Difference between revisions of "GPUs EMBO 2018"
| Line 3: | Line 3: | ||
= Creation of the project = | = Creation of the project = | ||
| − | * Create a tutorial project <br /> | + | * Create a tutorial project <br /> |
| − | <tt>dtutorial t -p | + | <tt>dtutorial t -p ptest -M 100 </tt> <br /> |
| − | This project contains 100 synthetic thermosomes. | + | This project <tt>ptest</tt>contains 100 synthetic thermosomes. |
* Adapt the project to be ran on a GPU environment <br /> | * Adapt the project to be ran on a GPU environment <br /> | ||
| − | <tt>dvput | + | <tt>dvput ptest destination matlab_gpu</tt> |
* Passes a group of GPU identifiers. Assuming that we just want to use 2 GPUs: <br /> | * Passes a group of GPU identifiers. Assuming that we just want to use 2 GPUs: <br /> | ||
| Line 17: | Line 17: | ||
<tt>dvunfold ptest</tt> | <tt>dvunfold ptest</tt> | ||
| − | It creates a script called <tt>ptest. | + | It creates a script called <tt>ptest.m</tt> that needs to be submitted to the GPU. |
= Submission of the project = | = Submission of the project = | ||
== Submission script model == | == Submission script model == | ||
| − | + | There is a sample submission script located in | |
<tt> /g/embo2018/cryo06/Dynamo/test/submit.scrip </tt> | <tt> /g/embo2018/cryo06/Dynamo/test/submit.scrip </tt> | ||
Latest revision as of 11:18, 26 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 ptestcontains 100 synthetic thermosomes.
- Adapt the project to be ran on a GPU environment
dvput ptest destination matlab_gpu
- Passes a group of GPU identifiers. Assuming that we just want to use 2 GPUs:
dvput ptest gpu_identifier_set 0:1
We assign temporarily the gpu identifiers 0 and 1. The queue will assign dynamically some other couple of free identifiers during runtime.
- Unfolds the project:
dvunfold ptest
It creates a script called ptest.m that needs to be submitted to the GPU.
Submission of the project
Submission script model
There is a sample submission script located in
/g/embo2018/cryo06/Dynamo/test/submit.scrip
containing:
#!/bin/bash
#SBATCH -p gpu
#SBATCH -N 1 #stay on a single node. remove for CPU jobs
#SBATCH -J jobname # change this
#SBATCH --ntasks=1;
#SBATCH -o run.out # STDOUT
#SBATCH -e run.err # STDERR
#SBATCH --gres=gpu:2 # XXXX CHANGE THIS
#SBATCH --mail-type=END,FAIL
#SBATCH --mem=12GB
#SBATCH --time=0-03:00:00
module load dynamo
export LD_LIBRARY_PATH=$EBROOTGCC/lib64:$LD_LIBRARY_PATH
module load CUDA/9.1.85_387.26-GCC-6.4.0-2.28
echo $CUDA_VISIBLE_DEVICES
MYPROJECT="ptest" # PUT HERE THE NAME OF YOUR PROJECT
echo "dvput $MYPROJECT -gpu_identifier_set $CUDA_VISIBLE_DEVICES" > dcommands.sh
echo "dvunfold $MYPROJECT" >> dcommands.sh
dynamo dcommands.sh
chmod u=rxw ./$MYPROJECT.m
./$MYPROJECT.m
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
cp /g/embo2018/cryo06/Dynamo/test/submit.script ptest.script
To edit the new script, use
emacs ptest.script
Operate the changes in the EMACS terminal. To leave, press Ctrl+x then Ctrl+c
Submit the script
srun ptest.script
