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tutorial:torque [2017/04/08 15:04] sertalpbilal [Options] |
tutorial:torque [2023/12/07 09:34] mjm519 [Useful MOAB Commands] |
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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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==== 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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However, first you have to have a permission to use GPU (given by Prof. Takac) -- this is just formality to allow to certain users to use video driver on polyp30 | However, first you have to have a permission to use GPU (given by Prof. Takac) -- this is just formality to allow to certain users to use video driver on polyp30 | ||
+ | |||
+ | If you are using TensorFlow in Python, you can set the limit on amount of GPU memory using: | ||
+ | < | ||
+ | config_tf.gpu_options.per_process_gpu_memory_fraction = p</ | ||
+ | in which **//p//** is the percent of GPU memory (a number between zero and one). | ||
==== Running MPI and Parallel Jobs ==== | ==== Running MPI and Parallel Jobs ==== | ||
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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:// |