The tools that are added to Galaxy can have a wide variance in the compute resources that they require and work efficiently on. To account for this, Galaxy’s job configuration needs to be tuned to run these tools properly. In addition, site-specific variables must be taken into consideration when choosing where to run jobs and what parameters to run them with.

Comment: Results may vary

Your results may be slightly different from the ones presented in this tutorial due to differing versions of tools, reference data, external databases, or because of stochastic processes in the algorithms.

Agenda

1. Installing Slurm
2. Using Slurm
3. Slurm-DRMAA
4. Galaxy and Slurm
   1. Running a Job
5. Recording Job Metrics
   1. Setting up Galaxy
   2. Generating Metrics
   3. What should I collect?
   4. Accessing the data
   5. Further Reading

Comment: Galaxy Admin Training Path

The yearly Galaxy Admin Training follows a specific ordering of tutorials. Use this timeline to help keep track of where you are in Galaxy Admin Training.

1. Step 1
   ansible-galaxy
2. Step 2
   backup-cleanup
3. Step 3
   customization
4. Step 4
   tus
5. Step 5
   cvmfs
6. Step 6
   apptainer
7. Step 7
   tool-management
8. Step 8
   reference-genomes
9. Step 9
   data-library
10. Step 10
    dev/bioblend-api
11. Step 11
    connect-to-compute-cluster
12. Step 12
    job-destinations
13. Step 13
    pulsar
14. Step 14
    celery
15. Step 15
    gxadmin
16. Step 16
    reports
17. Step 17
    monitoring
18. Step 18
    tiaas
19. Step 19
    sentry
20. Step 20
    ftp
21. Step 21
    beacon

Installing Slurm

Comment: Ansible Best Practices

If you’ve set up your Galaxy server using the Galaxy Installation with Ansible tutorial, you will have created a galaxyservers group in your inventory file, hosts, and placed your variables in group_vars/galaxyservers.yml. Although for the purposes of this tutorial, the Galaxy server and Slurm controller/node are one and the same, in a real world deployment they are very likely to be different hosts. We will continue to use the galaxyservers group for simplicity, but in your own deployment you should consider creating some additional groups for Slurm controller(s), Slurm nodes, and Slurm clients.

Tip: Do you need a DRM?

If you have a smaller server, do you still need a DRM? Yes! You should definitely run Slurm or a similar option. If you don’t, as soon as you restart Galaxy with local runners, any running jobs will be killed. Even with a handful of users, it is a good idea to keep 1-2 CPU cores/4GB RAM reserved for Galaxy.

Hands-on: Installing Slurm

1. Edit your requirements.yml and include the following contents:

   --- a/requirements.yml
   +++ b/requirements.yml
   @@ -23,3 +23,8 @@
    # Singularity/Apptainer
    - src: usegalaxy_eu.apptainer
      version: 0.0.1
   +# SLURM as our DRM
   +- src: galaxyproject.repos
   +  version: 0.0.3
   +- src: galaxyproject.slurm
   +  version: 1.0.2
      
   

   Tip: How to read a Diff

   If you haven’t worked with diffs before, this can be something quite new or different.

   If we have two files, let’s say a grocery list, in two files. We’ll call them ‘a’ and ‘b’.

   Input: Old

   $ cat old
   🍎
   🍐
   🍊
   🍋
   🍒
   🥑
   

   Output: New

   $ cat new
   🍎
   🍐
   🍊
   🍋
   🍍
   🥑
   

   We can see that they have some different entries. We’ve removed 🍒 because they’re awful, and replaced them with an 🍍

   Diff lets us compare these files

   $ diff old new
   5c5
   < 🍒
   ---
   > 🍍
   

   Here we see that 🍒 is only in a, and 🍍 is only in b. But otherwise the files are identical.

   There are a couple different formats to diffs, one is the ‘unified diff’

   $ diff -U2 old new
   --- old	2022-02-16 14:06:19.697132568 +0100
   +++ new	2022-02-16 14:06:36.340962616 +0100
   @@ -3,4 +3,4 @@
    🍊
    🍋
   -🍒
   +🍍
    🥑
   

   This is basically what you see in the training materials which gives you a lot of context about the changes:

   • --- old is the ‘old’ file in our view
   • +++ new is the ‘new’ file
   • @@ these lines tell us where the change occurs and how many lines are added or removed.
   • Lines starting with a - are removed from our ‘new’ file
   • Lines with a + have been added.

   So when you go to apply these diffs to your files in the training:

   1. Ignore the header
   2. Remove lines starting with - from your file
   3. Add lines starting with + to your file

   The other lines (🍊/🍋 and 🥑) above just provide “context”, they help you know where a change belongs in a file, but should not be edited when you’re making the above change. Given the above diff, you would find a line with a 🍒, and replace it with a 🍍

   Added & Removed Lines

   Removals are very easy to spot, we just have removed lines

   --- old	2022-02-16 14:06:19.697132568 +0100
   +++ new	2022-02-16 14:10:14.370722802 +0100
   @@ -4,3 +4,2 @@
    🍋
    🍒
   -🥑
   

   And additions likewise are very easy, just add a new line, between the other lines in your file.

   --- old	2022-02-16 14:06:19.697132568 +0100
   +++ new	2022-02-16 14:11:11.422135393 +0100
   @@ -1,3 +1,4 @@
    🍎
   +🍍
    🍐
    🍊
   

   Completely new files

   Completely new files look a bit different, there the “old” file is /dev/null, the empty file in a Linux machine.

   $ diff -U2 /dev/null old
   --- /dev/null	2022-02-15 11:47:16.100000270 +0100
   +++ old	2022-02-16 14:06:19.697132568 +0100
   @@ -0,0 +1,6 @@
   +🍎
   +🍐
   +🍊
   +🍋
   +🍒
   +🥑
   

   And removed files are similar, except with the new file being /dev/null

   --- old	2022-02-16 14:06:19.697132568 +0100
   +++ /dev/null	2022-02-15 11:47:16.100000270 +0100
   @@ -1,6 +0,0 @@
   -🍎
   -🍐
   -🍊
   -🍋
   -🍒
   -🥑
   

   The galaxyproject.repos role adds the Galaxy Packages for Enterprise Linux (GPEL) repository for RedHat/CentOS, which provides both Slurm and Slurm-DRMAA (neither are available in standard repositories or EPEL). For Ubuntu versions 18.04 or newer, it adds the Slurm-DRMAA PPA (Slurm-DRMAA was removed from Debian/Ubuntu in buster/bionic).

2. In the same directory, run:

   Input: Bash

   ansible-galaxy install -p roles -r requirements.yml
   

3. Add galaxyproject.repos, galaxyproject.slurm to the beginning of your roles section in your galaxy.yml playbook:

   --- a/galaxy.yml
   +++ b/galaxy.yml
   @@ -34,6 +34,8 @@
            dest: /libraries/
      roles:
        - galaxyproject.tusd
   +    - galaxyproject.repos
   +    - galaxyproject.slurm
        - usegalaxy_eu.apptainer
        - galaxyproject.galaxy
        - role: galaxyproject.miniconda
      
   

4. Add the slurm variables to your group_vars/galaxyservers.yml:

   --- a/group_vars/galaxyservers.yml
   +++ b/group_vars/galaxyservers.yml
   @@ -194,6 +194,16 @@ nginx_ssl_role: usegalaxy_eu.certbot
    nginx_conf_ssl_certificate: /etc/ssl/certs/fullchain.pem
    nginx_conf_ssl_certificate_key: /etc/ssl/user/privkey-www-data.pem
   
   +# Slurm
   +slurm_roles: ['controller', 'exec'] # Which roles should the machine play? exec are execution hosts.
   +slurm_nodes:
   +- name: localhost # Name of our host
   +  CPUs: 2         # Here you would need to figure out how many cores your machine has. For this training we will use 2 but in real life, look at `htop` or similar.
   +slurm_config:
   +  SlurmdParameters: config_overrides   # Ignore errors if the host actually has cores != 2
   +  SelectType: select/cons_res
   +  SelectTypeParameters: CR_CPU_Memory  # Allocate individual cores/memory instead of entire node
   +
    # TUS
    galaxy_tusd_port: 1080
    galaxy_tus_upload_store: /data/tus
      
   

5. Run the playbook

   Input: Bash

   ansible-playbook galaxy.yml
   

Note that the above Slurm config options are only those that are useful for this training exercise. In production, you would want to use a more appropriate configuration specific to your cluster (and setting SlurmdParameters to config_overrides is not recommended).

Installed with Slurm is MUNGE (MUNGE Uid ‘N Gid Emporium…) which authenticates users between cluster hosts. You would normally need to ensure the same Munge key is distributed across all cluster hosts (in /etc/munge/munge.key) - A great task for Ansible. However, the installation of the munge package has created a random key for you, and you will not need to distribute this since you’ll run jobs only on a single host.

You can now check that all of the daemons are running with the command systemctl status munge slurmd slurmctld

$ sudo systemctl status munge slurmd slurmctld
● munge.service - MUNGE authentication service
  Loaded: loaded (/usr/lib/systemd/system/munge.service; enabled; vendor preset: disabled)
   Active: active (running) since Sa 2019-01-26 22:38:13 CET; 28min ago
     Docs: man:munged(8)
 Main PID: 22930 (munged)
    Tasks: 4
   Memory: 128.0K
   CGroup: /system.slice/munge.service
           └─22930 /usr/sbin/munged

Jan 26 22:38:13 helena-test.novalocal systemd[1]: Starting MUNGE authentication service...
Jan 26 22:38:13 helena-test.novalocal systemd[1]: Started MUNGE authentication service.

● slurmd.service - Slurm node daemon
   Loaded: loaded (/usr/lib/systemd/system/slurmd.service; enabled; vendor preset: disabled)
   Active: active (running) since Sa 2019-01-26 23:04:21 CET; 2min 25s ago
  Process: 15051 ExecStart=/usr/sbin/slurmd $SLURMD_OPTIONS (code=exited, status=0/SUCCESS)
 Main PID: 15054 (slurmd)
    Tasks: 1
   Memory: 628.0K
   CGroup: /system.slice/slurmd.service
           └─15054 /usr/sbin/slurmd

Jan 26 23:04:21 helena-test.novalocal systemd[1]: Starting Slurm node daemon...
Jan 26 23:04:21 helena-test.novalocal systemd[1]: PID file /var/run/slurmd.pid not readable (yet?) after start.
Jan 26 23:04:21 helena-test.novalocal systemd[1]: Started Slurm node daemon.

● slurmctld.service - Slurm controller daemon
   Loaded: loaded (/usr/lib/systemd/system/slurmctld.service; enabled; vendor preset: disabled)
   Active: active (running) since Sa 2019-01-26 23:04:20 CET; 2min 26s ago
  Process: 15040 ExecStart=/usr/sbin/slurmctld $SLURMCTLD_OPTIONS (code=exited, status=0/SUCCESS)
 Main PID: 15042 (slurmctld)
    Tasks: 7
   Memory: 1.1M
   CGroup: /system.slice/slurmctld.service
           └─15042 /usr/sbin/slurmctld

Jan 26 23:04:20 helena-test.novalocal systemd[1]: Starting Slurm controller daemon...
Jan 26 23:04:20 helena-test.novalocal systemd[1]: PID file /var/run/slurmctld.pid not readable (yet?) after start.
Jan 26 23:04:20 helena-test.novalocal systemd[1]: Started Slurm controller daemon.

Running the playbook, the Slurm configuration, /etc/slurm/slurm.conf (or /etc/slurm-llnl/slurm.conf on Debian-based distributions) was created for you automatically. All of the variables were set by default. If you need to override the configuration yourself, Slurm provides an online tool which will help you configure it.

Using Slurm

You should now be able to see that your Slurm cluster is operational with the sinfo command. This shows the state of nodes and partitions (synonymous with queues in other DRMs). The “node-oriented view” provided with the -N flag is particularly useful:

$ sinfo
PARTITION AVAIL  TIMELIMIT  NODES  STATE NODELIST
debug*       up   infinite      1   idle localhost
$ sinfo -Nel
Fri Nov  4 16:51:24 2016
NODELIST   NODES PARTITION       STATE CPUS    S:C:T MEMORY TMP_DISK WEIGHT FEATURES REASON
localhost      1    debug*        idle    1    2:1:1      1        0      1   (null) none

If your node state is not idle, something has gone wrong. If your node state ends with an asterisk *, the Slurm controller is attempting to contact the Slurm execution daemon but has not yet been successful (the * next to the partition name is normal, it indicates the default partition).

We want to ensure that Slurm is actually able to run jobs. There are two ways this can be done:

• srun: Run an interactive job (e.g. a shell, or a specific program with its stdin, stdout, and stderr all connected to your terminal.
• sbatch: Run a batch job, with stdin closed and stdout/stderr redirected to a file.

Galaxy runs sbatch jobs but we can use both srun and sbatch to test:

Hands-on: Running commands with `srun`

1. Use srun to run the command uname -a

   Input: Bash

   srun uname -a
   

   Output

   Your output may look slightly different:

   $ srun uname -a
   Linux gat-1.oz.training.galaxyproject.eu 5.4.0-48-generic #52-Ubuntu SMP Thu Sep 10 10:58:49 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
   

Although it looks like this command ran as if I had not used srun, it was in fact routed through Slurm.

Hands-on: Running commands with `sbatch`

1. Create a test job script somewhere, such as in ~/sbatch-test.sh. It should be a batch script which runs uname -a, uptime, and sleeps for 30 seconds.

   Question

   What does your shell script look like?

   Solution

   #!/bin/bash
   uname -a
   uptime
   sleep 30
   

2. Make the script executable:

   Input: Bash

   chmod +x ~/sbatch-test.sh
   

3. Use sbatch to submit the job script

   Question

   What command did you run?

   Solution

   $ sbatch ~/sbatch-test.sh
   

4. Use squeue to check the queue

   Input: Bash

   squeue
   

   Output

   Your output may look slightly different:

   JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
      3     debug sbatch-t   ubuntu  R       0:22      1 localhost
   

If you’ve made it this far, your Slurm installation is working!

Slurm-DRMAA

Above Slurm in the stack is slurm-drmaa, a library that provides a translational interface from the Slurm API to the generalized DRMAA API in C.

Hands-on: Installing Slurm-DRMAA

1. Add a post_task to your playbook to install slurm-drmaa1 (Debian/Ubuntu) or slurm-drmaa (RedHat/CentOS).

   --- a/galaxy.yml
   +++ b/galaxy.yml
   @@ -52,3 +52,6 @@
            minute: "0"
            hour: "0"
            job: "SHELL=/bin/bash source {{ galaxy_venv_dir }}/bin/activate &&  GALAXY_LOG_DIR=/tmp/gxadmin/ GALAXY_ROOT={{ galaxy_root }}/server GALAXY_CONFIG_FILE={{ galaxy_config_file }} /usr/local/bin/gxadmin galaxy cleanup 60"
   +    - name: Install slurm-drmaa
   +      package:
   +        name: slurm-drmaa1
      
   

2. Run the playbook (ansible-playbook galaxy.yml)

   Input: Bash

   ansible-playbook galaxy.yml
   

Moving one level further up the stack, we find DRMAA Python. This is a Galaxy framework conditional dependency. Conditional dependencies are only installed if, during startup, a configuration option is set that requires that dependency. The galaxyproject.galaxy Ansible role will install these conditional dependencies, automatically.

Galaxy and Slurm

At the top of the stack sits Galaxy. Galaxy must now be configured to use the cluster we’ve just set up. The DRMAA Python documentation (and Galaxy’s own documentation) instruct that you should set the $DRMAA_LIBRARY_PATH environment variable so that DRMAA Python can find libdrmaa.so (aka slurm-drmaa). Because Galaxy runs under systemd, the environment that Galaxy starts under is controlled by the environment option in systemd service unit that the ansible role manages. The galaxy task should thus be updated to refer to the path to slurm-drmaa, which is /usr/lib/slurm-drmaa/lib/libdrmaa.so.1:

Hands-on: Making Galaxy aware of DRMAA

1. We need to configure the Slurm job runner. First, we instruct Galaxy’s job handlers to load the Slurm job runner plugin, and set the Slurm job submission parameters. A job runner plugin definition must have a unique name as its key, and a load attribute. Since we already have a good default destination that uses singularity, we will simply modify that to use the slurm runner. Galaxy will do the equivalent of submitting a job as sbatch /path/to/job_script.sh. In a job environment, the key is a unique identifier for that environment and the runner attribute must match the key of a defined runner plugin:

   --- a/group_vars/galaxyservers.yml
   +++ b/group_vars/galaxyservers.yml
   @@ -18,14 +18,27 @@ galaxy_job_config:
        local_runner:
          load: galaxy.jobs.runners.local:LocalJobRunner
          workers: 4
   +    slurm:
   +      load: galaxy.jobs.runners.slurm:SlurmJobRunner
   +      drmaa_library_path: /usr/lib/slurm-drmaa/lib/libdrmaa.so.1
      handling:
        assign: ['db-skip-locked']
      execution:
   -    default: singularity
   +    default: slurm
        environments:
          local_env:
            runner: local_runner
            tmp_dir: true
   +      slurm:
   +        runner: slurm
   +        singularity_enabled: true
   +        env:
   +        - name: LC_ALL
   +          value: C
   +        - name: APPTAINER_CACHEDIR
   +          value: /tmp/singularity
   +        - name: APPTAINER_TMPDIR
   +          value: /tmp
          singularity:
            runner: local_runner
            singularity_enabled: true
      
   

2. Run your Galaxy playbook

   Input: Bash

   ansible-playbook galaxy.yml
   

3. Watch the logs to check that everything loads correctly

   Input: Bash

   journalctl -f -u 'galaxy-*'
   

   Output

   Your output may look slightly different:

   Jan 12 15:46:01 gat-1.oz.training.galaxyproject.eu gunicorn[1821134]: galaxy.jobs.runners DEBUG 2021-01-12 15:46:01,109 [p:1821134,w:0,m:1] [MainThread] Starting 4 SlurmRunner workers
   Jan 12 15:46:01 gat-1.oz.training.galaxyproject.eu gunicorn[1821134]: galaxy.jobs DEBUG 2021-01-12 15:46:01,110 [p:1821134,w:0,m:1] [MainThread] Loaded job runner 'galaxy.jobs.runners.slurm:SlurmJobRunner' as 'slurm'
   

Running a Job

You should now be able to run a Galaxy job through Slurm. The simplest way to test is using the digest tool to calculate an md5sum.

Hands-on: Testing a Slurm Job

1. If you’re not still following the log files with journalctl, do so now.

   Input: Bash

   journalctl -f -u 'galaxy-*'
   

2. Click the upload button at the top of the tool panel (on the left side of the Galaxy UI).
3. In the resulting modal dialog, click the “Paste/Fetch data” button.
4. Type some random characters into the text field that has just appeared.
5. Click “Start” and then “Close”

6. Open Secure Hash / Message Digest tool

   Output

   Your output may look slightly different. In your journalctl terminal window you should see the following messages:

   galaxy.jobs.mapper DEBUG 2020-02-10 09:37:17,946 [p:9859,w:0,m:2] [JobHandlerQueue.monitor_thread] (1) Mapped job to destination id: slurm
   galaxy.jobs.handler DEBUG 2020-02-10 09:37:17,976 [p:9859,w:0,m:2] [JobHandlerQueue.monitor_thread] (1) Dispatching to slurm runner
   galaxy.jobs DEBUG 2020-02-10 09:37:18,016 [p:9859,w:0,m:2] [JobHandlerQueue.monitor_thread] (1) Persisting job destination (destination id: slurm)
   galaxy.jobs DEBUG 2020-02-10 09:37:18,021 [p:9859,w:0,m:2] [JobHandlerQueue.monitor_thread] (1) Working directory for job is: /srv/galaxy/jobs/000/1
   galaxy.jobs.runners DEBUG 2020-02-10 09:37:18,358 [p:9859,w:0,m:2] [JobHandlerQueue.monitor_thread] Job [1] queued (380.809 ms)
   galaxy.jobs.handler INFO 2020-02-10 09:37:18,372 [p:9859,w:0,m:2] [JobHandlerQueue.monitor_thread] (1) Job dispatched
   galaxy.jobs.command_factory INFO 2020-02-10 09:37:18,564 [p:9859,w:0,m:2] [SlurmRunner.work_thread-0] Built script [/srv/galaxy/jobs/000/1/tool_script.sh] for tool command [python '/srv/galaxy/server/tools/data_source/upload.py' /srv/galaxy/server /srv/galaxy/jobs/000/1/registry.xml /srv/galaxy/jobs/000/1/upload_params.json 1:/srv/galaxy/jobs/000/1/working/dataset_1_files:/data/000/dataset_1.dat]
   ...
   galaxy.jobs.runners.drmaa DEBUG 2020-02-10 09:37:18,645 [p:9859,w:0,m:2] [SlurmRunner.work_thread-0] (1) submitting file /srv/galaxy/jobs/000/1/galaxy_1.sh
   galaxy.jobs.runners.drmaa INFO 2020-02-10 09:37:18,654 [p:9859,w:0,m:2] [SlurmRunner.work_thread-0] (1) queued as 4
   galaxy.jobs DEBUG 2020-02-10 09:37:18,654 [p:9859,w:0,m:2] [SlurmRunner.work_thread-0] (1) Persisting job destination (destination id: slurm)
   

   At this point the job has been accepted by Slurm and is awaiting scheduling on a node. Once it’s been sent to a node and starts running, Galaxy logs this event:

   galaxy.jobs.runners.drmaa DEBUG 2020-02-10 09:37:19,537 [p:9859,w:0,m:2] [SlurmRunner.monitor_thread] (1/4) state change: job is running
   

   Finally, when the job is complete, Galaxy performs its job finalization process:

   galaxy.jobs.runners.drmaa DEBUG 2020-02-10 09:37:24,700 [p:9859,w:0,m:2] [SlurmRunner.monitor_thread] (1/4) state change: job finished normally
   galaxy.model.metadata DEBUG 2020-02-10 09:37:24,788 [p:9859,w:0,m:2] [SlurmRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 1
   galaxy.jobs INFO 2020-02-10 09:37:24,883 [p:9859,w:0,m:2] [SlurmRunner.work_thread-1] Collecting metrics for Job 1 in /srv/galaxy/jobs/000/1
   galaxy.jobs DEBUG 2020-02-10 09:37:24,917 [p:9859,w:0,m:2] [SlurmRunner.work_thread-1] job_wrapper.finish for job 1 executed (154.514 ms)
   

   Note a few useful bits in the output:

   • Persisting job destination (destination id: slurm): Galaxy has selected the slurm destination we defined
   • submitting file /srv/galaxy/server/database/jobs/000/2/galaxy_2.sh: This is the path to the script that is submitted to Slurm as it would be with sbatch
   • (1) queued as 4: Galaxy job id “1” is Slurm job id “4”, this can also be seen with the (1/4) in other output lines.
   • If job <id> ended is reached, the job should show as done in the UI

1-test-cat1.sh

Slurm allows us to query the exit state of jobs for a time period of the value of Slurm’s MinJobAge option, which defaults to 300 (seconds, == 5 minutes):

Input: Bash

Your job number is potentially different.

scontrol show job 4

Output

Your output may also look slightly different:

JobId=4 JobName=g1_upload1_admin_example_org
   UserId=galaxy(999) GroupId=galaxy(999) MCS_label=N/A
   Priority=4294901757 Nice=0 Account=(null) QOS=(null)
   JobState=COMPLETED Reason=None Dependency=(null)
   Requeue=1 Restarts=0 BatchFlag=1 Reboot=0 ExitCode=0:0
   RunTime=00:00:05 TimeLimit=UNLIMITED TimeMin=N/A
   SubmitTime=2020-02-10T09:37:18 EligibleTime=2020-02-10T09:37:18
   StartTime=2020-02-10T09:37:19 EndTime=2020-02-10T09:37:24 Deadline=N/A
   PreemptTime=None SuspendTime=None SecsPreSuspend=0
   LastSchedEval=2020-02-10T09:37:19
   Partition=debug AllocNode:Sid=gcc-1:9453
   ReqNodeList=(null) ExcNodeList=(null)
   NodeList=localhost
   BatchHost=localhost
   NumNodes=1 NumCPUs=1 NumTasks=1 CPUs/Task=1 ReqB:S:C:T=0:0:*:*
   TRES=cpu=1,mem=1M,node=1,billing=1
   Socks/Node=* NtasksPerN:B:S:C=0:0:*:* CoreSpec=*
   MinCPUsNode=1 MinMemoryNode=1M MinTmpDiskNode=0
   Features=(null) DelayBoot=00:00:00
   Gres=(null) Reservation=(null)
   OverSubscribe=OK Contiguous=0 Licenses=(null) Network=(null)
   Command=(null)
   WorkDir=/srv/galaxy/jobs/000/1
   StdErr=/srv/galaxy/jobs/000/1/galaxy_1.e
   StdIn=StdIn=/dev/null
   StdOut=/srv/galaxy/jobs/000/1/galaxy_1.o
   Power=

After the job has been purged from the active jobs database, a bit of information (but not as much as scontrol provides) can be retrieved from Slurm’s logs. However, it’s a good idea to set up Slurm’s accounting database to keep old job information in a queryable format.

Tip: Which directories need to be shared on a cluster?

The following directories need to be accesible via the same path on both the head node and compute nodes:

• galaxy_shed_tools_dir
• galaxy_tool_dependency_dir
• galaxy_file_path
• galaxy_job_working_directory
• galaxy_server_dir
• galaxy_venv_dir

Recording Job Metrics

Job metrics record properties of the jobs that are executed, information that can help you plan for trainings or plan capacity for further expansions of your Galaxy server. These properties include details such as the number of slots (cores) assigned to a job, the amount of memory available, details about the node on which the job executed, environment variables that were set at execution time, and more.

Galaxy collects and records very few job metrics by default, enabling more metrics plugins is recommended for any cluster-enabled Galaxy deployment. The metrics are stored in the Galaxy database, which can be queried externally to generate reports and debug job problems.

Some work has been done to try to analyse job runtime metrics to optimise cluster allocation based on job inputs, and enhance job submission (Tyryshkina et al. 2019). More work will be done in this area.

Comment: Note

Job metrics are only visible to Galaxy admin users, unless you set expose_potentially_sensitive_job_metrics: true, like UseGalaxy.eu does. EU’s intention with this is to empower users and make everything as transparent as possible.

This is the only option controlling which metrics general users see. Admins see all metrics collected, and by default general users see none. However most of the metrics exposed by this setting are quite safe (e.g. cgroups information on resource consumption, walltime, etc.)

Setting up Galaxy

By default, Galaxy enables the core metrics:

These include very basic submission parameters. We want more information!

Hands-on: Setting up the job metrics plugin configuration

1. Edit the global (for all hosts) group variables file, group_vars/all.yml:

   Details: Why are we editing "all" instead of "galaxyservers" vars?

   Both Galaxy and Pulsar use job metrics plugins, and when we configure Pulsar later, we will want it to have the same metrics plugin configuration as Galaxy. Putting this variable in all.yml will allow us to refer to it later when setting the corresponding variable for Pulsar.

   The variable we’ll set is named galaxy_job_metrics_plugins:

   --- a/group_vars/all.yml
   +++ b/group_vars/all.yml
   @@ -10,3 +10,13 @@ galaxy_db_name: galaxy
    cvmfs_role: client
    galaxy_cvmfs_repos_enabled: config-repo
    cvmfs_quota_limit: 500
   +
   +# Galaxy vars that will be reused by Pulsar
   +galaxy_job_metrics_plugins:
   +  - type: core
   +  - type: cpuinfo
   +  - type: meminfo
   +  - type: uname
   +  - type: env
   +  - type: cgroup
   +  - type: hostname
      
   

2. Run your Galaxy playbook

   Input: Bash

   ansible-playbook galaxy.yml
   

Currently, the job metrics plugin configuration is stored in a separate configuration file from Galaxy’s main configuration file (galaxy.yml). By setting galaxy_job_metrics_plugins, we instructed the galaxyproject.galaxy role to create this file, and update the option (job_metrics_config_file) in galaxy.yml that sets the path to this file. You can inspect the contents of the new config file on your Galaxy server:

Input: Bash

cat /srv/galaxy/config/job_metrics_conf.yml

Output: Bash

---
##
## This file is managed by Ansible.  ALL CHANGES WILL BE OVERWRITTEN.
##
-   type: core
-   type: cpuinfo
-   type: meminfo
-   type: uname
-   type: env
-   type: cgroup
-   type: hostname

Generating Metrics

With this, the job metrics collection and recording should be set up. Now when you run a job, you will see many more metrics:

Hands-on: Generate some metrics

1. Run a job (any tool is fine, even upload)

2. View the information of the output dataset (galaxy-info)

What should I collect?

There is not a good rule we can tell you, just choose what you think is useful or will be. Numeric parameters are “cheaper” than the text parameters (like uname to store), eventually you may find yourself wanting to remove old job metrics if you decide to collect the environment variables or similar.

Accessing the data

You can access the data via BioBlend (JobsClient.get_metrics), or via SQL with gxadmin.

Hands-on: Time to git commit

It’s time to commit your work! Check the status with

git status

Add your changed files with

git add ... # any files you see that are changed

And then commit it!

git commit -m 'Finished Connecting Galaxy to a compute cluster'

Comment: Got lost along the way?

If you missed any steps, you can compare against the reference files, or see what changed since the previous tutorial.

If you’re using git to track your progress, remember to add your changes and commit with a good commit message!

Further Reading

• Galaxy’s cluster documentation describes in detail alternative cluster configurations.
• The job_conf documentation fully describes the syntax of the job configuration file.
• The Distributed Resource Management Application API (DRMAA) page contains the DRMAA specification as well as documentation for various implementations. It also includes a list of DRMs supporting DRMAA.
• The Slurm documentation is extensive and covers all the features and myriad of ways in which you can configure slurm.
• PSNC slurm-drmaa’s page includes documentation and the SVN repository, which has a few minor fixes since the last released version. PSNC also wrote the initial implementations of the DRMAA libraries for PBSPro and LSF, so all three are similar.
• Our own fork of slurm-drmaa includes support for Slurms -M/--clusters multi-cluster functionality and newer versions of Slurm.
• Slurm Accounting documentation explains how to set up SlurmDBD.

Comment: Galaxy Admin Training Path

The yearly Galaxy Admin Training follows a specific ordering of tutorials. Use this timeline to help keep track of where you are in Galaxy Admin Training.

1. Step 1
   ansible-galaxy
2. Step 2
   backup-cleanup
3. Step 3
   customization
4. Step 4
   tus
5. Step 5
   cvmfs
6. Step 6
   apptainer
7. Step 7
   tool-management
8. Step 8
   reference-genomes
9. Step 9
   data-library
10. Step 10
    dev/bioblend-api
11. Step 11
    connect-to-compute-cluster
12. Step 12
    job-destinations
13. Step 13
    pulsar
14. Step 14
    celery
15. Step 15
    gxadmin
16. Step 16
    reports
17. Step 17
    monitoring
18. Step 18
    tiaas
19. Step 19
    sentry
20. Step 20
    ftp
21. Step 21
    beacon

You've Finished the Tutorial

Please also consider filling out the Feedback Form as well!

Key points

• Galaxy supports a variety of different DRMs.

• You should absolutely set one up, it prevents jobs from being killed during server restarts.

Frequently Asked Questions

References

1. Tyryshkina, A., N. Coraor, and A. Nekrutenko, 2019 Predicting runtimes of bioinformatics tools based on historical data: five years of Galaxy usage (J. Wren, Ed.). Bioinformatics 35: 3453–3460. 10.1093/bioinformatics/btz054

Feedback

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Citing this Tutorial

1. Nate Coraor, Björn Grüning, Helena Rasche, Connecting Galaxy to a compute cluster (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/admin/tutorials/connect-to-compute-cluster/tutorial.html Online; accessed TODAY
2. Hiltemann, Saskia, Rasche, Helena et al., 2023 Galaxy Training: A Powerful Framework for Teaching! PLOS Computational Biology 10.1371/journal.pcbi.1010752
3. Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012

BibTeX

@misc{admin-connect-to-compute-cluster,
author = "Nate Coraor and Björn Grüning and Helena Rasche",
	title = "Connecting Galaxy to a compute cluster (Galaxy Training Materials)",
	year = "",
	month = "",
	day = "",
	url = "\url{https://training.galaxyproject.org/training-material/topics/admin/tutorials/connect-to-compute-cluster/tutorial.html}",
	note = "[Online; accessed TODAY]"
}
@article{Hiltemann_2023,
	doi = {10.1371/journal.pcbi.1010752},
	url = {https://doi.org/10.1371%2Fjournal.pcbi.1010752},
	year = 2023,
	month = {jan},
	publisher = {Public Library of Science ({PLoS})},
	volume = {19},
	number = {1},
	pages = {e1010752},
	author = {Saskia Hiltemann and Helena Rasche and Simon Gladman and Hans-Rudolf Hotz and Delphine Larivi{\`{e}}re and Daniel Blankenberg and Pratik D. Jagtap and Thomas Wollmann and Anthony Bretaudeau and Nadia Gou{\'{e}} and Timothy J. Griffin and Coline Royaux and Yvan Le Bras and Subina Mehta and Anna Syme and Frederik Coppens and Bert Droesbeke and Nicola Soranzo and Wendi Bacon and Fotis Psomopoulos and Crist{\'{o}}bal Gallardo-Alba and John Davis and Melanie Christine Föll and Matthias Fahrner and Maria A. Doyle and Beatriz Serrano-Solano and Anne Claire Fouilloux and Peter van Heusden and Wolfgang Maier and Dave Clements and Florian Heyl and Björn Grüning and B{\'{e}}r{\'{e}}nice Batut and},
	editor = {Francis Ouellette},
	title = {Galaxy Training: A powerful framework for teaching!},
	journal = {PLoS Comput Biol}
}

                   

Go Further

Do you want to extend your knowledge? Follow one of our recommended follow-up trainings:

• tutorial Hands-on: Mapping Jobs to Destinations using TPV

Galaxy Administrators: Install the missing tools

You can use Ephemeris's shed-tools install command to install the tools used in this tutorial.

shed-tools install [-g GALAXY] [-a API_KEY] -t <(curl https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/connect-to-compute-cluster/tutorial.json | jq .admin_install_yaml -r)

Alternatively you can copy and paste the following YAML

---
install_tool_dependencies: true
install_repository_dependencies: true
install_resolver_dependencies: true
tools: []

Feedback

5 stars	14
1 stars	1

June 2021

• 5 stars: Liked: Very clear explanations

January 2021

• 5 stars: Liked: Easy and useful Disliked: Regarding 'expose_potentially_sensitive_job_metrics' , is there an option to expose different metrics for admins and general users? For example, creating different profiles in templates/galaxy/config/job_metrics_conf.xml.j2
• 5 stars: Liked: I really need this knowledge. Disliked: I have stuck in the part of editing templates/galaxy/config/job_conf.xml.j2 because some lines differ from the resulting file from previous session (namely singularity was set as default) and I had to compare the file showed in the video with the file I had. I took some time, but it worked at the end. It seems not so complicated now, but it will be when connecting to a living cluster. What happens when I have SLURM already configured at the server? And MUNGE (this guy made some nodes crash here because of very large log files), do I need to configure it in the cluster? It was not clear.
• 5 stars: Liked: Easily digestible
• 5 stars: Liked: fantastic, incredibly helpful. trainer is really great. Disliked: Would like info on adding to existing clusters (ie., SGE, etc)
• 5 stars: Liked: Just the right amount of content, Slurm is so large it would have been easy to get over complicated Disliked: Minor: the references to pulsar in the examples could be confusing, might be worth adding a warning for anyone who is going through this tutorial before the pulsar tutorial