diff --git a/_extras/miscellaneous.md b/_extras/miscellaneous.md index 8193d431..0ec760cd 100644 --- a/_extras/miscellaneous.md +++ b/_extras/miscellaneous.md @@ -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. @@ -251,4 +274,4 @@ If is not possible to change the input identifier, then you can use an alternati ```cwl valueFrom: $(inputs["sample-input"]) -``` +``` \ No newline at end of file