Slurm configuration

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Slurm configuration and slurm.conf

Starting from Slurm 17.11 you probably want to look at the example configuration files found in this RPM:

rpm -q slurm-example-configs

On the Head/Master node you should build a slurm.conf configuration file. When it has been fully tested, then slurm.conf must be copied to all other nodes.

It is mandatory that the slurm.conf file is identical on all nodes in the system!

Consult the Slurm_Quick_Start Administrator Guide. See also man slurm.conf or the on-line slurm.conf documentation.

Copy the HTML files to your $HOME directory, for example:

mkdir $HOME/slurm/
cp -rp /usr/share/doc/slurm-*/html $HOME/slurm/

Configless Slurm setup

With Slurm 20.02 there is a new configless feature that allows the compute nodes — specifically the slurmd process — and user commands running on login nodes to pull configuration information directly from the slurmctld instead of from a pre-distributed local file.

Notes:

  • Slurm versions 20.02.0 and 20.02.1 had a slurm_pam_adopt issue when using configless mode, see bug_8712.

  • Slurm versions up to an including 20.11.7 may start the slurmd service before the network is fully up, causing slurmd to fail. Observed on some CentOS 8 systems, see bug_11878. The workaround is to restart the slurmd service manually.

The order of precedence for determining what configuration source to use is listed in the configless page.

On startup the compute node slurmd will query the slurmctld server that you specify, and the configuration files will be pulled to the node’s local disk. The pulled slurmd conguration files are stored in this folder:

$ ls -ld /run/slurm/conf
lrwxrwxrwx. 1 root root 28 Mar 18 08:24 /run/slurm/conf -> /var/spool/slurmd/conf-cache
$ ls -la /var/spool/slurmd/conf-cache
total 24
drwxr-xr-x. 2 root  root     81 Mar 18 08:24 .
drwxr-xr-x. 3 slurm slurm    92 Mar 18 08:24 ..
-rw-r--r--. 1 root  root    506 Mar 18 08:24 cgroup.conf
-rw-r--r--. 1 root  root    165 Mar 18 08:24 gres.conf
-rw-r--r--. 1 root  root  11711 Mar 18 08:24 slurm.conf
-rw-r--r--. 1 root  root   2538 Mar 18 08:24 topology.conf

Testing configless setup

The slurmctld server information can preferably be provided in a DNS SRV record for your DNS zone, pointing to port 6817 on your slurmctld server(s):

_slurmctld._tcp 3600 IN SRV 10 0 6817 slurm-backup
_slurmctld._tcp 3600 IN SRV 0 0 6817 slurm-master

To verify the DNS setup, install these packages with tools required below:

yum install bind-utils hostname

Lookup the SRV record by either of:

dig +short -t SRV -n _slurmctld._tcp.`dnsdomainname`
host -t SRV _slurmctld._tcp.`dnsdomainname`

Add login and submit nodes to slurm.conf

The SLUG 2020 talk (see Slurm_Publications) Field Notes 4: From The Frontlines of Slurm Support by Jason Booth recommends on slide 31 to run slurmd on all login nodes in configless Slurm mode:

We generally suggest that you run a slurmd to manage the configs on those nodes that run client commands, including submit or login nodes

The simplest way to achieve this is described in bug_9832:

  1. Add the login and submit nodes to slurm.conf as default-configured nodes, for example:

    NodeName=login1,login2

    and do not add these nodes to any partitions!

    Remember to add these nodes to the topology.conf file as well, for example:

    SwitchName=switch1 Nodes=login1,login2

    and open the firewall on these nodes (see the firewall section below).

  2. Install the slurm-slurmd RPM on the login nodes and make sure to create the logging directory:

    mkdir /var/log/slurm
chown slurm.slurm /var/log/slurm

    Then start the slurmd service:

    systemctl enable slurmd
systemctl start slurmd

  3. Verify that the Slurm config files have been downloaded:

    ls -l /run/slurm/conf

Configuring a custom slurmd service

The SLURMD_OPTIONS can be defined in the file /etc/sysconfig/slurmd:

SLURMD_OPTIONS=-M --conf-server <name of slurmctld server>

which is read by the Systemd service file /usr/lib/systemd/system/slurmd.service.

Another way is to use systemctl edit slurmd to create an override file, see the systemctl manual page. The override files will be placed in the /etc/systemd/system/slurmd.service.d/ folder.

An example file /etc/systemd/system/slurmd.service.d/override.conf file could be:

[Service]
Environment="SLURMD_OPTIONS=-M --conf-server <name of slurmctld server>"

In this example the slurmd option -M locks slurmd in memory, and the slurmctld server name is given. See configless and the slurmd manual page.

Configurator for slurm.conf

You can generate an initial slurm.conf file using several tools:

  • The Slurm Version 17.02 Configuration Tool configurator.

  • The Slurm Version 17.02 Configuration Tool - Easy Version configurator.easy.

  • Build a configuration file using your favorite web browser and open file://$HOME/slurm/html/configurator.html or the simpler file configurator.easy.html.

  • Copy the more extensive sample configuration file .../etc/slurm.conf.example from the source tar-ball and use it as a starting point.

Save the resulting output to /etc/slurm/slurm.conf.

The parameters are documented in man slurm.conf and slurm.conf, and it’s recommended to read through the long list of parameters.

In slurm.conf it’s essential that the important spool directories and the slurm user are defined correctly:

SlurmUser=slurm
SlurmdSpoolDir=/var/spool/slurmd
StateSaveLocation=/var/spool/slurmctld

NOTE: These spool directories must be created manually and owned by user slurm (see below), as they are not part of the RPM installation.

Starting slurm daemons at boot time

Enable startup of services as appropriate for the given node:

systemctl enable slurmd      # Compute node
systemctl enable slurmctld   # Master/head server
systemctl enable slurmdbd    # Database server

The systemd service files are /usr/lib/systemd/system/slurm*.service.

Slurm 16.05 init script bug

The Slurm 16.05 RPM packages install and configure (it’s bug 3371) the init boot script /etc/init.d/slurm - even for systems like RHEL/CentOS 7 which use systemd! The bug has been fixed in Slurm 17.02.

If you have Slurm 16.05 (or older) on RHEL/CentOS 7, check if you have enabled the init script:

chkconfig --list slurm

We should modify this setup to use systemd exclusively. First disable the init script on all nodes, including login-nodes:

chkconfig --del slurm

In order to avoid accidentally starting services with /etc/init.d/slurm, it is best to also remove the offending script:

rm -f /etc/init.d/slurm

Then enable the services properly as shown above.

Beware that any update of the Slurm 16.05 RPMs will recreate the missing /etc/init.d/slurm file, so you must remember to remove it after every update.

Manual startup of services

If there is any question about:

  • The availability and sanity of the daemons’ spool directories (perhaps on remote storage)

  • The MySQL database

  • If Slurm has been upgraded to a new version

it may be a good idea to start each service manually in stead of automatically as shown above. For example:

slurmctld -Dvvvv

Watch the the output for any signs of problems. If the daemon looks sane, type Control-C and start the service in the normal way:

systemctl start slurmctld

E-mail notification setup

The slurm.conf variables MailProg and MailDomain determine the delivery of E-mail messages from Slurm. You may want to use smail from the slurm-contribs RPM package by setting:

MailProg=/usr/bin/smail

This will include some job statistics in the message.

Another possibility is Goslmailer (GoSlurmMailer).

Reconfiguration of slurm.conf

When changing the configuration files slurm.conf and cgroup.conf, they must first be distributed to all compute and login nodes. On the master node make the daemons reread the configuration files:

scontrol reconfigure

From the scontrol man-page about the reconfigure option:

  • Instruct all Slurm daemons to re-read the configuration file. This command does not restart the daemons. This mechanism would be used to modify configuration parameters (Epilog, Prolog, SlurmctldLogFile, SlurmdLogFile, etc.). The Slurm controller (slurmctld) forwards the request all other daemons (slurmd daemon on each compute node). Running jobs continue execution.

  • Most configuration parameters can be changed by just running this command, however, Slurm daemons should be shutdown and restarted if any of these parameters are to be changed:

    • AuthType, BackupAddr, BackupController, ControlAddr, ControlMach, PluginDir, StateSaveLocation, SlurmctldPort or SlurmdPort.

  • The slurmctld daemon and all slurmd daemons must be restarted if nodes are added to or removed from the cluster.

Adding nodes

According to the scontrol man-page, when adding or removing nodes to slurm.conf, it is necessary to restart slurmctld. However, it is also necessary to restart the slurmd daemon on all nodes, see bug_3973:

  1. Stop slurmctld

  2. Add/remove nodes in slurm.conf

  3. Restart slurmd on all nodes

  4. Start slurmctld

For a configless setup the slurmctld must be restarted first, in this case the order is:

  1. Stop slurmctld

  2. Add/remove nodes in slurm.conf

  3. Start slurmctld

  4. Quickly restart slurmd on all nodes

It is also possible to add nodes to slurm.conf with a state of future:

FUTURE
  Indicates the node is defined for future use and need not exist when the Slurm daemons are started.
  These nodes can be made available for use simply by updating the node state using the scontrol command rather than restarting the slurmctld daemon.
  After these nodes are made available, change their State in the slurm.conf file.
  Until these nodes are made available, they will not be seen using any Slurm commands or nor will any attempt be made to contact them.

However, such future nodes must not be members of any partition.

Cgroup configuration

Control Groups (Cgroups v1) provide a Linux kernel mechanism for aggregating/partitioning sets of tasks, and all their future children, into hierarchical groups with specialized behaviour.

Documentation about the usage of Cgroups:

To list current Cgroups use the command:

lscgroup
lscgroup -g cpu:/

To list processes that are not properly constrained by Slurm Cgroups:

ps --no-headers -eo pid,user,comm,cgroup | egrep -vw 'root|freezer:/slurm.*devices:/slurm.*cpuacct,cpu:/slurm.*memory:/slurm|cpuset:/slurm.*|dbus-daemon|munged|ntpd|gmond|polkitd|chrony|smmsp|rpcuser|rpc'

Usage of Cgroups within Slurm is described in the Cgroups_Guide. Slurm provides Cgroups versions of a number of plugins:

  • proctrack (process tracking)

  • task (task management)

  • jobacct_gather (job accounting statistics)

See also the cgroup.conf configuration file for the Cgroups support.

If you use jobacct_gather, change the default ProctrackType in slurm.conf:

ProctrackType=proctrack/linux

otherwise you’ll get this warning in the slurmctld log:

WARNING: We will use a much slower algorithm with proctrack/pgid, use Proctracktype=proctrack/linuxproc or some other proctrack when using jobacct_gather/linux

Notice: Linux kernel 2.6.38 or greater is strongly recommended, see the Cgroups_Guide General Usage Notes.

Getting started with Cgroups

In this example we want to constrain jobs to the number of CPU cores as well as RAM memory requested by the job.

Configure slurm.conf to use Cgroups as well as the affinity plugin:

TaskPlugin=affinity,cgroup

For a discussion see bug 3853.

You should probably also configure this (unless you have lots of short running jobs):

ProctrackType=proctrack/cgroup

see the section ProctrackType of slurm.conf.

Create cgroup.conf file:

cp /etc/slurm/cgroup.conf.example /etc/slurm/cgroup.conf

Edit the file to change these lines:

ConstrainCores=yes
ConstrainRAMSpace=yes
ConstrainSwapSpace=yes

The cgroup.conf page defines:

  • ConstrainCores=<yes|no>

    If configured to “yes” then constrain allowed cores to the subset of allocated resources. It uses the cpuset subsystem.

  • ConstrainRAMSpace=<yes|no>

    If configured to “yes” then constrain the job’s RAM usage. The default value is “no”, in which case the job’s RAM limit will be set to its swap space limit. Also see AllowedSwapSpace, AllowedRAMSpace and ConstrainSwapSpace.

  • ConstrainSwapSpace=<yes|no>

    If configured to “yes” then constrain the job’s swap space usage. The default value is “no”. Note that when set to “yes” and ConstrainRAMSpace is set to “no”, AllowedRAMSpace is automatically set to 100% in order to limit the RAM+Swap amount to 100% of job’s requirement plus the percent of allowed swap space. This amount is thus set to both RAM and RAM+Swap limits. This means that in that particular case, ConstrainRAMSpace is automatically enabled with the same limit than the one used to constrain swap space. Also see AllowedSwapSpace.

You may also consider defining MemSpecLimit in slurm.conf:

  • MemSpecLimit Amount of memory, in megabytes, reserved for system use and not available for user allocations. If the task/cgroup plugin is configured and that plugin constrains memory allocations (i.e. TaskPlugin=task/cgroup in slurm.conf, plus ConstrainRAMSpace=yes in cgroup.conf), then Slurm compute node daemons (slurmd plus slurmstepd) will be allocated the specified memory limit. The daemons will not be killed if they exhaust the memory allocation (ie. the Out-Of-Memory Killer is disabled for the daemon’s memory cgroup). If the task/cgroup plugin is not configured, the specified memory will only be unavailable for user allocations.

See an interesting discussion in bug 2713.

If compute nodes mount Lustre or NFS file systems, it may be a good idea to configure cgroup.conf with:

ConstrainKmemSpace=no

See the cgroup.conf man-page, bug_3874 and [slurm-dev] Interaction between cgroups and NFS. This requires Slurm 17.02.5 or later, see NEWS. After distributing the cgroup.conf file to all nodes, make a scontrol reconfigure.

Activating Cgroups

Now propagate the updated files slurm.conf and cgroup.conf to all compute nodes and restart their slurmd service.

Cgroup bugs

There may be some problems with Cgroups.

Jobs may crash with an error like:

slurmstepd: error: xcgroup_instantiate: unable to create cgroup '/sys/fs/cgroup/memory/slurm/uid_207887' : No space left on device

The bug_3890 explains this, it may be a kernel bug (CentOS 7 has kernel 3.10), see:

Workaround: Reboot the node.

Node Health Check

To insure the health status of Head/Master node and compute nodes, install the LBNL Node Health Check (NHC) package from LBL. The NHC releases are in https://github.com/mej/nhc/releases/.

It’s simple to configure NHC Slurm integration, see the NHC page. Add the following to slurm.conf on your Head/Master node and your compute nodes:

HealthCheckProgram=/usr/sbin/nhc
HealthCheckInterval=3600
HealthCheckNodeState=ANY

This will execute NHC every 60 minutes on nodes in ANY states, see the slurm.conf documentation about Health* variables. There are other criteria for when to execute NHC as defined by HealthCheckNodeState in slurm.conf: ALLOC, ANY, CYCLE, IDLE, MIXED.

We add the following lines in the NHC configuration file /etc/nhc/nhc.conf for nodes in the domain nifl.fysik.dtu.dk:

* || NHC_RM=slurm
# Flag df to list only local filesystems (omit NFS mounts)
* || DF_FLAGS="-Tkl"
* || DFI_FLAGS="-Til"
# Setting short hostname for compute nodes (default in our Slurm setup)
*.nifl.fysik.dtu.dk || HOSTNAME=$HOSTNAME_S
# Busy batch nodes may take a long time to run nhc
*.nifl.fysik.dtu.dk  || TIMEOUT=120
# Check OmniPath/Infiniband link
x*.nifl.fysik.dtu.dk  || check_hw_ib 100

If you want an E-mail alert from NHC you must add a crontab entry to execute the nhc-wrapper script, see the NHC page section Periodic Execution.

For example, to execute the NHC check once per hour with a specified E-mail interval of 1 day, add this to the system’s crontab:

# Node Health Check
3 * * * * /usr/sbin/nhc-wrapper -X 1d

NHC and GPU nodes

The NHC has a check for Nvidia GPU health, namely check_nv_healthmon. Unfortunately, it seems that Nvidia no longer offers the tool nvidia-healthmon for this purpose.

Nvidia has a new Data Center GPU Manager (DCGM) suite of tools which includes NVIDIA Validation Suite (NVVS). Download of DCGM requires membership of the Data Center GPU Manager (DCGM) Program. Install the RPM by:

yum install datacenter-gpu-manager-1.7.1-1.x86_64.rpm

Run the NVVS tool:

nvvs -g -l /tmp/nvvs.log

The (undocumented?) log file (-l) seems to be required.

See also https://docs.nvidia.com/datacenter/dcgm/latest/dcgm-user-guide/feature-overview.html#health-and-diagnostics

It does not seem obvious how to use NVVS as a fast running tool under NHC.

Perhaps it may be useful in stead to check for the presence of the GPU devices with a check similar to this (for 4 GPU devices):

gpu* || check_file_test -c -r /dev/nvidia0 /dev/nvidia1 /dev/nvidia2 /dev/nvidia3

It seems that these device files do not get created automatically at reboot, but only if you run this (for example, in /etc/rc.local):

/usr/bin/nvidia-smi

The physical presence of Nvidia devices can be tested by this command:

# lspci | grep NVIDIA

NHC bugs

It may be necessary to force the NHC configuration file /etc/nhc/nhc.conf to use the Slurm scheduler by adding this line near the top:

* || NHC_RM=slurm

because NHC (version 1.4.2) may autodetect NHC_RM=pbs if the file /usr/bin/pbsnodes is present (see issue 20).

Also, NHC 1.4.2 has a bug for Slurm multi-node jobs (see issue 15), so you have to comment out any lines in nhc.conf calling:

# check_ps_unauth_users

Both bugs should be fixed in NHC 1.4.3 (when it becomes available).

Reboot option

Nodes may occasionally have to be rebooted after firmware or kernel upgrades.

Reboot the nodes automatically as they become idle using the RebootProgram as configured in slurm.conf, see the scontrol reboot option and explanation in the man-page:

scontrol reboot [ASAP] [NodeList]

The ASAP flag is available from Slurm 17.02, see man scontrol for earlier versions.

Add this line to slurm.conf:

RebootProgram="/usr/sbin/reboot"

The path to reboot may be different on other OSes.

Notice: Command arguments to RebootProgram like:

RebootProgram="/sbin/shutdown -r now"

seem to be ignored for Slurm 16.05 until 17.02.3, see bug_3612.

Timeout options

A number of Timeout options may be configured in slurm.conf.

In bug_3941 is discussed the problem of nodes being drained due to the killing of jobs taking too long to complete. To extend this timeout configure in slurm.conf:

UnkillableStepTimeout=120

Values above 127 should not be used, see bug_11103.

This may also be accompanied by a custom command UnkillableStepProgram. If this timeout is reached, the node will also be drained with reason batch job complete failure.

ReturnToService option

The ReturnToService option in slurm.conf controls when a DOWN node will be returned to service, see slurm.conf and the FAQ Why is a node shown in state DOWN when the node has registered for service?.

MaxJobCount limit

In slurm.conf is defined:

MaxJobCount
  The maximum number of jobs Slurm can have in its active database at one time.
  Set the values of MaxJobCount and MinJobAge to insure the slurmctld daemon does not exhaust its memory or other resources.
  Once  this  limit  is  reached, requests to submit additional jobs will fail.
  The default value is 10000 jobs.

If you exceed 10000 jobs in the queue users will get an error when submitting jobs:

sbatch: error: Slurm temporarily unable to accept job, sleeping and retrying.
sbatch: error: Batch job submission failed: Resource temporarily unavailable

Add a higher value to slurm.conf, for example:

MaxJobCount=20000

Another parameter in slurm.conf may perhaps need modification with higher MaxJobCount:

MinJobAge
  The minimum age of a completed job before its record is purged from Slurm's active database.
  Set the values of MaxJobCount and to insure the slurmctld daemon does not exhaust its memory or other resources.
  The default value is 300 seconds.

In addition, it may be a good idea to implement MaxSubmitJobs and MaxJobs resource_limits for user associations or QOSes, for example:

sacctmgr modify user where name=<username> set MaxJobs=100 MaxSubmitJobs=500

Job arrays

The job_arrays offer a mechanism for submitting and managing collections of similar jobs quickly and easily; job arrays with millions of tasks can be submitted in milliseconds (subject to configured size limits).

A slurm.conf configuration parameter controls the maximum job array size:

  • MaxArraySize.

Be mindful about the value of MaxArraySize as job arrays offer an easy way for users to submit large numbers of jobs very quickly.

Requeueing of jobs

Jobs may be requeued explicitly by a system administrator, after node failure, or upon preemption by a higher priority job. The following parameter in slurm.conf may be changed for the default ability for batch jobs to be requeued:

JobRequeue=0

This function is:

  • If JobRequeue is set to a value of 1, then batch job may be requeued unless explicitly disabled by the user.

  • If JobRequeue is set to a value of 0, then batch job will not be requeued unless explicitly enabled by the user.

  • The default value is 1.

Use:

sbatch --no-requeue or --requeue

to change the default behavior for individual jobs.

Power monitoring and management

Slurm can be configured to monitor the power and energy usage of compute nodes, see the SLUG’18 presentation Workload Scheduling and Power Management. This paper also describes Slurm power management. See also the Slurm Power Management Guide.

The Slurm configuration file for the acct_gather plugins such as acct_gather_energy, acct_gather_profile and acct_gather_interconnect is described in acct_gather.conf.

Notice: Please beware that the power monitoring may or may not cover entire compute node cabinets and other infrastructure! For example, the RAPL method described below monitors CPUs and RAM only, and does not cover other power usage within the node such as GPUs, motherboard, fans, power supplies, PCIe network and storage adapters.

On most types of processors one may activate Running Average Power Limit (RAPL) sensors for CPUs and RAM memory, see these papers:

With Slurm several AcctGatherEnergyType types are defined in the slurm.conf manual page. RAPL data gathering can be enabled in Slurm by:

# Power and energy monitoring
AcctGatherEnergyType=acct_gather_energy/rapl
AcctGatherNodeFreq=30

and do a scontrol reconfig. After a minute the power values become available:

$ scontrol show node n123
...
  CurrentWatts=641 AveWatts=480

Please beware that the Slurm bug 9956 states: RAPL plugin: incorrect *Watts and ConsumedEnergy values.

A convenient script showpower is available for printing node power values as well as the total/average for sets of nodes with 1 line per node:

Usage: showpower < -w node-list | -p partition(s) | -a | -h > [ -S sorting-variable ]
where:
      -w node-list: Print this node-list
      -p partition(s): Print this partition
      -a: All nodes in the cluster
      -h: Print help information
      -S: Sort output by this column (e.g. CurrentWatts)

An example output is:

$ showpower -w d[001-005]
NodeName  #CPUs     CPU-  Current  Average       Cap ExtSensor ExtSensor
                    load    Watts    Watts     Watts     Watts    Joules
d001         56     56.7      681      605      n/a        0      n/s
d002         56     56.5      646      579      n/a        0      n/s
d003         56     56.8      655      582      n/a        0      n/s
d004         56     56.6      544      408      n/a        0      n/s
d005         56     56.6      643      415      n/a        0      n/s

NodeName  #CPUs     CPU-  Current  Average       Cap ExtSensor ExtSensor
                    load    Watts    Watts     Watts     Watts    Joules
TOTAL       280    283.2     3169     2589        0        0        0
Average      56     56.6      633      517        0        0        0

turbostat utility

A CLI utility turbostat is provided by the kernel-tools package for reporting processor topology, frequency, idle power-state statistics, temperature, and power usage on Intel® 64 processors, for example:

$ turbostat --quiet --Summary

The turbostat reads the model-specific registers (MSRs) /dev/cpu/CPUNUM/msr, see man 4 msr.

Power saving configuration

Slurm provides an integrated power_save mechanism for powering down idle nodes. Nodes that remain idle for a configurable period of time can be placed in a power saving mode, which can reduce power consumption or fully power down the node. The nodes will be restored to normal operation once work is assigned to them.

We describe the power_save configuration in the Slurm_cloud_bursting page section on Configuring slurm.conf for power saving.

High throughput configuration or large clusters

The following document contains Slurm administrator information specifically for high throughput computing, namely the execution of many short jobs. Getting optimal performance for high throughput computing does require some tuning and this document should help you off to a good start:

The following document contains Slurm administrator information specifically for clusters containing 1,024 nodes or more:

Head/Master server configuration

The following must be done on the Head/Master node. Create the spool and log directories and make them owned by the slurm user:

mkdir /var/spool/slurmctld /var/log/slurm
chown slurm: /var/spool/slurmctld /var/log/slurm
chmod 755 /var/spool/slurmctld /var/log/slurm

Create log files:

touch /var/log/slurm/slurmctld.log
chown slurm: /var/log/slurm/slurmctld.log

Create the (Linux default) accounting file:

touch /var/log/slurm/slurm_jobacct.log /var/log/slurm/slurm_jobcomp.log
chown slurm: /var/log/slurm/slurm_jobacct.log /var/log/slurm/slurm_jobcomp.log

NOTICE: If you plan to enable job accounting, it is mandatory to configure the database and accounting as explained in the Slurm accounting page.

slurmctld daemon

Start and enable the slurmctld daemon:

systemctl enable slurmctld.service
systemctl start slurmctld.service
systemctl status slurmctld.service

Warning: With Slurm 14.x and a compute node running RHEL 7 there is a bug systemctl start/stop does not work on RHEL 7. This problem has apparently been resolved in Slurm 15.08.

Copy slurm.conf to all nodes

Finally copy /etc/slurm/slurm.conf to all compute nodes:

scp -p /etc/slurm/slurm.conf nodeXXX:/etc/slurm/slurm.conf

It’s convenient to use the pdsh command, see PDSH.

It is important to keep this file identical on both the Head/Master server and all Compute nodes. Remember to include all of the NodeName= lines for all compute nodes.

Compute node configuration

The following must be done on each compute node. Create the slurmd spool and log directories and make the correct ownership:

mkdir /var/spool/slurmd /var/log/slurm
chown slurm: /var/spool/slurmd  /var/log/slurm
chmod 755 /var/spool/slurmd  /var/log/slurm

Create log files:

touch /var/log/slurm/slurmd.log
chown slurm: /var/log/slurm/slurmd.log

Executing the command:

slurmd -C

on each compute node will print its physical configuration (sockets, cores, real memory size, etc.), which must be added to the global slurm.conf file. For example a node may be defined as:

NodeName=test001 Boards=1 SocketsPerBoard=2 CoresPerSocket=2 ThreadsPerCore=1 RealMemory=8010 TmpDisk=32752 Feature=xeon

Warning: You should configure the RealMemory value slightly less than what is reported by slurmd -C, because kernel upgrades may give a slightly lower RealMemory value in the future and cause problems with the node’s health status.

For recent Xeon and EPYC CPUs, the Sub NUMA Cluster (SNC) BIOS setting has been shown to improve performance, see BIOS characterization for HPC with Intel Cascade Lake processors. This will cause each processor socket to have two NUMA domains, one for each of the memory controllers, so a dual-socket server will have 4 NUMA domains, for example:

$ slurmd -C
slurmd: Considering each NUMA node as a socket
CPUs=40 Boards=1 SocketsPerBoard=4 CoresPerSocket=10 ThreadsPerCore=1 RealMemory=385380

Note for Slurm 20.02: The Boards=1 SocketsPerBoard=2 configuration gives error messages, see bug_9241 and bug_9233. Use Sockets= in stead:

NodeName=test001 Sockets=2 CoresPerSocket=2 ThreadsPerCore=1 RealMemory=8010 TmpDisk=32752 Feature=xeon

This has been fixed in Slurm 20.02.4.

Here the TmpDisk is defined in slurm.conf as the size of the TmpFS file system (default: /tmp). It is possible to define another temporary file system in slurm.conf, for example:

TmpFS=/scratch

Start and enable the slurmd daemon:

systemctl enable slurmd.service
systemctl start slurmd.service
systemctl status slurmd.service

Partition limits

If EnforcePartLimits is set to “ALL” then jobs which exceed a partition’s size and/or limits will be rejected at submission time:

EnforcePartLimits=ALL

NOTE: The partition limits being considered are its configured MaxMemPerCPU, MaxMemPerNode, MinNodes, MaxNodes, MaxTime, AllocNodes, AllowAccounts, AllowGroups, AllowQOS, and QOS usage threshold.

Job limits

By default, Slurm will propagate all user limits from the submitting node (see ulimit -a) to be effective also within batch jobs.

It is important to configure slurm.conf so that the locked memory limit isn’t propagated to the batch jobs:

PropagateResourceLimitsExcept=MEMLOCK

as explained in https://slurm.schedmd.com/faq.html#memlock. A possible memory limit error with Omni-Path network fabric by Cornelis Networks was discussed in Slurm bug 3363.

In fact, if you have imposed any non-default limits in /etc/security/limits.conf or /etc/security/limits.d/\*.conf in the login nodes, you probably want to prohibit these from the batch jobs by configuring:

PropagateResourceLimitsExcept=ALL

See the slurm.conf page for the list of all PropagateResourceLimitsExcept limits.

PAM module restrictions

On Compute nodes you may additionally install the slurm-pam_slurm RPM package to prevent rogue users from logging in. A more important functions is the containment of SSH tasks, for example, by some MPI libraries not using Slurm for spawning tasks. The pam_slurm_adopt module makes sure that child SSH tasks are controlled by Slurm on the job’s master node.

SELinux may conflict with pam_slurm_adopt, so it might need to be disabled by this command:

setenforce 0

Disable SELinux permanently in /etc/selinux/config:

SELINUX=disabled

For further details, the pam_slurm_adopt module is described by its author in Caller ID: Handling ssh-launched processes in Slurm. Features include:

  • This module restricts access to compute nodes in a cluster where Slurm is in use. Access is granted to root, any user with an Slurm-launched job currently running on the node, or any user who has allocated resources on the node according to the Slurm.

Usage of pam_slurm_adopt is described in the source files pam_slurm_adopt. There is also a nice description in bug_4098. Documentation of pam_slurm_adopt is discussed in bug_3567.

The PAM usage of, for example, /etc/pam.d/system-auth on CentOS/RHEL is configured through the authconfig command.

Configure PrologFlags

Warning: Do NOT configure UsePAM=1 in slurm.conf (this advice can be found on the net). Please see bug_4098 (comment 3).

You need to configure slurm.conf with:

PrologFlags=contain

Then distribute the slurm.conf file to all nodes. Reconfigure the slurmctld service:

scontrol reconfigure

This can be done while the cluster is in production, see bug_4098 (comment 3).

PAM configuration

Warnings:

  • First make the PrologFlags=contain configuration described above.

  • Do NOT configure UsePAM=1 in slurm.conf.

  • Reconfiguration of the PAM setup should only be done on compute nodes that can’t run jobs (for example, drained nodes).

  • You should only configure this on Slurm 17.02.2 or later.

First make sure that you have installed this Slurm package:

rpm -q slurm-pam_slurm

Create a new file in /etc/pam.d/ where the line with pam_systemd.so has been removed:

cd /etc/pam.d/
grep -v pam_systemd.so < password-auth > password-auth-no-systemd

The reason is (quoting pam_slurm_adopt) that:

  • pam_systemd.so is known to not play nice with Slurm’s usage of cgroups. It is recommended that you disable it or possibly add pam_slurm_adopt.so after pam_systemd.so.

Insert some new lines in the file /etc/pam.d/sshd at this place:

...
account    required     pam_nologin.so
# - PAM config for Slurm - BEGIN
account    sufficient   pam_slurm_adopt.so
account    required     pam_access.so
# - PAM config for Slurm - END
account    include      password-auth
...

and also replace the line:

session    include      password-auth

by:

# - PAM config for Slurm - BEGIN
session    include      password-auth-no-systemd
# - PAM config for Slurm - END

Options to the pam_slurm_adopt.so module are documented in the pam_slurm_adopt page.

Now append these lines to /etc/security/access.conf (see man access.conf or access.conf for further possibilities):

+ : root   : ALL
- : ALL    : ALL

so that pam_access.so will:

  • Allow access to the root user.

  • Deny access to ALL other users.

This can be tested immediately by trying to make SSH logins to the node. Normal user logins should be rejected with the message:

Access denied by pam_slurm_adopt: you have no active jobs on this node
Connection closed by <IP address>

slurmd systemd limits

MPI jobs and other tasks using the Infiniband or Omni-Path network fabric by Cornelis Networks fabrics must have unlimited locked memory, see above. Limits defined in /etc/security/limits.conf or /etc/security/limits.d/\*.conf are not effective for systemd services, see https://access.redhat.com/solutions/1257953, so any limits must be defined in the service file, see man systemd.exec.

For slurmd running under systemd the default limits are configured in /usr/lib/systemd/system/slurmd.service as:

LimitNOFILE=51200
LimitMEMLOCK=infinity
LimitSTACK=infinity

If you want to modify/override these limits, create a new service file rather than editing the slurmd.service file. For example, create a file /etc/systemd/system/slurmd.service.d/core_limit.conf with the contents:

[Service]
LimitCORE=0

and do:

systemctl daemon-reload
systemctl restart slurmd

This file could be distributed to all compute nodes from a central location.

The possible process limit parameters are documented in the systemd.exec page section on Process Properties. The list is:

LimitCPU=, LimitFSIZE=, LimitDATA=, LimitSTACK=, LimitCORE=, LimitRSS=, LimitNOFILE=, LimitAS=, LimitNPROC=, LimitMEMLOCK=, LimitLOCKS=, LimitSIGPENDING=, LimitMSGQUEUE=, LimitNICE=, LimitRTPRIO=, LimitRTTIME=

To ensure that job tasks running under Slurm have the desired configuration, verify the slurmd daemon’s limits by:

cat /proc/$(pgrep -u 0 slurmd)/limits

If slurmd has a memory lock limited less than expected, it may be due to slurmd having been started at boot time by the old init-script /etc/init.d/slurm rather than by systemctl. To remedy this problem see the section Starting slurm daemons at boot time above.

Setting job limits with PAM

By default jobs started by slurmd do not use PAM and therefore do not honor the /etc/security/limits.conf file. This behavior may be changed by adding to slurm.conf (see the man-page):

UsePAM=1

Then you can create a file /etc/pam.d/slurm containing:

auth            required        pam_localuser.so
account         required        pam_unix.so
session         required        pam_limits.so

Temporary job directories

Jobs may be storing temporary files in /tmp, /scratch, and /dev/shm/. These directories may be filled up, and no clean-up is done after the job exits. There are several possible solutions:

  • The job_container_tmpfs plugin which was introduced in Slurm 20.11.5. You should read the tmpfs_jobcontainer FAQ as well as bug_11183 and bug_11135 for further details. The job_container_tmpfs plugin uses Linux_namespaces.

    WARNING: NFS automount and job_container/tmpfs do not play well together prior to 23.02: If a directory does not exist when the tmpfs is created, then that directory cannot be accessed by the job, see bug_14344 and bug_12567. The issue has been resolved in Slurm 23.02 according to bug_12567.

    The configuration file /etc/slurm/job_container.conf must be created, and it is important to configure the new 23.02 option:

    Shared=true

    See the job_container.conf manual page. An example job_container.conf file might contain:

    AutoBasePath=true
BasePath=/scratch Dirs=/tmp,/var/tmp,/dev/shm Shared=true

  • The auto_tmpdir SPANK plugin provides automated handling of temporary directories for jobs (see also this page).

    A great advantage of this plugin that it actually works correctly with NFS home directories automounted by autofs, in contrast to Slurm’s job_container_tmpfs plugin prior to 23.02 (see more below).

    You can build a customized RPM package for this plugin:

    • CMake version 3.6 (or greater) is required. Make sure the EPEL repo is enabled, then install this package:

      yum install epel-release
yum install cmake3    # CentOS 7 and other EL7 systems
dnf install cmake     # EL8 systems and newer

    • Download the source:

      git checkout git@github.com:University-of-Delaware-IT-RCI/auto_tmpdir.git
or:
git clone https://github.com/University-of-Delaware-IT-RCI/auto_tmpdir.git

cd auto_tmpdir
mkdir builddir
cd builddir

    • Configure the node local temporary directory as /scratch/slurm-<slurm_jobid> (choose whatever scratch disk is appropriate for your cluster installation):

      cmake3 -DSLURM_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release -DAUTO_TMPDIR_DEFAULT_LOCAL_PREFIX=/scratch/slurm- ..
make package

      Here the .. just refers to the parent directory. The generated RPM package may be named similar to auto_tmpdir-1.0.1-21.08.8.el8.x86_64.rpm.

    • Note: If you are upgrading Slurm to a new major version (like 21.08 to 22.05), you must use a test node to build the new auto_tmpdir RPM:

      1. Uninstall any preexisting RPM:

        yum remove auto_tmpdir

      2. Upgrade Slurm to the new version.

      3. Rebuild the auto_tmpdir RPM as shown above.

      4. Copy the auto_tmpdir RPM to where you keep the Slurm RPMs so that you can upgrade compute nodes with the slurm-* as well as auto_tmpdir simultaneously.

    • Install the auto_tmpdir RPM package on all slurmd compute nodes, as well as all submit/login nodes (see notes below).

    • Now you can create the file /etc/slurm/plugstack.conf (see the SPANK page) with contents:

      required    auto_tmpdir.so          mount=/tmp mount=/var/tmp

      Notes:

      • The /etc/slurm/plugstack.conf file name can be changed by the PlugStackConfig parameter in slurm.conf.

      • If you use configless Slurm the /etc/slurm/plugstack.conf file is automatically distributed from the slurmctld host.

      • It is not required that plugstack.conf is identical or even installed on every node in the cluster, since Slurm does not check for that. Therefore you can have different configurations on different nodes (except when you use configless Slurm).

      • If the plugstack.conf file is installed on a submit/login or compute node, it is mandatory that all plugins listed in the file are actually installed as well, otherwise user commands or slurmd will fail with errors. See a discussion in bug_14483.

    • Quickly restart the slurmd service on all compute nodes to actually activate the /etc/slurm/plugstack.conf feature:

      systemctl restart slurmd

      This is required in order for new srun commands etc. to run correctly with the SPANK plugin. See the SPANK manual page:

      Note: Plugins loaded in slurmd context persist for the entire time slurmd is running, so if configuration is changed or plugins are updated, slurmd must be restarted for the changes to take effect.

    • For information about Linux_namespaces currently mounted on the compute nodes use:

      lsns -t mnt

  • Another SPANK plugin is at https://github.com/hpc2n/spank-private-tmp. This plugin does not do any cleanup, so cleanup will have to be handled separately.

  • A manual cleanup could be made (if needed) by a crontab job on the compute node, for example for the /scratch directory:

    # Remove files > 7 days old under /scratch/XXX (mindepth=2)
find /scratch -depth -mindepth 2 -mtime +7 -exec rm -rf {} \;

Configure Prolog and Epilog scripts

It may be necessary to execute Prolog and/or Epilog scripts on the compute nodes when slurmd executes a task step (by default none are executed). See also the Prolog and Epilog Guide.

In the slurm.conf page this is described:

  • Prolog

    Fully qualified pathname of a program for the slurmd to execute whenever it is asked to run a job step from a new job allocation (e.g. /usr/local/slurm/prolog). A glob pattern (See glob(7)) may also be used to specify more than one program to run (e.g. /etc/slurm/prolog.d/*). The slurmd executes the prolog before starting the first job step. The prolog script or scripts may be used to purge files, enable user login, etc.

    By default there is no prolog. Any configured script is expected to complete execution quickly (in less time than MessageTimeout).

    If the prolog fails (returns a non-zero exit code), this will result in the node being set to a DRAIN state and the job being requeued in a held state, unless nohold_on_prolog_fail is configured in SchedulerParameters. See Prolog and Epilog Scripts for more information.

  • TaskProlog

    Fully qualified pathname of a program to be execute as the slurm job’s owner prior to initiation of each task. Besides the normal environment variables, this has SLURM_TASK_PID available to identify the process ID of the task being started. Standard output from this program can be used to control the environment variables and output for the user program. (further details in the slurm.conf page).

  • TaskEpilog

    Fully qualified pathname of a program to be execute as the slurm job’s owner after termination of each task. See TaskProlog for execution order details.

See also the items:

  • PrologEpilogTimeout

  • PrologFlags

  • SrunEpilog

Prolog and epilog examples

An example script is shown in the FAQ https://slurm.schedmd.com/faq.html#task_prolog:

#!/bin/sh
#
# Sample TaskProlog script that will print a batch job's
# job ID and node list to the job's stdout
#

if [ X"$SLURM_STEP_ID" = "X" -a X"$SLURM_PROCID" = "X"0 ]
then
  echo "print =========================================="
  echo "print SLURM_JOB_ID = $SLURM_JOB_ID"
  echo "print SLURM_NODELIST = $SLURM_NODELIST"
  echo "print =========================================="
fi

The script is supposed to output commands to be read by slurmd:

  • The task prolog is executed with the same environment as the user tasks to be initiated. The standard output of that program is read and processed as follows:

    • export name=value - sets an environment variable for the user task

    • unset name - clears an environment variable from the user task

    • print … - writes to the task’s standard output.

Configure partitions

System partitions are configured in slurm.conf, for example:

PartitionName=xeon8 Nodes=a[070-080] Default=YES DefaultTime=50:00:00 MaxTime=168:00:00 State=UP

Partitions may overlap so that some nodes belong to several partitions.

Access to partitions is configured in slurm.conf using AllowAccounts, AllowGroups, or AllowQos.

If some partition (like big memory nodes) should have a higher priority, this is controlled in slurm.conf using the multifactor plugin, for example:

PartitionName ... PriorityJobFactor=10
PriorityWeightPartition=1000

Sharing nodes and cons_tres

By default nodes are allocated exclusively to jobs, but it is possible to permit multiple jobs and/or multiple users per node. This is configured using Consumable Resource Allocation Plugin or cons_tres in slurm.conf. The cons_tres plugin has improved support for GPU nodes as compared to the older cons_res, and is described in the Presentations from Slurm User Group Meeting, September 2019, see Slurm_publications.

The required slurm.conf configuration is:

SelectType=select/cons_tres
SelectTypeParameters=CR_CPU_MEMORY

In this configuration CPU and Memory are consumable resources. It is mandatory to use OverSubscribe=NO for the partitions as stated in the cons_res page:

  • All CR_s assume OverSubscribe=No or OverSubscribe=Force EXCEPT for CR_MEMORY which assumes OverSubscribe=Yes

Strange behaviour will result if you use the wrong OverSubscribe parameter. The OverSubscribe parameter (default= NO) is defined in the section OverSubscribe in slurm.conf. See also the cons_res_share page.

Upgrade cons_res to cons_tres

The newer cons_tres plugin should be used in stead of cons_res. Upgrading from cons_res to cons_tres on a running system must be done very carefully, however, as discussed in bug_15470. The procedure is:

  1. In slurm.conf change into SelectType=select/cons_tres. The slurm.conf file must be distributed to all nodes (not needed with Configless).

  2. Then restart the slurmctld as well as all slurmd immediately:

    systemctl restart slurmctld
clush -ba systemctl restart slurmd

Here we have used ClusterShell to run the command on all nodes. One must not make a scontrol reconfig during this process!

Configure multiple nodes and their features

Some defaults may be configured in slurm.conf for similar compute nodes, for example:

NodeName=DEFAULT Boards=1 SocketsPerBoard=2 CoresPerSocket=2 ThreadsPerCore=1 RealMemory=8000 TmpDisk=32752 Weight=1
NodeName=q001
NodeName=q002
...

Note for Slurm 20.02: The Boards=1 SocketsPerBoard=2 configuration gives error messages, see bug_9241. Use this in stead:

NodeName=DEFAULT Sockets=2 CoresPerSocket=2 ThreadsPerCore=1 RealMemory=8000 TmpDisk=32752 Weight=1

Node features, similar to node properties used in the Torque resource manager are defined for each NodeName in slurm.conf by:

  • Feature:

    A comma delimited list of arbitrary strings indicative of some characteristic associated with the node. There is no value associated with a feature at this time, a node either has a feature or it does not. If desired a feature may contain a numeric component indicating, for example, processor speed. By default a node has no features.

Some examples are:

NodeName=DEFAULT Sockets=2 CoresPerSocket=2 ThreadsPerCore=1 RealMemory=8000 TmpDisk=32752 Feature=xeon8,ethernet Weight=1
NodeName=q001
NodeName=q002

NodeSet configuration

From Slurm 20.02 a new NodeSet configuration is available in slurm.conf.

The nodeset configuration allows you to define a name for a specific set of nodes which can be used to simplify the partition configuration section, especially for heterogenous or condo-style systems. Each nodeset may be defined by an explicit list of nodes, and/or by filtering the nodes by a particular configured feature.

This can be used to simplify partitions in slurm.conf, and some examples are:

NodeSet=a_nodes Nodes=a[001-100]
NodeSet=gpu_nodes Feature=GPU

Node weight

For clusters with heterogeneous node hardware it is useful to assign different Weight values to each type of node, see this slurm.conf parameter:

Weight
  The priority of the node for scheduling purposes. All things being equal, jobs will be allocated the nodes with the lowest weight which satisfies their requirements.

This enables prioritization based upon a number of hardware parameters such as GPUs, RAM memory size, CPU clock speed, CPU core number, CPU generation. For example, GPU nodes should be avoided for non-GPU jobs.

A nice method was provided by Kilian Cavalotti of SRCC where a weight mask is used in slurm.conf. Each digit in the weight mask represents a hardware parameter of the node (a weight prefix of 1 is prepended in order to avoid octal conversion). For example, the following weight mask example puts a higher weight on GPUs, then RAM memory, then number of cores, and finally the CPU generation:

# (A weight prefix of "1" is prepended)
#       #GRES           Memory          #Cores          CPU_generation
#        none: 0         24 GB: 0        8: 0           Nehalem:      1
#       1 GPU: 1         48 GB: 1        16: 1          Sandy Bridge: 2
#       2 GPU: 2         64 GB: 2        24: 2          Ivy Bridge:   3
#       3 GPU: 3        128 GB: 3        32: 3          Broadwell:    4
#       4 GPU: 4        256 GB: 4        36: 4          Skylake:      5
# Example: Broadwell (=4) with 24 cores (=2), 128 GB memory (=3), and 0 GPUs (=0): Weight=10324

This example would be used to assign a Weight value in slurm.conf for the relevant nodes:

NodeName=xxx Sockets=2 CoresPerSocket=12 ThreadsPerCore=1 RealMemory=128000 Weight=10324

A different prioritization of hardware can be selected with different columns and numbers in the mask, but a fixed number is the result of the mask calculation for each type of node.

Generic resources (GRES) and GPUs

The Generic resources (GRES) are a comma delimited list of generic resources (GRES) specifications for a node. Such resources may be occupied by jobs, for example, GPU accelerators. In this case you must also configure the gres.conf file.

An example with a gpu GRES may be a gres.conf file:

Nodename=h[001-002] Name=gpu Type=K20Xm File=/dev/nvidia[0-3]

If GRES is used, you must also configure slurm.conf, so define the named GRES in slurm.conf:

GresTypes=gpu

and append a list of GRES resources in the slurm.conf NodeName specifications:

NodeName=h[001-002] Gres=gpu:K20Xm:4

See also the examples in the gres.conf page.

Configure network topology

Slurm can be configured to support topology-aware resource allocation to optimize job performance, see the Topology_Guide and the topology.conf manual page.

Check consistency of /etc/slurm/topology.conf with nodelist in /etc/slurm/slurm.conf using the checktopology tool.

Configure firewall for Slurm daemons

The Slurm compute nodes must be allowed to connect to the Head/Master node’s slurmctld daemon. In the configuration file these ports are by default (see slurm.conf):

SlurmctldPort=6817
SlurmdPort=6818
SchedulerPort=7321

CentOS7/RHEL7 firewall

The CentOS7/RHEL7 default firewall service is firewalld and not the well-known iptables service. The dynamic firewall daemon firewalld provides a dynamically managed firewall with support for network “zones” to assign a level of trust to a network and its associated connections and interfaces. See Introduction to firewalld.

A nice introduction is RHEL7: How to get started with Firewalld.

Install firewalld by:

yum install firewalld firewall-config

Head/Master node

Open port 6817 (slurmctld):

firewall-cmd --permanent --zone=public --add-port=6817/tcp
firewall-cmd --reload

Alternatively, completely whitelist the compute nodes’ private subnet (here: 10.2.x.x):

firewall-cmd --permanent --direct --add-rule ipv4 filter INPUT_direct 0 -s 10.2.0.0/16 -j ACCEPT
firewall-cmd --reload

The configuration is stored in the file /etc/firewalld/direct.xml.

Database (slurmdbd) node

The slurmdbd service by default listens to port 6819, see slurmdbd.conf.

Open port 6819 (slurmdbd):

firewall-cmd --permanent --zone=public --add-port=6819/tcp
firewall-cmd --reload

Compute node firewall must be off

Quoting Moe Jette from [slurm-dev] No route to host: Which ports are used?:

Other communications (say between srun and the spawned tasks) are intended to operate within a cluster and have no port restrictions.

The simplest solution is to ensure that the compute nodes must have no firewall enabled:

systemctl stop firewalld
systemctl disable firewalld

However, you may run a firewall service, as long as you ensure that all ports are open between the compute nodes.

Login node firewall

A login node doesn’t need any special firewall rules for Slurm because no such daemons should be running on login nodes.

Warning: The srun command only works if the login node can:

  • Connect to the Head node port 6817.

  • Resolve the DNS name of the compute nodes.

  • Connect to the Compute nodes port 6818.

Therefore interactive batch jobs with srun seem to be impossible if your compute nodes are on an isolated private network relative to the Login node.

Firewall between slurmctld and slurmdbd

See advice from the Slurm_publications presentation Technical: Field Notes Mark 2: Random Musings From Under A New Hat, Tim Wickberg, SchedMD (2018).

SchedMD recommends to run slurmctld and slurmdbd daemons on separate servers, see the My Preferred Deployment Pattern slides in the presentation.

If you use this configuration, the firewall is an important issue.

See the Related Networking Notes slides in the presentation:

  • This is almost always an issue with a firewall in between slurmctld and slurmdbd.

  • slurmdbd opens a new connection to slurmctld to push changes.

  • If you’ve firewalled that off, the update will not be propogated.

Conclusion: Open the firewall for all ports between slurmctld and slurmdbd servers.

Open firewall between servers

On these servers, insert a firewalld direct_rule so that any incoming source IP packet (src) from a specific IP address (A.B.C.D) gets accepted, for example:

firewall-cmd --permanent --direct --add-rule ipv4 filter INPUT_direct 0 -s A.B.C.D/32 -j ACCEPT

Then reload the firewall for any changes to take effect:

firewall-cmd --reload

List the rules by:

firewall-cmd  --permanent --direct --get-all-rules

Checking the Slurm daemons

Check the configured daemons using the scontrol command:

scontrol show daemons

To verify the basic cluster partition setup:

scontrol show partition

To display the Slurm configuration:

scontrol show config

To display the compute nodes:

scontrol show nodes

One may also run the daemons interactively as described in Slurm_Quick_Start (Starting the Daemons). You can use one window to execute slurmctld -D -vvvvvv, a second window to execute slurmd -D -vvvvv.

Configure ARP cache for large networks

If the number of network devices (cluster nodes plus switches etc.) approaches or exceeds 512, you must consider the Linux kernel’s limited dynamic ARP-cache size. Please read the man-page man 7 arp about the kernel’s ARP-cache.

The best solution to this ARP-cache trashing problem is to increase the kernel’s ARP-cache garbage collection (gc) parameters by adding these lines to /etc/sysctl.conf:

# Don't allow the arp table to become bigger than(clusters containing 1024 nodes or more). this
net.ipv4.neigh.default.gc_thresh3 = 4096
# Tell the gc when to become aggressive with arp table cleaning.
# Adjust this based on size of the LAN.
net.ipv4.neigh.default.gc_thresh2 = 2048
# Adjust where the gc will leave arp table alone
net.ipv4.neigh.default.gc_thresh1 = 1024
# Adjust to arp table gc to clean-up more often
net.ipv4.neigh.default.gc_interval = 3600
# ARP cache entry timeout
net.ipv4.neigh.default.gc_stale_time = 3600

You may also consider increasing the SOMAXCONN limit:

# Limit of socket listen() backlog, known in userspace as SOMAXCONN
net.core.somaxconn = 1024

see Large Cluster Administration Guide.

Then reread this configuration file:

/sbin/sysctl -p

Slurm plugins

A Slurm plugin is a dynamically linked code object which is loaded explicitly at run time by the Slurm libraries. A plugin provides a customized implementation of a well-defined API connected to tasks such as authentication, interconnect fabric, and task scheduling.

Plugins include:

  • Job_Submit_Plugin.

  • Slurm scheduler plugins (schedplugins) are Slurm plugins that implement the Slurm scheduler API.

  • SPANK - Slurm Plug-in Architecture for Node and job (K)control.

  • cli_filter Plugin API.

  • The site_factor plugin is designed to provide the site a way to build a custom multifactor priority factor, and will only be loaded and operation alongside PriorityType=priority/multifactor.

Job submit plugins

The Job_Submit_Plugin (a Lua plugin) will execute a Lua script named /etc/slurm/job_submit.lua on the slurmctld host. Some clarification of the documentation is needed, however, see bug_14472 and bug_14500.

Sample Lua scripts can be copied from the Slurm source distribution in the directories contribs/lua/ and etc/:

We also provide a job submit plugin in https://github.com/OleHolmNielsen/Slurm_tools/tree/master/plugins

Please note that job_submit.lua.example has an issue with use of log.user() in job_modify() prior to Slurm 23.02, see bug_14539.

On the slurmctld server you may start with this example:

cp ~/rpmbuild/BUILD/slurm-22.05.8/etc/job_submit.lua.example /etc/slurm/job_submit.lua

(replace the 22.05 version number) and read in the Lua_manual about Lua programming. Install also the Lua package:

yum install lua

Inspiration for writing you custom job_submit.lua script can be found in:

It is strongly recommended to check your Lua code before using it with Slurm! Any error in the code might cause the slurmctld to crash! If possible, verify the code on a test cluster before using it in a production cluster.

A good starting point is to make a syntax check with the luac compiler:

luac -p /etc/slurm/job_submit.lua

Other Lua syntax checker tools can be found on the net, for example:

Lua functions for the job_submit plugin

When writing the Job_Submit_Plugin Lua script it is nice to have an overview of available functions and variables. This is not well documented at present.

We have discovered the following functions (TODO: is there a list of all functions?):

slurm.log_info
slurm.log_debug
slurm.log_debug2
slurm.log_debug3
slurm.log_user

The function _get_job_req_field in job_submit_lua.c lists all available job descriptor fields in job_desc, for example, the following may be useful:

job_desc.partition
job_desc.script
job_desc.environment
job_desc.gres
job_desc.num_tasks
job_desc.max_nodes
job_desc.cpus_per_task
job_desc.tres_per_node
job_desc.tres_per_socket
job_desc.tres_per_task
job_desc.user_name

NOTE: If some field is undefined in the user’s job script, for example max_nodes, slurmctld sets an “invalid” value (see bug_15012) which can be tested for in /etc/slurm/job_submit.lua:

  • Numeric values (a Lua double) if absent will be set to slurm.NO_VAL (32-bit, as defined in /usr/include/slurm/slurm.h).

    For completeness, there are both 16, 32, and 64-bit integer values NO_VAL16, NO_VAL, NO_VAL64 defined in slurm.h struct job_desc_msg_t.

  • String values (if absent) will be set to the nil Lua type.

Slurm error symbols ESLURM* and corresponding numeric values are defined in the file /usr/include/slurm/slurm_errno.h, see also bug_14500. Note that only a few selected symbols ESLURM* are exposed to the Lua script, but from Slurm 23.02 all the error codes in /usr/include/slurm/slurm_errno.h are exposed.

Your /etc/slurm/job_submit.lua script can test for undefined values like in this example:

slurm.ESLURM_INVALID_PARTITION_NAME=2000
if (job_desc.partition == nil) then
  slurm.log_user("No partition specified, please specify partition")
  return slurm.ESLURM_INVALID_PARTITION_NAME
end
if (job_desc.max_nodes == slurm.NO_VAL) then
  slurm.log_user("No max_nodes specified, please specify a number of nodes")
  return slurm.ESLURM_INVALID_PARTITION_NAME
end

Configure Slurm for Lua JobSubmitPlugins

The Job_Submit_Plugin will only execute the Lua script named /etc/slurm/job_submit.lua on the slurmctld host, and it is not used by any other nodes.

Then configure slurm.conf with this parameter (undocumented prior to 22.05.3):

JobSubmitPlugins=lua

which will make Slurm use the /etc/slurm/job_submit.lua script. Make sure to distribute slurm.conf to all nodes (or use a configless setup).

Then reconfigure slurmctld:

scontrol reconfig

If slurmctld gets an error when executing /etc/slurm/job_submit.lua, it will use any previously cached script and ignore the file on disk henceforth (see comment 15 in bug_14472).

WARNING: If slurmctld does not have a cached script (because it was just restarted, for example) it may crash!