From d216679d34019a703befe68e6c5956663948fa37 Mon Sep 17 00:00:00 2001 From: Manabu ISHII Date: Fri, 6 Sep 2019 23:12:54 +0900 Subject: [PATCH 1/5] Update miscellaneous.md --- _extras/miscellaneous.md | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/_extras/miscellaneous.md b/_extras/miscellaneous.md index 63399a9a..80d2f1ee 100644 --- a/_extras/miscellaneous.md +++ b/_extras/miscellaneous.md @@ -170,3 +170,25 @@ outputs: type: File outputSource: first/txt ``` + +### No space left on `/tmp` + +When you execute enough storage space ,sometimes you get this kind of error. + +> [Errno 28] No space left on device on device: '/tmp/q0aq3bde + +This kind of error is happens mainly two cases. + +1. tool using huge amount under `/tmp` . +2. You run on Mac. + +Both case one WORKAROUND is that temporary space is located under your home directory, or scratch storage if your computing environment has. + +WORKAROUND of `cwltool` is here . + +``` +--tmpdir-prefix TMPDIR_PREFIX +Path prefix for temporary directories +--tmp-outdir-prefix TMP_OUTDIR_PREFIX +Path prefix for intermediate output directories +``` From 45d97ccdde470967e8d60d09fd3974e33cd7b89d Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Wed, 11 Sep 2019 15:18:07 +0900 Subject: [PATCH 2/5] grammer tweak --- _extras/miscellaneous.md | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/_extras/miscellaneous.md b/_extras/miscellaneous.md index 80d2f1ee..e95c7a87 100644 --- a/_extras/miscellaneous.md +++ b/_extras/miscellaneous.md @@ -173,7 +173,7 @@ outputs: ### No space left on `/tmp` -When you execute enough storage space ,sometimes you get this kind of error. +When your storage space fills up, sometimes you get this kind of error. > [Errno 28] No space left on device on device: '/tmp/q0aq3bde @@ -184,11 +184,9 @@ This kind of error is happens mainly two cases. Both case one WORKAROUND is that temporary space is located under your home directory, or scratch storage if your computing environment has. -WORKAROUND of `cwltool` is here . +Workaround for `cwltool` is to use one of the following: ``` ---tmpdir-prefix TMPDIR_PREFIX -Path prefix for temporary directories ---tmp-outdir-prefix TMP_OUTDIR_PREFIX -Path prefix for intermediate output directories +--tmpdir-prefix TMPDIR_PREFIX Path prefix for temporary directories +--tmp-outdir-prefix TMP_OUTDIR_PREFIX Path prefix for intermediate output directories ``` From e0f815b4110b6d85e2a69506a60621e934898e0e Mon Sep 17 00:00:00 2001 From: Manabu ISHII Date: Wed, 11 Sep 2019 17:26:15 +0900 Subject: [PATCH 3/5] Describe the situation like sort --- _extras/miscellaneous.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/_extras/miscellaneous.md b/_extras/miscellaneous.md index e95c7a87..5c802517 100644 --- a/_extras/miscellaneous.md +++ b/_extras/miscellaneous.md @@ -173,7 +173,7 @@ outputs: ### No space left on `/tmp` -When your storage space fills up, sometimes you get this kind of error. +When you execute the tools like sort which consuming a lot of amount of `/tmp` space , you get this kind of error. > [Errno 28] No space left on device on device: '/tmp/q0aq3bde @@ -181,6 +181,7 @@ This kind of error is happens mainly two cases. 1. tool using huge amount under `/tmp` . 2. You run on Mac. + - Default Mac `/tmp` only has `1GB`. almost case is good but sometimes `1GB` is not enough. Both case one WORKAROUND is that temporary space is located under your home directory, or scratch storage if your computing environment has. From 3b64680ea23f3e25344b08a0980085f625b685a0 Mon Sep 17 00:00:00 2001 From: Manabu ISHII Date: Wed, 11 Sep 2019 17:28:57 +0900 Subject: [PATCH 4/5] About workaround for mac to increase /tmp --- _extras/miscellaneous.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/_extras/miscellaneous.md b/_extras/miscellaneous.md index 5c802517..57b6049f 100644 --- a/_extras/miscellaneous.md +++ b/_extras/miscellaneous.md @@ -191,3 +191,5 @@ Workaround for `cwltool` is to use one of the following: --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 `Memory` size (Default: `2GB` ) more bigger, the half of memory using as tmpfs. From 1f74177c69b518bc0e30956458b119d4c927657e Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Wed, 11 Sep 2019 17:44:29 +0900 Subject: [PATCH 5/5] clarifications --- _extras/miscellaneous.md | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/_extras/miscellaneous.md b/_extras/miscellaneous.md index 57b6049f..6a06d68f 100644 --- a/_extras/miscellaneous.md +++ b/_extras/miscellaneous.md @@ -173,23 +173,22 @@ outputs: ### No space left on `/tmp` -When you execute the tools like sort which consuming a lot of amount of `/tmp` space , you get this kind of error. +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 is happens mainly two cases. +This kind of error happens in mainly two cases: -1. tool using huge amount under `/tmp` . -2. You run on Mac. - - Default Mac `/tmp` only has `1GB`. almost case is good but sometimes `1GB` is not enough. +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. -Both case one WORKAROUND is that temporary space is located under your home directory, or scratch storage if your computing environment has. +Generic workaround: find a new temporary space, perhaps located under your home directory, or scratch storage if your computing environment has that. -Workaround for `cwltool` is to use one of the following: +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 `Memory` size (Default: `2GB` ) more bigger, the half of memory using as tmpfs. +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.