From a3ae950d2d011d9abfa9f742ad4ed59d06c7c5f2 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 15 Aug 2021 14:19:19 +0300 Subject: added issue about genecup running as root --- issues/genecup-running-as-root.gmi | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 issues/genecup-running-as-root.gmi (limited to 'issues/genecup-running-as-root.gmi') diff --git a/issues/genecup-running-as-root.gmi b/issues/genecup-running-as-root.gmi new file mode 100644 index 0000000..f1898c8 --- /dev/null +++ b/issues/genecup-running-as-root.gmi @@ -0,0 +1,31 @@ +# genecup is currently running as root on penguin2. + +Currently when run using shepherd it fails like this: + +guix system: warning: Consider running 'guix pull' followed by +'guix system reconfigure' to get up-to-date packages and security updates. + +guile: warning: failed to install locale +Backtrace: + 6 (primitive-load "/gnu/store/gkksaranscqwyzixgm4fk83by1n?") +In gnu/build/linux-container.scm: + 299:8 5 (call-with-temporary-directory #) + 327:16 4 (_ "/tmp/guix-directory.mkZ75V") + 270:12 3 (run-container _ _ (mnt pid ipc uts user) 65536 _ # _ # _) + 200:4 2 (initialize-user-namespace _ 65536 #:guest-uid _ # _) +In ice-9/ports.scm: + 465:8 1 (call-with-output-file _ _ #:binary _ #:encoding _) +In unknown file: + 0 (close-output-port #) + +ERROR: In procedure close-output-port: +In procedure fport_write: Operation not permitted + +A number of changes to different types of shepherd services (exec-command, make-system-constructor) still failed to actually run the container when started with `herd start genecup`. Ratspub is run from a `guix environment` rather than `guix system container` so we'll switch to that so we can go back to running all the services using shepherd. + +=> https://git.genenetwork.org/efraim/shepherd-services/commit/b3c96077c2ae3ebda05eb53d81fa6e377a55132d The commit to make genecup run in a guix environment, using shepherd. + +## Notes + +* It is unclear if the environmental-variables in the shepherd service are carried over to the shell script, but it seems not +* Had to run 'guix pull' to update the guix tree for genecup, since the guix-bioinformatics repository had made breaking changes since the last time. -- cgit v1.2.3