/bash -l
```
- If you're getting the error message

```
init.c(379):ERROR:109: Unknown shell type load
```

i.e. notice the trailing "-l". This tells bash to load the correct environment settings, which makes the module system usable.
when running your sbatch script, then your script is probably starting with the line

```
#!/bin/bash
```

To remedy this you need to make sure that your script starts with

```
#!/bin/bash -l
```

i.e. notice the trailing "-l". This tells bash to load the correct environment settings, which makes the module system usable.


???- question "How can I see my job's memory usage?"

Expand Down Expand Up @@ -227,18 +241,3 @@ If your job priority is zero or one, there are more serious problems, for exampl

If you ask for a longer run time (TimeLimit) than the maximum on the system, your job will not run. The maximum is currently ten days. If you must run a longer job, submit it with a ten-day runtime and contact UPPMAX support.

???- question "How do I use the modules in batch jobs?"

- In order to make running installed programs easier you should use the module command.
- The different module that are installed sets the correct environments that are needed for the programs to run, like ``PATH``, ``LD_LIBRARY_PATH`` and ``MANPATH``.
-To see what what modules that are available, type ``module avail``. To see what modules you have loaded, type ``module list``.

- Note. For the batch system slurm to work with modules you must have

```
#!/bin/bash -l
```

in your submit script.

- For more information, read the [module system guide](../modules.md)

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