Difference between revisions of "GPUs EMBO 2018"
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| − | We exemplify the process of sending projects to the GPU by a synthetic project. | + | We exemplify the process of sending projects to the GPU by the creation and running of a synthetic project. |
| + | = Creation of the project = | ||
* Create a tutorial project <br /> | * Create a tutorial project <br /> | ||
| − | <tt>dtutorial t -p ptest -M 100 </tt> | + | <tt>dtutorial t -p ptest -M 100 </tt> <br /> |
| + | This project contains 100 synthetic thermosomes. | ||
* Adapt the project to be ran on a GPU environment without matlab <br /> | * Adapt the project to be ran on a GPU environment without matlab <br /> | ||
| Line 15: | Line 17: | ||
It creates a script called <tt>ptest.sh</tt> that needs to be submitted to the a GPU. | It creates a script called <tt>ptest.sh</tt> that needs to be submitted to the a GPU. | ||
| + | |||
| + | = Submission of the project = | ||
| + | |||
| + | == Submission script model == | ||
| + | there is a sample script located in | ||
| + | <tt> path this and that </tt> | ||
| + | |||
| + | <pre> | ||
| + | #!/bin/bash | ||
| + | #SBATCH -p gpu | ||
| + | #SBATCH -N 1 #stay on a single node. remove for CPU jobs | ||
| + | #SBATCH -J jobname XXXX CHANGE THIS | ||
| + | #SBATCH --ntasks=7 | ||
| + | #SBATCH -o run.out # STDOUT | ||
| + | #SBATCH -e run.err # STDERR | ||
| + | #SBATCH --gres=gpu:2 XXXX CHANGE THIS | ||
| + | #SBATCH --mail-type=END,FAIL | ||
| + | #SBATCH --mem=120GB | ||
| + | #SBATCH --time=0-03:00:00 | ||
| + | module load dynamo | ||
| + | command | ||
| + | </pre> | ||
| + | |||
| + | == Adapt the script to the project == | ||
| + | |||
| + | You can copy the script to your local folder (where you have created the project) and edit it to match the requirements of the project. Basically, you need to change the number of GPUs, the name of the project. Rename it to something you can identify later, like <tt>ptest.script</tt> | ||
| + | |||
| + | == Submit the script == | ||
| + | <tt>srun ptest.script</tt> | ||
Revision as of 16:35, 22 August 2018
We exemplify the process of sending projects to the GPU by the creation and running of a synthetic project.
Contents
Creation of the project
- Create a tutorial project
dtutorial t -p ptest -M 100
This project contains 100 synthetic thermosomes.
- Adapt the project to be ran on a GPU environment without matlab
dvput ptest destination standalone_gpu
- Passes a group of GPU identifiers
dvput ptest gpu_identifier_set 0:3
- Unfolds the project:
dvunfold ptest
It creates a script called ptest.sh that needs to be submitted to the a GPU.
Submission of the project
Submission script model
there is a sample script located in
path this and that
#!/bin/bash #SBATCH -p gpu #SBATCH -N 1 #stay on a single node. remove for CPU jobs #SBATCH -J jobname XXXX CHANGE THIS #SBATCH --ntasks=7 #SBATCH -o run.out # STDOUT #SBATCH -e run.err # STDERR #SBATCH --gres=gpu:2 XXXX CHANGE THIS #SBATCH --mail-type=END,FAIL #SBATCH --mem=120GB #SBATCH --time=0-03:00:00 module load dynamo command
Adapt the script to the project
You can copy the script to your local folder (where you have created the project) and edit it to match the requirements of the project. Basically, you need to change the number of GPUs, the name of the project. Rename it to something you can identify later, like ptest.script
Submit the script
srun ptest.script
