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Batch_system

Timestamp:: Oct 15, 2021, 11:33:43 AM (3 years ago)
Author:: Jochen Kreutz
Comment:: Move heterogeneous and workflow stuff to own wiki pages

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Public/User_Guide/Batch_system

-                      v53
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 Hello World from rank 0 of 8 on dp-esb34
 }}}
-== Heterogeneous jobs ==
-As of version 17.11 of Slurm, heterogeneous jobs are supported. For example, the user can run:
-{{{
-srun --account=deep --partition=dp-cn -N 1 -n 1 hostname : --partition=dp-dam -N 1 -n 1 hostname
-dp-cn01
-dp-dam01
-}}}
-Please notice the `:` separating the definitions for each sub-job of the heterogeneous job. Also, please be aware that it is possible to have more than two sub-jobs in a heterogeneous job.
-The user can also request several sets of nodes in a heterogeneous allocation using `salloc`. For example:
-{{{
-salloc --partition=dp-cn -N 2 : --partition=dp-dam -N 4
-}}}
-In order to submit a heterogeneous job via `sbatch`, the user needs to set the batch script similar to the following one:
-{{{#!sh
-#!/bin/bash
-#SBATCH --job-name=imb_execute_1
-#SBATCH --account=deep
-#SBATCH --mail-user=
-#SBATCH --mail-type=ALL
-#SBATCH --output=job.out
-#SBATCH --error=job.err
-#SBATCH --time=00:02:00
-#SBATCH --partition=dp-cn
-#SBATCH --nodes=1
-#SBATCH --ntasks=12
-#SBATCH --ntasks-per-node=12
-#SBATCH --cpus-per-task=1
-#SBATCH packjob
-#SBATCH --partition=dp-dam
-#SBATCH --constraint=
-#SBATCH --nodes=1
-#SBATCH --ntasks=12
-#SBATCH --ntasks-per-node=12
-#SBATCH --cpus-per-task=1
-srun ./app_cn : ./app_dam
-}}}
-Here the `packjob` keyword allows to define Slurm parameters for each sub-job of the heterogeneous job. Some Slurm options can be defined once at the beginning of the script and are automatically propagated to all sub-jobs of the heterogeneous job, while some others (i.e. `--nodes` or `--ntasks`) must be defined for each sub-job. You can find a list of the propagated options on the [https://slurm.schedmd.com/heterogeneous_jobs.html#submitting Slurm documentation].
-When submitting a heterogeneous job with this colon notation using ParaStationMPI, a unique `MPI_COMM_WORLD` is created, spanning across the two partitions. If this is not desired, one can use the `--pack-group` key to submit independent job steps to the different node-groups of a heterogeneous allocation:
-{{{#!sh
-srun --pack-group=0 ./app_cn ; srun --pack-group=1 ./app_dam
-}}}
-Using this configuration implies that inter-communication must be established manually by the applications during run time, if needed.
-For more information about heterogeneous jobs please refer to the [https://slurm.schedmd.com/heterogeneous_jobs.html relevant page] of the Slurm documentation.
-=== Heterogeneous jobs with MPI communication across modules ===
-In order to establish MPI communication across modules using different interconnect technologies, some special Gateway nodes must be used. On the DEEP-EST system, MPI communication across gateways is needed only between Infiniband and Extoll interconnects.
-**Attention:** Only !ParaStation MPI supports MPI communication across gateway nodes.
-This is an example job script for setting up an Intel MPI benchmark between a Cluster and a DAM node using a IB <-> Extoll gateway for MPI communication:
-{{{#!sh
-#!/bin/bash
-# Script to launch IMB PingPong between DAM-CN using 1 Gateway
-# Use the gateway allocation provided by SLURM
-# Use the packjob feature to launch separately CM and DAM executable
-# General configuration of the job
-#SBATCH --job-name=modular-imb
-#SBATCH --account=deep
-#SBATCH --time=00:10:00
-#SBATCH --output=modular-imb-%j.out
-#SBATCH --error=modular-imb-%j.err
-# Configure the gateway daemon
-#SBATCH --gw_num=1
-#SBATCH --gw_psgwd_per_node=1
-# Configure node and process count on the CM
-#SBATCH --partition=dp-cn
-#SBATCH --nodes=1
-#SBATCH --ntasks-per-node=1
-#SBATCH packjob
-# Configure node and process count on the DAM
-#SBATCH --partition=dp-dam-ext
-#SBATCH --nodes=1
-#SBATCH --ntasks-per-node=1
-# Echo job configuration
-echo "DEBUG: SLURM_JOB_NODELIST=$SLURM_JOB_NODELIST"
-echo "DEBUG: SLURM_NNODES=$SLURM_NNODES"
-echo "DEBUG: SLURM_TASKS_PER_NODE=$SLURM_TASKS_PER_NODE"
-# Set the environment to use PS-MPI
-module --force purge
-module use $OTHERSTAGES
-module load Stages/Devel-2019a
-module load Intel
-module load ParaStationMPI
-# Show the hosts we are running on
-srun hostname : hostname
-# Execute
-APP="./IMB-MPI1 Uniband"
-srun ${APP}  : ${APP}
-}}}
-**Attention:** During the first part of 2020, only the DAM nodes will have Extoll interconnect (and only the nodes belonging to the `deep-dam-ext` partition will have Extoll active), while the CM and the ESB nodes will be connected via Infiniband. This will change later during the course of the project (expected end of Summer 2020), when the ESB will be equipped with Extoll connectivity (Infiniband will be removed from the ESB and left only for the CM).
-A general description of how the user can request and use gateway nodes is provided at [https://apps.fz-juelich.de/jsc/hps/jureca/modular-jobs.html#mpi-traffic-across-modules this section] of the JURECA documentation.
-**Attention:** some information provided on the JURECA documentation do not apply for the DEEP system. In particular:
-* as of 31/03/2020, the DEEP system has 2 gateway nodes.
-* As of 09/01/2020 the gateway nodes are exclusive to the job requesting them. Given the limited number of gateway nodes available on the system, this may change in the future.
-* As of 09/04/2020 the `xenv` utility (necessary on JURECA to load modules for different architectures - Haswell and KNL) is not needed any more on DEEP when using the latest version of ParaStationMPI (currently available in the `Devel-2019a` stage and soon available on the default production stage).
-{{{#!comment
-If you need to load modules before launching the application, it's suggested to create wrapper scripts around the applications, and submit such scripts with srun, like this:
-{{{#!sh
-...
-srun ./script_sdv.sh : ./script_knl.sh
-}}}
-where a script should contain:
-{{{#!sh
-#!/bin/bash
-module load ...
-./app_sdv
-}}}
-This way it will also be possible to load different modules on the different partitions used in the heterogeneous job.
-}}}
-== Workflows ==
-The version of Slurm installed on the system enables workflows (chains of jobs) with the possibility of having some overlap between the dependent jobs. This allows them to exchange data over the network rather than writing and reading it using a common file system.
-Workflows can be submitted in two ways:
-- using the new `--delay` option provided in `sbatch` command, which allows to start a job with a fixed delay from the start of the previous job;
-- submitting separate jobs using an `afterok` dependency and later requesting a change in dependency type from `afterok` to `after` (using our provided shared library), which allows the second job to start if resources are available.
-An example project that uses all the features discussed is provided [https://gitlab.version.fz-juelich.de/DEEP-EST/mpi_connect_test here].
-The following simple example script helps to understand the mechanism of new {{{delay}}} switch for workflows.
-{{{#!sh
-[huda1@deepv scripts]$ cat test.sh
-#!/bin/sh
-NAME=$(hostname)
-echo "$NAME: Going to sleep for $1 seconds"
-sleep $1
-echo "$NAME: Awake"
-[huda1@deepv scripts]$ cat batch_workflow.sh
-#!/bin/bash
-#SBATCH -p sdv -N2 -t3
-#SBATCH packjob
-#SBATCH -p sdv -N1 -t3 --delay 2
-srun test.sh 175
-[huda1@deepv scripts]$
-}}}
-In the above {{{sbatch}}} script, the usage of {{{--delay}}} can be seen. The option takes values in minutes and allows us to delay the subsequent job of by a user-defined number of minutes from the start of the first job in the job pack. After submission of this job pack (which uses the same syntax as a heterogeneous job), Slurm divides it into separate jobs. Also, Slurm ensures that the delay is respected by using reservations, rather than the usual scheduler.
-Here is the example execution of this script.
-{{{
-[huda1@deepv scripts]$ sbatch batch_workflow.sh
-Submitted batch job 81458
-[huda1@deepv scripts]$ squeue -u huda1
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-       sdv batch_wo    huda1 CF       0:01      2 deeper-sdv[02-03]
-       sdv batch_wo    huda1 PD       0:00      1 (Reservation)
-[huda1@deepv scripts]$
-}}}
-Here the second job (81459) will start 2 minutes after the start of the first job (81458), and it is listed as `PD` (`Pending`) with reason `Reservation` because it will start as soon as its reservation will begin.
-Similarly, the output files will be different for each separated job in the job pack. the final outputs are:
-{{{
-[huda1@deepv scripts]$ cat slurm-81458.out
-deeper-sdv02: Going to sleep for 175 seconds
-deeper-sdv03: Going to sleep for 175 seconds
-deeper-sdv02: Awake
-deeper-sdv03: Awake
-[huda1@deepv scripts]$ cat slurm-81459.out
-deeper-sdv01: Going to sleep for 175 seconds
-deeper-sdv01: Awake
-[huda1@deepv scripts]$
-}}}
-Another feature to note is that if there are multiple jobs in a job pack and any number of consecutive jobs have the same {{{delay}}} values, they are combined into a new heterogeneous job. This allows to have heterogeneous jobs within workflows. Here is an example of such a script:
-{{{#!sh
-[huda1@deepv scripts]$ cat batch_workflow_complex.sh
-#!/bin/bash
-#SBATCH -p sdv -N 2 -t 3
-#SBATCH -J first
-#SBATCH packjob
-#SBATCH -p sdv -N 1 -t 3 --delay 2
-#SBATCH -J second
-#SBATCH packjob
-#SBATCH -p sdv -N 1 -t 2 --delay 2
-#SBATCH -J second
-#SBATCH packjob
-#SBATCH -p sdv -N 2 -t 3 --delay 4
-#SBATCH -J third
-if [ "$SLURM_JOB_NAME" == "first" ]
-then
-        srun ./test.sh 150
-elif [ "$SLURM_JOB_NAME" == "second" ]
-then
-        srun ./test.sh 150 : ./test.sh 115
-elif [ "$SLURM_JOB_NAME" == "third" ]
-then
-        srun ./test.sh 155
-fi
-[huda1@deepv scripts]$
-}}}
-Note the {{{delay}}} values for the second and third job in the script are equal.
-**Attention** The {{{delay}}} value for the 4th job ({{{-J third}}}) is relative to the start of the first job and not from the start of middle 2 jobs. So it will start after 2 minutes of the start time of the middle jobs. Also, note the usage of the environment variable {{{SLURM_JOB_NAME}}} in the script to decide which command to run in which job. The example execution leads to the following:
-The example execution leads to the following:
-{{{
-[huda1@deepv scripts]$ sbatch batch_workflow_complex.sh
-Submitted batch job 81460
-[huda1@deepv scripts]$ squeue -u huda1
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-+0       sdv   second    huda1 PD       0:00      1 (Resources)
-+1       sdv   second    huda1 PD       0:00      1 (Resources)
-       sdv    third    huda1 PD       0:00      2 (Resources)
-       sdv    first    huda1 PD       0:00      2 (Resources)
-[huda1@deepv scripts]$
-}}}
-Note that the submitted heterogeneous job has been divided into a single job (81460), a job pack (81461) and again a single job (81643). Similarly, three different output files will be generated, one for each new job.
-{{{
-[huda1@deepv scripts]$ cat slurm-81460.out
-deeper-sdv03: Going to sleep for 150 seconds
-deeper-sdv04: Going to sleep for 150 seconds
-deeper-sdv03: Awake
-deeper-sdv04: Awake
-[huda1@deepv scripts]$ cat slurm-81461.out
-deeper-sdv01: Going to sleep for 150 seconds
-deeper-sdv02: Going to sleep for 115 seconds
-deeper-sdv02: Awake
-deeper-sdv01: Awake
-[huda1@deepv scripts]$ cat slurm-81463.out
-deeper-sdv01: Going to sleep for 155 seconds
-deeper-sdv02: Going to sleep for 155 seconds
-deeper-sdv01: Awake
-deeper-sdv02: Awake
-[huda1@deepv scripts]$
-}}}
-If a job exits earlier than the allocated time asked by the user, the corresponding reservation for this job is deleted 5 minutes after the end of the job, automatically and the resources become available for the other jobs. However, users should be careful with the requested time when submitting workflows as the larger time values can delay the scheduling of the workflows depending on the situation of the resources.
-The workflows created using {{{delay}}} switch ensure overlap between the applications. Instead, using the alternative method (which uses Slurm job dependencies) does not ensure a time overlap between two consecutive jobs of a workflow. Though, in this case users do not need to guess the time a job will take and how much should the delay between jobs starting times should be.
-Jobs can be chained in Slurm with the aid of the following script:
-{{{#!sh
-[huda1@deepv scripts]$ cat chain_jobs.sh
-#!/usr/bin/env bash
-if [ $# -lt 3 ]
-then
-    echo "$0: ERROR (MISSING ARGUMENTS)"
-    exit 1
-fi
-LOCKFILE=$1
-DEPENDENCY_TYPE=$2
-shift 2
-SUBMITSCRIPT=$*
-if  [ -f $LOCKFILE ]
-then
-    if [[ "$DEPENDENCY_TYPE" =~ ^(after|afterany|afterok|afternotok)$ ]]; then
-        DEPEND_JOBID=`head -1 $LOCKFILE`
-        echo "sbatch --dependency=${DEPENDENCY_TYPE}:${DEPEND_JOBID} $SUBMITSCRIPT"
-        JOBID=`sbatch --dependency=${DEPENDENCY_TYPE}:${DEPEND_JOBID} $SUBMITSCRIPT`
-    else
-        echo "$0: ERROR (WRONG DEPENDENCY TYPE: choose among 'after', 'afterany', 'afterok' or 'afternotok')"
-    fi
-else
-    echo "sbatch $SUBMITSCRIPT"
-    JOBID=`sbatch $SUBMITSCRIPT`
-fi
-echo "RETURN: $JOBID"
-# the JOBID is the last field of the output line
-echo ${JOBID##* } > $LOCKFILE
-exit 0
-}}}
-This is a modified version of the of the `chainJobs.sh` included in JUBE, which allows to select the desired dependency type between two consecutive jobs.
-Here is an example of submission of a workflow with Slurm dependencies using the previous script (here called `chain_jobs.sh`):
-{{{
-[huda1@deepv scripts]$ ./chain_jobs.sh lockfile afterok simple_job.sh
-sbatch simple_job.sh
-RETURN: Submitted batch job 98626
-[huda1@deepv scripts]$ ./chain_jobs.sh lockfile afterok simple_job.sh
-sbatch --dependency=afterok:98626 simple_job.sh
-RETURN: Submitted batch job 98627
-[huda1@deepv scripts]$ ./chain_jobs.sh lockfile afterok simple_job.sh
-sbatch --dependency=afterok:98627 simple_job.sh
-RETURN: Submitted batch job 98628
-[huda1@deepv scripts]$ squeue -u huda1
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-       sdv simple_j    huda1 PD       0:00      2 (Dependency)
-       sdv simple_j    huda1 PD       0:00      2 (Dependency)
-       sdv simple_j    huda1  R       0:21      2 deeper-sdv[01-02]
-[huda1@deepv scripts]$ scontrol show job 98628 | grep Dependency
-   JobState=PENDING Reason=Dependency Dependency=afterok:98627
-[huda1@deepv scripts]$ cat lockfile
-}}}
-Please note that `lockfile` must not exist previous to the first submission.
-After the first job submission, that file will contain the id of last submitted job, which is later used by the subsequent call to the `chain_job.sh` script to set the dependency.
-=== {{{slurm_workflow}}} Library ===
-In order to improve the usability of workflows, a library has been developed and deployed on the system to allow users to interact with the scheduler from within applications involved in a workflow.
-The library is called `slurm_workflow`.
-The library has two functions.
-The first function is relevant to workflows created using the `--delay` switch and  moves all the reservations of the remaining workflow jobs.
-{{{
-/*
-IN:    number of minutes from now. The start time of the next reservation of the workflow is moved to this time if doable.
-OUT:   0 successful, non zero unsuccessful.slurm_wf_error is set.
-*/
-int slurm_wf_move_all_res(uint32_t t);
-}}}
-The minimum value usable for the parameter is currently 2 (minutes).
-The second function changes the dependencies type of all jobs dependent on the current job from {{{afterok:job_id}}} to {{{after:job_id}}}.
-{{{
-/*
-OUT: 0 successful, error no otherwise.
-*/
-int slurm_change_dep();
-}}}
-This enables the jobs in workflow eligible for allocation by Slurm.
-Both functions allow an application to notify the scheduler that it is ready for the start of the subsequent jobs of a workflow.
-This is particularly relevant in case a network connection must be established between the two applications, but only after a certain time from the start of the first job.
-When using the library, the header file can be included using `#include <slurm/slurm_workflow.h>` and the library should be linked against using `-lslurm_workflow -lslurm`.