After logging into graham using:
ssh -Y [email protected]
you can use the command:
ls
to list all the files and directories in your home folder. Doing so you are going to find three main folders. Is this tutorial let's foccus on the $SCRATCH space and how to run a simple code.
After creating your environment in your /home directory (I really recomend you to create a folder called envs/environment and create your environment inside of it). Installing numpy using:
pip install numpy --no-index
You need to upload the python file to the $SCRATCH space and then run the code.
In order to access the scratch folder you do:
cd scratch
once inside you can create a folder for separate codes/projects that you are working on. For example, I am going to create a test folder inside $SCRATCH:
mkdir test
then I am going to enter test folder. Now I can either copy and paste the codes that I need inside this folder using text editors or cloning from a git repo.
In this case I am going to demostrate using a python code called basic_operations.py that you can clone from this git repo. Once you've transfered the code to the $SCRATCH space you can run it by:
python basic_operations.py
remember you environment needs to be activate in order to that work.
In this case we have a really dummy code that does not require a lot of memory or computer power, so its fine to run on the logging node. In the case you have a bigger code its necessary to run a scheduler, in this case our scheduler is going to be called sh_basic_operations.py and you can run it using:
python sh_basic_operations.py
Look at the ST column in the output of sq to determine the status of your jobs. The two most common states are PD for pending and R for running. When the job has finished, it no longer appears in the sq output.
If the code runs succesfully you should see a file .log like out_Opt_times_First1_Second10.0.log that you can open using a text editor or:
cat file.log
And you can check if you got any errors and, in this case, the print of our function.
This is a really simple example, but the srtucture of the sh file and your python code (main file) it will be similar.