Merge pull request #99 from glormph/deploy-change-to-different-setup-vms

Deploy change to different setup

deploy/analysis_deploy.yml

@@ -1,4 +1,15 @@
 ---
-- import_playbook: analysis_stop.yml
-- import_playbook: analysis_update.yml
-- import_playbook: analysis_start.yml
+- hosts: analysis
+  remote_user: "{{ analysis_connect_user }}"
+  tasks:
+    - name: Stop running workers
+      ansible.builtin.import_tasks:
+        file: stop_celery.yml
+
+    - name: Specific analysis tasks
+      ansible.builtin.import_tasks:
+        file: analysis_tasks.yml
+
+    - name: General kantele/celery updates
+      ansible.builtin.import_tasks:
+        file: update_analysis_storage_tasks.yml

deploy/analysis_from_scratch.yml

@@ -0,0 +1,56 @@
+---
+# Tasks to only run once when you get a provisioned VM
+# Installs packages, nextflow and prepares directories.
+#
+# Upgrading of these can later be done in another playbook (or in code)
+
+- hosts: analysis
+  remote_user: '{{ analysis_connect_user }}'
+  become: yes
+  tasks:
+    - name: Install packages
+      ansible.builtin.apt:
+        pkg:
+          - git
+          - docker.io
+          - docker-compose-v2
+          - default-jre-headless
+          - python3-venv
+          - libpq-dev
+          - python3-dev
+          - build-essential
+          - cifs-utils
+          - slurm-wlm
+          - slurm-client
+          - slurmdbd
+          - munge
+          - mariadb-server
+          - python3-mysqldb
+        state: present
+        update_cache: yes
+
+    - name: Create kantele group
+      ansible.builtin.group:
+        name: "{{ kantelegroup }}"
+        state: present
+
+    - name: Create kantele user
+      ansible.builtin.user:
+        name: "{{ kanteleuser }}"
+        group: "{{ kantelegroup }}"
+        create_home: yes
+
+    - name: Download nextflow
+      become_user: "{{ kanteleuser }}"
+      ansible.builtin.shell: 
+        cmd: "curl -s https://get.nextflow.io | bash"
+        chdir: "/home/{{ kanteleuser }}"
+
+    - name: Put NF in path
+      ansible.builtin.copy:
+        src: "/home/{{ kanteleuser }}/nextflow"
+        dest: /usr/local/bin/nextflow
+        mode: u=rwx,g=rx,a=rx
+        owner: kanteleadmin
+        group: kanteleadmin
+        remote_src: yes

deploy/analysis_tasks.yml

@@ -0,0 +1,104 @@
+---
+# Tasks for analysis node
+#
+- name: Create scratch dir for running
+  become: yes
+  ansible.builtin.file: 
+      path: "{{ baserun_dir }}"
+      state: directory
+      owner: "{{ kanteleuser }}"
+      group: "{{ kanteleuser }}"
+
+- name: Mount storages
+  become: yes
+  mount:
+      path: "{{ item.0 }}"
+      src: "{{ item.1 }}"
+      state: mounted
+      fstype: cifs
+      opts: "credentials={{ mount_cred }},uid={{ kanteleuser }},domain={{ mount_domain }}"
+  loop: "{{ storagedirs | zip(storageservers) | list }}"
+
+- name: Set mariaDB root password
+  become: yes
+  community.mysql.mysql_user:
+    name: root
+    host: "{{ item }}"
+    password: "{{ slurm_mysql_root_passwd }}"
+  with_items:
+    - localhost
+    # Default is no remote access, so do not set root password for below interfaces
+    #- 127.0.0.1
+    #- ::1
+
+- name: Set ~/.my.cnf file with root pass so prev task does not error on idempotent multiple runs
+  become: yes
+  template:
+    src: slurm_mariadb_my.cnf.j2
+    dest: /root/.my.cnf
+    mode: 0600
+
+- name: Slurm config file
+  become: yes
+  ansible.builtin.template:
+    src: slurm_conf.j2
+    dest: /etc/slurm/slurm.conf
+    mode: '755'
+    owner: slurm
+
+- name: Slurm DBD config file
+  become: yes
+  ansible.builtin.template:
+    src: slurmdbd.conf.j2
+    dest: /etc/slurm/slurmdbd.conf
+    mode: '600'
+    owner: slurm
+
+- name: Create Slurm dir in spool
+  become: yes
+  ansible.builtin.file: 
+      path: /var/spool/slurm
+      state: directory
+      owner: slurm
+      group: slurm
+
+- name: Set Slurm user in mariaDB
+  become: yes
+  community.mysql.mysql_user:
+    login_user: root
+    login_password: "{{ slurm_mysql_root_passwd }}"
+    host: localhost
+    name: slurm
+    password: "{{ slurm_mysql_user_passwd }}"
+    priv: 'slurm_acct.*:ALL'
+
+- name: Start Slurm
+  become: yes
+  systemd:
+      state: started 
+      enabled: true
+      daemon_reload: yes
+      name: "{{ item }}"
+  with_items:
+    - munge
+    - slurmctld
+    - slurmd
+    - slurmdbd
+
+- name: Get QOS in slurm
+  ansible.builtin.shell:
+    cmd: "sacctmgr show qos filter name=qc"
+  register: qos_qc
+
+- name: Set QOS in slurm if not set
+  become: yes
+  become_user: slurm
+  ansible.builtin.shell:
+    cmd: "{{ item }}"
+  # 3 lines if exists: headerfields, header-separator-horizontal-line, row-with-qc-qos
+  # so only run if 2 lines (no row-with-qc-qos)
+  when: qos_qc.stdout_lines | length == 2
+  # -i is for immediate (no prompt y/n)
+  with_items:
+    -  "sacctmgr -i add qos qc"
+    -  "sacctmgr -i modify qos qc set priority=100"

deploy/db-archive-restore.yml

@@ -1,9 +1,9 @@
 --- 
 # DB restoring on production from backup
 
-- hosts: kantele
+- hosts: web
   become: yes
-  become_user: '{{ web_user }}'
+  become_user: '{{ kanteleuser }}'
   tasks:
       - name: Remove running docker containers
         community.docker.docker_compose:

deploy/default_inventory/group_vars/all

@@ -6,55 +6,22 @@ mq_vhost: kantele_vhost
 rabbituser: kantele
 
 kanteledir: '{{ homedir }}/kantele'
+kantelevenv: "{{ kanteledir }}/venv"
 
+# DB accessed also from storage node for DB dumping
 kanteledb: kanteledb
 kanteledbuser: kanteleuser
-pgdatadir: "{{ homedir }}/pgdata"
-web_homedir: "/home/{{ web_user }}"
-host_pgbackup_path: "{{ web_homedir }}/pgbackups"
 
-compose_env_file: '{{ web_homedir }}/kantele/.compose.prod.env'
-
-tls_cert: server.crt
-tls_cert_key: server.key
-
-# DB backups in web container
+# DB dumping needs dir to dump in and uses compose so needs the env file
+host_pgbackup_path: "{{ homedir }}/pgbackups"
 container_backuppath: /pgbackups
+compose_env_file: '{{ homedir }}/kantele/.compose.prod.env'
 
-# Upload paths in nginx container
-container_uploadpath: /uploads
-host_uploadpath: "{{ kanteledir }}/uploads"
-upload_path_url: /uploads
-
-# Analysis paths in nginx container
-container_analysispath: /analysisfiles
-host_analysispath: "{{ kanteledir }}/srv_analysis"
-analysis_path_url: /analysisfiles
-
-# DEPRECATE if not used in backup DL script
-web_backupfolder: backups
-backup_dl_url: "https://{{ kantele_host }}{{ analysis_path_url }}/{{ web_backupfolder }}"
 
-storagesharenames: "storage,s3storage"
+celeryenv_file: "{{ kanteledir }}/celery.env"
+kantelelogdir: "{{ kanteledir }}/log"
 
-storage_env:
-    SECRET_KEY: "{{ secret_key }}"
-    PROTOCOL: https
-    KANTELEHOST: "{{ kantele_host }}"
-    RABBITHOST: "{{ kantele_host }}"
-    RABBIT_VHOST: '{{ mq_vhost }}'
-    RABBITPASS: "{{ amqppass }}"
-    RABBITUSER: "{{ rabbituser }}"
-    APIKEY: "{{ storage_apikey }}"
-    ADMIN_APIKEY: "{{ admin_apikey }}"
-    STORAGESHARENAMES: "{{ storagesharenames }}"
-    STORAGESHARES: "{{ storage_shares }}"
-    ANALYSISSHARE: "{{ analysis_share }}"
-    TMPSHARE: "{{ tmp_share }}"
-    MZMLINSHARE: "{{ mzml_in_share }}"
-    DSM_DIR: "{{ dsm_dir }}"
-    DATABASE_FTID: "{{ database_ftid }}" # for download/register ensembl
-    RSYNC_SSHPORT: 22 # ssh port on upload
-    RSYNC_SSHUSER: '{{ web_user }}'
-    RSYNC_SSHKEY: '{{ rsync_ssh_key }}'
-    PRIMARY_STORAGE: '{{ primary_storagename }}'
+queue_local: mv_md5_storage
+queue_dl: file_download
+queue_backup: backup_archive
+queue_scan: scaninbox

deploy/default_inventory/host_vars/analysis

@@ -0,0 +1 @@
+celery_env_template_file: celery_analysis_env.j2

deploy/default_inventory/host_vars/storadmin

@@ -0,0 +1,5 @@
+celery_env_template_file: celery_storage_env.j2
+
+tivoli_client_url: "https://aix.software.ibm.com/storage/tivoli-storage-management/maintenance/client/v8r1/Linux/LinuxX86_DEB/BA/v8122/8.1.22.0-TIV-TSMBAC-LinuxX86_DEB.tar"
+
+dsm_dir: "{{ homedir }}/dsmc_conf"