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Running jobs

Login nodes#

Login nodes are not for computing

Login nodes are shared among many users and therefore must not be used to run computationally intensive tasks. Those should be submitted to the scheduler which will dispatch them on compute nodes.

The key principle of a shared computing environment is that resources are shared among users and must be scheduled. It is mandatory to schedule work by submitting jobs to the scheduler on Sherlock. And since login nodes are a shared resource, they must not be used to execute computing tasks.

Acceptable use of login nodes include:

  • lightweight file transfers,
  • script and configuration file editing,
  • job submission and monitoring.

Resource limits are enforced

To minimize disruption and ensure a comfortable working environment for users, resource limits are enforced on login nodes, and processes started there will automatically be terminated if their resource usage (including CPU time, memory and run time) exceed those limits.

Slurm commands#

Slurm allows requesting resources and submitting jobs in a variety of ways. The main Slurm commands to submit jobs are listed in the table below:

Command Description Behavior
salloc Request resources and allocates them to a job Starts a new shell, but does not execute anything
srun Request resources and runs a command on the allocated compute node(s) Blocking command: will not return until the job ends
sbatch Request resources and runs a script on the allocated compute node(s) Asynchronous command: will return as soon as the job is submitted

Interactive jobs#

Dedicated nodes#

Interactive jobs allow users to log in to a compute node to run commands interactively on the command line. They could be an integral part of an interactive programming and debugging workflow. The simplest way to establish an interactive session on Sherlock is to use the sh_dev command:

$ sh_dev

This will open a login shell using one core and 4 GB of memory on one node for one hour. The sh_dev sessions run on dedicated compute nodes. This ensures minimal wait times when you need to access a node for testing script, debug code or any kind of interactive work.

sh_dev also provides X11 forwarding via the submission host (typically the login node you're connected to) and can thus be used to run GUI applications.

Compute nodes#

If you need more resources1, you can pass options to sh_dev, to request more CPU cores, more nodes, or even run in a different partition. sh_dev -h will provide more information:

$ sh_dev -h
sh_dev: start an interactive shell on a compute node.

Usage: sh_dev [OPTIONS]
    Optional arguments:
        -c      number of CPU cores to request (OpenMP/pthreads, default: 1)
        -n      number of tasks to request (MPI ranks, default: 1)
        -N      number of nodes to request (default: 1)
        -m      memory amount to request (default: 4GB)
        -p      partition to run the job in (default: dev)
        -t      time limit (default: 01:00:00)
        -r      allocate resources from the named reservation (default: none)
        -J      job name (default: sh_dev)
        -q      quality of service to request for the job (default: normal)

    Note: the default partition only allows for limited amount of resources.
    If you need more, your job will be rejected unless you specify an
    alternative partition with -p.

Another way to get an interactive session on a compute node is to use srun to execute a shell through the scheduler. For instance, to start a bash session on a compute node, with the default resource requirements (one core for 2 hours), you can run:

$ srun --pty bash

The main advantage of this approach is that it will allow you to specify the whole range of submission options that sh_dev may not support.

Finally, if you prefer to submit an existing job script or other executable as an interactive job, you can use the salloc command:

$ salloc script.sh

If you don't provide a command to execute, salloc will start a Slurm job and allocate resources for it, but it will not automatically connect you to the allocated node(s). It will only start a new shell on the same node you launched salloc from, and set up the appropriate $SLURM_* environment variables. So you will typically need to look at them to see what nodes have been assigned to your job. For instance:

$ salloc
salloc: Granted job allocation 655914
$ echo $SLURM_NODELIST
sh02-01n55
$ ssh sh02-01n55
[...]
sh02-01n55 ~ $

Connecting to nodes#

Login to compute nodes

Users are not allowed to login to compute nodes unless they have a job running there.

If you SSH to a compute node without any active job allocation, you'll be greeted by the following message:

$ ssh sh02-01n01
Access denied by pam_slurm_adopt: you have no active jobs on this node
Connection closed
$

Once you have a job running on a node, you can SSH directly to it and run additional processes2, or observe how you application behaves, debug issues, and so on.

The salloc command supports the same parameters as sbatch, and can override any default configuration. Note that any #SBATCH directive in your job script will not be interpreted by salloc when it is executed in this way. You must specify all arguments directly on the command line for them to be taken into account.

Batch jobs#

It's easy to schedule batch jobs on Sherlock. A job is simply an instance of your program, for example your R, Python or Matlab script that is submitted to and executed by the scheduler (Slurm). When you submit a job with the sbatch command it's called a batch job and it will either run immediately or will pend (wait) in the queue.

The length of time a job will pend is determined by several factors; how many other jobs are in the queue ahead or your job and how many resources your job is requesting are most the most important factors. One key principle when requesting resources is to always try to request as few resources as you need to get your job done. This will ensure your job pends in the queue for as little time as necessary. To get a rough idea of what resources are needed, you can profile your code/jobs in an sh_dev session in real-time with htop, nvtop, sacct etc. The basic concept is to tell the scheduler what resources your job needs and how long is should run. These resources are:

CPUs: How many CPUs the program you are calling the in the sbatch script needs, unless it can utilize multiple CPUs at once you should request a single CPU. Check your code's documentation or try running in an interactive session with sh_dev and run htop if you are unsure.

GPUs: If your code is GPU enabled, how many GPUs does your code need? Use the diagnostic tool nvtop to see if your code is capable of running on multiple GPUs and how much GPU memory it's using in real-time.

memory (RAM): How much memory your job will consume. Some things to consider, will it load a large file or matrix into memory? Does it consume a lot of memory on your laptop? Often the default memory is sufficient for many jobs.

time: How long will it take for your code to run to completion?

partition: What set of compute nodes on Sherlock will you run on, normal, gpu, owners, bigmem? Use the sh_part command to see what partitions you are allowed to run on. The default partition on Sherlock is the normal partition.

Next, you tell the scheduler what your job should should do: load modules and run your code. Note that any logic you can code into a bash script with the bash scripting language can also be coded into an sbatch script.

This example job, will run the Python script mycode.py for 10 minutes on the normal partition using 1 CPU and 8 GB of memory. To aid in debugging we are naming this job "test_job" and appending the Job ID (%j) to the two output files that Slurm creates when a job is run. The output files are written to the directory in which you launched your job in, you can also specify a different path. One file will contain any errors and the other will contain non-error output. Look in these 2 files ending in .err and .out for useful debugging information and error output.

Because it's a Python 3 script that uses some Numpy code, we need to load the python/3.6.1 and the py-numpy/1.19.2_py36 modules. The Python script is then called just as you would on the command line at the end of the sbatch script:

sbatch script:

#!/usr/bin/bash
#SBATCH --job-name=test_job
#SBATCH --output=test_job.%j.out
#SBATCH --error=test_job.%j.err
#SBATCH --time=10:00
#SBATCH -p normal
#SBATCH -c 1
#SBATCH --mem=8GB
module load python/3.6.1
module load py-numpy/1.19.2_py36
python3 mycode.py
Create and edit the sbatch script with a text editor like vim/nano or the OnDemand file manager. Then save the file, in this example we call it "test.sbatch".

Submit to the scheduler with the sbatch command:

$sbatch test.sbatch
Monitor your job and job ID in the queue with the squeue command:

$squeue -u $USER
   JOBID     PARTITION     NAME     USER    ST       TIME  NODES  NODELIST(REASON)
   44915821    normal    test_job  <userID>  PD       0:00      1 (Priority)

Notice that the jobs state (ST) in pending (PD)

Once the job starts to run that will change to R:

$squeue -u $USER
    JOBID     PARTITION     NAME     USER     ST      TIME  NODES   NODELIST(REASON)
    44915854    normal test_job  <userID>     R      0:10     1     sh02-01n49

Here you can see it has been running (R) on the compute node sh02-01n49 for 10 seconds. While your job is running you have ssh access to that node and can run diagnostic tools such as htop and nvtop in order to monitor your job's memory and CPU/GPU utilization in real-time. You can also manage this job based on the JobID assigned to it (44915854). For example the job can be cancelled with the scancel command.

Resource requests#

To get a better idea of the amount of resources your job will need, you can use the ruse command, available as a module:

$ module load system ruse

ruse is a command line tool developed by Jan Moren to measure a process' resource usage. It periodically measures the resource use of a process and its subprocesses, and can help you find out how much resource to allocate to your job. It will determine the actual memory, execution time and cores that individual programs or MPI applications need to request in their job submission options.

ruse periodically samples the process and its subprocesses and keeps track of the CPU, time and maximum memory use. It also optionally records the sampled values over time. The purpose or Ruse is not to profile processes in detail, but to follow jobs that run for many minutes, hours or days, with no performance impact and without changing the measured application in any way.

You'll find complete documentation and details about ruse's usage on the project webpage, but here are a few useful examples.

Sizing a job#

In its simplest form, ruse can help discover how much resources a new script or application will need. For instance, you can start a sizing session on a compute node with an overestimated amount of resources, and start your application like this:

$ ruse ./myapp

This will generate a <myapp>-<pid>/ruse output file in the current directory, looking like this:

Time:           02:55:47
Memory:         7.4 GB
Cores:          4
Total_procs:    3
Active_procs:   2
Proc(%): 99.9  99.9

It shows that myapp:

  • ran for almost 3 hours
  • used a little less than 8B of memory
  • had 4 cores available,
  • spawned 3 processes, among which at most 2 were active at the same time,
  • that both active processes each used 99.9% of a CPU core

This information could be useful in tailoring the job resource requirements to its exact needs, making sure that the job won't be killed for exceeding one of its resource limits, and that the job won't have to wait too long in queue for resources that it won't use. The corresponding job request could look like this:

#SBATCH --time 3:00:00
#SBATCH --mem 8GB
#SBATCH --cpus-per-task 2
Verifying a job's usage#

It's also important to verify that applications, especially parallel ones, stay in the confines of the resources they've requested. For instance, a number of parallel computing libraries will make the assumption that they can use all the resources on the host, will automatically determine the number of physical CPU cores present on the compute node, and start as many processes. This could be a significant issue if the job requested less CPUs, as more processes will be constrained on less CPU cores, which will result in node overload and degraded performance for the application.

To avoid this, you can start your application with ruse and report usage for each time step specified with -t. You can also request the reports to be displayed directly on stdout rather than stored in a file.

For instance, this will report usage every 10 seconds:

$ ruse -s -t10 --stdout ./myapp
   time         mem   processes  process usage
  (secs)        (MB)  tot  actv  (sorted, %CPU)
     10        57.5    17    16   33  33  33  25  25  25  25  25  25  25  25  20  20  20  20  20
     20        57.5    17    16   33  33  33  25  25  25  25  25  25  25  25  20  20  20  20  20
     30        57.5    17    16   33  33  33  25  25  25  25  25  25  25  25  20  20  20  20  20

Time:           00:00:30
Memory:         57.5 MB
Cores:          4
Total_procs:   17
Active_procs:  16
Proc(%): 33.3  33.3  33.2  25.0  25.0  25.0  25.0  25.0  25.0  24.9  24.9  20.0  20.0  20.0  20.0  19.9

Here, we can see that despite having being allocated 4 CPUs, the application started 17 threads, 16 of which were active running intensive computations, with the unfortunate consequence that each process could only use a fraction of a CPU.

In that case, to ensure optimal performance and system operation, it's important to modify the application parameters to make sure that it doesn't start more computing processes than the number of requested CPU cores.

Available resources#

Whether you are submitting a batch job, or an or interactive job, it's important to know the resources that are available to you. For this reason, we provide sh_part, a command-line tool to help answer questions such as:

  • which partitions do I have access to?
  • how many jobs are running on them?
  • how many CPUs can I use?
  • where should I submit my jobs?

sh_part can be executed on any login or compute node to see what partitions are available to you, and its output looks like this:

$ sh_part
     QUEUE STA   FREE  TOTAL   FREE  TOTAL RESORC  OTHER MAXJOBTIME    CORES       NODE   GRES
 PARTITION TUS  CORES  CORES  NODES  NODES PENDNG PENDNG  DAY-HR:MN    /NODE     MEM-GB (COUNT)
    normal   *    153   1792      0     84    23k    127    7-00:00    20-24    128-191 -
    bigmem         29     88      0      2      0      8    1-00:00    32-56   512-3072 -
       dev         31     40      0      2      0      0    0-02:00       20        128 -
       gpu         47    172      0      8    116      1    7-00:00    20-24    191-256 gpu:4(S:0-1)(2),gpu:4(S:0)(6)

The above example shows four possible partitions where jobs can be submitted: normal, bigmem, dev, or gpu. It also provides additional information such as the maximum amount of time allowed in each partition (MAXJOBTIME), the number of other jobs already in queue, along with the ranges of memory available on nodes in each partition.

  • in the QUEUE PARTITION column, the * character indicates the default partition.
  • the RESOURCE PENDING column shows the core count of pending jobs that are waiting on resources,
  • the OTHER PENDING column lists core counts for jobs that are pending for other reasons, such as licenses, user, group or any other limit,
  • the GRES column shows the number and type of Generic RESsources available in that partition (typically, GPUs), which CPU socket they're available from, and the number of nodes that feature that specific GRES combination. So for instance, in the output above, gpu:4(S:0-1)(2) means that the gpu partition features 2 nodes with 4 GPUs each, and that those GPUs are accessible from both CPU sockets (S:0-1).

Recurring jobs#

Warning

Cron tasks are not supported on Sherlock.

Users are not allowed to create cron jobs on Sherlock, for a variety of reasons:

  • resources limits cannot be easily enforced in cron jobs, meaning that a single user can end up monopolizing all the resources of a login node,
  • no amount of resources can be guaranteed when executing a cron job, leading to unreliable runtime and performance,
  • user cron jobs have the potential of bringing down whole nodes by creating fork bombs, if they're not carefully crafted and tested,
  • compute and login nodes could be redeployed at any time, meaning that cron jobs scheduled there could go away without the user being notified, and cause all sorts of unexpected results,
  • cron jobs could be mistakenly scheduled on several nodes and run multiple times, which could result in corrupted files.

As an alternative, if you need to run recurring tasks at regular intervals, we recommend the following approach: by using the --begin job submission option, and creating a job that resubmits itself once it's done, you can virtually emulate the behavior and benefits of a cron job, without its disadvantages: your task will be scheduled on a compute node, and use all of the resources it requested, without being impacted by anything else.

Depending on your recurring job's specificities, where you submit it and the state of the cluster at the time of execution, the starting time of that task may not be guaranteed and result in a delay in execution, as it will be scheduled by Slurm like any other jobs. Typical recurring jobs, such as file synchronization, database updates or backup tasks don't require strict starting times, though, so most users find this an acceptable trade-off.

The table below summarizes the advantages and inconvenients of each approach:

Cron tasks Recurring jobs
Authorized on Sherlock
Dedicated resources for the task
Persistent across node redeployments
Unique, controlled execution
Precise schedule

Recurrent job example#

The script below presents an example of such a recurrent job, that would emulate a cron task. It will append a timestamped line to a cron.log file in your $HOME directory and run every 7 days.

cron.sbatch
#!/bin/bash
#SBATCH --job-name=cron
#SBATCH --begin=now+7days
#SBATCH --dependency=singleton
#SBATCH --time=00:02:00
#SBATCH --mail-type=FAIL


## Insert the command to run below. Here, we're just storing the date in a
## cron.log file
date -R >> $HOME/cron.log

## Resubmit the job for the next execution
sbatch $0

If the job payload (here the date command) fails for some reason and generates and error, the job will not be resubmitted, and the user will be notified by email.

We encourage users to get familiar with the submission options used in this script by giving a look at the sbatch man page, but some details are given below:

Submission option or command Explanation
--job-name=cron makes it easy to identify the job, is used by the --dependency=singleton option to identify identical jobs, and will allow cancelling the job by name (because its jobid will change each time it's submitted)
--begin=now+7days will instruct the scheduler to not even consider the job for scheduling before 7 days after it's been submitted
--dependency=singleton will make sure that only one cron job runs at any given time
--time=00:02:00 runtime limit for the job (here 2 minutes). You'll need to adjust the value depending on the task you need to run (shorter runtime requests usually result in the job running closer to the clock mark)
--mail-type=FAIL will send an email notification to the user if the job ever fails
sbatch $0 will resubmit the job script by calling its own name ($0) after successful execution

You can save the script as cron.sbatch or any other name, and submit it with:

$ sbatch cron.sbatch

It will start running for the first time 7 days after you submit it, and it will continue to run until you cancel it with the following command (using the job name, as defined by the --job-name option):

$ scancel -n cron

Persistent jobs#

Recurring jobs described above are a good way to emulate cron jobs on Sherlock, but don't fit all needs, especially when a persistent service is required.

For instance, workflows that require a persistent database connection would benefit from an ever-running database server instance. We don't provide persistent database services on Sherlock, but instructions and examples on how to submit database server jobs are provided for MariaDB or PostgreSQL.

In case those database instances need to run pretty much continuously (within the limits of available resources and runtime maximums), the previous approach described in the recurring jobs section could fall a bit short. Recurring jobs are mainly designed for jobs that have a fixed execution time and don't reach their time limit, but need to run at given intervals (like synchronization or backup jobs, for instance).

Because a database server process will never end within the job, and will continue until the job reaches its time limit, the last resubmission command (sbatch $0) will actually never be executed, and the job won't be resubmitted.

To work around this, a possible approach is to catch a specific signal sent by the scheduler at a predefined time, before the time limit is reached, and then re-queue the job. This is easily done with the Bash trap command, which can be instructed to re-submit a job when it receives the SIGUSR1 signal.

Automatically resubmitting a job doesn't make it immediately runnable

Jobs that are automatically re-submitted using this technique won't restart right away: the will get back in queue and stay pending until their execution conditions (priority, resources, usage limits...) are satisfied.

Persistent job example#

Here's the recurring job example from above, modified to:

  1. instruct the scheduler to send a SIGUSR1 signal to the job 90 seconds3 before reaching its time limit (with the #SBATCH --signal option),
  2. re-submit itself upon receiving that SIGUSR1 signal (with the trap command)
persistent.sbatch
#!/bin/bash
#
#SBATCH --job-name=persistent
#SBATCH --dependency=singleton
#SBATCH --time=00:05:00
#SBATCH --signal=B:SIGUSR1@90

# catch the SIGUSR1 signal
_resubmit() {
    ## Resubmit the job for the next execution
    echo "$(date): job $SLURM_JOBID received SIGUSR1 at $(date), re-submitting"
    sbatch $0
}
trap _resubmit SIGUSR1

## Insert the command to run below. Here, we're just outputting the date every
## 10 seconds, forever

echo "$(date): job $SLURM_JOBID starting on $SLURM_NODELIST"
while true; do
    echo "$(date): normal execution"
    sleep 60
done

Long running processes need to run in the background

If your job's actual payload (the application or command you want to run) is running continuously for the whole duration of the job, it needs to be executed in the background, so the trap can be processed.

To run your application in the background, just add a & at the end of the command and then add a wait statement at the end of the script, to make the shell wait until the end of the job.

For instance, if you were to run a PostgreSQL database server, the while true ... done loop in the previous example could be replaced by something like this:

postgres -i -D $DB_DIR &
wait

Persistent $JOBID#

One potential issue with having a persistent job re-submit itself when it reaches its runtime limit is that it will get a different $JOBID each time it's (re-)submitted.

This could be particularly challenging when other jobs depend on it, like in the database server scenario, where client jobs would need to start only if the database server is running. This can be achieved with job dependencies, but those dependencies have to be expressed using jobids, so having the server job's id changing at each re-submission will be difficult to handle.

To avoid this, the re-submission command (sbatch $0) can be replaced by a re-queuing command:

scontrol requeue $SLURM_JOBID

The benefit of that change is that the job will keep the same $JOBID across all re-submissions. And now, dependencies can be added to other jobs using that specific $JOBID, without having to worry about it changing. And there will be only one $JOBID to track for that database server job.

The previous example can then be modified as follows:

persistent.sbatch
#!/bin/bash
#SBATCH --job-name=persistent
#SBATCH --dependency=singleton
#SBATCH --time=00:05:00
#SBATCH --signal=B:SIGUSR1@90

# catch the SIGUSR1 signal
_requeue() {
    echo "$(date): job $SLURM_JOBID received SIGUSR1, re-queueing"
    scontrol requeue $SLURM_JOBID
}
trap '_requeue' SIGUSR1

## Insert the command to run below. Here, we're just outputting the date every
## 60 seconds, forever

echo "$(date): job $SLURM_JOBID starting on $SLURM_NODELIST"
while true; do
    echo "$(date): normal execution"
    sleep 60
done

Submitting that job will produce an output similar to this:

Mon Nov  5 10:30:59 PST 2018: Job 31182239 starting on sh-06-34
Mon Nov  5 10:30:59 PST 2018: normal execution
Mon Nov  5 10:31:59 PST 2018: normal execution
Mon Nov  5 10:32:59 PST 2018: normal execution
Mon Nov  5 10:33:59 PST 2018: normal execution
Mon Nov  5 10:34:59 PST 2018: Job 31182239 received SIGUSR1, re-queueing
slurmstepd: error: *** JOB 31182239 ON sh-06-34 CANCELLED AT 2018-11-05T10:35:06 DUE TO JOB REQUEUE ***
Mon Nov  5 10:38:11 PST 2018: Job 31182239 starting on sh-06-34
Mon Nov  5 10:38:11 PST 2018: normal execution
Mon Nov  5 10:39:11 PST 2018: normal execution

The job runs for 5 minutes, then received the SIGUSR1 signal, is re-queued, restarts for 5 minutes, and so on, until it's properly scancelled.


  1. The dedicated partition that sh_dev uses by default only allows up to 2 cores and 8 GB or memory per user at any given time. So if you need more resources for your interactive session, you may have to specify a different partition. See the Partitions section for more details. 

  2. Please note that your SSH session will be attached to your running job, and that resources used by that interactive shell will count towards your job's resource limits. So if you start a process using large amounts of memory via SSH while your job is running, you may hit the job's memory limits, which will trigger its termination. 

  3. Due to the resolution of event handling by the scheduler, the signal may be sent up to 60 seconds earlier than specified.