diff options
| -rw-r--r-- | issues/gemma/gemma-wrapper-has-incomplete-files.gmi | 8 |
1 files changed, 7 insertions, 1 deletions
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. |