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tutorial:torque [2017/06/08 22:48] afo214 |
tutorial:torque [2024/02/28 13:12] mjm519 [Table] |
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| polyp1--polyp15 | | polyp1--polyp15 | ||
| polyp30 | 24 Intel(R) Xeon(R) CPU E5-2620 v3 @ 2.40GHz | 128 GB | 2x K80 (4GPUs) | | | polyp30 | 24 Intel(R) Xeon(R) CPU E5-2620 v3 @ 2.40GHz | 128 GB | 2x K80 (4GPUs) | | ||
+ | |||
+ | |||
+ | Configured Resources as provided in the Maui scheduler. This is pulled from Torque: | ||
+ | PROCS: 16 | ||
+ | MEM: 31G | ||
+ | SWAP: 63G | ||
===== Submitting Jobs ===== | ===== Submitting Jobs ===== | ||
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#PBS -o / | #PBS -o / | ||
#PBS -l nodes=1: | #PBS -l nodes=1: | ||
+ | #PBS -l pmem=2GB: | ||
#PBS -q batch | #PBS -q batch | ||
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</ | </ | ||
If you do not want to write the submission script you can do it just by calling | If you do not want to write the submission script you can do it just by calling | ||
- | < | + | < |
Now, we will run the code but we are setting the job parameters using '' | Now, we will run the code but we are setting the job parameters using '' | ||
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We have few queues '' | We have few queues '' | ||
< | < | ||
- | Queue | + | Queue |
- | ---------------- ------ -------- -------- ---- | + | ---------------- |
- | gpu -- -- | + | MOSEK |
- | medium | + | AMPL |
- | short -- -- | + | long 30 1 |
- | long | + | gpu 4 |
- | batch | + | verylong |
- | verylong | + | medium |
- | AMPL | + | coraverylong |
- | MOSEK -- -- | + | special |
+ | batch | ||
+ | short 0 | ||
+ | urgent | ||
+ | background | ||
+ | mediumlong | ||
</ | </ | ||
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You can see limits using this command '' | You can see limits using this command '' | ||
- | ^ Queue ^ Wall Time ^ | + | ^ Queue |
- | | batch | 01: | + | | urgent |
- | | short | 02: | + | | batch | 01: |
- | | medium | 04: | + | | short |
- | | long | 72: | + | | medium |
- | | very long | + | | mediumlong |
+ | | long | 72: | ||
+ | | verylong | ||
+ | | special | ||
+ | | background | ||
+ | | gpu | ||
+ | | AMPL | | 200 | 8 | 6 | ||
+ | | MOSEK | ||
+ | |||
+ | |||
+ | Notes: | ||
+ | * Urgent queue has no limits and jobs have a higher priority over all other jobs in the queues. Please be respectful of others if using this queue to complete time sensitive or critical jobs. | ||
+ | * background queue has no limits and jobs have a lower priority over all other jobs in the queues. | ||
===== Examples ===== | ===== Examples ===== | ||
==== Submitting a Small or Large Memory Job ==== | ==== Submitting a Small or Large Memory Job ==== | ||
- | You can use the option '' | + | You can use the option '' |
<code bash limited.sh> | <code bash limited.sh> | ||
- | qsub -l mem=4gb, | + | qsub -l pmem=4gb, |
</ | </ | ||
Sometimes your job needs more memory. You can choose a larger memory size with the same option: | Sometimes your job needs more memory. You can choose a larger memory size with the same option: | ||
- | <code bash large.pbs> | + | <code bash large.pbs> |
+ | |||
+ | To see what resources have been assigned by the batch queuing system run the ulimit command (bash) or limit comamnd: | ||
+ | <code bash pbs job submission command> | ||
+ | <code bash ulimit> | ||
+ | core file size (blocks, -c) 0 | ||
+ | data seg size | ||
+ | scheduling priority | ||
+ | file size | ||
+ | pending signals | ||
+ | max locked memory | ||
+ | max memory size | ||
+ | open files (-n) 65536 | ||
+ | pipe size (512 bytes, -p) 8 | ||
+ | POSIX message queues | ||
+ | real-time priority | ||
+ | stack size (kbytes, -s) unlimited | ||
+ | cpu time | ||
+ | max user processes | ||
+ | virtual memory | ||
+ | file locks (-x) unlimited</ | ||
+ | **[[https:// | ||
==== Running MATLAB ==== | ==== Running MATLAB ==== | ||
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#PBS -o / | #PBS -o / | ||
#PBS -l nodes=1: | #PBS -l nodes=1: | ||
+ | #PBS -l pmem=2GB: | ||
#PBS -q batch | #PBS -q batch | ||
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</ | </ | ||
and then schedule your jobs with Torque to perform experiments on GPU 1. | and then schedule your jobs with Torque to perform experiments on GPU 1. | ||
+ | |||
+ | |||
+ | ====== MOAB Scheduler ====== | ||
+ | PBS Torque is used to schedule and run jobs on our cluster. Two PBS processes are required to run jobs. On the PBS server, the pbs_server process runs to accept your job and add it to the queue. It will also dispatch the job to the nodes to run under the pbs_mom process. | ||
+ | |||
+ | |||
+ | ==== Useful MOAB Commands ==== | ||
+ | 1. [[https:// | ||
+ | |||
+ | 2. [[https:// | ||
+ | |||
+ | 3. [[https:// | ||
+ | |||
+ | ====Useful External Resources==== | ||
+ | [[https:// | ||
+ | |||
+ | [[https:// | ||
+ | |||
+ | [[http:// | ||
+ | |||
+ | [[https:// | ||
+ | |||
+ |