tutorial:torque
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tutorial:torque [2016/11/08 15:36] takac |
tutorial:torque [2017/03/15 17:58] afo214 |
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| ===== Submitting Jobs ===== | ===== Submitting Jobs ===== | ||
| - | |||
| - | <note tip> | ||
| Jobs can be submitted either using a submission file or directly from command line. First we explain how it is done and then we will discuss the options. | Jobs can be submitted either using a submission file or directly from command line. First we explain how it is done and then we will discuss the options. | ||
| Line 66: | Line 64: | ||
| 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 ===== |
| * '' | * '' | ||
| Line 93: | Line 90: | ||
| 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 | ||
| ---------------- ------ -------- -------- ---- --- --- -- ----- | ---------------- ------ -------- -------- ---- --- --- -- ----- | ||
| + | gpu -- -- | ||
| medium | medium | ||
| short -- -- | short -- -- | ||
| long | long | ||
| batch -- -- | batch -- -- | ||
| - | verylong | + | verylong |
| - | | + | AMPL -- -- |
| - | 0 | + | MOSEK |
| </ | </ | ||
| + | |||
| + | If you want to use AMPL or MOSEK, you have to use queue: AMPL or MOSEK, because we have limited licenses for them. | ||
| + | |||
| + | |||
| You can see limits using this command '' | You can see limits using this command '' | ||
| Line 118: | Line 128: | ||
| | very long | 240:00:00 | | | very long | 240:00:00 | | ||
| - | ==== Examples ==== | + | ===== Examples ===== |
| + | |||
| + | ==== Submitting a Small or Large Memory Job ==== | ||
| + | |||
| + | You can use the option '' | ||
| + | |||
| + | <code bash limited.sh> | ||
| + | qsub -l mem=4gb, | ||
| + | </ | ||
| - | === Submitting Large Memory Job === | + | Sometimes your job needs more memory. You can choose a larger memory size with the same option: |
| - | Sometimes your job needs more memory. This can be achieved by '' | + | < |
| - | < | + | |
| - | === Running MATLAB | + | ==== 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 | ||
| Line 138: | Line 155: | ||
| </ | </ | ||
| - | === Interactive Jobs === | + | <note tip>Use **-singleCompThread** [[https:// |
| + | ==== 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 '' | ||
| Line 148: | Line 166: | ||
| and you will be running interactive session on polyp15. | and you will be running interactive session on polyp15. | ||
| - | === Using GPU's === | + | ==== Using GPU' |
| Line 156: | Line 174: | ||
| 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 === | + | ==== Running MPI and Parallel Jobs ==== |
| <code bash mpi.pbs> | <code bash mpi.pbs> | ||
| Line 218: | Line 236: | ||
| c2 | c2 | ||
| </ | </ | ||
| - | |||
| - | ===== Advanced ===== | ||
| - | |||
| - | |||
| - | The qsub command will pass certain environment variables in the Variable_List attribute of the job. These variables will be available to the job. The value for the following variables will be taken from the environment of the qsub command: | ||
| - | * **HOME** (the path to your home directory) | ||
| - | * **LANG** (which language you are using) | ||
| - | * **LOGNAME** (the name that you logged in with) | ||
| - | * **PATH** (standard path to excecutables) | ||
| - | * **MAIL** (location of the users mail file) | ||
| - | * **SHELL** (command shell, i.e bash, | ||
| - | * **TZ** (time zone) | ||
| - | These values will be assigned to a new name which is the current name prefixed with the string " | ||
| - | * **PBS_O_HOST** (the name of the host upon which the qsub command is running) | ||
| - | * **PBS_SERVER** (the hostname of the pbs_server which qsub submits the job to) | ||
| - | * **PBS_O_QUEUE** (the name of the original queue to which the job was submitted) | ||
| - | * **PBS_O_WORKDIR** (the absolute path of the current working directory of the qsub command) | ||
| - | * **PBS_ARRAYID** (each member of a job array is assigned a unique identifier) | ||
| - | * **PBS_ENVIRONMENT** (set to PBS_BATCH to indicate the job is a batch job, or to PBS_INTERACTIVE to indicate the job is a PBS interactive job) | ||
| - | * **PBS_JOBID** (the job identifier assigned to the job by the batch system) | ||
| - | * **PBS_JOBNAME** (the job name supplied by the user) | ||
| - | * **PBS_NODEFILE** (the name of the file contain the list of nodes assigned to the job) | ||
| - | * **PBS_QUEUE** (the name of the queue from which the job was executed from) | ||
| - | * **PBS_WALLTIME** (the walltime requested by the user or default walltime allotted by the scheduler) | ||
| ===== Mass Operations ===== | ===== Mass Operations ===== | ||
| Line 277: | Line 271: | ||
| </ | </ | ||
| will cancel all jobs (both running jobs and queue). | will cancel all jobs (both running jobs and queue). | ||
| + | |||
| + | |||
| + | ===== Advanced ===== | ||
| + | |||
| + | |||
| + | The qsub command will pass certain environment variables in the Variable_List attribute of the job. These variables will be available to the job. The value for the following variables will be taken from the environment of the qsub command: | ||
| + | * **HOME** (the path to your home directory) | ||
| + | * **LANG** (which language you are using) | ||
| + | * **LOGNAME** (the name that you logged in with) | ||
| + | * **PATH** (standard path to excecutables) | ||
| + | * **MAIL** (location of the users mail file) | ||
| + | * **SHELL** (command shell, i.e bash, | ||
| + | * **TZ** (time zone) | ||
| + | These values will be assigned to a new name which is the current name prefixed with the string " | ||
| + | * **PBS_O_HOST** (the name of the host upon which the qsub command is running) | ||
| + | * **PBS_SERVER** (the hostname of the pbs_server which qsub submits the job to) | ||
| + | * **PBS_O_QUEUE** (the name of the original queue to which the job was submitted) | ||
| + | * **PBS_O_WORKDIR** (the absolute path of the current working directory of the qsub command) | ||
| + | * **PBS_ARRAYID** (each member of a job array is assigned a unique identifier) | ||
| + | * **PBS_ENVIRONMENT** (set to PBS_BATCH to indicate the job is a batch job, or to PBS_INTERACTIVE to indicate the job is a PBS interactive job) | ||
| + | * **PBS_JOBID** (the job identifier assigned to the job by the batch system) | ||
| + | * **PBS_JOBNAME** (the job name supplied by the user) | ||
| + | * **PBS_NODEFILE** (the name of the file contain the list of nodes assigned to the job) | ||
| + | * **PBS_QUEUE** (the name of the queue from which the job was executed from) | ||
| + | * **PBS_WALLTIME** (the walltime requested by the user or default walltime allotted by the scheduler) | ||
| + | |||
| + | |||
tutorial/torque.txt · Last modified: 2024/02/28 13:12 by mjm519
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