No modules loaded issue on dev environment

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1

Hello everyone,
I’m currently working on deploying IGV within our Open OnDemand 3.0.1 environment. However, I’ve encountered some issues with the modules not being loaded. I would greatly appreciate it if someone could provide assistance with this matter. I’ll be attaching the YAML files and output in my next replies.

Thank you.

This is form.yml

---
cluster: "slurm"
attributes:
  bc_num_hours:
    value: 1

  bc_num_slots:
    label: Number of CPU
    value: 1
    min: 1
    max: 24
    step: 1

  bc_num_mems:
    widget: "number_field"
    label: Memory per CPU (GB)
    value: 4
    min: 1
    max: 128
    step: 1

  bc_partition:
    widget: select
    label: Partition
    options:
      - ["compute", "compute"]


  modules:
     widget: select
     label: "igv 2.16.2"
     help: "This defines the version of igv you want to load."
     options:
       - [ "2.16.2", "igv/IGV_2.16.2" ]

form:
  - modules
  - bc_num_hours
  - bc_partition
  - bc_num_slots
  - bc_num_mems
  - bc_email_on_started
2

submit.yml.erb

---
batch_connect:
  template: "vnc"
script:
  native:
    - "-N 1"
    - "-n <%= bc_num_slots.blank? ? 1 : bc_num_slots.to_i %>"
    - "--mem-per-cpu=<%= bc_num_mems.blank? ? 4 : bc_num_mems.to_i %>G"
    - "--partition=<%= bc_partition %>"
    - "--time=<%= bc_num_hours.blank? ? 1 : bc_num_hours.to_i %>:00:00"
    - "--job-name=ood-igv"
3

template/script.sh.erb

#!/usr/bin/env bash


# Clean the environment
module reset

# Set working directory to home directory
cd "${HOME}"

#
# Launch Xfce Window Manager and Panel
#

(
  export SEND_256_COLORS_TO_REMOTE=1
  export XDG_CONFIG_HOME="<%= session.staged_root.join("config") %>"
  export XDG_DATA_HOME="<%= session.staged_root.join("share") %>"
  export XDG_CACHE_HOME="$(mktemp -d)"
  module restore
  set -x
  xfwm4 --compositor=off --daemon --sm-client-disable
  xsetroot -solid "#D3D3D3"
  xfsettingsd --sm-client-disable
  xfce4-panel --sm-client-disable
) &

#
# Start your GUI app
#

# Load the required environment
module load <%= context.modules %>
module list
set -x

# Launch your GUI app
#EXECUTE_COMMAND_TO_LAUNCH_GUI_APP
igvtools_gui.command &
igv.sh
4

output

Setting VNC password...
Starting VNC server...

Desktop 'TurboVNC: appliance-compute-0.novalocal:1 (kenny)' started on display appliance-compute-0.novalocal:1

Log file is vnc.log
Successfully started VNC server on appliance-compute-0:5901...
Script starting...
Starting websocket server...
The system default contains no modules
  (env var: LMOD_SYSTEM_DEFAULT_MODULES is empty)
  No changes in loaded modules

The system default contains no modules
  (env var: LMOD_SYSTEM_DEFAULT_MODULES is empty)
  No changes in loaded modules

++ xfwm4 --compositor=off --daemon --sm-client-disable
xfwm4: Unknown option --daemon.
Type "xfwm4 --help" for usage.
++ xsetroot -solid '#D3D3D3'
++ xfsettingsd --sm-client-disable
Lmod has detected the following error: The following module(s) are unknown:
"igv/IGV_2.16.2"

Please check the spelling or version number. Also try "module spider ..."
It is also possible your cache file is out-of-date; it may help to try:
  $ module --ignore_cache load "igv/IGV_2.16.2"

Also make sure that all modulefiles written in TCL start with the string
#%Module



No modules loaded
++ igv.sh
++ igvtools_gui.command
/home/kenny/ondemand/data/sys/dashboard/batch_connect/dev/igv/output/e8d1ac34-743e-4ad0-ad89-af8c610364e2/script.sh: line 81: igvtools_gui.command: command not found
/home/kenny/ondemand/data/sys/dashboard/batch_connect/dev/igv/output/e8d1ac34-743e-4ad0-ad89-af8c610364e2/script.sh: line 82: igv.sh: command not found
WebSocket server settings:
  - Listen on :63028
  - No SSL/TLS support (no cert file)
  - Backgrounding (daemon)
Scanning VNC log file for user authentications...
Generating connection YAML file...
Cleaning up...
Killing Xvnc process ID 246405
++ xfce4-panel --sm-client-disable
Unable to init server: Could not connect: Connection refused
xfce4-panel: Cannot open display: .
Type "xfce4-panel --help" for usage.
5

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