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| abstract:farber:runjobs:schedule_jobs [2019-02-19 10:32] – [Array jobs] anita | abstract:farber:runjobs:schedule_jobs [2019-02-22 11:36] – [Memory] ssunkara |
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| For memory you will be concerned about how much is free. Memory resources come as both consumable and sensor driven (not consumable). For example: | For memory you will be concerned about how much is free. Memory resources come as both consumable and sensor driven (not consumable). For example: |
| ^ memory resource ^ Consumable ^ Explanation ^ | ^ memory resource ^ Consumable ^ Explanation ^ |
| | mem_free | No |Memory that must be available BEFORE job can start | | | m_mem_free | Yes |Memory consumed per CPU DURING execution | |
| | m_mem_free | Yes |Memory consumed by the job DURING execution | | |
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| It is usually a good idea to add both resources. The ''mem_free'' complex is sensor driven, and is more reliable for choosing a node for your job. The ''m_mem_free'' is consumable, which means you are reserving the memory for future use. Other jobs, using ''m_mem_free'', may be barred from starting on the node. If you are specifying memory resources for a parallel environment job, the requested memory is multiplied by the slot count. By default, ''m_mem_free'' is defined as 1GB of memory per core (slot), if not specified. | The ''m_mem_free'' is consumable, which means you are reserving the memory for future use. Other jobs, using ''m_mem_free'', may be barred from starting on the node. If you are specifying memory resources for a parallel environment job, the requested memory is multiplied by the slot count. By default, ''m_mem_free'' is defined as 1GB of memory per core (slot), if not specified. |
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| <note tip>When using a shared memory parallel computing environment ''-pe threads'', divide the total memory needed by the number of slots. For example, to request 48G of shared memory for an 8 thread job, request 6G (6G per slot).</note> | <note tip>When using a shared memory parallel computing environment ''-pe threads'', divide the total memory needed by the number of slots. For example, to request 48G of shared memory for an 8 thread job, request 6G (6G per slot) i.e.,'-l m_mem_free=6G'</note> |
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| <note warning>Please note a job error will occur and prevent the queue from accepting jobs when: | <note warning>Please note a job error will occur and prevent the queue from accepting jobs when: |
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| <code> | <code> |
| qsub -l mem_free=20G,m_mem_free=20G -t 1-30 myjob.qs | qsub -l m_mem_free=20G -t 1-30 myjob.qs |
| </code> | </code> |
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| This will submit 30 jobs to the queue, with the SGE_TASK_ID variable set for use in the ''myjobs.qs'' script (an [[general:userguide:06_runtime_environ?&#array-jobs|array job]].) | This will submit 30 jobs to the queue, with the SGE_TASK_ID variable set for use in the ''myjobs.qs'' script (an [[:abstract:farber:runjobs:schedule_jobs#array-jobs|array job]].) |
| The ''mem_free'' resource will cause Grid Engine to find a node (or wait until one is available) with 20 Gbytes of memory free. | The ''m_mem_free'' resource will tell Grid Engine to not schedule a job on a node unless the specified amount of memory i.e., 20GB per CPU is available to consume on that node. Since this is a serial job that runs on a single CPU,20GB can be termed as total memory available for the job. |
| The ''m_mem_free'' resource will tell Grid Engine to not schedule a job on a node unless the specified amount of memory is available to consume on that node. | |
| ==== Parallel environments ==== | ==== Parallel environments ==== |
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| === The threads parallel environment === | === The threads parallel environment === |
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| Jobs such as those having openMP directives use the **//threads//** parallel environment, an implementation of the [[:general:userguide:05_development#programming-models|shared-memory programming model]]. These SMP jobs can only use the cores on a **single** node. | Jobs such as those having openMP directives use the **//threads//** parallel environment, an implementation of the [[:abstract:farber:app_dev:prog_env#programming-models|shared-memory programming model]]. These SMP jobs can only use the cores on a **single** node. |
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| For example, if your group only owns nodes with 24 cores, then your ''–pe threads'' request may only ask for 24 or fewer slots. Use Grid Engine's **qconf** command to determine the names and characteristics of the queues and compute nodes available to your investing-entity group on a cluster. | For example, if your group only owns nodes with 24 cores, then your ''–pe threads'' request may only ask for 24 or fewer slots. Use Grid Engine's **qconf** command to determine the names and characteristics of the queues and compute nodes available to your investing-entity group on a cluster. |