Job Execution
Job Execution
Overview
When a batch job is submitted from a work server, scheduling is handled by LSF (Platform Load Sharing Facility developed by IBM) which dispatches and executes the batch job on a calculation server. When submitting a job, it is necessary to choose a queue that is appropriate.
※See here for information on batch queues for workgroups.
Job Submission
Note
Info
In case that you submit over 100 jobs which run time are very short (less than 30 sec),these jobs should be merged into a shell script and submitted to LSF. (You can use LSF Session Scheduler if you submit the jobs to s queue) If many submitted jobs have run time shorter than the procedure interval of LSF manager service, these jobs have significant impact on system performance.
Info
When the availability of each servers' memory exceeds 90%, a series of processes which use large amount of memory may be forced to terminate for system protection. We appreciate your understandings.
Info
If free-space of your home directory less than 100MB, you cannot submit jobs temporarily due to prevent capacity depletion and job failure. You can submit jobs again when the free-space of your directory is over 100MB. Please check your status of home directory by Disk Quotas command.
Submit a Job
To submit a job into LSF, run the following command.
$> bsub [-q queue name -m "hostname" ] job name↓
［Example］
$> bsub -q s testjobs↓
- Normally, it is not necessary to specify a host name (i.e. the host where the job is executed) when submitting a job. LSF manages selectiion of appropriate calculation servers.
- You can't submit a job from calculation servers.
Also, this system supports jobs using OpenMPI/OpenMP. See Executing MPI Jobs or Executing OpenMP Jobs .
Sending completion notice by email
Info
If a large amount of notification emails are detected, the system administrator will delete them.
To send the completion notification from jobs by email, specify these options as shown below.
You must specify -o option to output the results as files, when you want to get notifications.
For detail, see Standard Output/Standard Error .
$> bsub -q s -u "email address" -o "filename or directoryname" -N jobname↓
［Example］
$> bsub -q s -u testuser01@post.kek.jp -o lsflog/result.log -N testjobs↓
Standard Output/Standard Error
It is not suitable output to HSM area.
So, if you conflict with these rule:
- To Specify output to HSM area
- To Execute bsub on HSM area
bsub will fail with the following messages:
--------------------------------------------------------- HSM area is not suitable to output logfiles from jobs. It may cause a system crash. Would you check your jobs and job-submission environment? See: http://kekcc.kek.jp/service/kekcc/html/Eng/JobExecution.html#sa89ac76 Thank you for your understanding and cooperation. ---------------------------------------------------------
Default
By default, the output file is “Job-ID.out” under the directory .lsf in your home directory.
Example： Group: CE, User: testuser1, Job ID: 111 ''/home/ce/testuser1/.lsf/111.out''
File Specification
You can specify a file name or a directory for the output file with the "-o" option. When only a directory is specified, the output file name is "Job-ID.out."
$> bsub -o "filename or directoryname" jobname↓
［Example］
$> bsub -o lsflog/ tetestjobs↓
※ The output file is created under lsflog, which is a sub-directory of the current directory. The file name is "Job-ID.out".
［Example2］
$> bsub -o lsflog/result.log tetestjobs2↓
※ The output file is created under lsflog, which is a sub-directory of the current directory. The file name is "result.log".
In case the specified output file already exists
If the same output file name is specified for several different jobs, the results are added at the end of the existing file
Limitation of output file size
When you use Default and File Specification , the output file size is limited up to 200MB by system.
To avoid it, you can control output file in your program or use shell redirection.
[Example] with csh
$> bsub "testjob >& lsflog/result.log"↓
[Example] with bsh
$> bsub "testjob > lsflog/result.log 2>&1"↓
Job Status
You can check the job status with the bjobs command.
$> bjobs jobID↓
[Example]
$> bjobs 111↓
If your jobs ware started, please check their status by using a command "/usr/local/bin/chk_runjob".
※This information is updated once per minute.
※The multi-core/multi-thread jobs, such as MPI/OpenMP, are not supported.
$> chk_runjob JOBS SLOT CPUTIME RUNTIME CPU/RUN 1500 1500 125649261 126740225 0.991
You can list your jobs in order of STARTTIME with "-l NUM" option.
NUM means the number of listed jobs.(default:show all)
$> chk_runjob -l 5 JOBS SLOT CPUTIME RUNTIME CPU/RUN 1500 1500 125649261 126740225 0.991 RUN JOB SUMMARY: JOBID QUEUE EXEC_HOST STARTTIME CPUTIME RUNTIME UTIL EXEC_JOB 30351511 l cb241 03/31-09:22:21 023:22:00 023:31:09 99.35% java 30351564 l cb241 03/31-09:22:42 023:21:36 023:30:48 99.35% java 30351774 l cb241 03/31-09:23:50 023:18:59 023:29:40 99.24% java 30351978 l cb241 03/31-09:25:03 023:19:30 023:28:27 99.36% java 30352009 l cb241 03/31-09:25:23 023:16:06 023:28:07 99.15% java
You can get details of your jobs with the "bjobs -l JOBID" command.
In a following case, execution efficiency becomes very low and CPU/RUN also falls.
- Mass or continuous submission of the extremely short (10-30 seconds or less) jobs.
- Submisson of jobs that cannot be run successfully (ex.command mistake)
- Too many jobs wire to one directory.
- Too many jobs read one file conqurently.
- Too many files in $HOME/.lsf/ .
- Home directory is full. --> you can check by "rquota", "bquota" ( = Only for Belle users ) or "hquota" command.
If "CPU/RUN < 0.6", please improve the utilization efficiency by performing the investigation of the cause.
Also, you can monitor the standard output during the job execution with the bpeek command.
$> bpeek jobID↓
［Example］
$> bpeek 111↓
You can get information on jobs with the "bhist -l" command after the job has finished.
If you get the message "No matching job found", you can add the option "-n 0" to look in all the previous LSF logs.
$> bhist -l jobID↓
［Example］
$> bhist -l 111↓
You can get information on jobs also with the "bacct -l" command.
$> bacct -l jobID↓
［Example］
$> bacct -l 111↓
Host Status
You can display load information for hosts using the lsload command.
$> lsload↓
［Example］
$> lsload↓
HOST_NAME status r15s r1m r15m ut pg ls it tmp swp mem ccb001 ok 0.0 0.2 0.2 0% 0.0 0 81 9769M 7.9G 155G ccb002 ok 0.6 0.1 0.2 0% 0.0 0 3153 10G 7.9G 155G ccb003 ok 0.0 0.2 0.2 1% 0.0 0 3152 10G 7.9G 163G .....
You can check the status of each host using the bhosts command.
$> bhosts↓
［Example］
$> bhosts↓
HOST_NAME STATUS JL/U MAX NJOBS RUN SSUSP USUSP RSV ccb001 ok - 40 0 0 0 0 0 ccb002 ok - 40 0 0 0 0 0 ccb003 ok - 40 0 0 0 0 0 ccb004 ok - 40 0 0 0 0 0 ccb005 ok - 40 0 0 0 0 0 .....
Cancellation
You can cancel jobs using the bkill command.
$> bkill jobID↓
When you set "0" instead of "jobID", all jobs you submitted will be canceled.
［Example］
$> bkill 111↓
If bkill fails to kill a job, the "-r" option can be used to force the termination. This option applies to situations such as;
- When executed bkill command, there is a message "Job
is being terminated" - bjobs command keeps showing the job that should have been terminated
$> bkill -r jobID↓
［Example］
$> bkill -r 111↓
Termination of jobs by system
- The jobs will be terminated for over the following thresholds by system.
| Reason of termination | Messages in bacct 4 |
|---|---|
| Reached maximum normalized execution time 1 | Completed |
| Reached maximum normalized CPU time 1 | Completed |
| Reached maximum resident set size (RSS) of a job 1 | Completed |
| Reached maximum virtual memory of a job 1 | Completed |
| Reached maximum processes of a job 1 | Completed |
| Reached maximum STDOUT output size 2 | Completed |
Scheduling Policies
LFS supports the "Fairshare" functions in order to provide a fair access to resources. Fairshare defines the priorities of jobs that are dispatched. The following command shows the current Fairshare values.
$> bqueues -l queue_name↓
［Example］
$> bqueues -l s↓
SHARE_INFO_FOR: s/ USER/GROUP SHARES PRIORITY STARTED RESERVED CPU_TIME RUN_TIME ADJUST GPU_RUN_TIME user-a 1 0.333 0 0 0.0 0 0.000 0 user-b 1 0.333 0 0 0.0 0 0.000 0 user-c 1 0.333 0 0 0.0 0 0.000 0 user-d 1 0.012 1 0 872.8 399993 0.000 0 user-e 1 0.008 1 0 0.0 574239 0.000 0 user-f 1 0.005 2 0 2588.0 1003056 0.000 0 user-g 1 0.004 31 0 36821.6 667907 0.000 0 user-h 1 0.003 98 0 94953.1 432167 0.000 0 user-i 1 0.001 17 0 17307.1 3447528 0.000 0 user-j 1 0.000 27 0 23340.3 12779340 0.000 0
Guaranteed Resource Allocation (GRA, Guaranteed Resource Allocation)
GRA (Guaranteed Resource Allocation) policy is applied in the a queue.
Jobs in this queue are dispatched in preference to other queues, but running jobs per user is limited to 4 (JL/U).
This queue is useful for jobs that need quick results when waiting job dispatch in the normal queues.
Note that the queue parameters are the same as the l queue.
How to use when using big memory for the queues sx, lx, hx, px, zx, adn cmb_px.
In the case of you use the queues sx, lx, hx, px, zx, and cmb_px, according to the amount of memory you are using. Specify the bsub option -n "parallel number X" within the TASKLIMIT setting value and submit the job.
［Example/sx queue］
6 for TASKLIMIT is set.
The available memory is as follows.
Specify 1 -> 8GB * 1 = MEMLIMIT = 8GB Specify 2 -> 8GB * 2 = MEMLIMIT = 16GB Specify 3 -> 8GB * 3 = MEMLIMIT = 24GB Specify 4 -> 8GB * 4 = MEMLIMIT = 32GB Specify 5 -> 8GB * 5 = MEMLIMIT = 40GB Specify 6 -> 8GB * 6 = MEMLIMIT = 48GB
MPI Job Execution
Job Submission
In the current computation system, it is possible to submit jobs that use OpenMPI/IntelMPI to LSF.
Regarding how to compile MPI applications, please refer to MPI Compilation.
Steps to rub MPI jobs.
Create job script file is needed to run MPI jobs.
The arguments for bsub command can discribed in the job script.
Here the way to describe in a script is shown.
Creating a job script
Set the environment with module command.
OpenMPI varies depends on compilers, chose the correct compiler used to build with.
Then run the programs with mpirun command.
［Example/IntelMPI］
1 2 3 4 5 6 7 8 | #!/bin/bash ##---- for bsub options #BSUB -n 24 #slot number #BSUB -q p #execution queue ##---- environment setting module load intel/2020 ##---- execution mpirun -np 24 ./a.out |
[Example/OpenMPI(gnu)]
1 2 3 4 5 6 7 8 | #!/bin/bash ##---- for bsub options #BSUB -n 24 #slot number #BSUB -q p #execution queue ##---- environment setting module load openmpi/2.1.6-gcc930 ##---- execution mpirun -np 24 ./a.out |
Job submission
$> bsub < job script↓
［Example］
$> cat mpijob_intel.sh ↓ #!/bin/bash #BSUB -n 24 #BSUB -q p module load intel/2020 mpirun -np 24 ./a.out $> $> bsub < mpijob_intel.sh↓
Limits of queues dedicated to parallel (MPI) jobs
MPI jobs must be submitted to the dedicated queues, p or px. When executing bsub, always specify either "-q p" or "-q px".
For the queues p and px, TASKLIMIT (Limit on the number of tasks used per job) is set to 24. Thus, parallel jobs using more than 24 processes cannot be submitted.
Your MPI job may get these errors and exit immediately after you submitted it. They show you to conflict with restriction of the system temporarily. Please re-submit MPI jobs again when you get them.
ipath_userinit: assign_context command failed: Network is down can't open /dev/ipath, network down (err=26)^
ipath_userinit: assign_context command failed: Invalid argument Driver initialization failure on /dev/ipath (err=23)
Selecting the Execution Nodes for a Parallel (MPI) Job
The KEK environment has been configured to assign job slots to MPI jobs as explained below. First, slots from the first node are assigned to the job, if the job requirements exceed the maximum number of slots per node, which is 28, slots from other nodes are also used.
Example) Case where a 12 process parallel job is submitted:
node01 ... 12 processes are executed node02 ... No process node03 ... No process node04 ... No process ... node12 ... No process
To have each process of the 12 process MPI job dispatched on 1 slot per node, add the option -R span[ptile=1] to the bsub command. It can be specified by the argument or in the job script.
[by argument]
$> bsub -R span[ptile=1] < job script↓
[specified in the job script]
Discribe the following line in the job script.
#BSUB -R span[ptile=1]
With this option, it is possible to have the MPI job dispatched as below.
node01 ... 1 process is executed node02 ... 1 process is executed node03 ... 1 process is executed node04 ... 1 process is executed ... node12 ... 1 process is executed
OpenMP Job Execution
Regarding how to compile OpenMP program applications, please refer to OpenMP program Compilation.
OpenMP job submission
OpenMP jobs can use the number of CPU cores specified by bsub -n ( default value is 1 ).
The maximum number of cores for OpenMP jobs is 24 ( per jobs ).
［Example ( Submitting OpenMP job to use 12 cores )］
$> bsub -R "span[hosts=1]" -q p -n 12 ./openmp_64↓
Limits of queues dedicated to OpenMP jobs
OpenMP jobs must be submitted to the dedicated queues, p or px. When executing bsub, always specify either "-q p" or "-q px". And when executing bsub, you need to specify "-R "span[hosts=1]", too.
Using LSF Session Scheduler
About LSF Session Scheduler
You can use LSF Session Scheduler (LSF SS) if you submit many jobs which satisfy following conditions:
- short RUNTIME (shorter than 30 seconds)
- do not use much CPU resources LSF SS makes these jobs get effectively.
Preparation
To use LSF SS, you have to make task file. This file is a list you want to execute in your job.
Example:my.task # cat my.task hostname date /home/xxx/user/script.sh
If you want to get the output of each commands, please use -o (standard output) or -e (standard error) options. For LSF SS, The output file of $HOME/.lsf have no output of command execution.
Example:my.task2 # cat my.task2 -o sample.out -e sample.err hostname
For above sample, sample.out contains standard output, and sample.err contains standard error.
In addition, you can use following parameters.
%J : Job ID %T : task ID
Job ID is JOBID of execute job, and task ID is the row of task file. For example, you can get four files, 10000.1.out,10000.1.err,10000.2.out,10000.2.err, if you submit follwoing task file.
Example:my.task3 # cat my.task3 -o %J.%T.out -e %J.%T.err hostname -o %J.%T.out -e %J.%T.err date
Job Submission
It shows the procedure to submit LSF SS job. You have to use s queue to use LSF SS.
$ bsub -app ssched <LSF option> ssched -tasks <task file>
Example: $ bsub -app ssched -q s ssched -tasks my.taks3
If you want to check job status, or cancel jobs, you can do them same as normal LSF job.
Others
If you submit LSF SS job to "not s queue", it has following errors.
LSF is Rejecting your job submission... ssched is available for only s queue. Job not submitted.
Additional Warnings
/tmp directory
/tmp shall be the location that makes basic system applications available to create temporary files. Please refrain from creating large size files or number of files in the /tmp by yourself. If the usage rate of the / tmp directory becomes high, large files are deleted. /tmp directory has been set quota, 1GB/users.
File staging during LSF jobs
Submitting many jobs reading "not staged files" (which do not exist on GHI disk) will make KEKCC system inefficiency.
If you can determine files using in your jobs, please stage files refer to "Staging files".