Working in Batch - Atos HPCF and ECS Introduction Tutorial

Let's explore how to use the Slurm Batch System to the ATOS HPCF or ECS.

Basic job submission

Access the default login node of the ATOS HPCF or ECS.

1. Create a directory for this tutorial so all the exercises and outputs are contained inside:

   mkdir ~/batch_tutorial
   cd ~/batch_tutorial

2. Create and submit a job called simplest.sh with just default settings that runs the command hostname. Can you find the output and inspect it? Where did your job run?

   Solution

   Using your favourite editor, create a file called simplest.sh with the following content

   simplest.sh

   #!/bin/bash
   hostname

   You can submit it with sbatch:

   sbatch simplest.sh

   The job should be run shortly. When finished, a new file called slurm-<jobid>.out should appear in the same directory. You can check the output with:

   $ cat $(ls -r1 slurm-*.out | head -n1)
   ab6-202.bullx
   [ECMWF-INFO -ecepilog] ----------------------------------------------------------------------------------------------------
   [ECMWF-INFO -ecepilog] This is the ECMWF job Epilogue
   [ECMWF-INFO -ecepilog] +++ Please report issues using the Support portal +++
   [ECMWF-INFO -ecepilog] +++ https://support.ecmwf.int                     +++
   [ECMWF-INFO -ecepilog] ----------------------------------------------------------------------------------------------------
   [ECMWF-INFO -ecepilog] Run at 2023-10-25T11:31:53 on ecs
   [ECMWF-INFO -ecepilog] JobName                   : simplest.sh
   [ECMWF-INFO -ecepilog] JobID                     : 64273363
   [ECMWF-INFO -ecepilog] Submit                    : 2023-10-25T11:31:36
   [ECMWF-INFO -ecepilog] Start                     : 2023-10-25T11:31:51
   [ECMWF-INFO -ecepilog] End                       : 2023-10-25T11:31:53
   [ECMWF-INFO -ecepilog] QueuedTime                : 15.0
   [ECMWF-INFO -ecepilog] ElapsedRaw                : 2
   [ECMWF-INFO -ecepilog] ExitCode                  : 0:0
   [ECMWF-INFO -ecepilog] DerivedExitCode           : 0:0
   [ECMWF-INFO -ecepilog] State                     : COMPLETED
   [ECMWF-INFO -ecepilog] Account                   : myaccount
   [ECMWF-INFO -ecepilog] QOS                       : ef
   [ECMWF-INFO -ecepilog] User                      : user
   [ECMWF-INFO -ecepilog] StdOut                    : /etc/ecmwf/nfs/dh1_home_a/user/slurm-64273363.out
   [ECMWF-INFO -ecepilog] StdErr                    : /etc/ecmwf/nfs/dh1_home_a/user/slurm-64273363.out
   [ECMWF-INFO -ecepilog] NNodes                    : 1
   [ECMWF-INFO -ecepilog] NCPUS                     : 2
   [ECMWF-INFO -ecepilog] SBU                       : 0.011
   [ECMWF-INFO -ecepilog] ----------------------------------------------------------------------------------------------------

   You can then see that the script has run on a different node than the one you are on.

   If you repeat the operation, you may get your job to run on a different node every time, whichever happens to be free at the time.

3. Configure your simplest.sh job to direct the output to simplest-<jobid>.out, the error to simplest-<jobid>.err both in the same directory, and the job name to just "simplest". Note you will need to use a special placeholder for the -<jobid>.

   Solution

   Using your favourite editor, open the simplest.sh job script and add the relevant #SBATCH directives:

   simplest.sh

   #!/bin/bash
   #SBATCH --job-name=simplest
   #SBATCH --output=simplest-%j.out
   #SBATCH --output=simplest-%j.err
   hostname

   You can submit it again with:

   sbatch simplest.sh

   After a few moments, you should see the new files appear in your directory (job id will be different than the one displayed here):

   $ ls simplest-*.*
   simplest-64274497.err  simplest-64274497.out

   You can check that the job name was also changed in the end of job report:

   $ grep -i jobname $(ls -r1 simplest-*.err | head -n1)
   [ECMWF-INFO -ecepilog] JobName                   : simplest

Basic job management

1. Create a new job script sleepy.sh with the contents below:

   sleepy.sh

   #!/bin/bash
   sleep 120

2. Submit  sleepy.sh to the batch system and check its status. Once it is running, cancel it and inspect the output.

   Solution

   Using your favourite editor, create sleepy.sh job script with the contents above. Then you can submit it with:

   sbatch sleepy.sh

   You can then check the state of your job with squeue:

   squeue -j <jobid>

   if you use the <jobid> of the job you just submitted, or just:

   squeue --me

   to list all your jobs.

   To cancel your job, just run scancel:

   scancel <jobid>

   If you inspect the output file from your last job, you will see a message like the following:

   slurmstepd: error: *** JOB 64281137 ON ab6-202 CANCELLED AT 2023-10-25T15:40:51 ***

3. Can you get information about the jobs you have run so far today, including those that have finished already?

   Solution

   When jobs finish, they will not appear in the squeue output any longer. You can then check the Accounting Database with sacct:

   sacct

   With no arguments, this command will show you the list of all jobs run by you on this day. 

   In the output you may see or more entries 3 entries such as:

   JobID                 JobName       QOS      State ExitCode    Elapsed   NNodes             NodeList 
   ------------ ---------------- --------- ---------- -------- ---------- -------- -------------------- 
   ...
   64281137            sleepy.sh        ef CANCELLED+      0:0   00:00:16        1              ab6-202 
   64281137.ba+            batch            CANCELLED     0:15   00:00:17        1              ab6-202 
   64281137.ex+           extern            COMPLETED      0:0   00:00:16        1              ab6-202 

   The first one corresponds to the job itself. The second one (always named batch) corresponds to the actual job script and the third (named extern) corresponds to the external step used to generate the end of job information. You may have more lines if your job contains more steps, which typically correspond to srun parallel executions.

   If you want to list just the entry for the job itself, you can do:

   sacct -X

4. Can you get information of all the jobs run today by you that were cancelled? 

   Solution

   You can filter jobs by state with the -s option. But If you run it naively:

   sacct -X -t CANCELLED

   You will get no output. That is because when using state you must also specify the start and end times of your query period. You can then do something like:

   sacct -X -s CANCELLED -S $(date +%Y-%m-%d) -E $(date +%Y-%m-%dT%H:%M:%S)

5. The default information shown on the screen when querying past jobs is limited. Can you extract the submit, start, and end times of your cancelled jobs today? What about their output and error path? Hint: use the corresponding man page for all the options.

   Solution

   You can use the following command to see all the possible output fields you can query for:

   sacct -e

   While there are dedicated fields for the job submit, start and end times, there is none for the output and error paths. However, the AdminComment field is used to carry that information. Since it is a long field, you may want to pass a length to the fieldname to avoid truncation:

   sacct -X -s CANCELLED -S $(date +%Y-%m-%d) -E $(date +%Y-%m-%dT%H:%M:%S) -o jobid,jobname,state,submit,start,end,AdminComment%150

   or you can also ask for a parsable output:

   sacct -X -s CANCELLED -S $(date +%Y-%m-%d) -E $(date +%Y-%m-%dT%H:%M:%S) -o jobid,jobname,state,submit,start,end,AdminComment -p

Common pitfalls

We will now attempt to troubleshoot some issues

1. Create a new job script broken1.sh with the contents below and try to submit the job. What happened? Can you fix the job and keep trying until it runs successfully?

   broken1.sh

   #SBATCH --job-name = broken 1
   #SBATCH --output = broken1-%J.out
   #SBATCH --error = broken1-%J.out
   #SBATCH --qos = express
   #SBATCH --time = 00:05:00 
   
   # This is the job
   echo "I was broken!"
   sleep 30

   Solution

   The job above has the following problems:

   • There is no shebang at the beginning of the script.
   • There should be no spaces in the directives
   • There should be no space
   • QoS "express" does not exist

   Here is an amended version:

   broken1_fixed.sh

   #!/bin/bash
   #SBATCH --job-name=broken1
   #SBATCH --output=broken1-%J.out
   #SBATCH --error=broken1-%J.out
   #SBATCH --time=00:05:00 
   
   # This is the job
   echo "I was broken!"
   sleep 30

   Note that the QoS line was removed, but you may also use the following if running on ECS:

   #SBATCH --qos=ef

   or the alternatively, if on Atos HPCF:

   #SBATCH --qos=nf

   Check that the actual job run and generated the expected output:

   $ grep -v ECMWF-INFO  $(ls -1 broken1-*.out | head -n1)
   I was broken!

2. Create a new job script broken2.sh with the contents below and try to submit the job. What happened? Can you fix the job and keep trying until it runs successfully?

   broken2.sh

   #!/bin/bash
   #SBATCH --job-name=broken2
   #SBATCH --output=broken2-%J.out
   #SBATCH --error=broken2-%J.out
   #SBATCH --qos=ns
   #SBATCH --time=10-00
   
   # This is the broken
   echo "I was broken!"

   Solution

   The job above has the following problems:

   • QoS "ns" does not exist. Either remove to use the default or use the corresponding queue on ECS (ef) or HPCF (nf)
   • The time requested is 10 days, which is longer than the maximum allowed. it was probably meant to be 10 minutes

   Here is an amended version:

   broken1.sh

   #!/bin/bash
   #SBATCH --job-name=broken2
   #SBATCH --output=broken2-%J.out
   #SBATCH --error=broken2-%J.out
   #SBATCH --time=10:00
   
   # This is the broken
   echo "I was broken!"

   Again, note that the QoS line was removed, but you may also use the following if running on ECS:

   #SBATCH --qos=ef

   or the alternatively, if on Atos HPCF:

   #SBATCH --qos=nf

   Check that the actual job run and generated the expected output:

   $ grep -v ECMWF-INFO  $(ls -1 broken2-*.out | head -n1)
   I was broken!

3. Create a new job script broken3.sh with the contents below and try to submit the job. What happened? Can you fix the job and keep trying until it runs successfully?

   broken3.sh

   #!/bin/bash
   #SBATCH --job-name=broken3
   #SBATCH --chdir=$SCRATCH
   #SBATCH --output=broken3output/broken3-%J.out
   #SBATCH --error=broken3output/broken3-%J.out
   
   # This is the job
   echo "I was broken!"

   Solution

   The job above has the following problems:

   • Variables are not expanded on job directives. You must specify your paths explicitly

   • The directory where the output and error files will go must exist beforehand. Otherwise the job will fail but you will not get any hint as to what may have happened to the job. The only hint would be if checking sacct:

     $ sacct -X --name=broken3
     JobID                 JobName       QOS      State ExitCode    Elapsed   NNodes             NodeList 
     ------------ ---------------- --------- ---------- -------- ---------- -------- -------------------- 
     64281800              broken3        ef     FAILED     0:53   00:00:02        1              ad6-201 

   You will need to create the output directory with:

   mkdir -p $SCRATCH/broken3output/

   Here is an amended version of the job:

   broken3.sh

   #!/bin/bash
   #SBATCH --job-name=broken3
   #SBATCH --chdir=/scratch/<your_user_id>
   #SBATCH --output=broken3output/broken3-%J.out
   #SBATCH --error=broken3output/broken3-%J.out
   
   # This is the job
   echo "I was broken!"

   Check that the actual job run and generated the expected output:

   $ grep -v ECMWF-INFO  $(ls -1 $SCRATCH/broken3output/broken3-*.out | head -n1)
   I was broken!

   You may clean up the output directory with

   rm -rf $SCRATCH/broken3output