Private Documentation Usegalaxy Deployment

Infrastructure creation using Terraform

• install terraform
• clone the infrastructure repository
• source the openstack v2 auth file
• create the infrastructure using terraform init, terraform plan -o galaxy, terraform apply galaxy
• the command terraform output gives in output all the ip of the newly created virtual machines, that can be used to populate the Ansible inventory file in the next configuration step

Configuration using Ansible

Ansible installation

Ansible by installing ansible-core + needed collections in order to have a more stable system

Install ansible core on ubuntu 20.04

sudo apt update
sudo apt install python3-venv
python3 -m venv master_env/
. master_env/bin/activate
pip install wheel ansible-core==2.11.3

Download roles and collections needed

git clone https://github.com/pmandreoli/infrastructure-playbook.git
git checkout dev_it
ansible-galaxy install -r requirements.yaml # install required collections and roles

Infrastructure-playbook

configuration

• hosts inventory file containing each infrastructure element created using Terraform
• yml files playbook to configure the services
• group_vars directory containing for each service a .yml file with variables
• secret_group_vars containing for the services that need secrets, the secret itself are encrypted using Ansible vault
• templates containing the configuration files to be created by each playbook/role
• roles Ansible role dir
• collection Ansible galaxy connection needed

services to configure

1. NFS
2. Postgresql
3. Rabbitmq
4. Galaxy
5. Nginx

NFS

to run proper job on the htcondor cluster the galaxy machine and condor workers has to share 2 main dir on NFS:

• /data/share
• /opt/galaxy

df -h result on the galaxy VM

Filesystem                 Size  Used Avail Use% Mounted on
devtmpfs                   3.9G     0  3.9G   0% /dev
tmpfs                      3.9G     0  3.9G   0% /dev/shm
tmpfs                      3.9G  656K  3.9G   1% /run
tmpfs                      3.9G     0  3.9G   0% /sys/fs/cgroup
/dev/vda2                   20G   15G  5.8G  72% /
172.30.16.133:/data/share  200G  2.7G  198G   2% /data/share
tmpfs                      783M     0  783M   0% /run/user/1000
172.30.16.133:/opt/galaxy   20G   13G  7.4G  64% /opt/galaxy

after the creation of the NFS you can mount it by using the mount.yml playbook

the configuration of the nfs, in order to allow to galaxy user and condor to write on that, is:

• /etc/exports

/data/share *(rw,sync,no_root_squash)
/opt/galaxy *(rw,sync,no_root_squash)

Postgresql

ansible-playbook --private-key ~/.ssh/ssh-priv.key -i hosts database.yml

control if postgresql is active and running on the database machine

# nmap -v -p 5432 127.0.0.1

Starting Nmap 7.60 ( https://nmap.org ) at 2022-10-12 14:06 UTC
Initiating SYN Stealth Scan at 14:06
Scanning localhost (127.0.0.1) [1 port]
Discovered open port 5432/tcp on 127.0.0.1
Completed SYN Stealth Scan at 14:06, 0.23s elapsed (1 total ports)
Nmap scan report for localhost (127.0.0.1)
Host is up (0.00024s latency).

PORT     STATE SERVICE
5432/tcp open  postgresql

Read data files from: /usr/bin/../share/nmap
Nmap done: 1 IP address (1 host up) scanned in 0.33 seconds
           Raw packets sent: 1 (44B) | Rcvd: 2 (88B)

control postgres configuration files /etc/postgresql/12/main/pg_hba.conf

## This file is maintained by Ansible - CHANGES WILL BE OVERWRITTEN
##

# DO NOT DISABLE!
# If you change this first entry you will need to make sure that the
# database superuser can access the database using some other method.
# Noninteractive access to all databases is required during automatic
# maintenance (custom daily cronjobs, replication, and similar tasks).
#
# Database administrative login by Unix domain socket
local   all             postgres                                peer

# "local" is for Unix domain socket connections only
local   all             all                                     peer
# IPv4 local connections:
host    all             all             127.0.0.1/32            md5
# IPv6 local connections:
host    all             all             ::1/128                 md5

# Entries configured in postgresql_pg_hba_conf follow

host    all             all        172.30.16.130/24              md5

• 172.30.16.130/24 is the galaxy private network /etc/postgresql/12/main/conf.d/25ansible_postgresql.conf contains:

listen_addresses = '<postgresql ip>'

secret_group_vars needed:

_galaxy_db_pass: "<passwd>"
_galaxy_db_host: "<database-ip>"
_galaxy_db_name: <db_name>
_galaxy_db_user: <db_user>
_galaxy_db_port: <db_port>


galaxy_db_connection: "postgresql://{{ _galaxy_db_user }}:{{ _galaxy_db_pass }}@{{ _galaxy_db_host }}/{{ _galaxy_db_name }}"
postgres_pass: "{{ _galaxy_db_pass }}"

RabbitMQ

ansible-playbook --private-key ~/.ssh/ssh-priv.key -i hosts rabbitmq.yml

check if created certificate are visible and mounted on the rabbitmq container to debug ssl connection check the throubleshooting doc rabbit will be installed and run on a the official docker container on the rabbitmq host check rabbit log:

docker logs rabbit_hole

check if the users were correctly created, in the docker container:

sudo rabbitmqctl authenticate_user <username> <password>

Galaxy

for python_macros and python-devel-2.7.5-80.el7_6.x86_64 conflicts: yum --enablerepo=cr update

ansible-playbook --private-key <key> -i hosts sn06.yml --extra-vars "__galaxy_dir_perms='0755'"

secret_group_vars the playbook includes both the db_main.yml and the all.yml:

• all.yml

---
galaxysession_cookie: test1
vault_sign_pass_secret: <random>

# rabbitmq
rabbitmq_password_galaxy: <rnadom>

# galaxy
galaxy_db_connection_ro: "<random>"

# proftpd
proftpd__galaxy_db_connection: "test6"

smtp_username: "<smtp server username>"
smtp_password: "<random>"


admin_users:
 - "<email>"

id_secret: "<random>"
certbot_admin_email: "<email>"
gapars_nginx_config: ""

⚠️ The installation do not set the nginx upload module, the nginx configuration has been modified

---

GALAXY troubleshooting

using journalctl check the galaxy unit

journalctl -fu galaxy-zergling*

---

Galaxy Managing storage

the storage is defined and managed by the file

/opt/galaxy/config/object_store_conf.xml this file is used to manage different object storages

<?xml version="1.0"?>
<object_store type="distributed" id="primary" order="0">
    <backends>
        <backend id="files11" type="disk" weight="1" store_by="uuid">
        <!-- galaxy-it  <files_dir path="/data/dnb05/galaxy_db/files"/>-->
        <files_dir path="/data/share/galaxy_db/files"/>
            <extra_dir type="temp" path="/data/share/jwd/tmp"/>
            <extra_dir type="job_work" path="/data/share/jwd/main"/>
        </backend>
        <backend id="secondary" type="disk" weight="0" store_by="id">
            <files_dir path="/data/0/galaxy_db/files"/>
            <extra_dir type="temp" path="/data/2/galaxy_db/tmp"/>
            <extra_dir type="job_work" path="/data/share/jwd/main"/>
        </backend>
    </backends>
</object_store> 

the tag weight determines where Galaxy write more is high more high is the priority

Sorting hat

source-code

location in galaxy at /opt/galaxy/dynamic_rules/usegalaxy

• destination_specifications.yaml -> definition of jobs destinations both local that on pulsar
• joint_destinations.yaml -> specific pulsar
• sorting_hat.py -> sorting hat executable
• sorting_hat.yaml -> specific configuration sorting hat
• tool_destinations.yaml -> tools requirements es: core, ram, gpus

Galaxy mantainment

tutorials

crontab jobs on the usegalaxy.eu

root@sn06:~$ crontab -l
#Ansible: Restart workflow schedulers
0 4 * * * /bin/bash -c 'for (( c=0; c<3; c++ )); do systemctl restart galaxy-workflow-scheduler@$c && sleep 240; done'
#Ansible: Restart handlers
0 3 * * * /bin/bash -c 'for (( c=0; c<6; c++ )); do systemctl restart galaxy-handler@$c && sleep 240; done'
#Ansible: Restart zerglings
30 3 * * * /bin/bash -c 'for (( c=0; c<6; c++ )); do systemctl restart galaxy-zergling@$c && sleep 240; done'
#Ansible: Clean up old logs
0 0 * * * journalctl --vacuum-time=1d -u galaxy-zergling@* galaxy-handler@* 2>/dev/null
#Ansible: Certbot automatic renewal.
40 20 * * * /opt/certbot/bin/certbot renew --quiet --no-self-upgrade 

galaxy@sn06:~$ crontab -l
#Ansible: Fix ftp
*/15 * * * * /usr/bin/fix-ftp
#Ansible: Fix unscheduled jobs
*/20 * * * * /usr/bin/galaxy-fix-unscheduled-jobs
#Ansible: Remove old FTP data
0 1 * * * cd "/data/jwd/incoming" && find . -type f -not -newermt "3 months ago" -exec rm '{}' +
#Ansible: Fix Missing API keys for IE users
*/5 * * * * /usr/bin/galaxy-fix-missing-api-keys
#Ansible: Recalculate user quotas
15 22 * * * /usr/bin/galaxy-fix-user-quotas
#Ansible: Attribute ELIXIR quota to ELIXIR AAI users
14 22 * * * /usr/bin/galaxy-fix-elixir-user-quotas
#Ansible: Slurp daily Galaxy stats into InfluxDB
0 0 * * * /usr/bin/galaxy-slurp
#Ansible: Slurp up-to-today galaxy stats into InfluxDB upto version
0 4 * * * /usr/bin/galaxy-slurp-upto
#Ansible: Condor maintenance tasks submitter
0 23 * * * /data/dnb01/maintenance/htcondor_crontab_scheduling_submitter.sh
#Ansible: Gxadmin Galaxy clean up
0 */6 * * * /usr/bin/env GDPR_MODE=1 PGUSER=galaxy PGHOST=sn05.galaxyproject.eu GALAXY_ROOT=/opt/galaxy/server GALAXY_CONFIG_FILE=/opt/galaxy/config/galaxy.yml GALAXY_LOG_DIR=/var/log/galaxy GXADMIN_PYTHON=/opt/galaxy/venv/bin/python /usr/bin/gxadmin galaxy cleanup 60
#Ansible: Docker clean up
30 2 * * * . /opt/galaxy/.bashrc && docker system prune -f > /dev/null

#Ansible: Call sync-to-nfs
30 2 * * * /usr/bin/galaxy-sync-to-nfs
#Ansible: Condor release held jobs increasing memory
*/15 * * * * /usr/bin/htcondor-release-held-jobs

gxadmin is widley used for the manteniance e.g:

gxadmin galaxy_cleanup 60 delete datasets older than 60 days

PULSAR configuration

connection with pulsar

message_queue_url: {{ message_queue_url }}

each manager is a instance

galaxy config