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tutorial:torque [2016/11/10 14:59] sertalpbilal Change of Order |
tutorial:torque [2023/10/25 13:50] mjm519 [Submitting a Small or Large Memory Job] |
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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 '' | ||
- | ===== Important | + | ===== Options ===== |
+ | ^ Option | ||
+ | | '' | ||
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- | * '' | + | You can find detailed information |
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- | + | ||
- | See [[http:// | + | |
+ | <note tip>You need to use option '' | ||
===== Monitoring and Removing jobs ===== | ===== Monitoring and Removing jobs ===== | ||
To show the jobs use '' | To show the jobs use '' | ||
< | < | ||
- | To show jobs of some user use '' | + | To show jobs of some user use '' |
+ | <code shell> | ||
+ | qdel JOB_ID | ||
+ | </ | ||
+ | Moreover, you can use the following command: | ||
+ | < | ||
+ | < | ||
+ | < | ||
==== Queues ==== | ==== Queues ==== | ||
- | We have few queues '' | + | We have few queues '' |
< | < | ||
Queue Memory CPU Time Walltime Node Run Que Lm State | Queue Memory CPU Time Walltime Node Run Que Lm State | ||
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| very long | 240:00:00 | | | very long | 240:00:00 | | ||
- | ==== Examples ==== | + | ===== Examples |
- | === Submitting Large Memory Job === | + | ==== Submitting |
- | Sometimes your job needs more memory. This can be achieved by '' | + | You can use the option |
- | < | + | |
- | === Running MATLAB | + | <code bash limited.sh> |
+ | qsub -l pmem=4gb,vmem=4gb test.pbs | ||
+ | </ | ||
+ | |||
+ | Sometimes your job needs more memory. You can choose a larger memory size with the same option: | ||
+ | |||
+ | <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 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</ | ||
+ | ==== Running MATLAB ==== | ||
You just have to create a submission job which looks like this | You just have to create a submission job which looks like this | ||
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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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</ | </ | ||
- | === Interactive Jobs === | + | <note tip>Use **-singleCompThread** [[https:// |
+ | ==== Running Solvers ==== | ||
+ | |||
+ | In order to run solvers (such as Gurobi/ | ||
+ | |||
+ | < | ||
+ | |||
+ | This flag enables the solver to find necessary authentication information. | ||
+ | |||
+ | ==== Interactive Jobs ==== | ||
If you do not care where you run your job just use '' | If you do not care where you run your job just use '' | ||
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and you will be running interactive session on polyp15. | and you will be running interactive session on polyp15. | ||
- | === Using GPU's === | + | ==== Using GPU' |
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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 | ||
- | === Running MPI and Parallel Jobs === | + | 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 ==== | ||
<code bash mpi.pbs> | <code bash mpi.pbs> | ||
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+ | ==== Tensorflow with GPU ==== | ||
+ | To use tensorflow with a specific GPU, say GPU 1, you can simply set | ||
+ | <code bash> | ||
+ | export CUDA_VISIBLE_DEVICES=1 | ||
+ | </ | ||
+ | and then schedule your jobs with Torque to perform experiments on GPU 1. |