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Batch System PBSPro (vulcan)

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Introduction

The only way to start a parallel job on the compute nodes of this system is to use the batch system. The installed batch system is based on PBSPro.

Writing a submission script is typically the most convenient way to submit your job to the batch system. You generally interact with the batch system in two ways: through options specified in job submission scripts (these are detailed below in the examples) and by using torque or moab commands on the login nodes. There are three key commands used to interact with torque:

  • qsub
  • qstat
  • qdel

Check the man page of torque for more advanced commands and options 

 man pbs_professional


Requesting Resources using batch system

You have to specify the resources you need for your batch job. These resources are specified by including them in the -l option argument on the qsub command or in the PBS job script. The 2 important resources you have to specify are number of nodes of a specific node type and the walltime you need for this job: 

  1. select=<number of nodes>:<node_resource_variable=type>
      2. To distinguish between different nodes 4 node resource variables are assigned to each node. The node_type, node_type_cpu, node_type_mem and node_type_core of each node. You have to specify at least one of the resource variable or you can specify a valid available combination of the resources for a specific type of nodes.
      Available node:
      node_type node_type_cpu node_type_mem node_type_core Graphic localscratch linkspeed describes notes # of nodes (laki) # of nodes (laki2)
      sb SandyBridge@2.60GHz 32gb 16c QDR cpu type intel sandy bridge, 32GB memory 2 octa core-CPU per node 98 178
      sb SandyBridge@2.60GHz 64gb 16c QDR cpu type intel sandy bridge, 64GB memory 2 octa core-CPU per node 6 10
      sb SandyBridge@2.60GHz 64gb 16c FDR cpu type intel sandy bridge, 64GB memory 2 octa core-CPU per node 24 0
      sb SandyBridge@2.60GHz 128gb 16c QDR cpu type intel sandy bridge, 128GB memory 2 octa core-CPU per node 0 4 (1 shared)
      hsw Haswell@2.60GHz 128gb 20c QDR cpu type intel haswell, 128GB memory 2 x 10 core-CPU 2.6 ghz per node 84 0
      hsw Haswell@2.60GHz 256gb 20c QDR cpu type intel haswell, 256GB memory 2 x 10 core-CPU 2.6 ghz per node 4 0
      hsw Haswell@2.50GHz 128gb 24c QDR cpu type intel haswell, 128GB memory 2 x 12 core-CPU 2.5 ghz per node 200 0
      hsw Haswell@2.50GHz 128gb 24c FDR cpu type intel haswell, 128GB memory 2 x 12 core-CPU 2.5 ghz per node 144 0
      hsw Haswell@2.50GHz 256gb 24c QDR cpu type intel haswell, 256GB memory 2 x 12 core-CPU 2.5 ghz per node 16 0
      il Interlagos@2.6GHz 256gb 48c QDR interlagos node with 256GB memory 6 0
      il Interlagos@2.6GHz 256gb 48c 4TB QDR interlagos node with 256GB memory, 4TB local scratch disk 4 0
      ib IvyBridge@3.3Ghz 384gb 16c Tesla K20Xm 11TB QDR node with intel IvyBridge@3.3Ghz, 16 cores, 384GB memory, 11TB local SSD scratch disk, Tesla K20Xm only for single node jobs available 3 0
      nh Nehalem_EX@2.67GHz 1024gb 48c SDR cpu type intel nehalem, 1TByte memory,8 socket 6 core CPU's will be shared with other jobs! Please use "qsub -q smp -l select=1:node_type=nh ..." 1 0
      nh Nehalem@2.8GHz 144gb 8c 6TB SDR cpu type intel nehalem, 148GB memory, 6TB local scratch 2 octa core-CPU per node + local scratch disk 1 0
      fx5800 Nehalem@2.93GHz 24gb 4c Quadro FX 5800 SDR Graphic node Nvidia Quadro FX 5800, 8 core intel W3540, 24GB memory only 1 node per job! Please use "qsub -q vis -l select=1:node_type=fx5800 ..." 4 1
      gtx680 Nehalem@2.53GHz 12gb 4c GTX680 SDR Cuda Node with GTX680, 8 core intel E5540, 12GB memory only 1 node per job! 2 0
      Multi nodes can be specified using a +: 
      nodes=2:tesla+3:nehalem
      The example above will allocate 2 nodes with feature tesla and 3 nodes with feature nehalem.
  2. walltime=<time>


Batch Mode

Production jobs are typically run in batch mode. Batch scripts are shell scripts containing flags and commands to be interpreted by a shell and are used to run a set of commands in sequence.

  • The number of required nodes, cores, wall time and more can be determined by the parameters in the job script header with "#PBS" before any executable commands in the script.
#!/bin/bash
#PBS -N job_name
#PBS -l select=2:node_type=hsw:mpiprocs=24
#PBS -l walltime=00:20:00             
  
# Change to the direcotry that the job was submitted from
cd $PBS_O_WORKDIR

module load mpi/your_mpi_version_for_your_application

# Launch the parallel job to the allocated compute nodes
mpirun opt1 opt2  ./my_mpi_executable arg1 arg2 > my_output_file 2>&1
  • The job is submitted by the qsub command (all script head parameters #PBS can also be adjusted directly by qsub command options).
 qsub my_batchjob_script.pbs
  • Setting qsub options on the command line will overwrite the settings given in the batch script:
 qsub -N other_name -l select=2:node_type=hsw:mpiprocs=24 -l walltime=00:20:00 my_batchjob_script.pbs
  • The batch script is not necessarily granted resources immediately, it may sit in the queue of pending jobs for some time before its required resources become available.
  • At the end of the execution output and error files are returned to your HOME directory
  • This example will run your executable "my_mpi_executable" in parallel with 48 MPI processes. The batch system will allocate 2 nodes to your job for a maximum time of 20 minutes and place 24 processes on each node. The batch systems allocates nodes exclusively only for one job. After the walltime limit is exceeded, the batch system will terminate your job. The mpirun example above will start the parallel executable "my_mpi_executable" with the arguments "arg1" and "arg2". The job will be started using 48 MPI processes with 24 processes placed on each of your allocated nodes. You need to have nodes allocated by the batch system (qsub) before starting mpirun.

Interactive batch Mode

Submit a batch job

You will get each requested node for your exclusive usage. There are 2 methods to use the batch system:

  1. interactive batch jobs:
    if requested resources are available, the job starts a interactive shell immediately. For interactive access the qsub command has the option -I example: 
    qsub -I ...
  1. normal batch jobs:
    jobs will be started by the MOAB scheduler after passing some rules configured by the administrator (FAIRSHARE, BACKFILLING, ...).

Command for submitting a batch job request

A short explanation follows here. For detailed information, see the man pages or the latest documentation in the WWW. 

man qsub
man pbs_resources
man pbs

Command to submit a batch job 

qsub <option>

On success, the qsub command returns a request ID.

You have to specify the resources you need for your batch job. These resources are specified by including them in the -l option argument on the qsub command or in the PBS job script. There are 2 important resources you need to specify: 

  1. nodes=<number of nodes>:<feature>
      2. To distinguish between different nodes, features are assigned to each node. These features describe the properties of each node. Please do only use exactly 1 feature for each node type.
      Available node:
      node_type node_type_cpu node_type_mem node_type_core graphic lokalescratch linkspeed describes notes '# of nodes (laki) # of nodes (laki2)
      nehalem, mem12gb No longer available !
      sb, mem32gb cpu type intel sandy bridge, 32GB memory 2 octa core-CPU per node 98 178
      hsw128gb10c cpu type intel haswell, 128GB memory 2 x 10 core-CPU 2.6 ghz per node 84 0
      hsw256gb10c cpu type intel haswell, 256GB memory 2 x 10 core-CPU 2.6 ghz per node 4 0
      hsw128gb12c cpu type intel haswell, 128GB memory 2 x 12 core-CPU 2.5 ghz per node 344 0
      hsw256gb12c cpu type intel haswell, 256GB memory 2 x 12 core-CPU 2.5 ghz per node 16 0
      tesla No longer available !
      mem64gb sb node with 64GB memory 30 10
      mem128gb sb node with 128GB memory 0 4 (1 shared)
      il Interlagos@2.6GHz 256gb 48c QDR interlagos node with 256GB memory 6 0
      il Interlagos@2.6GHz 256gb 48c 4TB QDR interlagos node with 256GB memory, 4TB local scratch disk 4 0
      mem384gb, scratch11tb,k20xm node with intel IvyBridge@3.3Ghz, 16 cores, 384GB memory, 11TB local SSD scratch disk, Tesla K20Xm only for single node jobs available 3 0
      smp cpu type intel nehalem, 1TByte memory,8 socket 6 core CPU's will be shared with other jobs! Please use "qsub -q smp -l nodes=1:smp..." 1
      mem144gb, scratch6tb, scratch2tb cpu type intel nehalem, 148GB memory, 2TB local scratch (1 nodes) or 6TB local scratch (1 nodes) 2 octa core-CPU per node + local scratch disk 1
      vis Graphic node Nvidia Quadro FX 5800, 8 core intel W3540, 24GB memory only 1 node per job! Please use "qsub -q vis -l nodes=1:vis..." 3 1
      gtx680 Cuda Node with GTX680, 8 core intel E5540, 12GB memory only 1 node per job! 2 0
      Multi nodes can be specified using a +: 
      nodes=2:tesla+3:nehalem
      The example above will allocate 2 nodes with feature tesla and 3 nodes with feature nehalem.
  2. walltime=<time>

Usage of multi-socket nodes and multi-core cpus

The batch system takes into account the number of cpus and nodes (summarized PE) for each node when assigning resources.

The resource request feature nodes. If the request has no option for the number of PE per node (ppn) set, then the system assumes that the requested nodes is equal the number of PE's. The batch system allocates a number of nodes that in total fulfill the sum of requested PE.


Example: 

 qsub -l nodes=2:nehalem ./myscript

The batch system allocates two node of feature nehalem. The file ${PBS_NODEFILE} contains: 

 node1
 node2

The ressource request feature nodes, Option ppn. If the request has the option ppn defined, then it is possible to allocate the defined PE's on a node. This option especially allow OpenMPI to place the MPI processes of ranks on a shared node or alternatively on distributed nodes.


Example: 

 qsub -l nodes=2:nehalem:ppn=2+1:nehalem:ppn=3 ./myscript

The batch system allocates 2 nodes of feature nehalem each for 2 PE's and 1 node of feature nehalem for 3 PE's. Then the file ${PBS_NODEFILE} contains: 

 node1
 node1
 node2
 node2
 node3
 node3
 node3

The resource request feature nodes, option pmem. For special applications it will be useful to allocate only 1 PE per node. In this case you need a little trick, because the batch system handle the option ppn=1 like the requests without this option (see the first example). Therefore you have to define an additional option in your request. A simple way to do this is to request the maximum of the node's memory.


Example: 

 qsub -l nodes=2:nehalem,pmem=11gb ./myscript

The batch system allocates 2 nodes of feature nehalem. Each of the nodes with feature nehalem have 12GByte RAM installed, so the batch system is constrained to allocate 2 nodes. And the file ${PBS_NODEFILE} should look like this: 

 node1
 node2

Defaults for Ressource Requests

If you don't set the resources for your job request, then you will get default resource limits for your job.

feature value notes
walltime 00:10:00
nodes 1
ppn 1

Please select your resource requests carefull. The higher your specified resource limits the lower the job priority. See also NEC_Cluster_QueuePolicies_for_(laki_+_laki2).

To have the same environmental settings (exported environment) of your current session in your batchjob, the qsub command needs the option argument -V.

Run job on other Account ID

There are Unix groups associated to the project account ID (ACID). To run a job on a non-default project budget, the groupname of this project has to be passed in the group_list: 

qsub -l nodes=1:nehalem -W group_list=<groupname>

Usage of a Reservation

For nodes which are reserved for special groups or users, you need to specify an additional option for this reservation:

E.g. a reservation named john.1 will be used with following command:
qsub -l nodes=1:nehalem,walltime=1:00 -W x=FLAGS:ADVRES:john.1 testjob.cmd

Job Arrays

Job arrays are groups of simlar jobs. Those jobs usually have slightly different parameters which depend on the current job index. This job index will be available in the $PBS_ARRAYID variable, which can be used in job scripts to calculate or generate any kind of job-specific (input)data.

Job arrays can be requested with '-t <range>[%<count_of_parallel_processes>]'.

The range is specifed as list of comma separated values. The values may be individual integers as well as integer ranges, spaces are not allowed. A count of parallel running processes can be requested. It must be specificed as last in the array request and is delimited from the array range by a percent sign (%). For further details see the documentation.

In order to request a job array with job IDs 0,9,1000-1017 and restrict parallel running jobs to two you can use the following: 

 qsub -t 1,9,1000-1017%2 myJobScript

or inside the job script 

#!/bin/bash
#PBS -l nodes=1,walltime=00:01:00
#PBS -t 1,9,1000-1017%2

# Replace the following line with your own code
echo "This is job with id '$PBS_ARRAYID' running on compute node '`hostname`'";
exit 0;

In case the job id returned by qsub was '23' then the job array will result in showq-output similar to the following: 

active jobs------------------------
JOBID              USERNAME	 STATE PROCS   REMAINING            STARTTIME

23[1]              testuser    Running     1    00:00:57  Thu Dec 20 17:38:10
23[9]              testuser    Running     1    00:00:57  Thu Dec 20 17:38:10

2 active jobs               2 of 3 processors in use by local jobs (66.67%)

eligible jobs----------------------
JOBID              USERNAME	 STATE PROCS     WCLIMIT            QUEUETIME


0 eligible jobs

blocked jobs-----------------------
JOBID              USERNAME	 STATE PROCS     WCLIMIT            QUEUETIME

23[1000]           testuser	  Hold     1    00:01:00  Thu Dec 20 17:35:39
23[1001]           testuser	  Hold     1    00:01:00  Thu Dec 20 17:35:39
23[1002]           testuser	  Hold     1    00:01:00  Thu Dec 20 17:35:39
23[1003]           testuser	  Hold     1    00:01:00  Thu Dec 20 17:35:39
23[1004]           testuser	  Hold     1    00:01:00  Thu Dec 20 17:35:39
 ..
23[1017]           testuser	  Hold     1    00:01:00  Thu Dec 20 17:35:39

Examples

Examples for PBS options in job scripts

You can submit batch jobs using qsub. A very simple qsub script for a MPI job with PBS (Torque) directives (#PBS ...) for the options of qsub looks like this: 

#!/bin/bash
#
# Simple PBS batch script that reserves two cpus and runs one
# MPI process on each node)
# The default walltime is 10min !
#
#PBS -l nodes=2:nehalem
cd $HOME/testdir
mpirun -np 2 -hostfile $PBS_NODEFILE ./mpitest

VERY important is that you specify a shell in the first line of your batch script.

VERY important in case you use the openmpi module is to omit the -hostfile option. Otherwise an error will occur like 

[n110402:02618] pls:tm: failed to poll for a spawned proc, return status = 17002
[n110402:02618] [0,0,0] ORTE_ERROR_LOG: In errno in file ../../../../../orte/mca/rmgr/urm/rmgr_urm.c at line 462
[n110402:02618] mpirun: spawn failed with errno=-11


If you want to use two MPI processes on each node this can be done like this: 

#!/bin/bash
#
# Simple PBS batch script that reserves two nodes and runs a
# MPI program on four processors (two on each node)
# The default walltime is 10min !
#
#PBS -l nodes=2:nehalem:ppn=2
cd $HOME/testdir
mpirun -np 4 -hostfile machines ./mpitest

If you need 2h wall time and one node you can use the following script: 

#
# Simple PBS batch script that runs a scalar job using 2h
#
#PBS -l nodes=1:nehalem,walltime=2:00:00
cd $HOME/jobdir
./my_executable

Examples for starting batch jobs:

  • Starting a script with all options specified inside the script file 
    qsub <script>
  • Starting a script using 3 nodes and a real time of 2 hours: 
    qsub -l nodes=3:nehalem,walltime=2:00:00 <script>
  • Starting a script using 5 cluster nodes using 4 processors on each node with PBS Feature nehalem: 
    qsub -l nodes=5:nehalem:ppn=4,walltime=2:00:00 <script>
  • Starting a script using 1 cluster node with PBS Feature mem24gb and 5 processors with PBS Feature mem12gb and real job time of 1.5 hours: 
    qsub -l nodes=1:mem24gb+5:mem12gb,walltime=1:30:00 <script>
  • Starting a interactive batch job using 5 processors with a job real time of 300 seconds: 
    qsub -I -l nodes=5:nehalem,walltime=300

    For interactive Batch jobs, you don't need a script.sh file. If the requested resources are available, you will get an interactive shell on one of the allocated compute nodes. Which nodes are allocated can be shown with the command cat $PBS_NODEFILE on the batch job shell or with the PBS status command qstat -n on the master node.

    You can log in from the frontend or any assigned node to all other assigned nodes by 
    ssh <nodename>

    If you exit the automatically established interactive shell to the node, it will be assumed that you finished your job and all other connections to the nodes will be terminated.

  • Possibilities to request 4 cluster nodes (with feature 'nehalem' i.e. 32 processors). 
    qsub -l nodes=4:nehalem:ppn=8 <script>
    qsub -l nodes=4:nehalem:pmem=11gb <script>

    The difference between both job submisson kinds is in the content of PBS_NODEFILE.

  • Starting a script which should run on other Account ID: First you have to know which Account ID's (groupnames) are valid for your login: 
    id

    Choose a valid groupname for your job (abc12345 will serve as a placeholder here): 

    qsub -l nodes=5:nehalem,walltime=300 -W group_list=abc12345

Get the batch job status

Please, don't run the commands qstat or showq in a iteration loop using e.g. watch. Those commands will block all other users. You can use nstat in place of qstat or showq. This command uses a SQL database which will be updated every 3 minutes.

  • Available commands 
      qstat [options]
showq [options] (showq -h for details)
nstat

      For detailed informations, see man pages: 

      nstat -h
man qstat
man pbsnodes
  • Examples
      list all batch jobs: 
      qstat -a

      lists all batch queues with resource limit settings: 

      qstat -q

      lists node information of a batch job ID: 

      qstat -n <JOB_ID>

      lists detailed information of a batch job ID: 

      qstat -f <JOB_ID>

      lists information of the PBS node status: 

      pbsnodes -a
pbsnodes -l

      gives informatioin of PBS node and job status: 

      nstat

      DISPLAY: X11 applications on interactive batch jobs

      For X11 applications you need to have SSH X11 Forwarding enabled. This is usually activated per default. But to be sure you can set 'ForwardX11 yes' in your $HOME/.ssh/config. To have the same DISPLAY of your current session in your batchjob, the qsub command needs the option argument -X. 

      frontend> qsub -l nodes=2:nehalem,walltime=300 -X -I
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