Running Jobs with Platform LSF

Platform LSF Version 7.0 Update 6 Release date: August 2009 Last modified: August 17, 2009

Copyright

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Contents
1 About Platform LSF .................................................................................................................... 5 Clusters, jobs, and queues ............................................................................................. 6 Hosts ............................................................................................................................... 9 LSF daemons ................................................................................................................ 11 Batch jobs and tasks ..................................................................................................... 14 Host types and host models .......................................................................................... 16 Users and administrators .............................................................................................. 17 Resources ..................................................................................................................... 18 Job lifecycle .................................................................................................................. 21 Working with Jobs .................................................................................................................... Submitting jobs (bsub) .................................................................................................. Modify pending jobs (bmod) .......................................................................................... Modify running jobs ....................................................................................................... About controlling jobs .................................................................................................... Using LSF with non-shared file space .......................................................................... operator ......................................................................................................................... About resource reservation ........................................................................................... 23 24 28 30 32 38 39 40 2

Monitoring Jobs ........................................................................................................................ 43 View information about jobs .......................................................................................... 44 About displaying resource allocation limits ................................................................... 48 Platform Management Console ................................................................................................ 49 Platform HPC Portal ...................................................................................................... 50

Running Jobs with Platform LSF 3

4 Running Jobs with Platform LSF

1
About Platform LSF

Running Jobs with Platform LSF 5

About Platform LSF

Clusters, jobs, and queues

Cluster
A group of computers (hosts) running LSF that work together as a single unit, combining computing power and sharing workload and resources. A cluster provides a single-system image for a network of computing resources. Hosts can be grouped into clusters in a number of ways. A cluster could contain:

All the hosts in a single administrative group All the hosts on one file server or sub-network Hosts that perform similar functions

Commands

lshosts View static resource information about hosts in the cluster bhosts View resource and job information about server hosts in the cluster lsid View the cluster name lsclusters View cluster status and size

Configuration

Define hosts in your cluster in lsf.cluster.cluster_name

Tip:
The name of your cluster should be unique. It should not be the same as any host or queue.

Job
A unit of work run in the LSF system. A job is a command submitted to LSF for execution. LSF schedules, controls, and tracks the job according to configured policies.

6 Running Jobs with Platform LSF

About Platform LSF Jobs can be complex problems, simulation scenarios, extensive calculations, anything that needs compute power.

Commands

bjobs View jobs in the system bsub Submit jobs

Job slot
A job slot is a bucket into which a single unit of work is assigned in the LSF system. Hosts are configured to have a number of job slots available and queues dispatch jobs to fill job slots.

Commands

bhosts View job slot limits for hosts and host groups bqueues View job slot limits for queues busers View job slot limits for users and user groups

Configuration

Define job slot limits in lsb.resources.

Job states
LSF jobs have the following states:

PEND Waiting in a queue for scheduling and dispatch RUN Dispatched to a host and running DONE Finished normally with zero exit value EXITED Finished with non-zero exit value PSUSP Suspended while pending USUSP Suspended by user SSUSP Suspended by the LSF system POST_DONE Post-processing completed without errors POST_ERR Post-processing completed with errors WAIT Members of a chunk job that are waiting to run

Queue
A clusterwide container for jobs. All jobs wait in queues until they are scheduled and dispatched to hosts. Queues do not correspond to individual hosts; each queue can use all server hosts in the cluster, or a configured subset of the server hosts. When you submit a job to a queue, you do not need to specify an execution host. LSF dispatches the job to the best available execution host in the cluster to run that job. Queues implement different job scheduling and control policies.

Commands

bqueues View available queues bsub -q Submit a job to a specific queue

Running Jobs with Platform LSF 7

About Platform LSF

bparams View default queues

Configuration

Define queues in lsb.queues

Tip:
The names of your queues should be unique. They should not be the same as the cluster name or any host in the cluster.

First-come, first-served scheduling (FCFS)

The default type of scheduling in LSF. Jobs are considered for dispatch based on their order in the queue.

8 Running Jobs with Platform LSF

About Platform LSF

Hosts
A host is an individual computer in the cluster. Each host may have more than 1 processor. Multiprocessor hosts are used to run parallel jobs. A multiprocessor host with a single process queue is considered a single machine, while a box full of processors that each have their own process queue is treated as a group of separate machines. Commands:

lsload View load on hosts lshosts View configuration information about hosts in the cluster including number of CPUS, model, type,

and whether the host is a client or server bhosts View batch server hosts in the cluster

Tip:
The names of your hosts should be unique. They should not be the same as the cluster name or any queue defined for the cluster.

Submission host
The host where jobs are submitted to the cluster. Jobs are submitted using the bsub command or from an application that uses the LSF API. Client hosts and server hosts can act as submission hosts.

Commands:

bsub Submit a job bjobs View jobs that are submitted

Execution host
The host where a job runs. Can be the same as the submission host. All execution hosts are server hosts. Commands

bjobs View where a job runs

Server host
Hosts that are capable of submitting and executing jobs. A server host runs sbatchd to execute server requests and apply local policies.

Commands

lshosts View hosts that are servers (server=Yes)

Configuration

server to 1

Server hosts are defined in the lsf.cluster.cluster_name file by setting the value of

Running Jobs with Platform LSF 9

About Platform LSF

Client host
Hosts that are only capable of submitting jobs to the cluster. Client hosts run LSF commands and act only as submission hosts. Client hosts do not execute jobs or run LSF daemons.

Commands

lshosts View hosts that are clients (server=No)

Configuration

Client hosts are defined in the lsf.cluster.cluster_name file by setting the value of server to 0

Master host
Where the master LIM and mbatchd run. An LSF server host that acts as the overall coordinator for that cluster. Each cluster has one master host to do all job scheduling and dispatch. If the master host goes down, another LSF server in the cluster becomes the master host. All LSF daemons run on the master host. The LIM on the master host is the master LIM.

Commands

lsid View the master host name

Configuration

The master host is the first host listed in the lsf.cluster.cluster_name file or is defined along with other candidate master hosts by LSF_MASTER_LIST in lsf.conf.

10 Running Jobs with Platform LSF

About Platform LSF

LSF daemons
LSF daemon Role

mbatchd mbschd sbatchd res

Job requests and dispatch Job scheduling Job execution

mbatchd

Master Batch Daemon running on the master host. Started by sbatchd. Responsible for the overall state of jobs in the system. Receives job submission, and information query requests. Manages jobs held in queues. Dispatches jobs to hosts as determined by mbschd.

Configuration

Port number defined in lsf.conf.

mbschd

Master Batch Scheduler Daemon running on the master host. Works with mbatchd. Started by mbatchd. Makes scheduling decisions based on job requirements, and policies, and resource availability. Sends scheduling decisions to the mbatchd.

sbatchd

Slave Batch Daemon running on each server host. Receives the request to run the job from mbatchd and manages local execution of the job. Responsible for enforcing local policies and maintaining the state of jobs on the host. The sbatchd forks a child sbatchd for every job. The child sbatchd runs an instance of res to create the execution environment in which the job runs. The child sbatchd exits when the job is complete.

Commands
badmin hstartup Starts sbatchd badmin hshutdown Shuts down sbatchd badmin hrestart Restarts sbatchd

Configuration

Port number defined in lsf.conf.

Running Jobs with Platform LSF 11

About Platform LSF

res

Remote Execution Server (res) running on each server host. Accepts remote execution requests to provide transparent and secure remote execution of jobs and tasks.

Commands

lsadmin resstartup Starts res lsadmin resshutdown Shuts down res lsadmin resrestart Restarts res

Configuration

Port number defined in lsf.conf.

lim

Load Information Manager (LIM) running on each server host. Collects host load and configuration information and forwards it to the master LIM running on the master host. Reports the information displayed by lsload and lshosts. Static indices are reported when the LIM starts up or when the number of CPUs (ncpus) change. Static indices are:

Number of CPUs (ncpus) Number of disks (ndisks) Total available memory (maxmem) Total available swap (maxswp) Total available temp (maxtmp) Dynamic indices for host load collected at regular intervals are: Hosts status (status) 15 second, 1 minute, and 15 minute run queue lengths (r15s, r1m, and r15m) CPU utilization (ut) Paging rate (pg) Number of login sessions (ls) Interactive idle time (it) Available swap space (swp) Available memory (mem) Available temp space (tmp) Disk IO rate (io)

Commands

lsadmin limstartup Starts LIM lsadmin limshutdown Shuts down LIM lsadmin limrestart Restarts LIM lsload View dynamic load values lshosts View static host load values

12 Running Jobs with Platform LSF

About Platform LSF

Configuration

Port number defined in lsf.conf.

Master LIM

The LIM running on the master host. Receives load information from the LIMs running on hosts in the cluster. Forwards load information to mbatchd, which forwards this information to mbschd to support scheduling decisions. If the master LIM becomes unavailable, a LIM on another host automatically takes over.

Commands

lsadmin limstartup Starts LIM lsadmin limshutdown Shuts down LIM lsadmin limrestart Restarts LIM lsload View dynamic load values lshosts View static host load values

Configuration

Port number defined in lsf.conf.

ELIM
External LIM (ELIM) is a site-definable executable that collects and tracks custom dynamic load indices. An ELIM can be a shell script or a compiled binary program, which returns the values of the dynamic resources you define. The ELIM executable must be named elim and located in LSF_SERVERDIR.

pim

Process Information Manager (PIM) running on each server host. Started by LIM, which periodically checks on pim and restarts it if it dies. Collects information about job processes running on the host such as CPU and memory used by the job, and reports the information to sbatchd.

Commands

bjobs View job information

Running Jobs with Platform LSF 13

About Platform LSF

Batch jobs and tasks

You can either run jobs through the batch system where jobs are held in queues, or you can interactively run tasks without going through the batch system, such as tests.

Job
A unit of work run in the LSF system. A job is a command submitted to LSF for execution, using the bsub command. LSF schedules, controls, and tracks the job according to configured policies. Jobs can be complex problems, simulation scenarios, extensive calculations, anything that needs compute power.

Commands

bjobs View jobs in the system bsub Submit jobs

Interactive batch job

A batch job that allows you to interact with the application and still take advantage of LSF scheduling policies and fault tolerance. All input and output are through the terminal that you used to type the job submission command. When you submit an interactive job, a message is displayed while the job is awaiting scheduling. A new job cannot be submitted until the interactive job is completed or terminated. The bsub command stops display of output from the shell until the job completes, and no mail is sent to you by default. Use Ctrl-C at any time to terminate the job.

Commands

bsub -I Submit an interactive job

Interactive task
A command that is not submitted to a batch queue and scheduled by LSF, but is dispatched immediately. LSF locates the resources needed by the task and chooses the best host among the candidate hosts that has the required resources and is lightly loaded. Each command can be a single process, or it can be a group of cooperating processes. Tasks are run without using the batch processing features of LSF but still with the advantage of resource requirements and selection of the best host to run the task based on load.

Commands

lsrun Submit an interactive task lsgrun Submit an interactive task to a group of hosts

See also LSF utilities such as ch, lsacct, lsacctmrg, lslogin, lsplace, lsload, lsloadadj, lseligible, lsmon, lstcsh.

Local task
An application or command that does not make sense to run remotely. For example, the ls command on UNIX.

14 Running Jobs with Platform LSF

About Platform LSF

Commands

lsltasks View and add tasks

Configuration

lsf.task Configure system-wide resource requirements for tasks lsf.task.cluster Configure cluster-wide resource requirements for tasks .lsftasks Configure user-specific tasks

Remote task
An application or command that can be run on another machine in the cluster.

Commands

lsrtasks View and add tasks

Configuration

lsf.task Configure system-wide resource requirements for tasks lsf.task.cluster Configure cluster-wide resource requirements for tasks .lsftasks Configure user-specific tasks

Running Jobs with Platform LSF 15

About Platform LSF

Host types and host models

Hosts in LSF are characterized by host type and host model. The following example has a host type of X86_64. Host models are Opteron240, Opteron840, Intel_EM64T, Intel_IA64.

Host type
The combination of operating system version and host CPU architecture. All computers that run the same operating system on the same computer architecture are of the same type in other words, binary-compatible with each other. Each host type usually requires a different set of LSF binary files. Commands

lsinfo -t View all host types defined in lsf.shared

Configuration Defined in lsf.shared Mapped to hosts in lsf.cluster.cluster_name

Host model
The combination of host type and CPU speed (CPU factor) of the computer. All hosts of the same relative speed are assigned the same host model. The CPU factor is taken into consideration when jobs are being dispatched. Commands

lsinfo -m View a list of currently running models lsinfo -M View all models defined in lsf.shared

Configuration Defined in lsf.shared Mapped to hosts in lsf.cluster.cluster_name

16 Running Jobs with Platform LSF

About Platform LSF

Users and administrators

LSF user
A user account that has permission to submit jobs to the LSF cluster.

LSF administrator
In general, you must be an LSF administrator to perform operations that will affect other LSF users. Each cluster has one primary LSF administrator, specified during LSF installation. You can also configure additional administrators at the cluster level and at the queue level.

Primary LSF administrator

The first cluster administrator specified during installation and first administrator listed in lsf.cluster.cluster_name. The primary LSF administrator account owns the configuration and log files. The primary LSF administrator has permission to perform clusterwide operations, change configuration files, reconfigure the cluster, and control jobs submitted by all users.

Cluster administrator
May be specified during LSF installation or configured after installation. Cluster administrators can perform administrative operations on all jobs and queues in the cluster. Cluster administrators have the same cluster-wide operational privileges as the primary LSF administrator except that they do not necessarily have permission to change LSF configuration files. For example, a cluster administrator can create an LSF host group, submit a job to any queue, or terminate another users job.

Queue administrator
An LSF administrator user account that has administrative permissions limited to a specified queue. For example, an LSF queue administrator can perform administrative operations on the specified queue, or on jobs running in the specified queue, but cannot change LSF configuration or operate on LSF daemons.

Running Jobs with Platform LSF 17

About Platform LSF

Resources
Resource usage
The LSF system uses built-in and configured resources to track resource availability and usage. Jobs are scheduled according to the resources available on individual hosts. Jobs submitted through the LSF system will have the resources they use monitored while they are running. This information is used to enforce resource limits and load thresholds as well as fairshare scheduling. LSF collects information such as:

Total CPU time consumed by all processes in the job Total resident memory usage in KB of all currently running processes in a job Total virtual memory usage in KB of all currently running processes in a job Currently active process group ID in a job Currently active processes in a job On UNIX, job-level resource usage is collected through PIM.

Commands

lsinfo View the resources available in your cluster bjobs -l View current resource usage of a job

Configuration

SBD_SLEEP_TIME in lsb.params Configures how often resource usage information is sampled by PIM, collected by sbatchd, and sent to mbatchd

Load indices
Load indices measure the availability of dynamic, non-shared resources on hosts in the cluster. Load indices built into the LIM are updated at fixed time intervals.

Commands

lsload -l View all load indices bhosts -l View load levels on a host

External load indices

Defined and configured by the LSF administrator and collected by an External Load Information Manager (ELIM) program. The ELIM also updates LIM when new values are received.

Commands

lsinfo View external load indices

18 Running Jobs with Platform LSF

About Platform LSF

Static resources
Built-in resources that represent host information that does not change over time, such as the maximum RAM available to user processes or the number of processors in a machine. Most static resources are determined by the LIM at start-up time. Static resources can be used to select appropriate hosts for particular jobs based on binary architecture, relative CPU speed, and system configuration.

Load thresholds
Two types of load thresholds can be configured by your LSF administrator to schedule jobs in queues. Each load threshold specifies a load index value:

loadSched determines the load condition for dispatching pending jobs. If a hosts load is beyond any defined loadSched, a job will not be started on the host. This threshold is also used as the condition for resuming suspended jobs. loadStop determines when running jobs should be suspended. To schedule a job on a host, the load levels on that host must satisfy both the thresholds configured for that host and the thresholds for the queue from which the job is being dispatched. The value of a load index may either increase or decrease with load, depending on the meaning of the specific load index. Therefore, when comparing the host load conditions with the threshold values, you need to use either greater than (>) or less than (<), depending on the load index.

Commands

bhosts-l View suspending conditions for hosts bqueues -l View suspending conditions for queues bjobs -l View suspending conditions for a particular job and the scheduling

thresholds that control when a job is resumed

Configuration

lsb.hosts Configure thresholds for hosts lsb.queues Configure thresholds for queues

Runtime resource usage limits

Limit the use of resources while a job is running. Jobs that consume more than the specified amount of a resource are signalled or have their priority lowered.

Configuration

lsb.queues Configure resource usage limits for queues

Hard and soft limits

Resource limits specified at the queue level are hard limits while those specified with job submission are soft limits. See setrlimit(2) man page for concepts of hard and soft limits.

Running Jobs with Platform LSF 19

About Platform LSF

Resource allocation limits

Restrict the amount of a given resource that must be available during job scheduling for different classes of jobs to start, and which resource consumers the limits apply to. If all of the resource has been consumed, no more jobs can be started until some of the resource is released.

Configuration

lsb.resources Configure queue-level resource allocation limits for hosts, users,

queues, and projects

Resource requirements (bsub -R)

Restrict which hosts the job can run on. Hosts that match the resource requirements are the candidate hosts. When LSF schedules a job, it collects the load index values of all the candidate hosts and compares them to the scheduling conditions. Jobs are only dispatched to a host if all load values are within the scheduling thresholds.

Commands

bsub-R Specify resource requirement string for a job

Configuration

lsb.queues Configure resource requirements for queues

20 Running Jobs with Platform LSF

About Platform LSF

Job lifecycle

1 Submit a job
You submit a job from an LSF client or server with the bsub command. If you do not specify a queue when submitting the job, the job is submitted to the default queue. Jobs are held in a queue waiting to be scheduled and have the PEND state. The job is held in a job file in the LSF_SHAREDIR/cluster_name/logdir/info/ directory.

Job ID
LSF assigns each job a unique job ID when you submit the job.

Job name
You can also assign a name to the job with the -J option of bsub. Unlike the job ID, the job name is not necessarily unique.

2 Schedule job
1. mbatchd looks at jobs in the queue and sends the jobs for scheduling to mbschd at a preset time interval (defined by the parameter JOB_SCHEDULING_INTERVAL in lsb.params). 2. mbschd evaluates jobs and makes scheduling decisions based on: Job priority Scheduling policies Available resources 3. mbschd selects the best hosts where the job can run and sends its decisions back to mbatchd.

Resource information is collected at preset time intervals by the master LIM from LIMs on server hosts. The master LIM communicates this information to mbatchd, which in turn communicates it to mbschd to support scheduling decisions.

3 Dispatch job
As soon as mbatchd receives scheduling decisions, it immediately dispatches the jobs to hosts.

Running Jobs with Platform LSF 21

About Platform LSF

4 Run job
sbatchd handles job execution. It:

1. 2. 3. 4.

Receives the request from mbatchd Creates a child sbatchd for the job Creates the execution environment Starts the job using res

The execution environment is copied from the submission host to the execution host and includes the following:

Environment variables needed by the job Working directory where the job begins running Other system-dependent environment settings, for example:

On UNIX and Linux, resource limits and umask On Windows, desktop and Windows root directory The job runs under the user account that submitted the job and has the status RUN.

5 Return output
When a job is completed, it is assigned the DONE status if the job was completed without any problems. The job is assigned the EXIT status if errors prevented the job from completing.
sbatchd communicates job information including errors and output to mbatchd.

6 Send email to client

mbatchd returns the job output, job error, and job information to the submission host through email. Use the -o and -e options of bsub to send job output and errors to a file.

Job report
A job report is sent by email to the LSF client and includes:

Job information such as: CPU use Memory use Name of the account that submitted the job Job output Errors

22 Running Jobs with Platform LSF

2
Working with Jobs

Running Jobs with Platform LSF 23

Working with Jobs

Submitting jobs (bsub)

Submit a job
To have your work run on the cluster, you must submit jobs. You have many options when submitting a job. The following is the most basic way of submitting a job. 1. To submit a job, run bsub. If you do not specify any options, the job is submitted to the default queue configured by the LSF administrator (usually queue normal) For example, if you submit the job my_job without specifying a queue, the job goes to the default queue.
bsub my_job Job <1234> is submitted to default queue <normal>

In the above example, 1234 is the job ID assigned to this job, and normal is the name of the default job queue. Your job remains pending until all conditions for its execution are met. Each queue has execution conditions that apply to all jobs in the queue, and you can specify additional conditions when you submit the job When you submit jobs, you can also specify an execution host or a range of hosts, a queue, and start and termination times, as well as a wide range of other job options.

About submitting a job to a specific queue

Job queues represent different job scheduling and control policies. All jobs submitted to the same queue share the same scheduling and control policy. Each job queue can use a configured subset of server hosts in the cluster; the default is to use all server hosts. System administrators can configure job queues to control resource access by different users and types of application. Users select the job queue that best fits each job. The default queue is normally suitable to run most jobs, but the default queue may assign your jobs a very low priority, or restrict execution conditions to minimize interference with other jobs. If automatic queue selection is not satisfactory, choose the most suitable queue for each job. The factors affecting which queue to choose are user access restrictions, size of job, resource limits of the queue, scheduling priority of the queue, active time windows of the queue, hosts used by the queue, scheduling load conditions, and the queue description displayed by the bqueues -l command.

View available queues

You can submit jobs to a queue as long as its STATUS is Open. However, jobs are not dispatched unless the queue is Active. To see available queues, run bqueues. To display only the queues that accept jobs from specific users or user groups, run bqueues -u user_name .

24 Running Jobs with Platform LSF

Working with Jobs To display only the queues that use specific host name or host group name to run jobs, run bqueues -m host_name.

Submit a job to a queue

The following examples are based on the queues defined in the default configuration. Your LSF administrator may have configured different queues. To run a job during off hours because the job generates very high load to both the file server and the network, you can submit it to the night queue:
bsub -q "night" my_job

If you have an urgent job to run, you may want to submit it to the priority queue:
bsub -q "priority" my_job

If you want to use hosts owned by others and you do not want to bother the owners, you may want to run your low priority jobs on the idle queue so that as soon as the owner comes back, your jobs get suspended:
bsub -q "idle" my_job

If you are running small jobs and do not want to wait too long to get the results, you can submit jobs to the short queue to be dispatched with higher priority:
bsub -q "short" my_job

Tip:
Make sure your jobs are short enough that they are not killed for exceeding the CPU time limit of the queue (check the resource limits of the queue, if any).

If your job requires a specific execution environment, you may need to submit it to a queue that has a particular job starter defined. LSF administrators are able to specify a queuelevel job starter as part of the queue definition; ask them for the name of the queue and configuration details.

Submit a job associated with a project (bsub -P)

Project names are logged in lsb.acct. You can use the bacct command to gather accounting information on a per-project basis. 1. To associate a project name with a job, run bsub -P project_name. On systems running IRIX 6, before the submitted job begins execution, a new array session is created and the project ID corresponding to the project name is assigned to the session.

Submit a job associated with a user group (bsub -G)

Note:
This task is only useful with fairshare scheduling.

You can specify any user group to which you belong as long as it does not contain any subgroups. You must be a direct member of the specified user group. User groups in non-leaf nodes cannot be specified because it will cause ambiguity in determining the correct shares given to a user. 1. To submit a job and associate it with a specified user group, run bsub -G user_group.

Running Jobs with Platform LSF 25

Working with Jobs For example, to submit the job myjob associated to user group special:
bsub -G special myjob

Submit a job with a job name (bsub -J)

You can associate a name with a job or job array. Job names can contain up to 4094 characters. You can later use the job name to identify the job. The job name need not be unique. 1. Use bsub -J job_name to submit a job and assign a job name to it. For example, to submit a job and assign the name my_job:
bsub -J my_job sleep 1000

Submit a job to a service class (bsub -sla)

You submit jobs to a service class as you would to a queue, except that a service class is a higher level scheduling policy that makes use of other, lower level ProductNameAbbreviation policies like queues and host partitions to satisfy the service-level goal that the service class expresses. The service class name where the job is to run is configured in lsb.serviceclasses. If the SLA does not exist or the user is not a member of the service class, the job is rejected. Outside of the configured time windows, the SLA is not active, and ProductNameAbbreviation schedules jobs without enforcing any service-level goals. Jobs will flow through queues following queue priorities even if they are submitted with -sla.

Tip:
You should submit your jobs with a run time limit (-W option) or the queue should specify a run time limit (RUNLIMIT in the queue definition in lsb.queues). If you do not specify a run time limit, ProductNameAbbreviation automatically adjusts the optimum number of running jobs according to the observed run time of finished jobs.

1. To submit a job to a service class for SLA-driven scheduling, run bsub -sla service_class_name. For example:
bsub -W 15 -sla Kyuquot sleep 100

submits the UNIX command sleep together with its argument 100 as a job to the service class named Kyuquot.

Submit a job under a job group (bsub -g)

The job group does not have to exist before submitting the job. 1. To submit a job into a job group, run bsub -g . For example:
bsub -g /risk_group/portfolio1/current myjob Job <105> is submitted to default queue.

Submits myjob to the job group /risk_group/portfolio1/current. If group /risk_group/portfolio1/current exists, job 105 is attached to the job group.

26 Running Jobs with Platform LSF

Working with Jobs If group /risk_group/portfolio1/current does not exist, ProductNameAbbreviation checks its parent recursively, and if no groups in the hierarchy exist, all three job groups are created with the specified hierarchy and the job is attached to group.

Running Jobs with Platform LSF 27

Working with Jobs

Modify pending jobs (bmod)

If your submitted jobs are pending (bjobs shows the job in PEND state), you can modify job submission parameters. You can also modify entire job arrays or individual elements of a job array. To replace the job command line, run bmod -Z "new_command". For example: bmod -Z "myjob file" 101. To change a specific job parameter, run bmod -b. The specified options replace the submitted options. The following example changes the start time of job 101 to 2:00 a.m.: bmod -b 2:00 101 To reset an option to its default submitted value (undo a bmod), append the n character to the option name and do not include an option value. The following example resets the start time for job 101 back to its default value: bmod -bn 101

Modify the service class of a job

You can attach or detach a service class of a job after the job has been submitted.

Restriction:
You cannot:

Use -sla with other bmod options Move job array elements from one service class to another, only entire job arrays Modify the service class of jobs already attached to a job group

Use the -sla option of bmod to modify the service class a job is attached to, or to attach a submitted job to a service class.
bmod -sla Kyuquot 2307

Attaches job 2307 to the service class Kyuquot. Use bmod -slan to detach a job from a service class. For example:
bmod -slan 2307

Detaches job 2307 from the service class Kyuquot.

Modify a job submitted to a job group

You can modify your own job groups and job groups that other users create under your job groups. The LSF administrator can modify job groups of all users.

Restriction:
The command bmod -g cannot be combined with other bmod options. It can only operate on pending jobs. It cannot operate on running or finished jobs.

28 Running Jobs with Platform LSF

Working with Jobs

You cannot move job array elements from one job group to another, only entire job arrays. A job array can only belong to one job group at a time. You cannot modify the job group of a job attached to a service class.

To specify a job group path to move a job or a job array from one job group to another, run bmod -g. For example:
bmod -g /risk_group/portfolio2/monthly 105

Moves job 105 to job group /risk_group/portfolio2/monthly. Like bsub -g, if the job group does not exist, LSF creates it.

Running Jobs with Platform LSF 29

Working with Jobs

Modify running jobs

Once you submit a job and it is running, you can modify some of the job options, including resource reservation, CPU limit, memory limit, and others.

Restriction:
You cannot modify remote running jobs in a MultiCluster environment.

Modify resource reservation Modify other selected job options

Modify resource reservation

A job is usually submitted with a resource reservation for the maximum amount required. Use this command to decrease the reservation, allowing other jobs access to the resource.

Note:
You can modify additional job options by setting LSB_MOD_ALL_JOBS in lsf.conf.

1. Run bmod -R to modify the resource reservation for a running job. For example, to set the resource reservation for job 101 to 25MB of memory and 50 MB of swap space:
bmod -R "rusage[mem=25:swp=50]" 101

Modify job options

LSB_MOD_ALL_JOBS is specified in lsf.conf. To modify the CPU limit of running jobs, LSB_JOB_CPULIMIT=Y must be defined in lsf.conf. To modify the memory limit of running jobs, LSB_JOB_MEMLIMIT=Y must be defined in lsf.conf. To modify the name of job error file for a running job, you must use bsub -e or bmod -e to specify an error file before the job starts running. If LSB_MOD_ALL_JOBS is specified in lsf.conf, the job owner or the LSF administrator can use the bmod command to modify some job options for running jobs. The modified resource limits cannot exceed the resource limits defined in the queue.

Restriction:
You cannot use these options in combination with other bmod options. An error message is issued and the modification fails if these options are used on running jobs in combination with other bmod options.

CPU limit (-c [hour:]minute[/host_name | /host_model] | -cn) Memory limit (-M mem_limit | -Mn) Rerunnable jobs (-r | -rn)

30 Running Jobs with Platform LSF

Working with Jobs Standard error file name (-e error_file | -en) Standard output file name (-o output_file | -on) Run limit (-W run_limit[/host_name | /host_model] | -Wn)

Running Jobs with Platform LSF 31

Working with Jobs

About controlling jobs

LSF controls jobs dispatched to a host to enforce scheduling policies or in response to user requests. The LSF system performs the following actions on a job:

Suspend by sending a SIGSTOP signal Resume by sending a SIGCONT signal Terminate by sending a SIGKILL signal On Windows, equivalent functions have been implemented to perform the same tasks.

Kill a job (bkill)

You can cancel a job from running or pending by killing it. If your job is part of a job group, the command bkill only kills jobs in the job group you specify. It does not kill jobs in lower level job groups in the path. 1. To kill job 3421:
bkill 3421

a) Use the -g option of bkill and specify a job group path to terminate jobs in a job group. For example:
bkill -g /risk_group 106

b) Use job ID 0 (zero) to terminate all jobs in a job group:

bkill -g /risk_group 0

Forcing removal of a job from LSF

If a job cannot be killed in the operating system, you can force the removal of the job from LSF. The bkill -r command removes a job from the system without waiting for the job to terminate in the operating system. This sends the same series of signals as bkill without r, except that the job is removed from the system immediately, the job is marked as EXIT, and job resources that LSF monitors are released as soon as LSF receives the first signal. 1. Use bkill -r to force the removal of the job from LSF.

About suspending and resuming jobs (bstop and bresume)

You can resume or suspend a job using the bstop and bresume commands. A job can be suspended by its owner or the LSF administrator with the bstop command. These jobs are considered user-suspended and are displayed by bjobs as USUSP. When the user restarts the job with the bresume command, the job is not started immediately to prevent overloading. Instead, the job is changed from USUSP to SSUSP (suspended by the system). The SSUSP job is resumed when host load levels are within the scheduling thresholds for that job, similarly to jobs suspended due to high load. If a user suspends a high priority job from a non-preemptive queue, the load may become low enough for LSF to start a lower priority job in its place. The load created by the low priority job can prevent the high priority job from resuming. This can be avoided by configuring preemptive queues.

32 Running Jobs with Platform LSF

Working with Jobs The command bstop sends the following signals to the job:

SIGTSTP for parallel or interactive jobs SIGTSTP is caught by the master process and passed to all the slave processes running on other hosts. SIGSTOP for sequential jobs SIGSTOP cannot be caught by user programs. The SIGSTOP signal can be configured with the LSB_SIGSTOP parameter in lsf.conf.

Allow users to resume jobs

If ENABLE_USER_RESUME=Y in lsb.params, you can resume your own jobs that have been suspended by the administrator.

Suspend a job

You can suspend or stop a job that is already running. You must be an administrator or the user who submitted the job. When you stop a job, it is suspended until you choose to resume it. Suspending a job causes your job to go into USUSP state if the job is already started, or to go into PSUSP state if your job is pending. By default, jobs that are suspended by the administrator can only be resumed by the administrator or root; users do not have permission to resume a job suspended by another user or the administrator. Administrators can resume jobs suspended by users or administrators. Administrators can also enable users to resume their own jobs that have been stopped by an administrator. 1. Use the -g option of bstop and specify a job group path to suspend jobs in a job group
bstop -g /risk_group 106 Job <106> is being stopped

Use job ID 0 (zero) to suspend all jobs in a job group:

bstop -g /risk_group/consolidate 0 Job <107> is being stopped Job <108> is being stopped Job <109> is being stopped

Resume a job

You can resume a job that was suspended using bstop. You must be the same user who suspended the job. If your job was suspended by the administrator, you cannot resume it; the administrator or root must resume the job for you. Resuming a user-suspended job does not put your job into RUN state immediately. If your job was running before the suspension, bresume first puts your job into SSUSP state and then waits for sbatchd to schedule it according to the load conditions. 1. From the command line, run bresume and specify a job group path to resume suspended jobs in a job group. For example, to resume job 3421, enter bresume 3421.

Running Jobs with Platform LSF 33

Working with Jobs

Move a job to the bottom of a queue (bbot)

Use bbot to move jobs relative to your last job in the queue.

You must be an LSF administrator or the user who submitted the job. By default, LSF dispatches jobs in a queue in the order of arrival (that is, first-come-first-served), subject to availability of suitable server hosts. Use the bbot command to change the position of pending jobs, or of pending job array elements, to affect the order in which jobs are considered for dispatch. Users can only change the relative position of their own jobs, and LSF administrators can change the position of any users jobs. To move a job to the bottom of the queue, run bbot. For example, bbot 5311. If invoked by a regular user, bbot moves the selected job after the last job with the same priority submitted by the user to the queue. If invoked by the LSF administrator, bbot moves the selected job after the last job with the same priority submitted to the queue.

Move a job to the top of a queue (btop)

Use btop to move jobs relative to your first job in the queue.

By default, LSF dispatches jobs in a queue in the order of arrival (that is, first-come-first-served), subject to availability of suitable server hosts. Use the btop command to change the position of pending jobs, or of pending job array elements, to affect the order in which jobs are considered for dispatch. Users can only change the relative position of their own jobs, and LSF administrators can change the position of any users jobs. To move a job to the top of the queue, run btop. In the following example, job 5311 is moved to the top of the queue. Since job 5308 is already running, job 5311 is placed in the queue after job 5308.

Tip:
Note that user1s job is still in the same position on the queue. user2 cannot use btop to get extra jobs at the top of the queue; when one of his jobs moves up the queue, the rest of his jobs move down.
bjobs -u all JOBID USER STAT QUEUE FROM_HOST 5308 user2 RUN normal hostA 5309 user2 PEND night hostA 5310 user1 PEND night hostB 5311 user2 PEND night hostA btop 5311 Job <5311> has been moved to position bjobs -u all JOBID USER STAT QUEUE FROM_HOST 5308 user2 RUN normal hostA 5311 user2 PEND night hostA 5310 user1 PEND night hostB 5309 user2 PEND night hostA EXEC_HOST hostD JOB_NAME /s500 /s200 /myjob /s700 SUBMIT_TIME Oct 23 10:16 Oct 23 11:04 Oct 23 13:45 Oct 23 18:17

1 from top. EXEC_HOST hostD JOB_NAME /s500 /s200 /myjob /s700 SUBMIT_TIME Oct 23 10:16 Oct 23 18:17 Oct 23 13:45 Oct 23 11:04

If invoked by a regular user, btop moves the selected job before the first job with the same priority submitted by the user to the queue.

34 Running Jobs with Platform LSF

Working with Jobs If invoked by the LSF administrator, btop moves the selected job before the first job with the same priority submitted to the queue.

Control jobs in job groups Stop jobs (bstop)

1. To suspend jobs in a job group, run bstop -g and specify a job group path.
bstop -g /risk_group 106

Job <106> is being stopped 2. To suspend all jobs in a job group, use job ID 0 (zero).
bstop -g /risk_group/consolidate 0
Job <107> is being stopped Job <108> is being stopped Job <109> is being stopped

Resume jobs (bresume)

1. To resume suspended jobs in a job group, run bresume -g and specify a job group path
bresume -g /risk_group 106

Job <106> is being resumed 2. To resume all jobs in a job group, use job ID 0 (zero).
bresume -g /risk_group 0 Job <109> is being resumed Job <110> is being resumed Job <112> is being resumed

Terminate jobs (bkill)

The command bkill only kills jobs in the job group you specify. It does not kill jobs in lower level job groups in the path. 1. To terminate jobs in a job group, run bkill -g and specify a job group path.
bkill -g /risk_group 106

Job <106> is being terminated 2. To terminate all jobs in a job group, run job ID 0 (zero).
bkill -g /risk_group 0
Job <1413> is being terminated Job <1414> is being terminated Job <1415> is being terminated Job <1416> is being terminated

Delete job groups (bgdel)

The job group cannot contain any jobs.

Running Jobs with Platform LSF 35

Working with Jobs 1. To remove a job group, run bgdel.

bgdel /risk_group Job group /risk_group is deleted.

The job group /risk_group and all its subgroups are deleted.

Submit a job to specific hosts

Specify which hosts a job can run on. When several hosts can satisfy the resource requirements of a job, the hosts are ordered by load. However, in certain situations it may be desirable to override this behavior to give preference to specific hosts, even if they are more heavily loaded.

Note:
By specifying a single host, you can force your job to wait until that host is available and then run on that host.

1. To indicate that a job must run on one of the specified hosts, use the bsub -m "hostA hostB ..." option. For example:
bsub -m "hostA hostD hostB" myjob

Submit a job with specific resources

You must be the LSF administrator.

Configure a new resource that your job runs with. If you have applications that need specific resources, you should create a new Boolean resource and configure that resource for the appropriate hosts in the cluster. If you specify a host list using the -m option of bsub, you must change the host list every time you add a new host that supports the desired resources. By using a Boolean resource, the LSF administrator can add, move, or remove resources without forcing users to learn about changes to resource configuration.

Queues and host preference

A queue can define host preferences for jobs. Host preferences specified by bsub -m override the queue specification. In the queue definition in lsb.queues, use the HOSTS parameter to list the hosts or host groups to which the queue can dispatch jobs. Use the not operator (~) to exclude hosts or host groups from the list of hosts to which the queue can dispatch jobs. This is useful if you have a large cluster, but only want to exclude a few hosts from the queue definition.

Specify different levels of host preference

Submit a job with varying levels of host preferences. You can indicate different levels of preference by specifying a number after the plus sign (+). The larger the number, the higher the preference for that host or host group. You can also specify the + with the keyword others.

1. Submit a job indicating a host preference.

36 Running Jobs with Platform LSF

Working with Jobs For example,

bsub -m "groupA+2 groupB+1 groupC" myjob

In this example, LSF gives first preference to hosts in groupA, second preference to hosts in groupB and last preference to those in groupC. Ordering within a group is still determined by load.

Submit a job with resource requirements

Submit a job that requires specific resources to run. 1. Submit a job indicating a resource requirement. For example, to submit a job which will run on Solaris 7 or Solaris 8:
bsub -R "sol7 || sol8" myjob

When you submit a job, you can also exclude a host by specifying a resource requirement using hname resource:
bsub -R "hname!=hostb && type==sgi6" myjob

Submit a job with SSH X11 forwarding

This task applies to UNIX execution and submissions hosts only. You cannot modify the DISPLAY environment variable. You can submit a job to run with SSH X11 forwarding. These jobs run securely between the X-Server host, the submission host, and the execution host. Allows you to run jobs through an SSH client without having the SSH daemon installed on the X-Server host. 1. 2. 3. 4. Log into the X-Server host. Enable SSH X11 forwarding in your SSH client. Use the SSH client to log into a submission host. Run bsub -XF or -XF -I. If required, provide the password for public or private keys. The job is scheduled by LSF and runs. The bsub command waits until the job is dispatched. If interactive (-I), the job displays throughout the lifecycle of the job.

Running Jobs with Platform LSF 37

Working with Jobs

Using LSF with non-shared file space

LSF is usually used in networks with shared file space. When shared file space is not available, use the bsub -f command to have LSF copy needed files to the execution host before running the job, and copy result files back to the submission host after the job completes. LSF attempts to run the job in the directory where the bsub command was invoked. If the execution directory is under the users home directory, sbatchd looks for the path relative to the users home directory. This handles some common configurations, such as cross-mounting user home directories with the /net automount option. If the directory is not available on the execution host, the job is run in /tmp. Any files created by the batch job, including the standard output and error files created by the -o and -e options to bsub, are left on the execution host. LSF provides support for moving user data from the submission host to the execution host before executing a batch job, and from the execution host back to the submitting host after the job completes. The file operations are specified with the -f option to bsub. LSF uses the lsrcp command to transfer files. lsrcp contacts RES on the remote host to perform file transfer. If RES is not available, the UNIX rcp command is used.

bsub -f
The -f "[local_file operator [remote_file]]" option to the bsub command copies a file between the submission host and the execution host. To specify multiple files, repeat the -f option. local_file

File name on the submission host.

remote_file

File name on the execution host. The files local_file and remote_file can be absolute or relative file path names. You must specify at least one file name. When the file remote_file is not specified, it is assumed to be the same as local_file. Including local_file without the operator results in a syntax error.

38 Running Jobs with Platform LSF

Working with Jobs

operator
Operation to perform on the file. The operator must be surrounded by white space. Valid values for operator are:

> local_file on the submission host is copied to remote_file on the execution host before job execution. remote_file is overwritten if it exists. < remote_file on the execution host is copied to local_file on the submission host after the job completes. local_file is overwritten if it exists. << remote_file is appended to local_file after the job completes. local_file is created if it does not exist. ><, <> Equivalent to performing the > and then the < operation. The file local_file is copied to remote_file before the job executes, and remote_file is copied back, overwriting local_file, after the job completes. <> is the same as ><

If the submission and execution hosts have different directory structures, you must ensure that the directory where remote_file and local_file will be placed exists. ProductNameAbbreviation tries to change the directory to the same path name as the directory where the bsub command was run. If this directory does not exist, the job is run in your home directory on the execution host. You should specify remote_file as a file name with no path when running in non-shared file systems; this places the file in the jobs current working directory on the execution host. This way the job will work correctly even if the directory where the bsub command is run does not exist on the execution host. Be careful not to overwrite an existing file in your home directory.

Running Jobs with Platform LSF 39

Working with Jobs

About resource reservation

When a job is dispatched, the system assumes that the resources that the job consumes will be reflected in the load information. However, many jobs do not consume the resources they require when they first start. Instead, they will typically use the resources over a period of time. For example, a job requiring 100 MB of swap is dispatched to a host having 150 MB of available swap. The job starts off initially allocating 5 MB and gradually increases the amount consumed to 100 MB over a period of 30 minutes. During this period, another job requiring more than 50 MB of swap should not be started on the same host to avoid over-committing the resource. You can reserve resources to prevent overcommitment by LSF. Resource reservation requirements can be specified as part of the resource requirements when submitting a job, or can be configured into the queue level resource requirements.

How resource reservation works

When deciding whether to schedule a job on a host, LSF considers the reserved resources of jobs that have previously started on that host. For each load index, the amount reserved by all jobs on that host is summed up and subtracted (or added if the index is increasing) from the current value of the resources as reported by the LIM to get amount available for scheduling new jobs:
available amount = current value - reserved amount for all jobs

View resource information

You can view host - or queue-level resource information. 1. View host-level resource information. a) To view the amount of resources reserved on each host, run bhosts -l. b) To view information about shared resources, run bhosts -s. 2. View the queue-level resource information. a) To see the resource usage configured at the queue level, run bqueues -l.

Submit a job with resource requirements

1. To specify resource reservation at the job level, use bsub -R and include the resource usage section in the resource requirement (rusage) string. For example:
bsub -R "rusage[tmp=30:duration=30:decay=1]" myjob

LSF reserves 30 MB of temp space for the job. As the job runs, the amount reserved will decrease at approximately 1 MB/minute such that the reserved amount is 0 after 30 minutes.

Submit a job with start or termination times

You can specify a time of day at which to start or stop a job. By default, LSF dispatches jobs as soon as possible, and then allows them to finish, although resource limits might terminate the job before it finishes. If you do not want to start your job immediately when you submit it, specify a start time for LSF to start it. You can also specify a time after which the job should be terminated.

40 Running Jobs with Platform LSF

Working with Jobs 1. Submit a job with a start time.

bsub -b 5:00 myjob

This example submits a job that remains pending until after the local time on the master host reaches 5 a.m. 2. Submit a job with a termination time.
bsub -t 11:12:20:30 myjob

The job called myjob is submitted to the default queue. If the job is still running on November 12 at 8:30 p.m., it will be killed.

Submit a job with resource requirements

Submit a job that requires specific resources to run. 1. Submit a job indicating a resource requirement. For example, to submit a job which will run on Solaris 7 or Solaris 8:
bsub -R "sol7 || sol8" myjob

When you submit a job, you can also exclude a host by specifying a resource requirement using hname resource:
bsub -R "hname!=hostb && type==sgi6" myjob

Submit a job with compute unit resource requirements

Submit a job with compute unit resource requirements. 1. Submit a job to run on a certain number of compute units or fewer using the keyword maxcus in the resource requirement cu string. To submit a job which will run over 4 or fewer compute units of type rack for example:
bsub -R "cu[type=rack:maxcus=4]" my_job

2. Submit a job to run balanced over the fewest possible compute units using the keyword balance in the resource requirement cu string. To submit a job which will run evenly distributed over the fewest compute units and use a total of 64 slots, for example:
bsub -n 64 -R "cu[balance]" my_job

Possible resource allocations (in order of preference) are: 64 slots on 1 enclosure 32 slots on 2 enclosures 22 slots on 1 enclosure and 21 slots on 2 enclosures 16 slots on 4 enclosures 3. Submit a job to run on compute units few or many available slots use the keyword pref.

To submit a job to run on compute units with the fewest slots for example:
bsub -R "cu[pref=minavail]" my_job

Running Jobs with Platform LSF 41

Working with Jobs

42 Running Jobs with Platform LSF

3
Monitoring Jobs

Running Jobs with Platform LSF 43

Monitoring Jobs

View information about jobs

1. Use the bjobs and bhist commands to view information about jobs:

bjobs reports the status of jobs and the various options allow you to display specific information. bhist reports the history of one or more jobs in the system.

You can also find jobs on specific queues or hosts, find jobs submitted by specific projects, and check the status of specific jobs using their job IDs or names.

View unfinished jobs

1. Run bjobs to view the status of LSF jobs. When no options are specified, bjobs displays information about jobs in the PEND, RUN, USUSP, PSUSP, and SSUSP states for the current user.

View all jobs

You can display information about jobs that are both running and those recently finished (PEND, RUN, USUSP, PSUSP, SSUSP, DONE, and EXIT statuses) 1. Run bjobs -a . All your jobs that are still in the system and jobs that have recently finished are displayed.

View running jobs

You can display information about only jobs that are running (RUN status). 1. Run bjobs -r. All your running jobs are displayed.

View pending reasons for jobs

When you submit a job, it may be held in the queue before it starts running and it may be suspended while running. You can find out why jobs are pending or in suspension with the bjobs -p option. 1. Run bjobs -p. Displays information for pending jobs (PEND state) and their reasons. There can be more than one reason why the job is pending. The pending reasons alsodisplay the number of hosts for each condition. 2. To get specific host names along with pending reasons, run bjobs -lp. 3. To view the pending reasons for all users, run bjobs -p -u all.

View suspending reasons for jobs

When you submit a job, it may be held in the queue before it starts running and it may be suspended while running. 1. Run bjobs -s.

44 Running Jobs with Platform LSF

Monitoring Jobs Displays information for suspended jobs (SUSP state) and their reasons. There can be more than one reason why the job is suspended. The pending reasons alsodisplay the number of hosts for each condition. 2. To get specific host names along with suspend reasons, run bjobs -ls. 3. To view the suspend reasons for all users, run bjobs -s -u all.

View detailed job information

The -l option of bjobs displays detailed information about job status and parameters, such as the jobs current working directory, parameters specified when the job was submitted, and the time when the job started running.
bjobs -l with a job ID displays all the information about a job, including:

Submission parameters Execution environment Resource usage

1. Run bjobs -l.

bjobs -l 7678
Job Id <7678>, User <user1>, Project <default>, Status <PEND>, Queue <priority>, Command <verilog> Mon Oct 28 13:08:11: Submitted from host <hostD>,CWD <$HOME>, Requested Resources <type==any && swp>35>; PENDING REASONS: Queues resource requirements not satisfied:3 hosts; Unable to reach slave lsbatch server: 1 host; Not enough job slots: 1 host; SCHEDULING PARAMETERS: r15s r1m r15m ut pg io ls it tmp swp mem loadSched 0.7 1.0 4.0 loadStop 1.5 2.5 8.0 -

View job group information

You can view information about jobs in job groups or view jobs by job group. To see all job groups, run bjgroup. To see jobs by job group, run bjobs -g /group_name.

Monitor SLA progress

You can display the properties of service classes configured in lsb.serviceclasses and the dynamic state information for each service class. 1. Run bsla 2. Run bacct -sla to display historical performance of a service class.

View job output

You must be logged on as the job owner. The output from a job is normally not available until the job is finished. However, LSF provides the bpeek command for you to look at the output the job has produced so far. By default, bpeek shows the output from the most recently submitted job. You can also select the job by queue or execution host, or specify the job ID or job name on the command line.

Running Jobs with Platform LSF 45

Monitoring Jobs To save time, you can use this command to check if your job is behaving as you expected and kill the job if it is running away or producing unusable results. 1. Run bpeek job_id. For example:
bpeek 1234
<< output from stdout >> Starting phase 1 Phase 1 done Calculating new parameters ...

View chronological history of jobs

By default, the bhist command displays information from the job event history file, lsb.events, on a per job basis. Use the -t option of bhist to display the events chronologically instead of grouping all events for each job. Use the -T option to select only those events within a given time range. For example, the following displays all events which occurred between 14:00 and 14:30 on a given day:
bhist -t -T 14:00,14:30
Wed Oct 22 14:01:25: Job <1574> Wed Oct 22 14:03:09: Job <1575> Command , Requested Resources ; Wed Oct 22 14:03:18: Job <1575> Wed Oct 22 14:03:18: Job <1575> Wed Oct 22 14:03:18: Job <1575> Pid <210>; Wed Oct 22 14:05:06: Job <1577> Command , Requested Resources ; Wed Oct 22 14:05:11: Job <1577> Wed Oct 22 14:05:11: Job <1577> Wed Oct 22 14:05:12: Job <1577> Pid <429>; Wed Oct 22 14:08:26: Job <1578> Command; Wed Oct 22 14:10:55: Job <1577> Wed Oct 22 14:16:55: Job <1578> Wed Oct 22 14:17:04: Job <1575> done successfully; submitted from host to Queue , CWD , User , Project , dispatched to ; starting (Pid 210); running with execution home , Execution CWD , Execution submitted from host to Queue, CWD , User , Project ,

dispatched to ; starting (Pid 429); running with execution home, Execution CWD , Execution submitted from host to Queue, CWD , User , Project , done successfully; exited; done successfully;

View history of jobs not listed in active event log

LSF periodically backs up and prunes the job history log. By default, bhist only displays job history from the current event log file. You can display the history for jobs that completed some time ago and are no longer listed in the active event log. The -n num_logfiles option tells the bhist command to search through the specified number of log files instead of only searching the current log file. Log files are searched in reverse time order. For example, the command bhist -n 3 searches the current event log file and then the two most recent backup files. 1. Run bhist -n num_logfiles.

46 Running Jobs with Platform LSF

Monitoring Jobs

bhist -n 1 bhist -n 2 bhist -n 3 bhist -n 0

Searches the current event log file lsb.events Searches lsb.events and lsb.events.1 Searches lsb.events, lsb.events.1, lsb.events.2 Searches all event log files in LSB_SHAREDIR

View job history

You can check on the status of your job since it was submitted. The bhist command displays a summary of the pending, suspended, and running time of jobs for the user who invoked the command. 1. Run bhist. a) Run bhist -l to display the time information and a complete history of scheduling events for each job. b) Use bhist -u all to display a summary for all users in the cluster.

Update interval
The job-level resource usage information is updated at a maximum frequency of every SBD_SLEEP_TIME seconds. The update is done only if the value for the CPU time, resident memory usage, or virtual memory usage has changed by more than 10 percent from the previous update or if a new process or process group has been created.

Job-level information
Job-level information includes:

Total CPU time consumed by all processes of a job Total resident memory usage in KB of all currently running processes of a job Total virtual memory usage in KB of all currently running processes of a job Currently active process group ID of a job Currently active processes of a job

Running Jobs with Platform LSF 47

Monitoring Jobs

About displaying resource allocation limits

The command blimits displays:

Configured limit policy name Users (-u option) Queues (-q option) Hosts (-m option) Project names (-P option)

Resources that have no configured limits or no limit usage are indicated by a dash (-). Limits are displayed in a USED/ LIMIT format. For example, if a limit of 10 slots is configured and 3 slots are in use, then blimits displays the limit for SLOTS as 3/10. If limits MEM, SWP, or TMP are configured as percentages, both the limit and the amount used are displayed in MB. For example, lshosts displays maximum memory (maxmem) of 249 MB, and MEM is limited to 10% of available memory. If 10 MB out of are used, blimits displays the limit for MEM as 10/25 (10 MB USED from a 25 MB LIMIT). Configured limits and resource usage for builtin resources (slots, mem, tmp, and swp load indices) are displayed as INTERNAL RESOURCE LIMITS separately from custom external resources, which are shown as EXTERNAL RESOURCE LIMITS. Limits are displayed for both the vertical tabular format and the horizontal format for Limit sections. If a vertical format Limit section has no name, blimits displays NONAMEnnn under the NAME column for these limits, where the unnamed limits are numbered in the order the vertical-format Limit sections appear in the lsb.resources file. If a resource consumer is configured as all, the limit usage for that consumer is indicated by a dash (-). PER_HOST slot limits are not displayed. The bhosts commands displays these as MXJ limits. In MultiCluster, blimits returns the information about all limits in the local cluster.

View information about resource allocation limits

Your job may be pending because some configured resource allocation limit has been reached. You can display the dynamic counters of resource allocation limits configured in the Limit sections in lsb.resources. 1. Run blimits to display the current resource usage, including any limits that may be blocking your job.

48 Running Jobs with Platform LSF

4
Platform Management Console

Running Jobs with Platform LSF 49

Platform Management Console

Platform HPC Portal

The HPC Portal allows users and administrators to monitor hosts and to submit and monitor jobs.

Open the HPC Portal for the first time

Make sure the HPC Portal is installed.

Launch the interactive HPC Portal to monitor hosts and jobs and run jobs. The HPC Portal allows you to monitor hosts and jobs, as well as submit jobs. When logging in for the first time, the LSF administrator must log on as root. All administrators and non-administrator users logging on to the HPC Portal must provide an OS user name and password. 1. Open the HPC Portal in a supported Web browser.
http://master_host_name:8080/platform

2. Log on with your UNIX or Windows username and password. 3. If the log on failed or the URL could not be found, restart the HPC Portal by running pmcadmin from the command line. In most cases, the daemons and services required to run the HPC Portal start automatically; however, if the HPC Portal goes down, you may need to restart HPC Portal services and daemons.

Enable cookies
The HPC Portal requires that Web browsers accept first-party and third-party cookies. In some cases, your browser default settings may block these cookies. In this case, you need to manually change this setting.

Note:
By default, IE7 blocks cookies, while IE6, Firefox 1.5, and Firefox 2.0 allow cookies.

For IE7: 1. In your browser, go to Tools > Internet Options > Privacy > Advanced. 2. Select Override automatic cookie handling. 3. Select Accept for both first-party and third-party cookies. 4. Click OK to save your settings.

50 Running Jobs with Platform LSF

A
automount option /net 38

Index
associated to a user group 25 to a specific queue 24 btop changing job order within queues 34

B
bacct command 45 batch jobs accessing files 38 file access 38 scheduling 40 bbot changing job order within queues 34 bhist viewing chronological history of jobs 46 viewing job history 47 viewing jobs not listed in active event log 46 bhosts -l viewing host-level resource information 40 bjobs viewing status of jobs 44 bmod modifying resource reservation for jobs 30 modifying running jobs 30 bpeek viewing job output 45 bqueues -l viewing queue-level resource information 40 bresume resuming jobs 32 bsla 45 bstop SIGSTOP and SIGTSTP signals 33 suspending jobs 32 bsub remote file access 38 submitting a job associated to a service class 26

C
CPU time limit small jobs 25

D
directories remote access 38

G
goal-oriented scheduling. See SLA scheduling

H
history viewing 46, 47 home directories remote file access 39 hosts specifying on job submission 36 specifying preference at job submission 36 viewing resource allocation limits (blimits) 48

J
job limits modifying for running jobs 30 job output options modifying for rerunnable jobs 30 modifying for running jobs 31 job rerun modifying running jobs 30 job-level resource reservation 40

Running Jobs with Platform LSF 51

jobs assigning job names 26 changing execution order 34 checking output 45 modifying resource reservation 30 resuming 32 specifying resource requirements 37, 41 submitting for a user group 25 resources 36 specifying host preference 36 to a service class 26 to specific queues 24 submitting to a project 25 submitting with start/end time 40 suspending 32 view information 45 viewing chronological history 46 history 47 status of 44

Q
queues and host preference 36 changing job order within 34 specifying at job submission 24 viewing resource allocation limits (blimits) 48

R
rcp command for remote file access 38 rerunnable jobs modifying running jobs 30 resource requirements specifying at job submission 37, 41 resource reservation description 40 modifying for jobs 30 resource usage limits CPU limit for small jobs 25 modifying for running jobs 30 resources and job submission 36 resuming jobs when suspended by administrator 33 RUN job state 33

L
limits modifying for running jobs 30 logs viewing jobs not listed in active event log 46 lsb.resources file viewing limit configuration (blimits) 48 lsrcp command for remote file access 38

S
sbatchd (slave batch daemon) remote file access 38 SBD_SLEEP_TIME 47 service classes bacct command 45 bsla command 45 service level agreement. See SLA scheduling signals bstop command 33 SIGCONT in job control actions 32 SIGKILL in job control actions 32 SIGSTOP bstop command 33 job control actions 32 SIGTSTP bstop command 33 SIGSTOPand SIGTSTP signals

N
names assigning to jobs 26 non-shared file space 38

O
order of job execution 34

P
project names viewing resource allocation limits (blimits) 48 projects associating jobs with 25 collecting information 25 PSUSP job state 33

52 Running Jobs with Platform LSF

bstop command 33 SLA scheduling bacct command 45 bsla command 45 submitting jobs description 26 SSH X11 forwarding 37 SSUSP job state 33 standard error output file

modifying for running jobs 31 standard output file modifying for running jobs 31

U
update interval 47 user groups associating with jobs at job submission 25 users viewing resource allocation limits (blimits) 48 USUSP job state 32, 33

Running Jobs with Platform LSF 53