From d326fd0036a43b4e2b1edfe8137ff5c36570d221 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Thu, 25 Nov 2021 09:25:55 +0100
Subject: Fixed incomplete output for parallel gemma

---
 issues/gemma/gemma-wrapper-has-incomplete-files.gmi | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

(limited to 'issues/gemma')

diff --git a/issues/gemma/gemma-wrapper-has-incomplete-files.gmi b/issues/gemma/gemma-wrapper-has-incomplete-files.gmi
index 6cb92f6..d530fb4 100644
--- a/issues/gemma/gemma-wrapper-has-incomplete-files.gmi
+++ b/issues/gemma/gemma-wrapper-has-incomplete-files.gmi
@@ -8,7 +8,7 @@ Gemma wrapper caches files - but it can happen a cached file is incomplete and n
 
 ## Tasks
 
-* [ ] parse parallel job log for failed tasks and remove the output files.
+* [X] parse parallel job log for failed tasks and remove the output files.
 * [X] create a (global) lock file for gemma-wrapper
 
 ## Info
@@ -23,6 +23,12 @@ The problem is that it is NOT a catch all. If there is a hardware fault or a pro
 
 It turns out that GNU parallel can keep track of jobs in a job log - and even rerun the ones missing using the `--joblog` and `--resume` switches. The last we don't need because we are using a cache. But we can use the log file to remove any incomplete output files! To me this is the obvious solution because 'parallel' is monitoring outside the GEMMA process and is a hardened piece of software. On failure it simply designates runs that way and we can clean up any (partly) produced files followed by a safe rerun. The lock routine below ascertains no processes are creating the same output at the same time.
 
+## Delete files on failure
+
+Implemented in
+
+=> https://github.com/genetics-statistics/gemma-wrapper/commit/624ed0d805f29ab682cffbe46bc104dffd0d713c
+
 ## Dealing with locks
 
 There is another parallel issue (pun intended) where gemma-wrapper is invoked twice for the same job. This is quite possible when people get impatient waiting for a first job to finish.
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