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TechDarting TechDarting Propelling Technology ≡TechDarting Home ▼ About-Us Contact-us Advertise Sitemap Parallel Programming Linux Android Programming Languages Thursday, 4 June 2015 PBS Pro Tutorial Posted by Krishna Arutwar at Thursday, June 04, 2015 What is PBS Pro? Portable Batch System (PBS) is a software which is used in cluster computing to schedule jobs on multiple nodes. PBS was started as contract project by NASA. PBS is available in three different versions as below 1) Torque: Terascale Open-source Resource and QUEue Manager (Torque) is developed from OpenPBS. It is developed and maintain by Adaptive Computing Enterprises. It is used as a distributed resource manager can perform well when integrated with Maui cluster scheduler to improve performance. 2) PBS Professional (PBS Pro): It is commercial version of PBS offered by Altair Engineering. 3) OpenPBS: It is open source version released in 1998 developed by NASA. It is not actively developed. In this article we are going to concentrate on tutorial of PBS Pro it is similar to some extent with Torque. Fig. 1.1 PBS complex cluster with eight execution host PBS contain three basic units server, MoM (execution host), scheduler. 1) Server: It is heart of the PBS, with executable named “pbs_server”. It uses IP network to communicate with the MoMs. PBS server create a batch job, modify the job requested from different MoMs. It keeps track of all resources available, assigned in the PBS complex from different MoMs. It will also monitor the PBS license for jobs. If your license expires it will throw an error. 2) Scheduler: PBS scheduler uses various algorithms to decide when job should get executed on which node or vnode by using detail of resources available from server. It has executable as “pbs_sched”. 3) MoM: MoM is the mother of all execution job with executable “pbs_mom”. When MoM gets job from server it will actually execute that job on the host. Each node must have MoM running to get participate in execution. Installation and Setting up of environment (cluster with multiple nodes) Extract compressed software of PBS Pro and go the path of extracted folder it contain “INSTALL” file, make that file executable you may use command like “chmod +x ./INSTALL”. As shown in the image below run this executable. It will ask for the “execution directory” where you want to store the executable (such as qsub, pbsnodes, qdel etc.) used for different PBS operations and “home directory” which contain different configuration files. Keep both as default for simplicity. There are three kind of installation available as shown in figure: Fig. 1.2 PBS installation 1) Server node: PBS server, scheduler, MoM and commands are installed on this node. PBS server will keep track of all execution MoMs present in the cluster. It will schedule jobs on this execution nodes. As MoM and commands are also installed on server node it can be used to submit and execute the jobs. 2) Execution node: This type installs MoM and commands. This nodes are added as available nodes for execution in a cluster. They are also allowed to submit the jobs at server side with specific permission by server as we are going to see below. They are not involved in scheduling. This kind of installation ask for PBS server which is used to submit jobs, get status of jobs etc. 3) Client node: This are the nodes which are only allowed to submit a PBS job at server with specific permission by the server and allowed to see the status of the jobs. They are not involved in execution or scheduling. Creating vnode in PBS Pro: We can create multiple vnodes in a single node which contain some part of resources in a node. We can execute job on this vnodes with specified allocated resources. We can create vnode using qmgr command which is command line interface to PBS server. We can use command given below to create vnode using qmgr. Qmgr: create node Vnode1,Vnode2 resources_available.ncpus=8, resources_available.mem=10gb,? resources_available.ngpus=1, sharing=default_excl? The command above will create two vnodes named Vnode1 and Vnode2 with 8 cpus cores, 10gb of memory and 1 GPU with sharing mode as default_excl which means this vnode can execute exclusively only one job at a time independent of number of resources free. This sharing mode can be default_shared which means any number of jobs can run on that vnode until all resources are busy. To know more about all attributes which can be used with vnode creation are available in PBS Pro reference guide. You can also create a file in "/var/spool/PBS/mom_priv/config.d/" this folder with any name you want I prefer hostname-vnode with sample given below. It will select all files even temporary files with (~) and replace configuration for same vnode so delete unnecessary files to get proper configuration of vnodes. e.g. $configversion 2 hostname:resources_available.ncpus=0hostname:resources_available.mem=0hostname:resources_available.ngpus=0hostname[0]:resources_available.ncpus=8 ?hostname[0]:resources_available.mem=16gbhostname[0]:resources_available.ngpus=1 hostname[0]:sharing=default_exclhostname[1]:resources_available.ncpus=8hostname[1]:resources_available.mem=16gbhostname[1]:resources_available.ngpus=1 hostname[1]:sharing=default_exclhostname[2]:resources_available.ncpus=8hostname[2]:resources_available.mem=16gbhostname[2]:resources_available.ngpus=1 hostname[2]:sharing=default_exclhostname[3]:resources_available.ncpus=8hostname[3]:resources_available.mem=16gbhostname[3]:resources_available.ngpus=1 hostname[3]:sharing=default_excl Here in this example we assigned default node configuration to resource available as 0 because by default it will detect and allocate all available resources to default node with sharing attribute as is default_shared. Which cause problem as all the jobs will by default get scheduled on that default vnode because its sharing type is default_shared. If you want to schedule jobs on your customized vnodes you should allocate resources available as 0 on default vnode. Every time whenever you restart the PBS server this vnodes get create unlike vnodes created manually using command line. PBS get status: get status of Jobs: qstat will give details about jobs there states etc. useful options: To print detail about all jobs which are running or in hold state: qstat -a To print detail about subjobs in JobArray which are running or in hold state: qstat -ta To print all finished jobs: qstat -x get status of PBS nodes and vnodes: "pbsnode -a" command will provide list of all nodes present in PBS complex with there resources available, assigned, status etc. To get details of all nodes and vnodes you created use "pbsnodes -av" command. You can also specify node or vnode name to get detail information of that specific node or vnode. e.g. pbsnodes wolverine (here wolverine is hostname of the node in PBS complex which is mapped with IP address in /etc/hosts file) Job submission (qsub): PBS MoM will submit jobs to the ...

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