sge_pe man page
sge_pe — Sun Grid Engine parallel environment configuration file format
Parallel environments are parallel programming and runtime environments allowing for the execution of shared memory or distributed memory parallelized applications. Parallel environments usually require some kind of setup to be operational before starting parallel applications. Examples for common parallel environments are shared memory parallel operating systems and the distributed memory environments Parallel Virtual Machine (PVM) or Message Passing Interface (MPI).
sge_pe allows for the definition of interfaces to arbitrary parallel environments. Once a parallel environment is defined or modified with the -ap or -mp options to qconf(1) and linked with one or more queues via pe_list in queue_conf(5) the environment can be requested for a job via the -pe switch to qsub(1) together with a request of a range for the number of parallel processes to be allocated by the job. Additional -l options may be used to specify the job requirement to further detail.
Note, Sun Grid Engine allows backslashes (\) be used to escape newline (\newline) characters. The backslash and the newline are replaced with a space (" ") character before any interpretation.
The format of a sge_pe file is defined as follows:
The name of the parallel environment as defined for pe_name in sge_types(1). To be used in the qsub(1) -pe switch.
The number of parallel processes being allowed to run in total under the parallel environment concurrently. Type is number, valid values are 0 to 9999999.
A comma separated list of user access list names (see access_list(5)). Each user contained in at least one of the enlisted access lists has access to the parallel environment. If the user_lists parameter is set to NONE (the default) any user has access being not explicitly excluded via the xuser_lists parameter described below. If a user is contained both in an access list enlisted in xuser_lists and user_lists the user is denied access to the parallel environment.
The xuser_lists parameter contains a comma separated list of so called user access lists as described in access_list(5). Each user contained in at least one of the enlisted access lists is not allowed to access the parallel environment. If the xuser_lists parameter is set to NONE (the default) any user has access. If a user is contained both in an access list enlisted in xuser_lists and user_lists the user is denied access to the parallel environment.
The invocation command line of a start-up procedure for the parallel environment. The start-up procedure is invoked by sge_shepherd(8) prior to executing the job script. Its purpose is to setup the parallel environment correspondingly to its needs. An optional prefix "user@" specifies the user under which this procedure is to be started. The standard output of the start-up procedure is redirected to the file REQNAME.poJID in the job's working directory (see qsub(1)), with REQNAME being the name of the job as displayed by qstat(1) and JID being the job's identification number. Likewise, the standard error output is redirected to REQNAME.peJID
The following special variables being expanded at runtime can be used (besides any other strings which have to be interpreted by the start and stop procedures) to constitute a command line:
The pathname of a file containing a detailed description of the layout of the parallel environment to be setup by the start-up procedure. Each line of the file refers to a host on which parallel processes are to be run. The first entry of each line denotes the hostname, the second entry the number of parallel processes to be run on the host, the third entry the name of the queue, and the fourth entry a processor range to be used in case of a multiprocessor machine.
The name of the host on which the start-up or stop procedures are started.
The user name of the job owner.
Sun Grid Engine's unique job identification number.
The name of the job.
The name of the parallel environment in use.
Number of slots granted for the job.
The processors string as contained in the queue configuration (see queue_conf(5)) of the master queue (the queue in which the start-up and stop procedures are started).
The cluster queue of the master queue instance.
The invocation command line of a shutdown procedure for the parallel environment. The shutdown procedure is invoked by sge_shepherd(8) after the job script has finished. Its purpose is to stop the parallel environment and to remove it from all participating systems. An optional prefix "user@" specifies the user under which this procedure is to be started. The standard output of the stop procedure is also redirected to the file REQNAME.poJID in the job's working directory (see qsub(1)), with REQNAME being the name of the job as displayed by qstat(1) and JID being the job's identification number. Likewise, the standard error output is redirected to REQNAME.peJID
The same special variables as for start_proc_args can be used to constitute a command line.
The allocation rule is interpreted by the scheduler thread and helps the scheduler to decide how to distribute parallel processes among the available machines. If, for instance, a parallel environment is built for shared memory applications only, all parallel processes have to be assigned to a single machine, no matter how much suitable machines are available. If, however, the parallel environment follows the distributed memory paradigm, an even distribution of processes among machines may be favorable.
The current version of the scheduler only understands the following allocation rules:
An integer number fixing the number of processes per host. If the number is 1, all processes have to reside on different hosts. If the special denominator $pe_slots is used, the full range of processes as specified with the qsub(1) -pe switch has to be allocated on a single host (no matter which value belonging to the range is finally chosen for the job to be allocated).
Starting from the best suitable host/queue, all available slots are allocated. Further hosts and queues are "filled up" as long as a job still requires slots for parallel tasks.
From all suitable hosts a single slot is allocated until all tasks requested by the parallel job are dispatched. If more tasks are requested than suitable hosts are found, allocation starts again from the first host. The allocation scheme walks through suitable hosts in a best-suitable-first order.
This parameter can be set to TRUE or FALSE (the default). It indicates whether Sun Grid Engine is the creator of the slave tasks of a parallel application via sge_execd(8) and sge_shepherd(8) and thus has full control over all processes in a parallel application, which enables capabilities such as resource limitation and correct accounting. However, to gain control over the slave tasks of a parallel application, a sophisticated PE interface is required, which works closely together with Sun Grid Engine facilities. Such PE interfaces are available through your local Sun Grid Engine support office.
Please set the control_slaves parameter to false for all other PE interfaces.
The job_is_first_task parameter can be set to TRUE or FALSE. A value of TRUE indicates that the Sun Grid Engine job script already contains one of the tasks of the parallel application (the number of slots reserved for the job is the number of slots requested with the -pe switch), while a value of FALSE indicates that the job script (and its child processes) is not part of the parallel program (the number of slots reserved for the job is the number of slots requested with the -pe switch + 1).
If wallclock accounting is used (execd_params ACCT_RESERVED_USAGE and/or SHARETREE_RESERVED_USAGE set to TRUE) and control_slaves is set to FALSE, the job_is_first_task parameter influences the accounting for the job: A value of TRUE means that accounting for cpu and requested memory gets multiplied by the number of slots requested with the -pe switch, if job_is_first_task is set to FALSE, the accounting information gets multiplied by number of slots + 1.
For pending jobs with a slot range PE request the number of slots is not determined. This setting specifies the method to be used by Sun Grid Engine to assess the number of slots such jobs might finally get.
The assumed slot allocation has a meaning when determining the resource-request-based priority contribution for numeric resources as described in sge_priority(5) and is displayed when qstat(1) is run without -g t option.
The following methods are supported:
The specified integer number is directly used as prospective slot amount.
The slot range minimum is used as prospective slot amount. If no lower bound is specified with the range 1 is assumed.
The of the slot range maximum is used as prospective slot amount. If no upper bound is specified with the range the absolute maximum possible due to the PE's slots setting is assumed.
The average of all numbers occurring within the job's PE range request is assumed.
This parameter is only checked if control_slaves (see above) is set to TRUE and thus Sun Grid Engine is the creator of the slave tasks of a parallel application via sge_execd(8) and sge_shepherd(8). In this case, accounting information is available for every single slave task started by Sun Grid Engine.
The accounting_summary parameter can be set to TRUE or FALSE. A value of TRUE indicates that only a single accounting record is written to the accounting(5) file, containing the accounting summary of the whole job including all slave tasks, while a value of FALSE indicates an individual accounting(5) record is written for every slave task, as well as for the master task.
Note: When running tightly integrated jobs with SHARETREE_RESERVED_USAGE set, and with having accounting_summary enabled in the parallel environment, reserved usage will only be reported by the master task of the parallel job. No per parallel task usage records will be sent from execd to qmaster, which can significantly reduce load on qmaster when running large tightly integrated parallel jobs.
Note, that the functionality of the start-up, shutdown and signaling procedures remains the full responsibility of the administrator configuring the parallel environment. Sun Grid Engine will just invoke these procedures and evaluate their exit status. If the procedures do not perform their tasks properly or if the parallel environment or the parallel application behave unexpectedly, Sun Grid Engine has no means to detect this.
sge_intro(1), sge__types(1), qconf(1), qdel(1), qmod(1), qsub(1), access_list(5), sge_qmaster(8), sge_shepherd(8).
See sge_intro(1) for a full statement of rights and permissions.
qconf(1), qmake-ge(1), qmon(1), qrsub(1), sge_access_list(5), sge_queue_conf(5), sge_resource_quota(5), sge_sched_conf(5), sge_shepherd(8), sge_types(1), submit(1).