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Slurm

From ALICE Documentation

Running a job on ALICE using Slurm

Slurm (Simple Linux Utility for Resource Management) is an open-source job scheduler that allocates compute resources on clusters for queued researcher defined jobs. Slurm has been deployed at various national and international computing centres, and by approximately 60% of the TOP500 supercomputers in the world.

You can learn more about SLURM and its commands from the official Slurm website.

To use Slurm commands, you must first log in to either of the head nodes of ALICE, login1 or login2. For information on how to login to the ALICE long nodes see section Login to cluster.

Best practices

  1. Don't ask for more time than you really need.  The scheduler will have an easier time finding a slot for the 2 hours you need rather than the 48 hours you request.  When you run a job it will report back on the time used which you can use as a reference for future jobs.  However, don't cut the time too tight.  If something like shared I/O activity slows it down and you run out of time, the job will fail.
  2. Test your submission scripts.  Start small.  You can use the debug queue which has a higher priority but a short run time.
  3. Respect memory limits.  If your application needs more memory than is available, your job could fail and leave the node in a state that requires manual intervention.
  4. Use the debug queue.  It has a higher priority which is useful for running tests that can complete in less than 10 minutes.
  5. Do not run scripts automating job submissions. Executing large numbers of sbatch's in rapid succession can overload the system's scheduler leading to problems with overall system performance. A better alternative is to submit job arrays.

Requesting job resources

ATTENTION: We recommend that you submit sbatch Slurm jobs with the #sbatch--export=none option to establish a clean environment, otherwise Slurm will propagate current environmental variables to the job. This could impact the behavior of the job, particularly for MPI jobs.

In order to use the HPC Slurm compute nodes, you must first login to a head node, hpc-login3 or hpc-login2, and submit a job.

  • To request an interactive job, use the salloc command.
  • To submit a job script, use the sbatch command.
  • To check on the status of a job already in the Slurm queue, use the squeue and sinfo commands.

Creating a job script

One option for running a job on ALICE is to set up a job script. In this script, you specify the cluster resources that the job needs and list, in sequence, the commands that you want to execute. A job script is a plain text file that can be edited with a UNIX editor such as vi, nano or emacs.

To properly configure a job script, you will need to know the general script format, the commands you wish to use, how to request the resources required for the job to run, and, possibly, some of the Slurm environmental variables.

Common SLURM commands

The following is a list of common Slurm commands that will be discussed in more detail on this page. To learn about all the options available for each command, enter man <command> while logged into the ALICE.

Command Definition
sbatch Submit a job script for execution (queued)
scancel Delete a job
scontrol Job status (detailed), several options only available to root
sinfo Display state of partitions and nodes
squeue Display state of all (queued) jobs
salloc Submit a job for execution or initiate job in real-time (interactive job)

Specify Resources Submitting a Job

Slurm has its syntax to request compute resources. Below is a summary table of some commonly requested resources and the Slurm syntax to get it. For a complete listing of request syntax, run the command man sbatch.

Syntax Meaning
sbatch/salloc Submit batch/interactive job
   --ntasks=<number> Number of processes to run (default is 1)
  --mem=<number> Total memory (single node)
  --mem-per-cpu=<number> Memory per processor core
  --constraint=<attribute> Node property to request (e.g. avx, IB)
  --partition=<partition_name> Request specified partition/queue

For more details on Slurm syntax, see below or the Slurm documentation at slurm.schedmd.com/sbatch.html

Determining what resources to request

Before you submit a job for batch processing, it is important to know what the requirements of your program are so that it can run properly. Each program and workflow has unique requirements so we advise that you determine what resources you need before you write your script.

Keep in mind that increasing the amount of compute resources may also increase the amount of time that your job spends waiting in the queue. You may request whatever resources you need but bear in mind that other researchers need to be able to use those resources as well.

Below are some tips for determining the resources to ask for in your job script. These are options defined for the sbatch and salloc commands. There are additional options that you can find by checking the man pages for each command.

Tasks and CPU's per task

In Slurm terminology, a task is an instance of a running a program.

If your program supports communication across computers or you plan on running independent tasks in parallel, request multiple tasks with the following command. The default value is set to 1. 

--ntasks=<number>

For more advanced programs, you can request both multiple tasks and multiple CPUs per task.

Memory

All programs require a certain amount of memory to function properly. To see how much memory your program needs, you can check the documentation or run it in an interactive session and use the top command to profile it. To specify the memory for your job, use the mem-per-cpu option. 

--mem-per-cpu=<number>

Where <number> is memory per processor core. The default is 1GB.

Walltime

If you do not define how long your job will run, it will default to 30 minutes. The maximum walltime for the main partition (queue) is 24 hours. If you are running a job in the main partition and it will not complete in 24 hours, please contact XXX. If a job does not complete within the runtime specified in the script, it will terminate. To specify the walltime for your job, use the time option. 

--time=<hh:mm:ss>

Here, <hh:mm:ss> represents hours, minutes and seconds requested.

GPU's

Some programs can take advantage of the unique hardware architecture in a graphics processing unit (GPU). You have to check your documentation for compatibility. To request a GPU, add one of the following lines to your script: 

--gres=gpu:<number>

or 

--gres=gpu:<GPU_type>:<number>

where:

  • <number> is the number of GPUs per node requested.
  • <GPU_type> is one of the following: 2080ti.

Use the chart below to determine which of the above GPU_type's you wish to request:

GPU_type Max Number of GPUs Per Node GPU Model
2080ti 4 NVIDIA 2080TI

For interactive sessions utilizing GPUs, after salloc has run and you are on a compute node, you need to use the srun command to execute your commands: 

               $ nvidia-smi
               No devices were found
               
               $ srun -n1 nvidia-smi
               +-----------------------------------------------------------------------------+
               | NVIDIA-SMI 390.25                 Driver Version: 390.25                    |
               |-------------------------------+----------------------+----------------------|
               | GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr. ECC |
               | Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute M. |
               |===============================+======================+======================|
               |   0  RTX 2080TI          On   | 00000000:08:00.0 Off |                    0 |
               | N/A   29C    P8    25W / 225W |      0MiB /  4743MiB |      0%      Default |
               +-------------------------------+----------------------+----------------------+


Network/Cluster

Some programs solve problems that can be broken up into pieces and distributed across multiple computers that communicate over a network. This strategy often delivers greater performance. ALICE has compute nodes on two separate networks, Infiniband (100Gbps). To see these performance increases, your application or code must be specifically designed to take advantage of these low latency networks.

To request a specific network, you can add the following line to your resource request: 

--constraint=<network>

where <network> is IB.

Other

Besides the network a compute node lives on, there may be other features about it that you might need to specify for your program to run efficiently. Below is a table of some commonly requested node attributes that can be defined within the constraints of the sbatch and salloc commands.

Constraint What It Does
avx/avx2 Advanced Vector eXtensions, optimized math operations
Xeon Request compute nodes with Intel Xeon processors
Opteron Request compute nodes with AMD Opteron processors

Note: ALICE currently has avx/avx2 only.

Environment variables

Any environment variables that you have set with the sbatch command will be passed to your job. For this reason, if your program needs certain environment variables set to function properly, it is best to put them in your job script. This also makes it easier to reproduce your job results later, if necessary.

NOTE: Environment variables override any options set in a batch script. Command-line options override any previously set environment variables.

Information on some of the common input and output environment variables available within the sbatch job script is listed in the chart below. For additional information, see the man page for sbatch.

Environmental Variable Definition
$SLURM_JOB_ID ID of job allocation
$SLURM_SUBMIT_DIR Directory job where was submitted
$SLURM_JOB_NODELIST File containing allocated hostnames
$SLURM_NTASKS Total number of cores for job

Interactive jobs

Interactive jobs use the command salloc to allocate resources and put you in an interactive shell on compute node(s). Review the Determining What Resources to Request section above to determine which resources you may need to include as options for these commands.

Interactive jobs can be a helpful debugging tool for creating job scripts for batch job submission, described in the next section. This allows you to experiment on compute nodes with command options, and environmental variables, providing immediate feedback, which can help determine your workflow. 

salloc [options]

Recommendation: use of the option --ntasks enables Slurm to be efficient when allocating resources.

For testing, we recommend the following script as a starting point: 

salloc --ntasks=8 --time=1:00:00 --mem-per-cpu=2GB

Examples of Interactive Jobs in Slurm

To request a job to run 8 tasks on an IB node: 

 salloc --ntasks=8 --constraint=IB

Job scripts

After determining what your workflow will be and the compute resources needed, you can create a job script and submit it. To submit a script for a batch run you can use the command sbatch as in: 

sbatch <job_script>

Here is a sample job script. We'll break this sample script down, line by line, so you can see how a script is put together. 

#!/bin/bash
#SBATCH --ntasks=8
#SBATCH --time=01:00:00
          
cd /home/rcf-proj/tt1/test/ 
source /usr/alice/python/3.6.0/setup.sh 
python my.py

In general, a job script can be split into three parts:

Line 1: Interpreter

#!/bin/bash
  • Specifies the shell that will be interpreting the commands in your script. Here, the bash shell is used.
  • To avoid confusion, this should match your login shell.

Line 2-3: Slurm options

#SBATCH --ntasks=8
#SBATCH --time=01:00:00
  • Request cluster resources.
  • Lines that begin with #SBATCH will be ignored by the interpreter and read by the job scheduler
  • #SBATCH --ntasks=<number>: specifies the number of tasks (processes) that will run in this job. In this example, 8 tasks will run.
  • #SBATCH --time=<hh:mm:ss>: sets the maximum runtime for the job. In this example, the maximum runtime is 1 hour.

NOTE: Since 8 processor cores in total are being requested, the job will consume 8 core-hours. This is the unit of measurement that the job scheduler uses to keep track of compute time usage.

We recommend that you use #SBATCH --export=NONE to establish a clean environment, otherwise, Slurm will propagate current environmental variables to the job. This could impact the behaviour of the job, particularly for MPI jobs.

Lines 4-6: Job commands

cd /home/rcf-proj/tt1/test/ 
source /usr/alice/python/3.6.0/setup.sh 
python my.py
  • These lines provide the sequence of commands needed to run your job.
  • These commands will be executed on the allocated resources.
  • cd /home/rcf-proj/tt1/test/: Changes the working directory to /home/rcf-proj/tt1/test/
  • source /usr/alice/python/3.6.0/setup.sh: Prepares the environment to run Python 3.6.0.
  • python my.py: Runs the program on the resources allocated. In this example it runs python, specifying my.py in the current directory, /home/rcf-proj/tt1/test, as the argument.

Example of a simple MPI script: Hello World MPI

This is an example of a simple MPI program that runs on multiple processors. It demonstrates the use of Slurm's interactive mode and ALICE's OpenMP setup.

__HelloWorldMPI.c__ 

  1 #include "mpi.h"
  2 #include
  3 #include
  4
  5 int main (int argc, char *argv[])
  6 {
  7 int i, rank, size, namelen;
  8 char name [MPI_MAX_PROCESSOR_NAME];
  9 
  10 MPI_Init (&argc, &argv);
  11
  12 MPI_Comm_size (MPI_COMM_WORLD, &size);
  13 MPI_Comm_rank (MPI_COMM_WORLD, &rank);
  14 MPI_Get_processor_name (name, &namelen);
  15
  16 printf ("Hello World from rank %d running on %s!\n", rank, name);
  17
  18 if (rank == 0 )
  19 printf ("MPI World size = %d processes\n", size);
  20
  21 MPI_Finalize ();
  22 
  23 }

You will need to source the OpenMP software based on your shell, compile and test the code. Here is an example using the copy command in a bash shell and testing in your home directory. 

  [me@nodelogin01~]$ cp /home/rcf-proj/workshop/introSLURM/helloMPI/helloWorldMPI.c ~
  [me@nodelogin01~]$ source /usr/alice/openmp/setup.sh
  [me@nodelogin01~]$ mpicc -o helloWorldMPI helloWorldMPI.c
  [me@nodelogin01~]$ ls -l helloWorldMPI
  -rwxr-xr-x 1 user nobody 8800 Feb 21 14:32 helloWorldMPI
  [me@nodelogin01~]$ salloc --ntasks=30  
  ----------------------------------------
  Begin SLURM Prolog Wed 21 Feb 2018 02:34:35 PM PST
  Job ID:        767
  Username:      user
  Accountname:   lc_alice1
  Name:          bash
  Partition:     quick
  Nodes:         node[001,007]
  TasksPerNode:  15(x2)
  CPUSPerTask:   Default[1]
  TMPDIR:        /tmp/767.quick
  Cluster:       alice
  HSDA Account:  false
  End SLURM Prolog
  ----------------------------------------
  [me@node015~]$ source /usr/alice/openmp/setup.sh
  [me@node015~]$ srun --ntasks=30 --mpi=pmi2 ./helloWorldMPI
  Hello World from rank 10 running on node001!
  Hello World from rank 19 running on node002!
  Hello World from rank 11 running on node003!
  Hello World from rank 3 running on node004!
  Hello World from rank 17 running on node005!
  Hello World from rank 4 running on node006!
  Hello World from rank 7 running on node007!
  Hello World from rank 2 running on node008!
  Hello World from rank 12 running on node009!
  Hello World from rank 21 running on node010!
  Hello World from rank 26 running on node011!
  Hello World from rank 9 running on node012!
  Hello World from rank 13 running on node013!
  Hello World from rank 22 running on node014!
  Hello World from rank 6 running on node015!
  Hello World from rank 5 running on node016!
  Hello World from rank 20 running on node017!
  Hello World from rank 15 running on node018!
  Hello World from rank 18 running on node019!
  Hello World from rank 14 running on node020!
  Hello World from rank 23 running on node851!
  Hello World from rank 28 running on node852!
  Hello World from rank 8 running on node0853!
  Hello World from rank 27 running on node0854!
  Hello World from rank 16 running on node0855!
  Hello World from rank 25 running on node0856!
  Hello World from rank 1 running on node857!
  Hello World from rank 29 running on node858!
  Hello World from rank 24 running on node859!
  Hello World from rank 0 running on node860!
  MPI World size = 30 processes
  [me@node015~]$ logout
  salloc: Relinquishing job allocation 767
  [me@nodelogin01~]$

The srun command runs the helloWorldMPI program on 30 tasks. Slurm provides information about the job. Most of the information is self-explanatory. Only 1 cpu was used per task, and the job ran across 2 nodes. Note that for multi-node jobs, the number of tasks per node lines up with the nodes utilized by the job. In this example, 22 tasks were run on node014, while 8 were run on node853.

Monitoring Your Jobs

To monitor the status of your jobs in the Slurm partitions, use the squeue command. You will only have access to see your queued jobs. Options to this command will help filter and format the output to meet your needs. See the man page for more information.

Squeue Option Action
  ---user=<username> Lists entries only belonging to username, only available to administrator
  ---jobs=<job_id> List entry, if any, for job_id
  ---partition=<partition_name> Lists entries only belonging to partition_name

Here is an example of using squeue. 

         [me@nodelogin01~]$ squeue
             JOBID PARTITION      NAME     USER ST      TIME  NODES NODELIST(REASON)
             537   cpu-short      helloWor user R       0:47      2 node[004,010]

The output of squeue provides the following information:

Squeue Output Column Header Definition
JOBID Unique number assigned to each job
PARTITION Partition id the job is scheduled to run or is running, on
NAME Name of the job, typically the job script name
USER User id of the job
ST Current state of the job (see table below for meaning)
TIME Amount of time job has been running
NODES Number of nodes job is scheduled to run across
NODELIST(REASON) If running, the list of the nodes the job is running on. If pending, the reason the job is waiting

Valid Job States

Code State Meaning
CA Canceled Job was cancelled
CD Completed Job completed
CF Configuring Job resources being configured
CG Completing Job is completing
F Failed Job terminated with non-zero exit code
NF Node Fail Job terminated due to failure of node(s)
PD Pending Job is waiting for compute node(s)
R Running Job is running on compute node(s)
TO Timeout Job terminated upon reaching its time limit

Job in Queue

Sometimes a long queue time is an indication that something is wrong or the cluster could simply be busy. You can check to see how much longer your job will be in the queue with the command: 

squeue --start --job <job_id>

Please note that this is only an estimate based on current and historical utilization and results can fluctuate. Here is an example of using squeue with the start and job options. 

[me@nodelogin01~]$ squeue --start --job 384
 JOBID PARTITION 	NAME 	USER ST          START_TIME  NODES SCHEDNODES   NODELIST(REASON)

  384      main    star-lac     user PD 2018-02-12T16:09:31  	 2 (null)       (Resources)

In the above example, the job is in a pending to run state, because there are no resources available that will allow it to launch. The job is expected to start at approximately 16:09:31 on 02-12-2018. This is an estimation, as jobs ahead of it may complete sooner, freeing up necessary resources for this job. If you believe there is a problem with your job starting, and have checked your scripts for typos, send email to helpdesk@alice.leidenuniv.nl. Let us know your job ID along with a description of your problem and we can check to see if anything is wrong.

Job is Running

Another mechanism for obtaining job information is with the command scontrol show job <job_id>. This provides more detail on the resources requested and reserved for your job. It will be able to tell the status of your job, but not the status of the programs running within the job. Here is an example using scontrol. 

[me@nodelogin01~]$ scontrol show job 384
JobId=390 JobName=star-ali
   UserId=ttrojan(12345) GroupId=uscno1(01) MCS_label=N/A
   Priority=1 Nice=0 Account=lc_ucs1 QOS=lc_usc1_maxcpumins
   JobState=PENDING Reason=Resources Dependency=(null)
   Requeue=1 Restarts=0 BatchFlag=0 Reboot=0 ExitCode=0:0
   RunTime=00:00:00 TimeLimit=00:30:00 TimeMin=N/A
   SubmitTime=2018-02-12T15:39:57 EligibleTime=2018-02-12T15:39:57
   StartTime=2018-02-12T16:09:31 EndTime=2018-02-12T16:39:31 Deadline=N/A
   PreemptTime=None SuspendTime=None SecsPreSuspend=0
   Partition=quick AllocNode:Sid=node-login3:21524
   ReqNodeList=(null) ExcNodeList=(null)
   NodeList=(null) SchedNodeList=node[001,010]
   NumNodes=2-2 NumCPUs=2 NumTasks=2 CPUs/Task=1 ReqB:S:C:T=0:0:*:*
   TRES=cpu=2,mem=2048,node=2
   Socks/Node=* NtasksPerN:B:S:C=0:0:*:1 CoreSpec=*
   MinCPUsNode=1 MinMemoryCPU=1G MinTmpDiskNode=0
   Features=[myri|IB] DelayBoot=00:00:00
   Gres=(null) Reservation=(null)
   OverSubscribe=NO Contiguous=0 Licenses=(null) Network=(null)
   Command=(null)
   WorkDir=/auto/rcf-00/ttrojan
   Power=
[me@nodelogin01~]$

When your job is done, check the log files to make sure everything has completed without incident.

Job Organization

Slurm has some handy features to help you keep organized, when you add them to the job script, or the salloc command.

Syntax Meaning
  --mail-user=<email> Where to send email alerts
  ---mail-type="<BEGIN|END|FAIL|REQUEUE|ALL>" When to send email alerts
  ---output=<out_file> Name of output file
  ---error=<error_file> Name of error file
  ---account=<account_id> Which account to charge cpu time
  ---job-name=<job_name> Job name (will display in squeue output)

Get Job Usage Statistics

It can be helpful to fine-tune your job or requests knowing the resources that were used. The 

sacct --jobs=<job_id>

command can provide some usage statistics for jobs that are running, and those that have completed.

Output can be filtered and formatted to provide specific information, including requested memory and peak memory used during job execution. See the man pages for more information. 


      [me@nodelogin01~]$ sacct --jobs=383 --format=User,JobID,account,Timelimit,elapsed,ReqMem,MaxRss,ExitCode
           User         JobID      Account     Timelimit      Elapsed       ReqMem      MaxRSS ExitCode
      --------- ------------- ------------ ------------- ------------ ------------ ----------- --------
           user 383                lc_alice1      02:00:00     01:28:59  	 1Gc                  0:0
            	383.extern         lc_alice1                   01:28:59          1Gc                  0:0
      [me@nodelogin01~]$

Canceling a Job

Whether your job is running or waiting in the queue, you can cancel the job using the Canceling <job_id> command. Use squeue if you do not recall the job id. 


     [me@nodelogin01~]$ scancel 384
     [me@nodelogin01~]$

Monitoring the Partitions in the Clusters

To see the overall status of the partitions and nodes in the clusters run the sinfo command. As with the other monitoring commands, there are additional options and formatting available. 

 [me@nodelogin01~]$ sinfo
 PARTITION      AVAIL  TIMELIMIT  NODES  STATE NODELIST
 testing           up    1:00:00      2   idle nodelogin[01-02]
 cpu-short*        up    3:00:00      5    mix node[002,005,007,012-013]
 cpu-short*        up    3:00:00      2  alloc node[001,003]
 cpu-short*        up    3:00:00     13   idle node[004,006,008-011,014-020]
 cpu-medium        up 1-00:00:00      5    mix node[002,005,007,012-013]
 cpu-medium        up 1-00:00:00      2  alloc node[001,003]
 cpu-medium        up 1-00:00:00     13   idle node[004,006,008-011,014-020]
 cpu-long          up 7-00:00:00      5    mix node[002,005,007,012-013]
 cpu-long          up 7-00:00:00      2  alloc node[001,003]
 cpu-long          up 7-00:00:00     13   idle node[004,006,008-011,014-020]
 gpu-short         up    3:00:00      6    mix node[852,855,857-860]
 gpu-short         up    3:00:00      4  alloc node[851,853-854,856]
 gpu-medium        up 1-00:00:00      6    mix node[852,855,857-860]
 gpu-medium        up 1-00:00:00      4  alloc node[851,853-854,856]
 gpu-long          up 7-00:00:00      6    mix node[852,855,857-860]
 gpu-long          up 7-00:00:00      4  alloc node[851,853-854,856]
 mem               up   infinite      1  alloc node801
 notebook-cpu      up   infinite      2    mix node[002,005]
 notebook-cpu      up   infinite      2  alloc node[001,003]
 notebook-cpu      up   infinite      1   idle node004
 notebook-gpu      up   infinite      1    mix node852
 notebook-gpu      up   infinite      1  alloc node851
 playground-cpu    up   infinite      2    mix node[002,005]
 playground-cpu    up   infinite      2  alloc node[001,003]
 playground-cpu    up   infinite      1   idle node004
 playground-gpu    up   infinite      1    mix node852
 playground-gpu    up   infinite      1  alloc node851
 [me@nodelogin01~]$

Monitor the nodes in the cluster

To get detailed information on a particular compute node, use the scontrol show node=<nodename> command. 

     [me@nodelogin01~]$ scontrol show node="node020"
     NodeName=node020 Arch=x86_64 CoresPerSocket=8
        CPUAlloc=16 CPUErr=0 CPUTot=16 CPULoad=1.01
        AvailableFeatures=IB,avx,avx2,xeon,E5-2640v3,nx360
        ActiveFeatures=IB,avx,avx2,xeon,E5-2640v3,nx360
        Gres=(null)
        NodeAddr=node020 NodeHostName=node020 Version=17.02
        OS=Linux RealMemory=63000 AllocMem=16384 FreeMem=45957 Sockets=2 Boards=1
        MemSpecLimit=650
        State=ALLOCATED ThreadsPerCore=1 TmpDisk=0 Weight=16 Owner=N/A MCS_label=N/A
        Partitions=route_queue,quick,main,large,long,testSharedQ,restrictedQ,preemptMeQ,preemptYouQ
        BootTime=2018-02-08T04:08:36 SlurmdStartTime=2018-02-09T12:55:53
        CfgTRES=cpu=16,mem=63000M
        AllocTRES=cpu=16,mem=63000M
        CapWatts=n/a
        CurrentWatts=0 LowestJoules=0 ConsumedJoules=0
        ExtSensorsJoules=n/s ExtSensorsWatts=0 ExtSensorsTemp=n/s
     
     
     [me@nodelogin01~]$

Getting Help

If you need help with using Slurm, please email us at helpdesk@alice.leidenuniv.nl

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