This repository houses Guix configuration for GeneNetwork machines and containers. The git repo lives at https://git.genenetwork.org/gn-machines/ * GeneNetwork development container The GeneNetwork development container is currently run on /tux02/. It runs continuous integration and continuous deployment services for genenetwork2, genenetwork3 and several other associated projects. To build and install the container, you will need the [[https://gitlab.com/genenetwork/guix-bioinformatics][guix-bioinformatics]] and [[https://git.systemreboot.net/guix-forge/][guix-forge]] channels. Once these channels are pulled and available, on /tux02/, run #+BEGIN_SRC shell $ ./genenetwork-development-deploy.sh #+END_SRC /tux02/ is configured with a systemd service to run this container. Restart it. #+BEGIN_SRC shell $ sudo systemctl restart genenetwork-development-container #+END_SRC * Virtuoso container for tux01 production The virtuoso container is run on /tux01/ production. It runs virtuoso alone. To build and install the container, you will need the guix-bioinformatics channel. Once guix-bioinformatics is pulled and available, on /tux01/, run #+begin_src shell $ ./virtuoso-deploy.sh #+end_src /tux01/ is configured with a systemd service to run this container. Restart it. #+begin_src shell $ sudo systemctl restart virtuoso-container #+end_src * Secure virtuoso authentication In containers containing virtuoso instances, it is important to secure authentication by changing default user passwords and disabling unnecessary users. See [[https://issues.genenetwork.org/topics/systems/virtuoso][virtuoso gemtext documentation]] on passwords for more details. * Getting a Shell into the Container You can get a shell into the container with something like: #+BEGIN_SRC sh sudo guix container exec 89086 /run/current-system/profile/bin/bash --login #+END_SRC When you start the container, you can get a shell into the container using the ~nsenter~ command. You will need the process ID of the container, which you can see on container startup or on your can get with something like: #+BEGIN_SRC sh ps -u root -f --forest | grep -A4 '/usr/local/bin/genenetwork-development-container' | grep 'shepherd' #+END_SRC Where =/usr/local/bin/genenetwork-development-container= is the path used for invoking (running) the system container. That will give you output of the form: #+BEGIN_EXAMPLE 11869 pts/3 00:00:00 shepherd #+END_EXAMPLE From the guix [/operating-system/ Reference](https://guix.gnu.org/manual/en/html_node/operating_002dsystem-Reference.html) under the *packages* option, the list of packages installed under the global profile are found in */run/current-system/profile*, for example: #+BEGIN_SRC sh /run/current-system/profile/ls /gnu/store #+END_SRC to list the files under */gnu/store* With that knowledge, we can now get a shell using ~nsenter~ as follows: #+BEGIN_SRC sh sudo nsenter -a -t 11869 /run/current-system/profile/bin/bash \ --init-file /run/current-system/profile/etc/profile #+END_SRC which will give you a bash shell with the ~PATH~ environment variable setup correctly to give you access to all packages in the global profile. * Troubleshooting Tips ** Use Profiles When troubleshooting, we need to be using the correct profile that has all the necessary dependencies. Use a [[https://ci.genenetwork.org/channels.scm][channels]] file to set up a profile. An example of a channel that was fixed at Python 3.9: #+begin_src scheme (list (channel (name 'gn-bioinformatics) (url "https://gitlab.com/genenetwork/guix-bioinformatics") (branch "master") (commit "9939feb61ea29881d42628bc58a43886f7da6573")) (channel (name 'guix-forge) (url "https://git.systemreboot.net/guix-forge/") (branch "main") (introduction (make-channel-introduction "0432e37b20dd678a02efee21adf0b9525a670310" (openpgp-fingerprint "7F73 0343 F2F0 9F3C 77BF 79D3 2E25 EE8B 6180 2BB3"))))) #+end_src Activate a profile by: #+begin_src bash export GUIX_PROFILE=~/.guix-extra-profiles/genenetwork . $GUIX_PROFILE/etc/profile #+end_src Double-check to confirm that you are using the correct channel using =guix describe=. The use of profiles is well documented [[https://issues.genenetwork.org/topics/guix-profiles][here]]---it should match your channels.scm file. ** View Logs When troubleshooting our containers, all our log files are located in "/export2/guix-containers/genenetwork-development/var/log": #+begin_src sh tail /export2/guix-containers/genenetwork-development/var/log/cd/genenetwork2.log tail /export2/guix-containers/genenetwork-development/var/log/cd/genenetwork3.log #+end_src Note that to be able to view log files, you have to have root permissions. ** Back-ups When running borg, you can run into the following error: #+begin_src text root@tux02:/export3/local/home/bonfacem# borg list /export3/backup/tux01/borg/borg-tux01/ Cache, or information obtained from the security directory is newer than repository - this is either an attack or unsafe (multiple repos with same ID) #+end_src To fix it: : borg config repo id : rm ~/.config/borg/security/REPO_ID/manifest-timestamp : borg delete --cache-only REPO