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| -rw-r--r-- | issues/genecup-running-as-root.gmi | 31 |
1 files changed, 31 insertions, 0 deletions
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 #<procedure 7ff547853640?>) + 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 #<output: /proc/15090/uid_map 8>) + +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. |