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GN3 Setup on tux01 - Non-Deterministic Behavior


  • assigned: bonfacem, zachs
  • priority: high
  • type: ops, guix
  • keywords: gn3
  • status: closed


Zach and Munyoki attempted to set up GN3 on tux01 following the provided channels file:

(list (channel
       (name 'gn-bioinformatics)
       (url "https://git.genenetwork.org/guix-bioinformatics")
       (branch "master")
       (name 'guix-forge)
       (url "https://git.systemreboot.net/guix-forge/")
       (branch "main")
	  "7F73 0343 F2F0 9F3C 77BF  79D3 2E25 EE8B 6180 2BB3")))))

... and execution steps:

source /var/guix/profiles/per-user/aruni/current-guix/etc/profile

guix pull -C channels.scm -p ~/.guix-extra-profiles/genenetwork

.  .guix-extra-profiles/genenetwork/etc/profile

guix install genenetwork3 genenetwork2 -p ~/.guix-extra-profiles/genenetwork

git clone https://github.com/genenetwork/genenetwork3.git

cd genenetwork3/

/export2/local/home/zas1024/gn3-zach/genenetwork3/run_dev.sh run --port=8090

Despite our efforts, attempting a CURL on GN3 using Zach's username consistently resulted in an empty response.

Even when Zach switched to my user (bonfacem) and repeated the steps with my ".guix-extra-profile", the CURL still produced an empty result. We tried various troubleshooting steps, such as running the commands in a shell with no specific environment set up and using su to switch to bonfacem from Zach's userspace, but the issue persists.


The error caused was due to missing SSL certificates. This was resolved by exporting the right SSL paths before starting the server. The simple fix was adding:

export SSL_CERT_DIR="$GUIX_PROFILE/etc/ssl/certs"
export SSL_CERT_FILE="$GUIX_PROFILE/etc/ssl/certs/ca-certificates.crt"

Also, debugging was difficult because of poor logging. This is being tracked here:

  • closed
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