Changes between Version 27 and Version 28 of gridEngineUsers
- Timestamp:
- 07/02/09 10:11:10 (5 months ago)
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gridEngineUsers
v27 v28 24 24 25 25 {{{ 26 #!/bin/bash27 26 date 28 27 }}} 29 28 It is a simple script that calls '''date''' on whatever machine SGE decides to run your job on. Let's have a look at another submit file that does the same thing: 30 29 {{{ 31 #!/bin/bash32 30 #$ -cwd 33 31 #$ -j y … … 52 50 Rather than explain everything all at once, here is a submit script for a parallel job: 53 51 {{{ 54 #!/bin/bash55 56 52 #$ -N parallel-job 57 53 #$ -cwd 58 54 #$ -pe ompi* 4 59 #$ -l i_ mx=true,h_rt=08:00:0055 #$ -l i_ib=true,h_rt=08:00:00 60 56 #$ -j y 61 57 #$ -o output.$JOB_ID … … 76 72 * `-e`: `-e` does the same thing as `-o` except that it redirects your standard error stream to some file or a file in a path. 77 73 78 * `-l i_ mx=true`: This tells the scheduler that you only want your job to run on resources where `i_mx` is true. `i_mx` is a '''complex''' ([wiki:UsingComplexes "More Information"]) that tells you which queues have Myrinet capability. Any job that requests `i_mx=true` will run only on hosts which have this capability.74 * `-l i_ib=true`: This tells the scheduler that you only want your job to run on resources where `i_ib` is true. `i_ib` is a '''complex''' ([wiki:UsingComplexes "More Information"]) that tells you which queues are connected via !InfiniBand. Any job that requests `i_ib=true` will run only on hosts which have this capability. 79 75 80 76 === Interactive jobs === … … 153 149 == Storing !GridEngine Options == 154 150 Commonly used options in submit scripts or calls to `qstat` can be stored in dot files within your home directory in order to prevent you from needlessly using them repeatedly. 151 155 152 === `qstat` Options === 156 153 Options for the `qstat` command may be stored in the `~/.sge_qstat` file, in your home directory. This allows you to add default options to the `qstat` command. An example of this follows: … … 163 160 164 161 Adding these options to the `~/.sge_qstat` file ensures that the default call to `qstat` will show jobs for all users and provide a view of the process distribution throughout the cluster. You can add any of the options defined in the `qstat` man pages to this file to make them defaults for your account. 162 165 163 === `qsub` and Submit Script Options === 166 164 Even more useful is the `~/.sge_request` file which stores default options for submit scripts and calls to `qsub`. This is extremely useful for creating a consistent environment for your jobs. In the following file, we have defined defaults for the treatment of STDOUT, STDERR, the name of the output files, to use the current working directory, and what shell I want. These defaults will be used by all of your submit scripts unless overridden in the submit script itself. Below is an example of an `~/.sge_request` file and an example submit script using those defaults: 165 167 166 ==== ~/.sge_request ==== 168 167 {{{ … … 172 171 -o output.$JOB_NAME.$JOB_ID 173 172 }}} 173 174 174 And now a job script. Notice the lack of the above options as they are assumed from the `~/.sge_request` file: 175 175 {{{ 176 #!/bin/bash177 176 #$ -N job_name 178 177 #$ -pe ompi* 12-16 179 #$ -l h_rt=08:00:00,h_data=2.0G 180 #$ -l i_ib=true,mem_request=2.0G 178 #$ -l h_rt=08:00:00,mem_free=2.0G,i_ib=true 181 179 182 180 sge_mpirun my_parallel_job
