Hi,
I am trying to install a local Galaxy instance and connect it to a Grid engine cluster to run the jobs. However, following the guidelines at Connecting to a Cluster — Galaxy Project 24.1.dev0 documentation for creating the configuration files, I cannot get the cluster to perform any execution or receive any trace in the logs. Meanwhile, if I run a job from the grid engine cluster directly the job does run. Is there any extra documentation about Galaxy integration with Grid Engine?
These are the configuration files:
job_conf.xml
<?xml version="1.0"?>
<!-- A sample job config that describes all available options -->
<job_conf>
<plugins>
<!-- "workers" is the number of threads for the runner's work queue.
The default from <plugins> is used if not defined for a <plugin>.
For all asynchronous runners (i.e. everything other than
LocalJobRunner), this is the number of threads available for
starting and finishing jobs. For the LocalJobRunner, this is the
number of concurrent jobs that Galaxy will run.
-->
<plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner">
<!-- Override the $DRMAA_LIBRARY_PATH environment variable -->
<param id="drmaa_library_path">/sched/sge/sge-2011.11/lib/linux-x64/libdrmaa.so</param>
</plugin>
</plugins>
<destinations default="htc">
<!-- Destinations define details about remote resources and how jobs
should be executed on those remote resources.
-->
<destination id="htc" runner="drmaa">
<!-- SGE DRMAA to send to a specific request 7GB of RAM (2 per CPU) and 4 CPUs -->
<param id="nativeSpecification">-w n -l slot_type=htc</param>
<env file="/shared/Galaxy/.venv/bin/activate" />
</destination>
<destination id="mpi" runner="drmaa">
<!-- SGE DRMAA to send to a specific request 420 GB of RAM and 116 CPUs for MPI job -->
<param id="nativeSpecification">-w n -pe mpi 116</param>
<env file="/shared/Galaxy/.venv/bin/activate" />
</destination>
</destinations>
</job_conf>
galaxy.yml
uwsgi:
shared-socket: :80
http: =0
uid: azureuser
gid: azureuser
buffer-size: 16384
processes: 2
threads: 4
offload-threads: 2
# Mapping to serve static content.
static-map: /static=static
# Mapping to serve the favicon.
static-map: /favicon.ico=static/favicon.ico
# Allow serving certain assets out of `client`. Most modern Galaxy
# interfaces bundle all of this, but some older pages still serve
# these via symlink, requiring this rule.
static-safe: client/src/assets
# Enable the master process manager. Disabled by default for maximum
# compatibility with CTRL+C, but should be enabled for use with
# --daemon and/or production deployments.
master: true
# Path to the application's Python virtual environment. If using Conda
# for Galaxy's framework dependencies (not tools!), do not set this.
virtualenv: /shared/Galaxy/.venv
# Path to the application's Python library.
pythonpath: lib
# The entry point which returns the web application (e.g. Galaxy,
# Reports, etc.) that you are loading.
module: galaxy.webapps.galaxy.buildapp:uwsgi_app()
# Mount the web application (e.g. Galaxy, Reports, etc.) at the given
# URL prefix. Cannot be used together with 'module:' above.
#mount: /galaxy=galaxy.webapps.galaxy.buildapp:uwsgi_app()
# Make uWSGI rewrite PATH_INFO and SCRIPT_NAME according to
# mount-points. Set this to true if a URL prefix is used.
manage-script-name: false
# It is usually a good idea to set this to ``true`` if processes is
# greater than 1.
thunder-lock: true
# Cause uWSGI to respect the traditional behavior of dying on SIGTERM
# (its default is to brutally reload workers)
die-on-term: true
# Cause uWSGI to gracefully reload workers and mules upon receipt of
# SIGINT (its default is to brutally kill workers)
hook-master-start: unix_signal:2 gracefully_kill_them_all
# Cause uWSGI to gracefully reload workers and mules upon receipt of
# SIGTERM (its default is to brutally kill workers)
hook-master-start: unix_signal:15 gracefully_kill_them_all
py-call-osafterfork: false
# Ensure application threads will run if `threads` is unset.
enable-threads: true
umask: 022
galaxy:
new_file_path: tmp
cluster_files_directory: sge
admin_users: azureuser
drmaa_external_runjob_script: sudo -E /shared/Galaxy/galaxy_env/bin/python3 /shared/Galaxy/galaxy-app/scripts/drmaa_external_runner.py
external_chown_script: sudo -E /shared/Galaxy/galaxy_env/bin/python3 /shared/Galaxy/galaxy-app/scripts/external_chown_script.py
real_system_username: username
Thanks and greetings
