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abstract:farber:runjobs:queues [2018-10-08 16:00] – anita | abstract:farber:runjobs:queues [2018-10-08 16:01] (current) – anita | ||
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==== Mapping jobs to nodes ==== | ==== Mapping jobs to nodes ==== | ||
+ | |||
Once Grid Engine determines the appropriate standby queue, it maps the job to available, idle, nodes (hosts) to fill all the slots. For openmpi jobs, Grid Engine is configured to use the //fill up// allocation rule, by default. | Once Grid Engine determines the appropriate standby queue, it maps the job to available, idle, nodes (hosts) to fill all the slots. For openmpi jobs, Grid Engine is configured to use the //fill up// allocation rule, by default. | ||
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| | ||
</ | </ | ||
- | |||
- | ===== Farber Exclusive access ===== | ||
- | |||
- | If a job is submitted with the '' | ||
- | |||
- | * promote any serial jobs to 20-core threaded (-pe threads 20) | ||
- | * modify any parallel jobs to round-up the slot count to the nearest multiple of 20 | ||
- | * ignore any memory resources and make all memory available on all nodes assigned to the job | ||
- | |||
- | A job running on a node with '' | ||
- | |||
- | Job script example: | ||
- | <code bash> | ||
- | # | ||
- | # The exclusive flag asks to run this job only on all nodes required to fulfill requested slots | ||
- | #$ -l exclusive=1 | ||
- | # | ||
- | # This job needs an openmpi parallel environment using 32 slots = 2 nodes exclusively. | ||
- | #$ -pe openmpi 32 | ||
- | # | ||
- | # By default the slot count granted by Grid Engine will be | ||
- | # used, one MPI worker per slot. Set this variable if you | ||
- | # want to use fewer cores than Grid Engine granted you (e.g. | ||
- | # when using exclusive=1): | ||
- | # | ||
- | # | ||
- | |||
- | ... | ||
- | </ | ||
- | |||
- | <note tip>In the script example, this job would be rounded up to 40 and would be assigned 2 nodes. If you really want your job to run with only 32 slots, uncomment and set '' | ||
- | |||
- | Grid Engine is configured to "fill up" nodes by allocating as many slots as possible before proceeding to another node to fulfill the total number of requested slots for the job. Unfortunately, | ||
- | |||
- | To assure that your job will be the only job running on a node (or all nodes needed to satisfy the slots requested), specify the '' | ||
- | |||
- | <code text> | ||
- | qsub -l exclusive=1 ... | ||
- | </ | ||
- | |||
- | |||
- | If a job is submitted with the general resource, Grid Engine will | ||
- | |||
- | * promote any serial jobs to 20-core threaded (-pe threads 20) | ||
- | * modify any parallel jobs to round-up the slot count to the nearest multiple of 20 | ||
- | * ignore any memory resources and make all memory available on all nodes assigned to the job | ||
- | |||
- | A job running on a node with '' | ||
- | |||
- | Job script example: | ||
- | <code bash> | ||
- | # | ||
- | # The exclusive flag asks to run this job only on all nodes required to fulfill requested slots | ||
- | #$ -l exclusive=1 | ||
- | # | ||
- | # This job needs an openmpi parallel environment using 32 slots = 2 nodes exclusively. | ||
- | #$ -pe openmpi 32 | ||
- | # | ||
- | # By default the slot count granted by Grid Engine will be | ||
- | # used, one MPI worker per slot. Set this variable if you | ||
- | # want to use fewer cores than Grid Engine granted you (e.g. | ||
- | # when using exclusive=1): | ||
- | # | ||
- | # | ||
- | |||
- | ... | ||
- | </ | ||
- | |||
- | <note tip>In the script example, this job would be rounded up to 40 and would be assigned 2 nodes. If you really want your job to run with only 32 slots, uncomment and set '' | ||
- | |||
==== Actions at the run-time limit ===== | ==== Actions at the run-time limit ===== | ||
Line 313: | Line 244: | ||
The first '' | The first '' | ||
+ | ===== Farber Exclusive access ===== | ||
+ | |||
+ | If a job is submitted with the '' | ||
+ | |||
+ | * promote any serial jobs to 20-core threaded (-pe threads 20) | ||
+ | * modify any parallel jobs to round-up the slot count to the nearest multiple of 20 | ||
+ | * ignore any memory resources and make all memory available on all nodes assigned to the job | ||
+ | |||
+ | A job running on a node with '' | ||
+ | |||
+ | Job script example: | ||
+ | <code bash> | ||
+ | # | ||
+ | # The exclusive flag asks to run this job only on all nodes required to fulfill requested slots | ||
+ | #$ -l exclusive=1 | ||
+ | # | ||
+ | # This job needs an openmpi parallel environment using 32 slots = 2 nodes exclusively. | ||
+ | #$ -pe openmpi 32 | ||
+ | # | ||
+ | # By default the slot count granted by Grid Engine will be | ||
+ | # used, one MPI worker per slot. Set this variable if you | ||
+ | # want to use fewer cores than Grid Engine granted you (e.g. | ||
+ | # when using exclusive=1): | ||
+ | # | ||
+ | # | ||
+ | |||
+ | ... | ||
+ | </ | ||
+ | |||
+ | <note tip>In the script example, this job would be rounded up to 40 and would be assigned 2 nodes. If you really want your job to run with only 32 slots, uncomment and set '' | ||
+ | |||
+ | Grid Engine is configured to "fill up" nodes by allocating as many slots as possible before proceeding to another node to fulfill the total number of requested slots for the job. Unfortunately, | ||
+ | |||
+ | To assure that your job will be the only job running on a node (or all nodes needed to satisfy the slots requested), specify the '' | ||
+ | |||
+ | <code text> | ||
+ | qsub -l exclusive=1 ... | ||
+ | </ | ||
+ | |||
+ | |||
+ | If a job is submitted with the general resource, Grid Engine will | ||
+ | |||
+ | * promote any serial jobs to 20-core threaded (-pe threads 20) | ||
+ | * modify any parallel jobs to round-up the slot count to the nearest multiple of 20 | ||
+ | * ignore any memory resources and make all memory available on all nodes assigned to the job | ||
+ | |||
+ | A job running on a node with '' | ||
+ | |||
+ | Job script example: | ||
+ | <code bash> | ||
+ | # | ||
+ | # The exclusive flag asks to run this job only on all nodes required to fulfill requested slots | ||
+ | #$ -l exclusive=1 | ||
+ | # | ||
+ | # This job needs an openmpi parallel environment using 32 slots = 2 nodes exclusively. | ||
+ | #$ -pe openmpi 32 | ||
+ | # | ||
+ | # By default the slot count granted by Grid Engine will be | ||
+ | # used, one MPI worker per slot. Set this variable if you | ||
+ | # want to use fewer cores than Grid Engine granted you (e.g. | ||
+ | # when using exclusive=1): | ||
+ | # | ||
+ | # | ||
+ | |||
+ | ... | ||
+ | </ | ||
+ | |||
+ | <note tip>In the script example, this job would be rounded up to 40 and would be assigned 2 nodes. If you really want your job to run with only 32 slots, uncomment and set '' |