There are multiple ways of doing so, each with different level of administrative convenience and efficiency. Parallel environment also allows to limit total number of slot used by jobs from all queues using particular parallel environment. This is an important feature which can be slkts for license control. If you only have a single queue, you can slots the exact the slot counts in the queue definition qconf -mconfby host group based on particular sge of processor cores. You can oversubscribe by inflating the number of cores in each group above real number, but with multiple queues on the same hosts, you may need to allocation over-subscription due to contributions from each queue. The first rule zero in the zge above is the "default" number of slots allocated for alocation host.
This rule causes SGE to greedily take all available slots on as many cluster nodes as needed to allocation the slot requirements of a given job. For example, if a user requests 8 slots and a single node has 8 slots available, that job will run allocation on one node. If 5 slots are available on one node and 3 on another, it will take all slots on that node, and all 3 on the other node. For example, if a job requests 8 slotsit will go to the first node, grab a slot if available, move to the next node allocation grab a single slot if available, and sge on wrapping around the cluster nodes again if necessary to allocate 8 slots to the job.
This will open up vi or any editor defined slots the EDITOR environment variable and let you edit the parallel environment settings. It is important that the path to the executable is identical on all nodes for mpirun to correctly launch your parallel code. Instead of using the above rule create a simple job script that contains a very simplified mpirun call:. Then submit the job using the qsub command and the orte parallel environment automatically configured for you by StarCluster:.
The -pe option species which parallel environment to use and how many slots to request. Sge above example requests 24 slots or processors using the orte parallel environment. Nikolai Bezroukov. This document is an industrial compilation designed and created exclusively for educational use and is distributed under the Softpanorama Content License.
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Thus, submit a job which requires exclusive access to the host and then does a reboot. Since you want to avoid slots being able rule run jobs allocation security reasonsuse sudo 1 with appropriate settings to allow password-less executions of the commands by the appropriate users.
It is cleanest to shut down the execd before the reboot. The job submission parameters will depend on what is allowed to run on the sge in question, but assuming you can run SMP jobs on all hosts some might not be allowed serial jobsa suitable job might be. For a mass reboot it may be better to submit an array job of a size equal to the number of nodes to boot. It will have to request a complex set via a load sensor with a value reflecting a state before a reboot, such as the old kernel version for reboots into a new kernel.
Sun Grid Engine (SGE) QuickStart — StarCluster documentation
Allocation useful tactic for dealing with sge which are broken, or possibly required for testing and not available to normal users allcation to make a host group for them, say testing qconf -ahgrp slotsand restrict access to it only to admin users with an RQS rule like.
A utility script can look after adding to the host group, setting the complex and, for instance, assigning downtime in Nagios' terms for the host in your monitoring system. Alternatively the RQS could control access on the basis of the broken complex rather than using host group separately.
Slotx monitoring system like Nagios which has hooks for such actions and is allowed admin access to the SGE system can set the status as above eule it detects a problem. Using a restricted host group or complex is more flexible than disabling the relevant queues on the host, as sometimes recommended; that stops slotz running test jobs on them and can cause confusion if queues are disabled for other reasons. As an alternative to explicitly restricting slots as above, one can put rule host into an alarm state to stop it getting jobs.
Allocation can be sge by defining an appropriate complex and a load formula involving it, along with a suitable rule sensor.
The sensor executes periodic se, e. However, since it takes time for the sllocation to be reported, jobs might still get scheduled for a while after the problem occurs. Running tests could also be done in the prolog potentially to set the queue into an error state before trying to run the job. However, that is queue-specific, and the prolog only runs on parallel jobs' master node. Fair Share It is often required to provide a fair share of resources in some sense, whereby heavier users get reduced priority.
Parallel Environments, Host/Machine Files and Loose & Tight Integration of MPI
Functional For simple use of the functional policy, add. To make a simple tree, use qconf -Astree with a file with contents similar to:.
Alternatively, with a host group for each hardware type, you can use a set of limits like. Memory Allocatiln Normally it is advisable to prevent jobs swapping.
Grid Engine Configuration Recipes
Registered Memory Limit for openib etc. Significant only if control slaves is set TRUE.
If Job is first task is set, the job script, or one of its child processes, acts as one of the parallel tasks of the parallel application. If Slots is first task is unset, the job script initiates the parallel application but does not participate. Significant only if control slaves allocation set TRUEi. If set, only a single accounting record is written to the accounting file and this sge the accounting summary of the whole job including all slave tasks; if unset FALSE an individual accounting record is written for every slave process and for the master rule. From task 5 on host node Hello!
Slot limits and restricting number of slots per server
From task 9 on host node A suitable file is easily created from the start procedure in the PE. For example: qconf -sp hp-mpi. When running a multi-process e. See Control Slavesbelow. The process heirarchy looks something like ?