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High Throughput Computing Administration Guide

This 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. A working knowledge of Slurm should be considered a prerequisite for this material.

Performance Results

Slurm has also been validated to execute 500 simple batch jobs per second on a sustained basis with short bursts of activity at a much higher level. Actual performance depends upon the jobs to be executed plus the hardware and configuration used.

System configuration

Several system configuration parameters may require modification to support a large number of open files and TCP connections with large bursts of messages. Changes can be made using the /etc/rc.d/rc.local or /etc/sysctl.conf script to preserve changes after reboot. In either case, you can write values directly into these files (e.g. "echo 32832 > /proc/sys/fs/file-max").

  • /proc/sys/fs/file-max: The maximum number of concurrently open files. We recommend a limit of at least 32,832.
  • /proc/sys/net/ipv4/tcp_max_syn_backlog: The maximum number of SYN requests to keep in memory that we have yet to get the third packet in a 3-way handshake from. The tcp_max_syn_backlog variable is overridden by the tcp_syncookies variable, which needs to be turned on for this variable to have any effect. The default value is 1024 for systems with more than 128Mb of memory, and 128 for low memory machines. If server suffers of overload, try to increase this number.
  • /proc/sys/net/ipv4/tcp_syncookies: Used to send out syncookies to hosts when the kernels syn backlog queue for a specific socket is overflowed. The default value is 0, which disables this functionality. Set the value to 1.
  • /proc/sys/net/ipv4/tcp_synack_retries: How many times to retransmit the SYN,ACK reply to an SYN request. In other words, this tells the system how many times to try to establish a passive TCP connection that was started by another host. This variable takes an integer value, but should under no circumstances be larger than 255. Each retransmission will take aproximately 30 to 40 seconds. The default value of 5, which results in a timeout of passive TCP connections of aproximately 180 seconds and is generally satisfactory.
  • /proc/sys/net/core/somaxconn: Limit of socket listen() backlog, known in userspace as SOMAXCONN. Defaults to 128. The value should be raised substantially to support bursts of request. For example, to support a burst of 1024 requests, set somaxconn to 1024.
  • /proc/sys/net/ipv4/ip_local_port_range: Identify the ephermeral ports available, which are used for many Slurm communcations. The value may be raised to support a high volume of communcations. For example, write the value "32768 65535" into the ip_local_port_range file in order to make that range of ports available.

The transmit queue length (txqueuelen) may also need to be modified using the ifconfig command. A value of 4096 has been found to work well for one site with a very large cluster (e.g. "ifconfig txqueuelen 4096").

Munge configuration

By default the Munge daemon runs with two threads, but a higher thread count can improve its throughput. We suggest starting the Munge daemon with ten threads for high throughput support (e.g. "munged --num-threads 10").

User limits

The ulimit values in effect for the slurmctld daemon should be set quite high for memory size, open file count and stack size.

Slurm Configuration

Several Slurm configuration parameters should be adjusted to reflect the needs of high throughput computing. The changes described below will not be possible in all environments, but these are the configuration options that you may want to consider for higher throughput.

  • AccountingStorageType: Disabling accounting will improve job throughput. Disable storing of accounting by using the accounting_storage/none plugin. Starting in Slurm 14.11 there was work done to improve the speedup of the database which makes turning accounting off a minimal improvement in performance. If using the SlurmDBD even greater speedup can be achieved by setting the CommitDelay option in the slurmdbd.conf
  • JobAcctGatherType: Disabling the collection of job accounting information will improve job throughput. Disable collection of accounting by using the jobacct_gather/none plugin.
  • JobCompType: Disabling recording of job completion information will improve job throughput. Disable recording of job completion information by using the jobcomp/none plugin.
  • MaxJobCount: Controls how many jobs may be in the slurmctld daemon records at any point in time (pending, running, suspended or completed[temporarily]). The default value is 10,000.
  • MessageTimeout: Controls how long to wait for a response to messages. The default value is 10 seconds. While the slurmctld daemon is highly threaded, its responsiveness is load dependent. This value might need to be increased somewhat.
  • MinJobAge: Controls how soon the record of a completed job can be purged from the slurmctld memory and thus not visible using the squeue command. The record of jobs run will be preserved in accounting records and logs. The default value is 300 seconds. The value should be reduced to a few seconds if possible. Use of accounting records for older jobs can increase the job throughput rate compared with retaining old jobs in the memory of the slurmctld daemon.
  • ProctrackType: Avoid using proctrack/cgroup it is considerably slower than other alternatives. proctrack/pgid (the default) is advised.
  • PriorityType: The priority/builtin is considerably faster than other options, but schedules jobs only on a First In First Out (FIFO) basis.
  • SchedulerParameters: Several scheduling parameters are available.
    • Setting option batch_sched_delay will control how long the scheduling of batch jobs can be delayed. This effects only batch jobs. For example, if many jobs are submitted each second, the overhead of trying to schedule each one will adversely impact the rate at which jobs can be submitted. The default value is 3 seconds.
    • Setting option defer will avoid attempting to schedule each job individually at job submit time, but defer it until a later time when scheduling multiple jobs simultaneously may be possible. This option may improve system responsiveness when large numbers of jobs (many hundreds) are submitted at the same time, but it will delay the initiation time of individual jobs.
    • sched_min_interval is yet another configuration parameter to control how frequently the scheduling logic runs. It can still be triggered on each job submit, job terminiation, or other state change which could permit a new job to be started. However that triggering does not cause the scheduling logic to be started immediately, but only within the configured sched_interval. For example, if sched_min_interval=2 (seconds) and 100 jobs are submitted within a 2 second time window, then the scheduling logic will be executed one time rather than 100 times (with the default configuration).
    • Besides controlling how frequently the scheduling logic is executed, the default_queue_depth configuration parameter controls how many jobs are considered to be started in each scheduler iteration. The default value of default_queue_depth is 100 (jobs), which should be fine in most cases.
    • The sched/backfill plugin has relatively high overhead if used with large numbers of job. Configuring bf_max_job_test to a modest size (say 100 jobs or less) and bf_interval to 30 seconds or more will limit the overhead of backfill scheduling (NOTE: the default values are fine for both of these parameters). Other backfill options available for tuning backfill scheduling include bf_max_job_user, bf_resolution and bf_window. See the slurm.conf man page for details.
  • SchedulerType: If most jobs are short lived then use of the sched/builtin plugin is recommended. This manages a queue of jobs on a First-In-First-Out (FIFO) basis and eliminates logic used to sort the queue by priority.
  • SelectType: If only serial jobs (single CPU jobs) are to be executed, use of the select/serial plugin is recommended. This plugin eliminates much of the logic found in other select plugins to optimize job allocations with respect to network topology. It also reduces communications required to executed batch jobs by 75 percent through the use of a "pull" model, where the completeion of each job by the slurmd daemon initiates a single message to the slurmctld daemon upon completion of the job's epilog script. The response to this message can be information required to initiate another job utilizing the resources just released by the previous job. NOTE: The use of select/serial prevents the job's Epilog program from being initiated with any SPANK environment variables.
  • SlurmctldPort: It is desirable to configure the slurmctld daemon to accept incoming messages on more than one port in order to avoid having incoming messages discarded by the operating system due to exceeding the SOMAXCONN limit described above. Using between two and ten ports is suggested when large numbers of simultaneous requests are to be supported.
  • SlurmctldDebug: More detailed logging will decrease system throughput. Set to 2 (log errors only) or 3 (general information logging). Each increment in the logging level will increase the number of message by a factor of about 3.
  • SlurmdDebug: More detailed logging will decrease system throughput. Set to 2 (log errors only) or 3 (general information logging). Each increment in the logging level will increase the number of message by a factor of about 3.
  • SlurmdLogFile: Writing to local storage is recommended.
  • TaskPlugin: Avoid using task/cgroup it is slower than other alternatives. It is not as heavy as the cgroup proctrack plugin, but still added overhead. On the same note task/affinity does not appear to add any measurable overhead.
  • Other: Configure logging, accounting and other overhead to a minimum appropriate for your environment.

SlurmDBD Configuration

Starting in Slurm 14.11 there was work done to improve the speedup of the database which makes turning accounting off a minimal improvement in performance. If using the SlurmDBD even greater speedup can be achieved by setting the CommitDelay option in the slurmdbd.conf

You might also consider setting the 'Purge*' options in your slurmdbd.conf to clear out old Data. A Typical configuration would look like this...

  • PurgeEventAfter=12months
  • PurgeJobAfter=12months
  • PurgeResvAfter=2months
  • PurgeStepAfter=2months
  • PurgeSuspendAfter=1month

Last modified 28 December 2015

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IBM Parallel Environment
User and Administrator Guide

Overview
User Tools
System Administration

Overview

This document describes the unique features of Slurm on the IBM computers with the Parallel Environment (PE) software. You should be familiar with the Slurm's mode of operation on Linux clusters before studying the relatively few differences in operation on systems with PE, which are described in this document.

Note that Slurm is designed to be a replacement for IBM's LoadLeveler. They are not designed to concurrently schedule resources. Slurm provides manages network resources and provides the POE command with a library that emulates LoadLeveler functionality.

User Tools

The normal set of Slurm user tools: srun, scancel, sinfo, squeue, scontrol, etc. provide all of the expected services. The onl. Slurm command not supported is sattach. Job steps are launched using the srun command, which translates its options and invokes IBM's poe command. The poe command actually launches the tasks. The poe command may also be invoked directly if desired. The actual task launch process is as follows:

  1. Invoke srun command with desired options.
  2. The srun command creates a job allocation (if necessary).
  3. The srun command translates its options and invokes the poe command.
  4. The poe command loads a Slurm library that provides various resource management functionality.
  5. The poe command, through the Slurm library, creates a Slurm step allocation and launches a process named "pmdv12" on the appropriate compute nodes. Note that the "v12" on the end of the process name represents the version number of the "pmd" process and is subject to change.
  6. The poe command interacts with the pmdv12 process to launch the application tasks, handle their I/O, etc. Since the task launch procedure occurs outside of Slurm's control, none of the normal task-level Slurm support is available.
  7. The poe command, through the Slurm library, reports the completion of the job step.

Network Options

Each job step can specify it's desired network options. For example, one job step may use IP mode communications and the next use User Space (US) mode communications. Network specifications may be specified using srun's --network option or the SLURM_NETWORK environment variable. Supported network options include:

  • Network protocol
    • ip Internet protocol, version 4
    • ipv4 Internet protocol, version 4 (default)
    • ipv6 Internet protocol, version 6
    • us User Space protocol, may be combined with ibv4 or ipv6
  • Programming interface
    • lapi Low-level Application Programming Interface
    • mpi Message Passing Interface (default)
    • pami Parallel Active Message Interface
    • pgas Partitioned Global Address Programming
    • shmem OpenSHMEM interface
    • test Test Protocol
    • upc Unified Parallel C Interface

      • NOTE: Slurm supports the values listed above, and does not support poe user_defined_parallelAPI values.
  • Other options
    • bulk_xfer [=resources] Enable bulk transfer of data using Remote Direct-Memory Access (RDMA). The optional resources specification is a numeric value which can have a suffix of "k", "K", "m", "M", "g" or "G" for kilobytes, megabytes or gigabytes. NOTE: The resources specification is not supported by the underlying IBM infrastructure as of Parallel Environment version 2.2 and no value should be specified at this time.
    • cau=count Specify the count of Collective Acceleration Units (CAU) required per programming interface. Default value is zero. Applies only to IBM Power7-IH processors. POE requires that if cau has a non-zero value then us, devtype=IB or devtype=HFI must be explicitly specified otherwise the request may attempt to allocate CAU with IP communications and fail.
    • devname=name Specify the name of an individual network adapter to use. For example: "eth0" or "mlx4_0".
    • devtype=type Specify the device type to use for communications. The supported values of type are: "IB" (InfiniBand), "HFI" (P7 Host Fabric Interface), "IPONLY" (IP-Only interfaces), "HPCE" (HPC Ethernet), and "KMUX" (Kernel Emulation of HPCE). The devices allocated to a job must all be of the same type. The default value depends upon depends upon what hardware is available and in order of preferences is IPONLY (which is not considered in User Space mode), HFI, IB, HPCE, and KMUX.
    • immed=count Specify the count of immediate send slots per adapter window. Default value is zero. Applies only to IBM Power7-IH processors.
    • instances=count Specify number of network connections for each task on each network connection. The default instance count is 1.
    • sn_all Use all available switch adapters (default). This option can not be combined with sn_single.
    • sn_single Use only one switch adapters. This option can not be combined with sn_all. If multiple adapters of different types exist, the devname and/or devtype option can also be used to select one of them.

Examples of network option use:

--network=sn_all,mpi
Allocate one switch window per task on each node and every network supporting MPI.

--network=sn_all,mpi,bulk_xfer,us
Allocate one switch window per task on each node and every network supporting MPI and user space communications. Reserve resources for RDMA.

--network=sn_all,instances=3,mpi
Allocate three switch window per task on each node and every network supporting MPI.

--network=sn_all,mpi,pami
Allocate one switch window per task on each node and every network supporting MPI and a second window supporting PAMI.

--network=devtype=ib,instances=2,lapi,mpi
On every InfiniBand network connection, allocate two switch windows each for both lapi and mpi interfaces. If each node has one InfiniBand network connection, this would result in four switch windows per task.

NOTE: Switch resources on a node are shared between all job steps on that node. If a job step can not be initiated due to insufficient switch resources being available, that job step will periodically retry allocating resources for the lifetime of the job unless srun's --immediate option is used.

Debugging

Most debuggers require detailed information about launched tasks such as host name, process ID, etc. Since that information is only available from poe (which launches those tasks), the srun command wrapper can not be used for most debugging purposes. You or the debugging tool must invoke the poe command directly. In order to facilitate the direct use of poe, srun's
--launch-cmd option may be used with the options normally used. srun will then print the equivalent poe command line, which can subsequently be used with the debugger. The poe options must be explicitly set even if the command is executed from within an existing Slurm allocation (i.e. from within an allocation created by the salloc or sbatch command).

Checkpoint

Checkpoint/restart is only supported with LoadLeveler. The checkpoint/poe plugin is based Slurm support for checkpoint support of poe in in the 2005 time frame and does not work with the current versions of poe.

Unsupported Options

Some Slurm options can not be supported by PE and the following srun options are silently ignored:

  • -D, --chdir (set working directory)
  • -K, --kill-on-bad-exit (terminate step if any task has a non-zero exit code)
  • -k, --no-kill (set to not kill job upon node failure)
  • --ntasks-per-core (number of tasks to invoke per code)
  • --ntasks-per-socket (number of tasks to invoke per socket)
  • -O, --overcommit (over subscribe resources)
  • --resv-ports (communication ports reserved for OpenMPI)
  • --runjob-opts (used only on IBM BlueGene/Q systems)
  • --signal (signal to send when near time limit and the remaining time required)
  • --sockets-per-node (number of sockets per node required)
  • --task-epilog (per-task epilog program)
  • --task-prolog (per-task prolog program)
  • -u, --unbuffered (avoid line buffering)
  • -W, --wait (specify job swait time after first task exit)
  • -Z, --no-allocate (launch tasks without creating job allocation>

A limited subset of srun's --cpu-bind options are supported as shown below. If the --cpus-per-task option is not specified, a value of one is used by default. Note tha. Slurm's mask_cpu and map_cpu options are not supported, nor are options to bind to sockets or boards.

Slurm option POE equivalent
--cpu-bind=threads --cpus-per-task=# -task_affinity=cpu:#
--cpu-bind=cores --cpus-per-task=# -task_affinity=core:#
--cpu-bind=rank --cpus-per-task=# -task_affinity=cpu:#

In addition, file name specifications with expression substitution (e.g. file names including "%j" for job_ID, "%J" for job_ID.step_ID, "%s" for step_ID, "%t" for task_ID, or "%n" for node_ID) are not supported. This effects the following options:

  • -e, --error
  • -i, --input
  • -o, --output

For the srun command's --multi-prog option (Multiple Program, Multiple Data configurations), the command file will be translated from Slurm's format to a POE format. POE does not suppor. Slurm expressions in the MPMD configuration file (e.g. "%t" will not be replaced with the task's number and "%o" will not be replaced with the task's offset within this range). The command file will be stored in a temporary file in the ".slurm" subdirectory of your home directory. The file name will have a prefix of "slurm_cmdfile." followed by srun's process id. If the srun command does not terminate gracefully, this file may persist after the job step's termination and not be purged. You can find and purge these files using commands of the form shown below. You should only purge older files, after their job steps are completed.

$ ls -l ~/.slurm/slurm_cmdfile.*
$ rm    ~/.slurm/slurm_cmdfile.*

The -L/--label option differs slightly in that when the output from multiple tasks are identical, they are combined on a single line with the prefix identifying which task(s) generated the output. In addition, there is a colon but no space between the task IDs and output. For example:

# Slurm OUTPUT
0: foo
1: foo
2: foo
0: bar
1: barr
2: bar

# POE OUTPUT
0-2:foo
0 2:bar
1:barr

In addition, when srun's --multi-prog option (for Multiple Program, Multiple Data configurations) is used with the -L/--label option then a job step ID, colon and space will precede the task ID and colon. For example:

# Slurm OUTPUT
0: zero
1: one
2: two

# POE OUTPUT (FOR STEP ID 1)
1: 0: zero
1: 1: one
1: 2: two

The srun command is not able to report task status upon receipt of a SIGINT signal (ctrl-c interrupt from keyboard), however two SIGINT signals within a one second interval will terminate the job as on other Slurm configurations.

Environment Variables

Since Slurm is not directly launching user tasks, the following environment variables are NOT available with POE:

  • SLURM_CPU_BIND_LIST
  • SLURM_CPU_BIND_TYPE
  • SLURM_CPU_BIND_VERBOSE
  • SLURM_CPUS_ON_NODE
  • SLURM_GTIDS
  • SLURM_LAUNCH_NODE_IPADDR
  • SLURM_LOCALID
  • SLURM_MEM_BIND_LIST
  • SLURM_MEM_BIND_TYPE
  • SLURM_MEM_BIND_VERBOSE
  • SLURM_NODEID
  • SLURM_PROCID
  • SLURM_SRUN_COMM_HOST
  • SLURM_SRUN_COMM_PORT
  • SLURM_TASK_PID
  • SLURM_TASKS_PER_NODE
  • SLURM_TOPOLOGY_ADDR
  • SLURM_TOPOLOGY_ADDR_PATTERN

Note that POE sets a variety of environment variables that provide similar information to some the missing Slurm environment variables. Particularly note the following environment variables:

  • MP_I_UPMD_HOSTNAME (local hostname)
  • MP_CHILD (global task ID)

Gang Scheduling

Slurm can be configured to gang schedule (time slice) parallel jobs by alternately suspending and resuming them. Depending upon the number of jobs configured to time slice and the time slice interval (as specified in the slurm.conf file using the OverSubscribe and SchedulerTimeSlice options), the job may experience communication timeouts. Set the environment variable MP_TIMEOUT to specify an appropriate communication timeout value. Note that the default timeout is 150 seconds. See Gang Scheduling for more information.

export MP_TIMEOUT=600

Other User Notes

POE can not support a step ID of zero. In POE installations, a job's first step ID will be 1 rather than 0.

Since the Slurm step launches the PE PMD process instead of the users tasks the exit code stored in accounting will be that of the PMD instead of the users tasks. The exit code of the job allocation if started with srun will be correct as we will grab the exit code from the wrapped poe.

Use of the srun command rather than the poe command is recommeded to launch tasks. If the poe command is used with a hostlist file (e.g. "-hfile" option or "MP_HOSTFILE" environment variable or a "host.list" file in the current working directory), the resd option must be set to yes (e.g. "-resd yes" option or "MP_RESD=yes" environment variable).

System Administration

There are several critical Slurm configuration parameters for use with PE. These configuration parameters should be set in your slurm.conf file. LaunchType defines the task launch mechanism to be used and must be set to launch/poe. This configuration means that poe will be used to launch all applications. SwitchType defines the mechanism used to manage the network switch and it must be set to switch/nrt and use IBM's Network Resource Table (NRT) interface on ALL nodes in the cluster (only a few of them will actually interact with IBM's NRT library, but all need to work with the NRT data structures). Task launch is slower in this environment than with a typical Linux cluster and the MessageTimeout must be configured to a sufficiently large value so that large parallel jobs can be launched withou. Slurm's job step credentials expiring. When switch resources are allocated to a job, all processes spawned by that job must be terminated before the switch resources can be released for use by another program. This means that reliable tracking of all spawned processes is critical for switch use. Use of ProctrackType=proctrack/cgroup is strongly recommended. Use of any other process tracking plugin significantly increases the likelihood of orphan processes that must be manually identified and killed in order to release switch resources. While it is possible to to configure distinct NodeName and NodeHostName parameters for the compute nodes, this is discouraged for performance reasons (the switch/nrt plugin is not optimized for such a configuration).

# Excerpt of slurm.conf
LaunchType=launch/poe
SwitchType=switch/nrt
MessageTimeout=30
ProctrackType=proctrack/cgroup

In order for these plugins to be built, the locations of the POE Resource Manager header file (permapi.h) the NRT header file (nrt.h) and NRT library (libnrt.so) must be identified at the time the Slurm is built. The header files are needed at build time to get NRT data structures, function return codes, etc. The NRT library location is needed to identify where the library is to be loaded from by Slurm's switch/nrt plugin, but the library is only actually when needed and only by the slurmd daemon.

Slurm searches for the header files in the /usr/include directory by default. If the files are not installed there, you can specify a different location using the --with-nrth=PATH option to the configure program, where "PATH" is the fully qualified pathname of the parent directory(ies) of the nrt.h and permapi.h files. Slurm searches for the libnrt.so file in the /usr/lib and /usr/lib64 directories by default. If the file is not installed there, you can specify a different location using the --with-nrtlib=PATH option to the configure program, where "PATH" is the fully qualified pathname of the parent directory of the libnrt.so file. Alternately these values may be specified in your ~/.rpmmacros file. For example:

%_with_nrth      "/opt/ibmhpc/pecurrent/base/include"
%_with_libnrt    "/opt/ibmhpc/pecurrent/base/intel/lib64"

IMPORTANT:The poe command interacts with Slurm by loading a Slurm library providing a variety of functions for its use. The library name is "libpermapi.so" and it is in installed with the other Slurm libraries in the subdirectory "lib/slurm". You must modify the link of /usr/lib64/libpermapi.so to point to the location of the slurm version of this library.

Modifying the "/etc/poe.limits" file is not enough. The poe command is loading and using the libpermapi.so library initially from the /usr/lib64 directory. It later reads the /etc/poe.limits file and loads the library listed there. In order for poe to work with Slurm, it needs to use the "libpermapi.so" generated by Slurm for all of its functions. Until poe is modified to only load the correct library, it is necessary for /usr/lib64/libpermapi.so to contain Slurm's library or a link to it.

If you are having problems running on more than 32 nodes this is most likely your issue.

Changes to the count of dynmamic switch windows necessitate cold-starting Slurm (without jobs). The procedure is as follows:

  1. Prevent new jobs from being started (e.g. Drain the compute nodes).
  2. Cancel all jobs.
  3. Change the dynamic window count on the compute nodes.
  4. Restart Slurm daemons without preserving state (e.g. "/etc/init.d/slurm startclean" or initiate the daemons using the "-c" option).

Job Scheduling

Slurm can be configured to gang schedule (time slice) parallel jobs by alternately suspending and resuming them. Depending upon the number of jobs configured to time slice and the time slice interval (as specified in the slurm.conf file using the OverSubscribe and SchedulerTimeSlice options), the job may experience communication timeouts. Set the environment variable MP_TIMEOUT to specify an appropriate communication timeout value. Note that the default timeout is 150 seconds. See Gang Scheduling for more information.

export MP_TIMEOUT=600

Slurm also can support long term job preemption with IBM's Parallel Environment. Job's can be explicitly preempted and later resumed using the scontrol suspend <jobid> and scontrol resume <jobid> commands. This functionality relies upon NRT functions to suspend/resume programs and reset MPI timeouts. Note tha. Slurm supports the preemption only of whole jobs rather than individual job steps. A suspended job will relinquish CPU resources, but retain memory and switch window resources. Note that the long term suspension of jobs with any allocated Collective Acceleration Units (CAU) is disabled and an error message to that effect will be generated in response to such a request. In addition, version 1200 or higher of IBM's NRT API is required to support this functionality.

Cold Starting

If the slurmctld daemon is cold started (without saved state), then information about previously allocated network resources is lost. Slurm will release those resources to the best of its ability based upon information available from the Network Resource Table (NRT) library functions. These function provide sufficient information to release all resources except for CAU on a Torrent network (e.g. a PERCS system). In order to release CAU, it is necessary to cold start the Protocol Network Services Daemon (PNSD) on compute nodes following the sequence shown below.

Stop  Slurm daemons:       /etc/init.d/slurm stop
Stop  PNSD:                stopsrc -s pnsd
Start PNSD clean:          startsrc -s pnsd -a -c
Start Slurm daemons clean: /etc/init.d/slurm startclean

Design Notes

It is necessary for all nodes that can be used for scheduling a single job have the same network adapter types and count. For example, if node "tux1" has two ethernet adapters then the node "tux2" in the same cluster must also have two ethernet adapters on the same networks or be in a different Slurm partition so that one job can not be allocated resources on both nodes. Without this restriction, a job may allocated adapter resources on one node and be unable to allocate the corresponding adapter resources on another node.

It is possible to configure Slurm and LoadLeveler to simultaneously exist on a cluster, however each scheduler must be configured to manage different compute nodes (e.g. LoadLeveler can manage compute nodes "tux[1-8]" and Slurm can manage compute nodes "tux[9-16]" on the same cluster). In addition, the /etc/poe.limits file on each node must identify the MP_PE_RMLIB appropriate for that node (e.g. IBM's or Slurm's libpermapi.so). If Slurm and LoadLeveler are configured to simultaneously manage the same nodes, you should expect both resource managers to try assigning the same resources. This will result in job failures.

The srun command uses the launch/poe plugin to launch the poe program. Then poe uses the launch/slurm plugin to launch the "pmd" process on the compute nodes, so two launch plugins are actually used.

Depending upon job size and network options, allocating and deallocating switch resources can take multiple seconds per node and the process of launching applications on multiple nodes is not well parallelized. This is outside of Slurm's control.

The two figures below show a high-level overview of the switch/nrt and launch/poe plugins. A typical Slurm installation with IBM PE would make use of both plugins, but the operation of each is shown independently for improved clarity. Note the the switch/nrt plugin is needed by not only the slurmd daemon, but also the slurmctld daemon (for managing switch allocation data structures) and the srun command (for packing and unpacking switch allocation information used at task launch time). In figure 2, note that the libpermapi library issues the job and job step creation requests. The srun command is an optional front-end for the poe command and the poe command can be invoked directly by the user if desired.

Figure 1: Use of the switch/nrt plugin

Figure 2: Use of the launch/poe plugin

Debugging Notes

It is possible to generate detailed logging of all switch/nrt actions and data by configuring DebugFlags=switch.

The environment variable MP_INFOLEVEL can be used to enable the logging of POE debug messages. To enable fairly detailed logging, set MP_INFOLEVEL=6.

The Protocol Network Services Daemon (PNSD) manages the Network Resource Table (NRT) information on each node. It's logs are written to the file /tmp/serverlog, which may be useful to diagnose problems. In order to execute PNSD in debug node (for extra debugging information), run the following commands as user root:

stopsrc -s pnsd
startsrc -s pnsd -a -D

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Last modified 31 March 2016

slurm-slurm-16-05-9-1/doc/html/ibm.shtml000066400000000000000000000077731304416576200177110ustar00rootroot00000000000000

IBM AIX User and Administrator Guide

Overview

This document describes the unique features of Slurm on the IBM AIX computers with a Federation switch. Slurm support for AIX has been thoroughly tested, but we know of no AIX installations using Slurm after 2008. You should be familiar with the Slurm's mode of operation on Linux clusters before studying the relatively few differences in IBM system operation described in this document.

User Tools

The normal set of Slurm user tools: srun, scancel, sinfo, smap, squeue and scontrol provide all of the expected services except support for job steps. While the srun command will launch the tasks of a job step on an IBM AIX system, it does not support use of the Federation switch or IBM's MPI. Job steps should be launched using IBM's poe command. This architecture insures proper operation of all IBM tools.

You will use srun to submit a batch script to Slurm. This script should contain one or more invocations of poe to launch the tasks. If you want to run a job interactively, just execute poe directly. Poe will recognize that it lacks a Slurm job allocation (the SLURM_JOB_ID environment variable will be missing) and create the Slurm allocation prior to launching tasks.

Each poe invocation (or Slurm job step) can have it's own network specification. For example one poe may use IP mode communications and the next use User Space (US) mode communications. This enhancement to normal poe functionality may be accomplished by setting the SLURM_NETWORK environment variable. The format of SLURM_NETWORK is "network.[protocol],[type],[usage],[mode]". For example "network.mpi,en0,shared,ip". See LoadLeveler documentation for more details.

Checkpoint

Slurm supports checkpoint via poe. In order to enable checkpoint, the shell executing the poe command must itself be initiated with the environment variable CHECKPOINT=yes. One file is written for each node on which the job is executing, plus another for the script executing poe.a By default, the checkpoint files will be written to the current working directory of the job. Names and locations of these files can be controlled using the environment variables MP_CKPTFILE and MP_CKPTDIR. Use the squeue command to identify the job and job step of interest. To initiate a checkpoint in which the job step will continue execution, use the command:
scontrol check create job_id.step_id
To initiate a checkpoint in which the job step will terminate afterwards, use the command:
scontrol check vacate job_id.step_id

System Administration

Three unique components are required to use Slurm on an IBM system.

  1. The Federation switch plugin is required. This component is packaged with the Slurm distribution.
  2. There is a process tracking kernel extension required. This is used to insure that all processes associated with a job are tracked. Slurm normally uses session ID and process group ID on Linux systems, but these mechanisms can not prevent user processes from establishing their own session or process group and thus "escape" from Slurm tracking. This kernel extension is not packaged with Slurm, but is available upon request.
  3. The final component is a library that accepts poe library calls and performs actions in Slurm to satisfy these requests, such as launching tasks. This library is based upon IBM Confidential information and is not at this time available for distribution. Interested parties are welcome to pursue the possible distribution of this library with IBM and Slurm developers.

Until this last issue is resolved, use of Slurm on an IBM AIX system should not be viewed as a supported configuration (at least outside of LLNL, which established a contract with IBM for this purpose).

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Last modified 5 October 2012

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Intel Knights Landing (KNL) User and Administrator Guide

Overview

This document describes the unique features of Slurm on the computers with the Intel Knights Landing processor. You should be familiar with the Slurm's mode of operation on Linux clusters before studying the relatively few differences in Intel KNL system operation described in this document.

User Tools

The desired NUMA and MCDRAM modes for a KNL processor should be specified using the -C or --constraints option of Slurm's job submission commands: salloc, sbatch, and srun. Currently available NUMA and MCDRAM modes are shown in the table below. Each node's available and current NUMA and MCDRAM modes are visible in the "available features" and "active features" fields respectively, which may be seen using the scontrol, sinfo, or sview commands. Note that a node may need to be rebooted to get the desired NUMA and MCDRAM modes and nodes may only be rebooted when they contain no running jobs (i.e. sufficient resources may be available to run a pending job, but until the node is idle and can be rebooted, the pending job may not be allocated resources). Also note that the job will be charged for resources from the time of resource allocation, which may include time to reboot a node into the desired NUMA and MCDRAM configuration.

While Slurm generally supports a very rich set of options for the node constraint options (exclusive OR, node counts for each constraint, etc.), only a simple AND operation is supported for KNL systems (specified using a comma or ampersand separator between specified constraints). Jobs may specify their desired NUMA and/or MCDRAM configuration. If no NUMA and/or MCDRAM configuration is specified, then a node with any possible value for that configuration will be used.

Type Name Description
MCDRAMcacheAll of MCDRAM to be used as cache
MCDRAMequalMCDRAM to be used partly as cache and partly combined with primary memory
MCDRAMflatMCDRAM to be combined with primary memory into a "flat" memory space
NUMAa2aAll to all
NUMAhemiHemisphere
NUMAsnc2Sub-NUMA cluster 2
NUMAsnc4Sub-NUMA cluster 4 (NOTE)
NUMAquadQuadrant (NOTE)

Jobs requiring some or all of the KNL high bandwidth memory (HBM) should explicitly request that memory using Slurm's Generic RESource (GRES) options. The HBM will always be known by Slurm GRES name of "hbm". Examples below demonstrate use of HBM.

NOTE: Slurm version 16.05 provides limited support for restricting use of HBM. At some point in the future, the amount of HBM requested by the job will be compared with the total amount of HBM and number of memory-containing NUMA nodes available on the KNL processor. The job will then be bound to specific NUMA nodes in order to limit the total amount of HBM available to the job, and thus reserve the remaining HBM for other jobs running on that KNL processor.

NOTE: Slurm version 16.05 and earlier can only support homogeneous nodes (e.g. the same number of cores per NUMA node). KNL processors with 68 cores (a subset of KNL models) will not have homogeneous NUMA nodes in snc4 mode, but each each NUMA node will have either 16 or 18 cores. This will result in Slurm using the lower core count, finding a total of 256 threads rather than 272 threads and setting the node to a DOWN state.

Accounting

If a node requires rebooting for a job's required configuration, the job will be charged for the resource allocation from the time of allocation through the lifetime of the job, including the time consumed for booting the nodes. The job's time limit will be calculated from the time that all nodes are ready for use. For example, a job with a 10 minute time limit may be allocated resources at 10:00:00. If the nodes require rebooting, they might not be available for use until 10:20:00, 20 minutes after allocation, and the job will begin execution at that time. The job must complete no later than 10:30:00 in order to satisfy it's time limit (10 minutes after execution actually begins). However, the job will be charged for 30 minutes of resource use, which includes the boot time.

Sample Use Cases

$ sbatch -C flat,a2a -N2 --gres=hbm:8g --exclusive my.script
$ srun --constraint=hemi,cache -n36 a.out
$ srun --constraint=flat --gres=hbm:2g -n36 a.out

$ sinfo -o "%30N %20b %f"
NODELIST       ACTIVE_FEATURES  AVAIL_FEATURES
nid000[10-11]
nid000[12-35]  flat,a2a         flat,a2a,snc2,hemi
nid000[36-43]  cache,a2a        flat,equal,cache,a2a,hemi

Network Topology

Slurm will optimize performance using those resources available without rebooting. If node rebooting is required, then it will optimize layout with respect to network bandwidth using both nodes currently in the desired configuration and those which can be made available after rebooting. This can result in more nodes being rebooted than strictly needed, but will improve application performance.

Users can specify they want all resources allocated on a specific count of leaf switches (Dragonfly group) using Slurm's --switches option. They can also specify how much additional time they are willing to wait for such a configuration. If the desired configuration can not be made available within the specified time interval, the job will be allocated nodes optimized with respect to network bandwidth to the extent possible. On a Dragonfly network, this means allocating resources over either single group or distributed evenly over as many groups as possible. For example:

srun --switches=1@10:00 N16 a.out

Note that system administrators can disable use of the --switches option or limit the amount of time the job can be deferred using the SchedulerParameters max-switch-wait option.

Booting Problems

If node boots fail, those nodes are drained and the job is requeued so that it can be allocated a different set of nodes. The nodes originally allocated to the job will remain available to the job, so likely a small number of additional nodes will be required.

System Administration

Four important components are required to use Slurm on an Intel KNL system.

  1. Slurm needs a mechanism to determine the node's current topology (e.g. how many NUMA exist and which cores are associated with each NUMA). Slurm relies upon Portable Hardware Locality (HWLOC) for this functionality. Please install HWLOC before building Slurm.
  2. The node features plugin manages the available and active features information available for each KNL node.
  3. A configuration file is used to define various timeouts, default configuration, etc. The configuration file name and contents will depend upon the node features plugins used. See the knl.conf man page for more information.
  4. A mechanism is required to boot nodes in the desired configuration. This mechanism must be integrated with existing Slurm infrastructure for rebooting nodes on user request (--reboot) plus (for Cray systems only) power saving (powering down idle nodes and restarting them on demand).

In addition, there is a DebugFlags option of "NodeFeatures" which will generate detailed information about KNL operations.

The KNL-specific available and active features are configured differently based upon the plugin configured.
For the knl_cray plugin, KNL-specific available and active features are not included in the "slurm.conf" configuration file, but are set and the managed by the NodeFeatures plugin when the slurmctld daemon starts.
For the knl_generic plugin, KNL-specific features should be defined in the "slurm.conf" configuration file. When the slurmd daemon starts on each compute node, it will update the available and active features as needed.
Features which are not KNL-specific (e.g. rack number, "knl", etc.) will be copied from the node's "Features" configuration in "slurm.conf" to both the available and active feature fields and not modified by the NodeFeatures plugin.

Slurm version 16.05 does not support the concept of multiple NUMA nodes within a single socket. If a KNL node is booted with multiple NUMA, then each NUMA node will appear in Slurm as a separate socket. In the slurm.conf configuration file, set "FastSchedule=1" and node socket and core counts to values which are appropriate for some NUMA mode to be used on the node. When the node boots and the slurmd daemon on the node starts, it will report to the slurmctld daemon the node's actual socket (NUMA) and core counts, which will update Slurm data structures for the node to the values which are currently configured. Note that Slurm (version 16.05) current does not support the concept of differing numbers of cores in each socket (or NUMA node). We are currently working to address these issues.

Mode of Operation

  1. The node's configured "Features" are copied to the available and active feature fields.
  2. The node features plugin determines the node's current MCDRAM and NUMA values as well as those which are available and adds those values to the node's active and available feature fields respectively. Note that these values may not be available until the node has booted and the slurmd daemon on the compute node sends that information to the slurmctld daemon.
  3. Jobs will be allocated nodes already in the requested MCDRAM and NUMA mode if possible. If insufficient resources are available with the requested configuration then other nodes will be selected and booted into the desired configuration once no other jobs are active on the node. Until a node is idle, its configuration can not be changed. Note that node reboot time is roughly on the order of 20 minutes.

Cray Configuration

On Cray systems, NodeFeaturesPlugins should be configured as "knl_cray".

The configuration file will be named "knl_cray.conf". The file will include the path to the capmc program (CapmcPath), which is used to get a node's available MCDRAM and NUMA modes, change the modes, power the node down, reboot it, etc. Note the "CapmcTimeout" parameter is the time required for the capmc program to respond to a request and NOT the time for a boot operation to complete.

Power saving mode is integrated with rebooting nodes in the desired mode. Programs named "capmc_resume" and "capmc_suspend" are provided to boot nodes in the desired mode. The programs are included in the main Slurm RPM and installed in the "sbin" directory and must be installed on the Cray "sdb" node. If powering down of idle nodes is not desired, then configure "ResumeProgram" in "slurm.conf" to the path of the "capmc_resume" file and configure "SuspendTime" to a huge value (e.g. "SuspendTime=30000000" will only power down a node which has been idle for about one year).

Note that getting a compute node's current MCDRAM and NUMA mode, modifying its MCDRAM and NUMA mode, and rebooting it are operations performed by the slurmctld daemon on the head node.

The GresTypes configuration parameter should include "hbm" to identify High Bandwidth Memory (HBM) as being a consumable resources on compute nodes. Additional GresTypes can be specified as needed in a comma separated list. The amount of HBM on each node should not be configured in a Slurm configuration file, but that information will be loaded by the knl_cray plugin using information provided by the capmc program.

Sample slurm.conf file for knl_cray plugin

# Sample slurm.conf
NodeFeaturesPlugins=knl_cray
DebugFlags=NodeFeatures
GresTypes=hbm
#
ResumeProgram=/opt/slurm/default/sbin/capmc_resume
SuspendTime=30000000
ResumeTimeout=1800
...
Nodename=default Sockets=1 CoresPerSocket=68 ThreadsPerCore=4 RealMemory=128000 Feature=knl
NodeName=nid[00000-00127] State=UNKNOWN

Sample knl_cray.conf file

# Sample knl_cray.conf
CapmcPath=/opt/cray/capmc/default/bin/capmc
CapmcTimeout=2000	# msec
DefaultNUMA=a2a         # NUMA=all2all
AllowNUMA=a2a,snc2,hemi
DefaultMCDRAM=cache     # MCDRAM=cache

Sample slurm.conf File

# Sample slurm.conf
NodeFeaturesPlugins=knl_cray
DebugFlags=NodeFeatures
GresTypes=hbm
#
ResumeProgram=/opt/slurm/default/sbin/capmc_resume
SuspendProgram=/opt/slurm/default/sbin/capmc_suspend
SuspendTime=30000000
ResumeTimeout=1800
...
Nodename=default Sockets=1 CoresPerSocket=68 ThreadsPerCore=4 RealMemory=128000 Feature=knl
NodeName=nid[00000-00127] State=UNKNOWN

Generic Cluster Configuration

All other clusters should have NodeFeaturesPlugins configured to "knl_generic". This plugin performs all operations directly on the compute nodes using Intel's syscfg program to get and modify the node's MCDRAM and NUMA mode and uses the Linux reboot program to reboot the compute node in order for modifications in MCDRAM and/or NUMA mode to take effect. Make sure that RebootProgram is defined in the slurm.conf file. This plugin currently does not permit the specification of ResumeProgram, SuspendProgram, SuspendTime, etc. in slurm.conf, however that limitation may be removed in the future (the ResumeProgram currently has no means of changing the node's MCDRAM and/or NUMA mode prior to reboot).

NOTE:The syscfg program reports the MCDRAM and NUMA mode to be used when the node is next booted. If the syscfg program is used to modify the MCDRAM or NUMA mode of a node, but it is not rebooted, then Slurm will be making scheduling decisions based upon incorrect state information. If you want to change node state information outside of Slurm then use the following proceedure:

  1. Drain the nodes of interest
  2. Change their MCDRAM and/or NUMA mode
  3. Reboot the nodes, then
  4. Restore them to service in Slurm

Sample knl_generic.conf File

# Sample knl_generic.conf
SyscfgPath=/usr/bin/syscfg
DefaultNUMA=a2a         # NUMA=all2all
AllowNUMA=a2a,snc2,hemi
DefaultMCDRAM=cache     # MCDRAM=cache

Sample slurm.conf File

# Sample slurm.conf
NodeFeaturesPlugins=knl_generic
DebugFlags=NodeFeatures
GresTypes=hbm
RebootProgram=/sbin/reboot
...
Nodename=default Sockets=1 CoresPerSocket=68 ThreadsPerCore=4 RealMemory=128000 Feature=knl
NodeName=nid[00000-00127] State=UNKNOWN

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Last modified 5 December 2016

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Job Array Support

Overview

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). All jobs must have the same initial options (e.g. size, time limit, etc.), however it is possible to change some of these options after the job has begun execution using the scontrol command specifying the JobID of the array or individual ArrayJobID.

$ scontrol update job=101 ...
$ scontrol update job=101_1 ...

Job arrays are only supported for batch jobs and the array index values are specified using the --array or -a option of the sbatch command. The option argument can be specific array index values, a range of index values, and an optional step size as shown in the examples below. Note that the minimum index value is zero and the maximum value is a Slurm configuration parameter (MaxArraySize minus one). Jobs which are part of a job array will have the environment variable SLURM_ARRAY_TASK_ID set to its array index value.

# Submit a job array with index values between 0 and 31
$ sbatch --array=0-31    -N1 tmp

# Submit a job array with index values of 1, 3, 5 and 7
$ sbatch --array=1,3,5,7 -N1 tmp

# Submit a job array with index values between 1 and 7
# with a step size of 2 (i.e. 1, 3, 5 and 7)
$ sbatch --array=1-7:2   -N1 tmp

A maximum number of simultaneously running tasks from the job array may be specified using a "%" separator. For example "--array=0-15%4" will limit the number of simultaneously running tasks from this job array to 4.

Job ID and Environment Variables

Job arrays will have two additional environment variable set. SLURM_ARRAY_JOB_ID will be set to the first job ID of the array. SLURM_ARRAY_TASK_ID will be set to the job array index value. For example a job submission of this sort
sbatch --array=1-3 -N1 tmp
will generate a job array containing three jobs. If the sbatch command responds
Submitted batch job 36
then the environment variables will be set as follows:

SLURM_JOB_ID=36
SLURM_ARRAY_JOB_ID=36
SLURM_ARRAY_TASK_ID=1

SLURM_JOB_ID=37
SLURM_ARRAY_JOB_ID=36
SLURM_ARRAY_TASK_ID=2

SLURM_JOB_ID=38
SLURM_ARRAY_JOB_ID=36
SLURM_ARRAY_TASK_ID=3

All Slurm commands and APIs recognize the SLURM_JOB_ID value. Most commands also recognize the SLURM_ARRAY_JOB_ID plus SLURM_ARRAY_TASK_ID values separated by an underscore as identifying an element of a job array. Using the example above, "37" or "36_2" would be equivalent ways to identify the second array element of job 36. A set of APIs has been developed to operate on an entire job array or select tasks of a job array in a single function call. The function response consists of an array identifying the various error codes for various tasks of a job ID. For example the job_resume2() function might return an array of error codes indicating that tasks 1 and 2 have already completed; tasks 3 through 5 are resumed successfully, and tasks 6 through 99 have not yet started.

File Names

Two additional options are available to specify a job's stdin, stdout, and stderr file names: %A will be replaced by the value of SLURM_ARRAY_JOB_ID (as defined above) and %a will be replaced by the value of SLURM_ARRAY_TASK_ID (as defined above). The default output file format for a job array is "slurm-%A_%a.out". An example of explicit use of the formatting is:
sbatch -o slurm-%A_%a.out --array=1-3 -N1 tmp
which would generate output files names of this sort "slurm-36_1.out", "slurm-36_2.out" and "slurm-36_3.out". If these file name options are used without being part of a job array then "%A" will be replaced by the current job ID and "%a" will be replaced by 4,294,967,294 (equivalent to 0xfffffffe or NO_VAL).

Scancel Command Use

If the job ID of a job array is specified as input to the scancel command then all elements of that job array will be cancelled. Alternately an array ID, optionally using regular expressions, may be specified for job cancellation.

# Cancel array ID 1 to 3 from job array 20
$ scancel 20_[1-3]

# Cancel array ID 4 and 5 from job array 20
$ scancel 20_4 20_5

# Cancel all elements from job array 20
$ scancel 20

# Cancel the current job or job array element (if job array)
if [[-z $SLURM_ARRAY_JOB_ID]]; then
  scancel $SLURM_JOB_ID
else
  scancel ${SLURM_ARRAY_JOB_ID}_${SLURM_ARRAY_TASK_ID}
fi

Squeue Command Use

When a job array is submitted to Slurm, only one job record is created. Additional job records will only be created when the state of a task in the job array changes, typically when a task is allocated resources or its state is modified using the scontrol command. By default, the squeue command will report all of the tasks associated with a single job record on one line and use a regular expression to indicate the "array_task_id" values as shown below.

$ squeue
 JOBID     PARTITION  NAME  USER  ST  TIME  NODES NODELIST(REASON)
1080_[5-1024]  debug   tmp   mac  PD  0:00      1 (Resources)
1080_1         debug   tmp   mac   R  0:17      1 tux0
1080_2         debug   tmp   mac   R  0:16      1 tux1
1080_3         debug   tmp   mac   R  0:03      1 tux2
1080_4         debug   tmp   mac   R  0:03      1 tux3

An option of "--array" or "-r" has also been added to the squeue command to print one job array element per line as shown below. The environment variable "SQUEUE_ARRAY" is equivalent to including the "--array" option on the squeue command line.

$ squeue -r
 JOBID PARTITION  NAME  USER  ST  TIME  NODES NODELIST(REASON)
1082_3     debug   tmp   mac  PD  0:00      1 (Resources)
1082_4     debug   tmp   mac  PD  0:00      1 (Priority)
  1080     debug   tmp   mac   R  0:17      1 tux0
  1081     debug   tmp   mac   R  0:16      1 tux1
1082_1     debug   tmp   mac   R  0:03      1 tux2
1082_2     debug   tmp   mac   R  0:03      1 tux3

The squeue --step/-s and --job/-j options can accept job or step specifications of the same format.

$ squeue -j 1234_2,1234_3
...
$ squeue -s 1234_2.0,1234_3.0
...

Two additional job output format field options have been added to squeue:
%F prints the array_job_id value
%K prints the array_task_id value
(all of the obvious letters to use were already assigned to other job fields).

Scontrol Command Use

Use of the scontrol show job option shows two new fields related to job array support. The JobID is a unique identifier for the job. The ArrayJobID is the JobID of the first element of the job array. The ArrayTaskID is the array index of this particular entry, either a single number of an expression identifying the entries represented by this job record (e.g. "5-1024"). Neither field is displayed if the job is not part of a job array. The optional job ID specified with the scontrol show job or scontrol show step commands can identify job array elements by specifying ArrayJobId and ArrayTaskId with an underscore between them (eg. <ArrayJobID>_<ArrayTaskId>).

The scontrol command will operate on all elements of a job array if the job ID specified is ArrayJobID. Individual job array tasks can be modifed using the ArrayJobID_ArrayTaskID as shown below.

$ sbatch --array=1-4 -J array ./sleepme 86400
Submitted batch job 21845

$ squeue
 JOBID   PARTITION     NAME     USER  ST  TIME NODES NODELIST
 21845_1    canopo    array    david  R  0:13  1     dario
 21845_2    canopo    array    david  R  0:13  1     dario
 21845_3    canopo    array    david  R  0:13  1     dario
 21845_4    canopo    array    david  R  0:13  1     dario

$ scontrol update JobID=21845_2 name=arturo
$ squeue
 JOBID   PARTITION     NAME     USER  ST   TIME  NODES NODELIST
 21845_1    canopo    array    david  R   17:03   1    dario
 21845_2    canopo   arturo    david  R   17:03   1    dario
 21845_3    canopo    array    david  R   17:03   1    dario
 21845_4    canopo    array    david  R   17:03   1    dario

The scontrol hold, holdu, release, requeue, requeuehold, suspend and resume commands can also either operate on all elements of a job array or individual elements as shown below. 

$ scontrol suspend 21845
$ squeue
 JOBID PARTITION      NAME     USER  ST TIME  NODES NODELIST
21845_1    canopo    array    david  S 25:12  1     dario
21845_2    canopo   arturo    david  S 25:12  1     dario
21845_3    canopo    array    david  S 25:12  1     dario
21845_4    canopo    array    david  S 25:12  1     dario
$ scontrol resume 21845
$ squeue
 JOBID PARTITION      NAME     USER  ST TIME  NODES NODELIST
21845_1    canopo    array    david  R 25:14  1     dario
21845_2    canopo   arturo    david  R 25:14  1     dario
21845_3    canopo    array    david  R 25:14  1     dario
21845_4    canopo    array    david  R 25:14  1     dario

scontrol suspend 21845_3
$ squeue
 JOBID PARTITION      NAME     USER  ST TIME  NODES NODELIST
21845_1    canopo    array    david  R 25:14  1     dario
21845_2    canopo   arturo    david  R 25:14  1     dario
21845_3    canopo    array    david  S 25:14  1     dario
21845_4    canopo    array    david  R 25:14  1     dario
scontrol resume 21845_3
$ squeue
 JOBID PARTITION      NAME     USER  ST TIME  NODES NODELIST
21845_1    canopo    array    david  R 25:14  1     dario
21845_2    canopo   arturo    david  R 25:14  1     dario
21845_3    canopo    array    david  R 25:14  1     dario
21845_4    canopo    array    david  R 25:14  1     dario

Job Dependencies

A job which is to be dependent upon an entire job array should specify itself dependent upon the ArrayJobID. Since each array element can have a different exit code, the interpretation of the afterok and afternotok clauses will be based upon the highest exit code from any task in the job array.

When a job dependency specifies the job ID of a job array:
The after clause is satisfied after all tasks in the job array start.
The afterany clause is satisfied after all tasks in the job array complete.
The afterok clause is satisfied after all tasks in the job array complete successfully.
The afternotok clause is satisfied after all tasks in the job array complete with at least one tasks not completing successfully.

Examples of use are shown below:

# Wait for specific job array elements
sbatch --depend=after:123_4 my.job
sbatch --depend=afterok:123_4:123_8 my.job2

# Wait for entire job array to complete
sbatch --depend=afterany:123 my.job

# Wait for entire job array to complete successfully
sbatch --depend=afterok:123 my.job

# Wait for entire job array to complete and at least one task fails
sbatch --depend=afternotok:123 my.job

Other Command Use

The following Slurm commands do not currently recognize job arrays and their use requires the use of Slurm job IDs, which are unique for each array element: sacct, sbcast, smap, sreport, sshare, sstat, and strigger. The sattach, sprio and sstat commands have been modified to permit specification of either job IDs or job array elements. The sview command has been modified to permit display of a job's ArrayJobId and ArrayTaskId fields. Both fields are displayed with a value of "N/A" if the job is not part of a job array.

System Administration

A new configuration parameter has been added to control the maximum job array size: MaxArraySize. The smallest index that can be specified by a user is zero and the maximum index is MaxArraySize minus one. The default value of MaxArraySize is 1001. The maximum MaxArraySize supported in Slurm version 14.03 and earlier is 65,533. Slurm version 14.11 has a new job array data structure, which can support job arrays with millions of tasks. Be mindful about the value of MaxArraySize as job arrays offer an easy way for users to submit large numbers of jobs very quickly.

The sched/backfill plugin has been modified to improve performance with job arrays. Once one element of a job array is discovered to not be runable or impact the scheduling of pending jobs, the remaining elements of that job array will be quickly skipped.

Slurm creates a single job record when a job array is submitted. Additional job records are only created as needed, typically when a task of a job array is started, which provides a very scalable mechanism to manage large job counts. Each task of the job array will have a unique Slurm "job_id", but all will have the same "array_job_id" value.

Last modified 22 June 2016

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Job Container Plugin API

Overview

This document describes Slurm job container plugins and the API that defines them. It is intended as a resource to programmers wishing to write their own Slurm job container plugins. Note that job container plugin is designed for use with Slurm jobs. It also applies to the sbcast server process on compute nodes. There is a proctrack plugin designed for use with Slurm job steps.

Slurm job container plugins are Slurm plugins that implement the Slurm job container API described herein. They must conform to the Slurm Plugin API with the following specifications:

const char plugin_type[]
The major type must be "job_container." The minor type can be any recognizable abbreviation for the type of proctrack. We recommend, for example:

  • cncu — Designed for use on Cray systems only and interface with Compute Node Clean Up (CNCU) the Cray infrastructure.
  • none — Designed for all other systems.

const char plugin_name[]
Some descriptive name for the plugin. There is no requirement with respect to its format.

const uint32_t plugin_version
If specified, identifies the version of Slurm used to build this plugin and any attempt to load the plugin from a different version of Slurm will result in an error. If not specified, then the plugin may be loadeed by Slurm commands and daemons from any version, however this may result in difficult to diagnose failures due to changes in the arguments to plugin functions or changes in other Slurm functions used by the plugin.

The programmer is urged to study src/plugins/proctrack/job_container/job_container_cncu.c for an example implementation of a Slurm proctrack plugin.

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Data Objects

The implementation must support a container ID of type uint64_t. This container ID is generated by the proctrack plugin.

The implementation must maintain (though not necessarily directly export) an enumerated errno to allow Slurm to discover as practically as possible the reason for any failed API call. These values must not be used as return values in integer-valued functions in the API. The proper error return value from integer-valued functions is Slurm_ERROR. The implementation should endeavor to provide useful and pertinent information by whatever means is practical. Successful API calls are not required to reset errno to a known value.

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API Functions

The following functions must appear. Functions which are not implemented should be stubbed.

int init (void)

Description:
Called when the plugin is loaded, before any other functions are called. Put global initialization here.

Returns:
SLURM_SUCCESS on success, or
SLURM_ERROR on failure.

void fini (void)

Description:
Called when the plugin is removed. Clear any allocated storage here.

Returns: None.

Note: These init and fini functions are not the same as those described in the dlopen (3) system library. The C run-time system co-opts those symbols for its own initialization. The system _init() is called before the SLURM init(), and the SLURM fini() is called before the system's _fini().

int container_p_create (uint32_t job_id);

Description: Create a container. The caller should insure that be valid container_p_delete() is called.

Argument: job_id    (input) Job ID.

Returns: Slurm_SUCCESS if successful. On failure, the plugin should return Slurm_ERROR and set the errno to an appropriate value to indicate the reason for failure.

int container_p_add_cont (uint32_t job_id, uint64_t cont_id);

Description: Add a specific process tracking container (PAGG) to a given job's container.

Arguments:
job_id    (input) Job ID.
cont_id    (input) Process tracking container value as set by the proctrack plugin.

Returns: Slurm_SUCCESS if successful. On failure, the plugin should return Slurm_ERROR and set the errno to an appropriate value to indicate the reason for failure.

int container_p_add_pid (uint32_t job_id, pid_t pid, uid_t uid);

Description: Add a specific process ID to a given job's container. The process is first placed into a process tracking container (PAGG).

Arguments:
job_id    (input) Job ID.
pid    (input) Process ID.
uid    (input) Owning user ID.

Returns: Slurm_SUCCESS if successful. On failure, the plugin should return Slurm_ERROR and set the errno to an appropriate value to indicate the reason for failure.

int container_p_delete (uint32_t job_id);

Description: Destroy or otherwise invalidate a job container. This does not imply the container is empty, just that it is no longer needed.

Arguments: job_id    (input) Job ID.

Returns: Slurm_SUCCESS if successful. On failure, the plugin should return Slurm_ERROR and set the errno to an appropriate value to indicate the reason for failure.

void container_p_reconfig (void);

Description: Note change in configuration, especially the value of the DebugFlags with respect to JobContainer.

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Last modified 27 March 2015

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Job Exit Codes

A job's exit code (aka exit status, return code and completion code) is captured by Slurm and saved as part of the job record. For sbatch jobs, the exit code that is captured is the output of the batch script. For salloc jobs, the exit code will be the return value of the exit call that terminates the salloc session. For srun, the exit code will be the return value of the command that srun executes.

Any non-zero exit code will be assumed to be a job failure and will result in a Job State of FAILED with a Reason of "NonZeroExitCode".

The exit code is an 8 bit unsigned number ranging between 0 and 255. While it is possible for a job to return a negative exit code, Slurm will display it as an unsigned value in the 0 - 255 range.

Job Step Exit Codes

When a job contains multiple job steps, the exit code of each executable invoked by srun is saved individually to the job step record.

Signaled Jobs

When a job or step is sent a signal that causes its termination, Slurm also captures the signal number and saves it to the job or step record.

Displaying Exit Codes and Signals

Slurm displays a job's exit code in the output of the scontrol show job and the sview utility. Slurm displays job step exit codes in the output of the scontrol show step and the sview utility.

When a signal was responsible for a job or step's termination, the signal number will be displayed after the exit code, delineated by a colon(:).

Database Job/Step Records

The Slurm control daemon sends job and step records to the Slurm database when the Slurm accounting_storage plugin is installed. Job and step records sent to the Slurm db can be viewed using the sacct command. The default sacct output contains an ExitCode field whose format mirrors the output of scontrol and sview described above.

Derived Exit Code and Comment String

After reading the above description of a job's exit code, one can imagine a scenario where a central task of a batch job fails but the script returns an exit code of zero, indicating success. In many cases, a user may not be able to ascertain the success or failure of a job until after they have examined the job's output files.

The job includes a "derived exit code" field. It is initially set to the value of the highest exit code returned by all of the job's steps (srun invocations). The job's derived exit code is determined by the Slurm control daemon and sent to the database when the accounting_storage plugin is enabled.

In addition to the derived exit code, the job record in the Slurm database contains a comment string. This is initialized to the job's comment string (when AccountingStoreJobComment parameter in the slurm.conf is set) and can only be changed by the user.

A new option has been added to the sacctmgr command to provide the user the means to modify these two fields of the job record. No other modification to the job record is allowed. For those who prefer a simpler command specifically designed to view and modify the derived exit code and comment string, the sjobexitmod wrapper has been created (see below).

The user now has the means to annotate a job's exit code after it completes and provide a description of what failed. This includes the ability to annotate a successful completion to jobs that appear to have failed but actually succeeded.

The sjobexitmod command

The sjobexitmod command is available to display and update the two derived exit fields of the Slurm db's job record. sjobexitmod can first be used to display the existing exit code / string for a job:

> sjobexitmod -l 123
JobID Account NNodes NodeList     State ExitCode DerivedExitCode Comment
----- ------- ------ -------- --------- -------- --------------- -------
123        lc      1     tux0 COMPLETED      0:0             0:0
If a change is desired, sjobexitmod can modify the derived fields: 
> sjobexitmod -e 49 -r "out of memory" 123

 Modification of job 123 was successful.

> sjobexitmod -l 123
JobID Account NNodes NodeList     State ExitCode DerivedExitCode Comment
----- ------- ------ -------- --------- -------- --------------- -------
123        lc      1     tux0 COMPLETED      0:0            49:0 out of memory

The existing sacct command also supports the two new derived exit fields:

> sacct -X -j 123 -o JobID,NNodes,State,ExitCode,DerivedExitcode,Comment
JobID   NNodes      State ExitCode DerivedExitCode        Comment
------ ------- ---------- -------- --------------- --------------
123          1  COMPLETED      0:0            49:0  out of memory

Last modified 15 April 2015

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Job Launch Design Guide

Overview

This guide describes at a high level the processes which occur in order to initiate a job including the daemons and plugins involved in the process. It describes the process of job allocation, step allocation, task launch and job termination. The functionality of tens of thousands of lines of code has been distilled here to a couple of pages of text, so much detail is missing.

Job Allocation

The first step of the process is to create a job allocation, which is a claim on compute resources. A job allocation can be created using the salloc, sbatch or srun command. The salloc and sbatch commands create resource allocations while the srun command will create a resource allocation (if not already running within one) plus launch tasks. Each of these commands will fill in a data structure identifying the specifications of the job allocation requirement (e.g. node count, task count, etc.) based upon command line options and environment variables and send the RPC to the slurmctld daemon. If the new job request is the highest priority, the slurmctld daemon will attempt to select resources for it immediately, otherwise it will validate that the job request can be satisfied at some time and queue the request. In either case the request will receive a response almost immediately containing one of the following:

  • A job ID and the resource allocation specification (nodes, cpus, etc.)
  • A job ID and notification of the job being in a queued state OR
  • An error code

The process of selecting resources for a job request involves multiple steps, some of which involve plugins. The process is as follows:

  1. Call job_submit plugins to modify the request as appropriate
  2. Validate that the options are valid for this user (e.g. valid partition name, valid limits, etc.)
  3. Determine if this job is the highest priority runnable job, if so then really try to allocate resources for it now, otherwise only validate that it could run if no other jobs existed
  4. Determine which nodes could be used for the job. If the feature specification uses an exclusive OR option, then multiple iterations of the selection process below will be required with disjoint sets of nodes
  5. Call the select plugin to select the best resources for the request
  6. The select plugin will consider network topology and the topology within a node (e.g. sockets, cores, and threads) to select the best resources for the job
  7. If the job can not be initiated using available resources and preemption support is configured, the select plugin will also determine if the job can be initiated after preempting lower priority jobs. If so then initiate preemption as needed to start the job

Step Allocation

The srun command is always used for job step creation. It fills in a job step request RPC using information from the command line and environment variables then sends that request to the slurmctld daemon. It is important to note that many of the srun options are intended for job allocation and are not supported by the job step request RPC (for example the socket, core and thread information is not supported). If a job step uses all of the resources allocated to the job then the lack of support for some options is not important. If one wants to execute multiple job steps using various subsets of resources allocated to the job, this shortcoming could prove problematic. It is also worth noting that the logic used to select resources for a job step is relatively simple and entirely contained within the slurmctld daemon code (the select plugin is not used for job steps). If the request can not be immediately satisfied due to a request for exclusive access to resources, the appropriate error message will be sent and the srun command will retry the request on a periodic basis. (NOTE: It would be desirable to queue the job step requests to support job step dependencies and better performance in the initiation of job steps, but that is not currently supported.) If the request can be satisfied, the response contains a digitally signed credential (by the crypto plugin) identifying the resources to be used.

Task Launch

The srun command builds a task launch request data structure including the credential, executable name, file names, etc. and sends it to the slurmd daemon on node zero of the job step allocation. The slurmd daemon validates the signature and forwards the request to the slurmd daemons on other nodes to launch tasks for that job step. The degree of fanout in this message forwarding is configurable using the TreeWidth parameter. Each slurmd daemon tests that the job has not been cancelled since the credential was issued (due to a possible race condition) and spawns a slurmstepd program to manage the job step. Note that the slurmctld daemon is not directly involved in task launch in order to minimize the overhead on this critical resource.

Each slurmstepd program executes a single job step. Besides the functions listed below, the slurmstepd program also executes several SPANK plugin functions at various times.

  1. Performs MPI setup (using the appropriate plugin)
  2. Calls the switch plugin to perform any needed network configuration
  3. Creates a container for the job step using a proctrack plugin
  4. Change user ID to that of the user
  5. Configures I/O for the tasks (either using files or a socket connection back to the srun command
  6. Sets up environment variables for the tasks including many task-specific environment variables
  7. Fork/exec the tasks

Job Step Termination

There are several ways in which a job step or job can terminate, each with slight variation in the logic executed. The simplest case is if the tasks run to completion. The srun will note the termination of output from the tasks and notify the slurmctld daemon that the job step has completed. slurmctld will simply log the job step termination. The job step can also be explicitly cancelled by a user, reach the end of its time limit, etc. and those follow a sequence of steps very similar to that for job termination, which is described below.

Job Termination

Job termination can either be user initiated (e.g. scancel command) or system initiated (e.g. time limit reached). The termination ultimately requires the slurmctld daemon to notify the slurmd daemons on allocated nodes that the job is to be ended. The slurmd daemon does the following:

  1. Send a SIGCONT and SIGTERM signal to any user tasks
  2. Wait KilLWait seconds if there are any user tasks
  3. Send a SIGKILL signal to any user tasks
  4. Wait for all tasks to complete
  5. Execute any Epilog program
  6. Send an epilog_complete RPC to the slurmctld daemon

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Last modified 18 May 2011

slurm-slurm-16-05-9-1/doc/html/job_submit_plugins.shtml000066400000000000000000000300001304416576200230130ustar00rootroot00000000000000

Job Submit Plugin API

Overview

This document describes Slurm job submit plugins and the API that defines them. It is intended as a resource to programmers wishing to write their own Slurm job submit plugins. This is version 100 of the API.

Slurm job submit plugins must conform to the Slurm Plugin API with the following specifications:

const char plugin_name[]="full text name"

A free-formatted ASCII text string that identifies the plugin.

const char plugin_type[]="major/minor"

The major type must be "job_submit." The minor type can be any suitable name for the type of job submission package. We include samples in the Slurm distribution for

  • all_partitions — Set default partition to all partitions on the cluster.
  • defaults — Set default values for job submission or modify requests.
  • logging — Log select job submission and modification parameters.
  • lua — Interface to Lua scripts implementing these functions (actually a slight variation of them). Sample Lua scripts can be found with the Slurm distribution in the directory contribs/lua. The default installation location of the Lua scripts is the same location as the Slurm configuration file, slurm.conf.
  • partition — Sets a job's default partition based upon job submission parameters and available partitions.

const uint32_t plugin_version
If specified, identifies the version of Slurm used to build this plugin and any attempt to load the plugin from a different version of Slurm will result in an error. If not specified, then the plugin may be loadeed by Slurm commands and daemons from any version, however this may result in difficult to diagnose failures due to changes in the arguments to plugin functions or changes in other Slurm functions used by the plugin.

Slurm can be configured to use multiple job_submit plugins if desired, however the lua plugin will only execute one lua script named "job_submit.lua" located in the default script directory (typically the subdirectory "etc" of the installation directory).

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API Functions

All of the following functions are required. Functions which are not implemented must be stubbed.

int init (void)

Description:
Called when the plugin is loaded, before any other functions are called. Put global initialization here.

Returns:
SLURM_SUCCESS on success, or
SLURM_ERROR on failure.

void fini (void)

Description:
Called when the plugin is removed. Clear any allocated storage here.

Returns: None.

Note: These init and fini functions are not the same as those described in the dlopen (3) system library. The C run-time system co-opts those symbols for its own initialization. The system _init() is called before the Slurm init(), and the Slurm fini() is called before the system's _fini().

int job_submit(struct job_descriptor *job_desc, uint32_t submit_uid, char **error_msg)

Description:
This function is called by the slurmctld daemon with job submission parameters supplied by the salloc, sbatch or srun command. It can be used to log and/or modify the job parameters supplied by the user as desired. Note that this function has access to the slurmctld's global data structures, for example to examine the available partitions, reservations, etc.

Arguments:
job_desc (input/output) the job allocation request specifications.
submit_uid (input) user ID initiating the request.
error_msg (output) If the argument is not null, then a plugin generated error message can be stored here. The error message is expected to have allocated memory which Slurm will release using the xfree function. The error message is propagated to the caller only when the return code of this function is not SLURM_SUCCESS.

Returns:
SLURM_SUCCESS on success, or
SLURM_ERROR on failure.

int job_modify(struct job_descriptor *job_desc, struct job_record *job_ptr, uint32_t modify_uid)

Description:
This function is called by the slurmctld daemon with job modification parameters supplied by the scontrol or sview command. It can be used to log and/or modify the job parameters supplied by the user as desired. Note that this function has access to the slurmctld's global data structures, for example to examine the available partitions, reservations, etc.

Arguments:
job_desc (input/output) the job allocation request specifications.
job_ptr (input/output) slurmctld daemon's current data structure for the job to be modified.
modify_uid (input) user ID initiating the request.

Returns:
SLURM_SUCCESS on success, or
SLURM_ERROR on failure.

Lua Functions

The Lua functions differ slightly from those implemented in C for better ease of use. Sample Lua scripts can be found with the Slurm distribution in the directory contribs/lua. The default installation location of the Lua scripts is the same location as the Slurm configuration file, slurm.conf. Reading and writing of job environment variables using Lua is possible by referencing the environment variables as a data structure containing named elements. For example:
if (job_desc.environment.LANGUAGE == "en_US") then
....

int job_submit(struct job_descriptor *job_desc, List part_list, uint32_t submit_uid)

Description:
This function is called by the slurmctld daemon with job submission parameters supplied by the salloc, sbatch or srun command. It can be used to log and/or modify the job parameters supplied by the user as desired. Note that this function has access to the slurmctld's global data structures, for example to examine the available partitions, reservations, etc.

Arguments:
job_desc (input/output) the job allocation request specifications.
part_list (input) List of pointer to partitions which this user is authorized to use.
submit_uid (input) user ID initiating the request.

Returns:
0 on success, or an errno on failure. Slurm specific error numbers from slurm/slurm_errno.h may be used. On failure, the request will be rejected and the user will have an appropriate error message printed for that errno.

int job_modify(struct job_descriptor *job_desc, struct job_record *job_ptr, List part_list, int modify_uid)

Description:
This function is called by the slurmctld daemon with job modification parameters supplied by the scontrol or sview command. It can be used to log and/or modify the job parameters supplied by the user as desired. Note that this function has access to the slurmctld's global data structures, for example to examine the available partitions, reservations, etc.

Arguments:
job_desc (input/output) the job allocation request specifications.
job_ptr (input/output) slurmctld daemon's current data structure for the job to be modified.
part_list (input) List of pointer to partitions which this user is authorized to use.
modify_uid (input) user ID initiating the request.
0 on success, or an errno on failure. Slurm specific error numbers from slurm/slurm_errno.h may be used. On failure, the request will be rejected and the user will have an appropriate error message printed for that errno.

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Building

Generally using a LUA interface for a job submit plugin is best: It is simple to write and maintain with minimal dependencies upon the Slurm data structures. However using C does provide a mechanism to get more information than available using LUA including full access to all of the data structures and functions in the slurmctld daemon. The simplest way to build a C program would be to just replace one of the job submit plugins included in the Slurm distribution with your own code (i.e. use a patch with your own code). Then just build and install Slurm with that new code. Building a new plugin outside of the Slurm distribution is possible, but far more complex. It also requires access to a multitude of Slurm header files as shown in the proceedure below.

  1. You will need to at least partly build Slurm first. The "configure" command must be executed in order to build the "config.h" file in the build directory.
  2. Create a local directory somewhere for your files to build with. Also create subdirectories named ".libs" and ".deps".
  3. Copy a ".deps/job_submit_*Plo" file from another job_submit plugin's ".deps" directory (made as part of the build process) into your local ".deps" subdirectory. Rename the file as appropriate to reflect your plugins name (e.g. rename "job_submit_partition.Plo" to be something like "job_submit_mine.Plo").
  4. Compile and link your plugin. Those options might differ depending upon your build environment. Check the options used for building the other job_submit plugins and modify the example below as required.
  5. Install the plugin.
# Example:
# The Slurm source is in ~/SLURM/slurm.git
# The Slurm build directory is ~/SLURM/slurm.build
# The plugin build is to take place in the directory
#   "~/SLURM/my_submit"
# The installation locaiton is "/usr/local"

# Build Slurm from ~/SLURM/slurm.build
# (or at least run "~/SLURM/slurm.git/configure")

# Set up your plugin files
cd ~/SLURM
mkdir my_submit
cd my_submit
mkdir .libs
mkdir .deps
# Create your plugin code
vi job_submit_mine.c

# Copy up a dependency file
cp ~/SLURM/slurm.build/src/plugins/job_submit/partition/.deps/job_submit_partition.Plo \
   .deps/job_submit_nine.Plo

# Compile
gcc -DHAVE_CONFIG_H -I~/SLURM/slurm.build -I~/slurm.git \
   -g -O2 -pthread -fno-gcse -Werror -Wall -g -O0       \
   -fno-strict-aliasing -MT job_submit_mine.lo          \
   -MD -MP -MF .deps/job_submit_mine.Tpo                \
   -c job_submit_mine.c -o job_submit_mine.o

# Some clean up
mv -f .deps/job_submit_mine.Tpo .deps/job_submit_mine.Plo
rm -fr .libs/job_submit_mine.a .libs/job_submit_mine.la \
   .libs/job_submit_mine.lai job_submit_mine.so

# Link
gcc -shared -fPIC -DPIC .libs/job_submit_mine.o -O2         \
   -pthread -O0 -pthread -Wl,-soname -Wl,job_submit_mine.so \
   -o job_submit_mine.so

# Install
cp job_submit_mine.so file \
   /usr/local/lib/slurm/job_submit_mine.so

Last modified 13 April 2015

slurm-slurm-16-05-9-1/doc/html/jobacct_gatherplugins.shtml000066400000000000000000000356241304416576200234770ustar00rootroot00000000000000

Slurm Job Accounting Gather Plugin API

Overview

This document describes Slurm job accounting gather plugins and the API that defines them. It is intended as a resource to programmers wishing to write their own Slurm job accounting gather plugins.

Slurm job accounting gather plugins must conform to the Slurm Plugin API with the following specifications:

const char plugin_name[]="full text name"

A free-formatted ASCII text string that identifies the plugin.

const char plugin_type[]="major/minor"

The major type must be "jobacct_gather." The minor type can be any suitable name for the type of accounting package. We currently use

  • aix — Gathers information from AIX /proc table and adds this information to the standard rusage information also gathered for each job.
  • cgroup — Gathers information from Linux cgroup infrastructure and adds this information to the standard rusage information also gathered for each job. (Experimental, not to be used in production.)
  • linux — Gathers information from Linux /proc table and adds this information to the standard rusage information also gathered for each job.
  • none — No information gathered.

const uint32_t plugin_version
If specified, identifies the version of Slurm used to build this plugin and any attempt to load the plugin from a different version of Slurm will result in an error. If not specified, then the plugin may be loadeed by Slurm commands and daemons from any version, however this may result in difficult to diagnose failures due to changes in the arguments to plugin functions or changes in other Slurm functions used by the plugin.

The sacct program can be used to display gathered data from regular accounting and from these plugins.

The programmer is urged to study src/plugins/jobacct_gather/linux and src/common/slurm_jobacct_gather.[c|h] for a sample implementation of a Slurm job accounting gather plugin.

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API Functions

All of the following functions are required. Functions which are not implemented must be stubbed.

int init (void)

Description:
Called when the plugin is loaded, before any other functions are called. Put global initialization here.

Returns:
SLURM_SUCCESS on success, or
SLURM_ERROR on failure.

void fini (void)

Description:
Called when the plugin is removed. Clear any allocated storage here.

Returns: None.

Note: These init and fini functions are not the same as those described in the dlopen (3) system library. The C run-time system co-opts those symbols for its own initialization. The system _init() is called before the Slurm init(), and the Slurm fini() is called before the system's _fini().

int jobacct_gather_p_poll_data(List task_list, bool pgid_plugin, uint64_t cont_id)

Description:
Build a table of all current processes.

Arguments:
task_list (in/out) List containing current processes
pgid_plugin (input) if we are running with the pgid plugin
cont_id (input) container id of processes if not running with pgid

int jobacct_gather_p_endpoll(void)

Description:
Called when the process is finished to stop the polling thread.

Arguments:
none

Returns:
SLURM_SUCCESS on success, or
SLURM_ERROR on failure.

int jobacct_gather_p_add_task(pid_t pid, uint16_t tid)

Description:
Used to add a task to the poller.

Arguments:
pid (input) Process id
tid (input) slurm global task id

Returns:
SLURM_SUCCESS on success, or
SLURM_ERROR on failure.

Job Account Gathering

All of the following functions are not required but may be used.

int jobacct_gather_init(void)

Description:
Loads the job account gather plugin.

Returns:
SLURM_SUCCESS on success, or
SLURM_ERROR on failure.

int jobacct_gather_fini(void)

Description:
Unloads the job account gathering plugin.

Returns:
SLURM_SUCCESS on success, or
SLURM_ERROR on failure.

int jobacct_gather_startpoll(uin16_t frequency)

Description:
Creates and starts the polling thread.

Arguments:
frequency (input) frequency of the polling.

Returns:
SLURM_SUCCESS on success, or
SLURM_ERROR on failure.

void jobacct_gather_change_poll(uint16_t frequency)

Description:
Changes the polling thread to a new frequency.

Arguments:
frequency (input) frequency of the polling

Returns:
SLURM_SUCCESS on success, or
SLURM_ERROR on failure.

void jobacct_gather_suspend_poll(void)

Description:
Temporarily stops the polling thread.

Returns:
SLURM_SUCCESS on success, or
SLURM_ERROR on failure.

void jobacct_gather_resume_poll(void)

Description:
Resumes the polling thread that was stopped.

Returns:
SLURM_SUCCESS on success, or
SLURM_ERROR on failure.

jobacctinfo_t *jobacct_gather_stat_task(pid_t pid)

Description:
Gets the basis of the information of the task.

Arguments:
pid (input) process id.

Returns:
SLURM_SUCCESS on success, or
SLURM_ERROR on failure.

jobacctinfo_t *jobacct_gather_remove_task(pid_t pid)

Description:
Removes the task.

Arguments:
pid (input) process id.

Returns:
SLURM_SUCCESS on success, or
SLURM_ERROR on failure.

int jobacct_gather_set_proctrack_container_id(uint64_t id)

Description:
Sets the proctrack container to a given id.

Arguments:
id (input) id to set.

Returns:
SLURM_SUCCESS on success, or
SLURM_ERROR on failure.

int jobacct_gather_set_mem_limit(uint32_t job_id, uint32_t step_id,uint32_t mem_limit)

Description:
Sets the memory limit of the job account.

Arguments:
job_id (input) id of the job.
sted_id (input) id of the step.
mem_limit (input) memory limit in megabytes.

Returns:
SLURM_SUCCESS on success, or
SLURM_ERROR on failure.

void jobacct_gather_handle_mem_limit(uint32_t total_job_mem, uint32_t total_job_vsize)

Description:
Called to find out how much memory is used.

Arguments:
total_job_mem (input) total amount of memory for jobs.
total_job_vsize (input) the total job size.

Returns:
SLURM_SUCCESS on success, or
SLURM_ERROR on failure.

Job Account Info

All of the following functions are not required but may be used.

jobacctinfo_t *jobacctinfo_create(jobacct_id_t *jobacct_id)

Description:
Creates the job account info.

Arguments:
jobacct_id (input) the job account id.

Returns:
SLURM_SUCCESS on success, or
SLURM_ERROR on failure.

void jobacctinfo_destroy(void *object)

Description:
Destroys the job account info.

Arguments:
object (input) the job that needs to be destroyed

Returns:
SLURM_SUCCESS on success, or
SLURM_ERROR on failure.

int jobacctinfo_setinfo(jobacctinfo_t *jobacct, enum jobacct_data_type type, void *data)

Description:
Set the information for the job.

Arguments:
jobacct (input) job account
type(input) enum telling the plugin how to transform the data.
data (input/output) Is a void * and the actual data type depends upon the first argument to this function (type).

Returns:
SLURM_SUCCESS on success, or
SLURM_ERROR on failure.

int jobacctinfo_getinfo(jobacctinfo_t *jobacct, enum jobacct_data_type type, void *data)

Description:
Gets the information about the job.

Arguments:
jobacct (input) job account.
type (input) the data type of the job account. data

Returns:
SLURM_SUCCESS on success, or
SLURM_ERROR on failure.

void jobacctinfo_pack(jobacctinfo_t *jobacct, uint16_t rpc_version, Buf buffer)

Description:
Packs the job account information.

Arguments:
jobacct (input) the job account.
rpc_version (input) the rpc version.
buffer (input) the buffer.

Returns:
SLURM_SUCCESS on success, or
SLURM_ERROR on failure.

int jobacctinfo_unpack(jobacctinfo_t **jobacct, uint16_t rpc_version, Buf buffer)

Description:
Unpacks the job account information.

Arguments:
jobacct (input) the job account.
rpc_version (input) the rpc version.
buffer (input) the buffer.

Returns:
SLURM_SUCCESS on success, or
SLURM_ERROR on failure.

void jobacctinfo_aggregate(jobacctinfo_t *dest, jobacctinfo_t *from)

Description:
Aggregates the jobs.

Arguments:
dest (input) New destination of the job.
from (input) Original location of job.

Returns:
SLURM_SUCCESS on success, or
SLURM_ERROR on failure.

void jobacctinfo_2_stats(slurmdb_stats_t *stats, jobacctinfo_t *jobacct)

Description:
Gets the stats of the job in accounting.

Arguments:
stats (input) slurm data base stat.
jobacct (input) the job account.

Returns:
SLURM_SUCCESS on success, or
SLURM_ERROR on failure.

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Parameters

These parameters can be used in the slurm.conf to configure the plugin and the frequency at which to gather information about running jobs.

JobAcctGatherType
Specifies which plugin should be used.
JobAcctGatherFrequency
Time interval between pollings in seconds.

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Last modified 27 March 2015

slurm-slurm-16-05-9-1/doc/html/jobcompplugins.shtml000066400000000000000000000210371304416576200221620ustar00rootroot00000000000000

Slurm Job Completion Logging Plugin API

Overview

This document describes Slurm job completion logging plugins and the API that defines them. It is intended as a resource to programmers wishing to write their own SLURM job completion logging plugins.

Slurm job completion logging plugins are Slurm plugins that implement the SLURM API for logging job information upon their completion. This may be used to log job information to a text file, database, etc. The plugins must conform to the Slurm Plugin API with the following specifications:

const char plugin_type[]
The major type must be "jobcomp." The minor type can be any recognizable abbreviation for the type of scheduler. We recommend, for example:

  • none — No job logging.
  • filetxt — Log job information to a text file.
  • mysql — Job completion is written to a mysql database.
  • script — Execute a script passing in job information in environment variables.

const char plugin_name[]
Some descriptive name for the plugin. There is no requirement with respect to its format.

const uint32_t plugin_version
If specified, identifies the version of Slurm used to build this plugin and any attempt to load the plugin from a different version of Slurm will result in an error. If not specified, then the plugin may be loadeed by Slurm commands and daemons from any version, however this may result in difficult to diagnose failures due to changes in the arguments to plugin functions or changes in other Slurm functions used by the plugin.

The programmer is urged to study src/plugins/jobcomp/filetxt/jobcomp_filetxt.c and src/plugins/jobcomp/none/jobcomp_none.c for sample implementations of a Slurm job completion logging plugin.

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Data Objects

The implementation must maintain (though not necessarily directly export) an enumerated errno to allow Slurm to discover as practically as possible the reason for any failed API call. Plugin-specific enumerated integer values should be used when appropriate. It is desirable that these values be mapped into the range ESLURM_JOBCOMP_MIN and ESLURM_JOBCOMP_MAX as defined in slurm/slurm_errno.h. The error number should be returned by the function slurm_jobcomp_get_errno() and this error number can be converted to an appropriate string description using the slurm_jobcomp_strerror() function described below.

These values must not be used as return values in integer-valued functions in the API. The proper error return value from integer-valued functions is SLURM_ERROR. The implementation should endeavor to provide useful and pertinent information by whatever means is practical. Successful API calls are not required to reset any errno to a known value. However, the initial value of any errno, prior to any error condition arising, should be SLURM_SUCCESS.

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API Functions

The following functions must appear. Functions which are not implemented should be stubbed.

int init (void)

Description:
Called when the plugin is loaded, before any other functions are called. Put global initialization here.

Returns:
SLURM_SUCCESS on success, or
SLURM_ERROR on failure.

void fini (void)

Description:
Called when the plugin is removed. Clear any allocated storage here.

Returns: None.

Note: These init and fini functions are not the same as those described in the dlopen (3) system library. The C run-time system co-opts those symbols for its own initialization. The system _init() is called before the SLURM init(), and the SLURM fini() is called before the system's _fini().

int slurm_jobcomp_set_location (char * location);

Description: Specify the location to be used for job logging.

Argument: location    (input) specification of where logging should be done. The interpretation of this string is at the discretion of the plugin implementation.

Returns: SLURM_SUCCESS if successful. On failure, the plugin should return SLURM_ERROR and set the errno to an appropriate value to indicate the reason for failure.

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int slurm_jobcomp_log_record (struct job_record *job_ptr);

Description: Note that a job is about to terminate or change size. The job's state will include the JOB_RESIZING flag if and only if it is about to change size. Otherwise the job is terminating. Note the existence of resize_time in the job record if one wishes to record information about a job at each size (i.e. a history of the job as its size changes through time).

Argument:
job_ptr   (input) Pointer to job record as defined in src/slurmctld/slurmctld.h

Returns: SLURM_SUCCESS if successful. On failure, the plugin should return SLURM_ERROR and set the errno to an appropriate value to indicate the reason for failure.

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int slurm_jobcomp_get_errno (void);

Description: Return the number of a job completion logger specific error.

Arguments: None

Returns: Error number for the last failure encountered by the job completion logging plugin.

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const char *slurm_jobcomp_strerror(int errnum);

Description: Return a string description of a job completion logger specific error code.

Arguments: errnum    (input) a job completion logger specific error code.

Returns: Pointer to string describing the error or NULL if no description found in this plugin.

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List slurm_jobcomp_get_jobs(acct_job_cond_t *job_cond);

Description: Get completed job info from storage.

Arguments:
job_cond     (input) specification of filters to identify the jobs we wish information about (start time, end time, cluster name, user id, etc). acct_job_cond_t is defined in common/slurm_accounting_storage.h.

Returns: A list of job records or NULL on error. Elements on the list are of type jobcomp_job_rec_t, which is defined in common/slurm_jobcomp.h. Any returned list must be destroyed to avoid memory leaks.

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void slurm_jobcomp_archive(List selected_parts, void *params)

Description: used to archive old data.

Arguments:
List selected_parts (input) list containing char *'s of names of partitions to query against.
void *params (input) to be cast as sacct_parameters_t in the plugin.

Returns: None

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Last modified 27 March 2015

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