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About no space on /tmp #163

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25 changes: 24 additions & 1 deletion _extras/miscellaneous.md
Original file line number Diff line number Diff line change
Expand Up @@ -170,6 +170,29 @@ outputs:
type: File
outputSource: first/txt
```

### No space left on `/tmp`

When you execute tools like `sort` which consume a lot of `/tmp` space, you can get this kind of error:

> [Errno 28] No space left on device on device: '/tmp/q0aq3bde

This kind of error happens in mainly two cases:

1. The tool using huge amount of disk space under `/tmp` (perhaps via `$(runtime.tmpdir)`)
2. You are running on Mac with Docker and the `/tmp` in the Docker Virtual Machine is only 1GB in size and this is not enough.

Generic workaround: find a new temporary space, perhaps located under your home directory, or scratch storage if your computing environment has that.

Specific workaround for `cwltool` is to use one of the following options:

```
--tmpdir-prefix TMPDIR_PREFIX Path prefix for temporary directories
--tmp-outdir-prefix TMP_OUTDIR_PREFIX Path prefix for intermediate output directories
```

Or if you using a Mac, increase the Docker Virtual Machine `Memory` size (Default: `2GB` ) to be bigger, as half of VM memory is used for the `/tmp` tmpfs.

### `cwltool` errors due to filenames with space characters inside

`cwltool` does not allow some characters in filenames by default.
Expand Down Expand Up @@ -251,4 +274,4 @@ If is not possible to change the input identifier, then you can use an alternati

```cwl
valueFrom: $(inputs["sample-input"])
```
```