From 3787440fb80f3d0e0f6834aaf9fda07d6dd9b2e1 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sun, 14 Nov 2021 16:15:19 -0600
Subject: gemma-wrapper transactions

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 .../gemma/gemma-wrapper-has-incomplete-files.gmi   | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 issues/gemma/gemma-wrapper-has-incomplete-files.gmi

diff --git a/issues/gemma/gemma-wrapper-has-incomplete-files.gmi b/issues/gemma/gemma-wrapper-has-incomplete-files.gmi
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+# gemma-wrapper has incomplete files
+
+Gemma wrapper caches files - but it can happen a cached file is incomplete and never updated again. The problem appears when GNU parallel is invoked and hits an error. The task here is to make gemma-wrapper transactional.
+
+## Tags
+
+* assigned: pjotrp, zachs
+
+## Tasks
+
+* [ ] parse parallel job log for failed tasks and remove the output files.
+* [ ] create a (global) lock file for gemma-wrapper
+
+## Info
+
+GNU parallel can fail, but does not tell how individual processes did. Need to check if it can return a thread (number). If not we have the option of checking the GEMMA status file and/or see if the output file is complete (by counting number of lines).
+
+Turns out GNU parallel can keep track of jobs in a job log - and even rerun the ones missing. 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!
+
+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.
+
+One solution is to write a lock file using the inputs as a hash. The lock file can contain a PID and we can check if that is still alive. I should do the same for sheepdog locks(!)
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