Running DeepHSI from a SIF File#
Download the files using git and cd into the DeepHSI folder on your local computer
git clone https://github.com/shighton/DeepHSI.git && cd DeepHSI
Build a SIF container using the test.def file in DeepHSI
singularity build new.sif test.def
Copy the new SIF file into your project folder in the supercomputer (Bridges2 for this example)
scp new.sif <Username>@bridges2.psc.edu:/ocean/projects/cts090005p/<Username>
SSH into the supercomputer, navigate to your project folder, and make sure there are data and images folders
mkdir data && mkdir images
Run the new SIF file.
singularity run --bind ./data:/mnt,./:/images new.sif
The stable sif file as of June 8th 2022 can be found here or by command line:
singularity pull --arch amd64 library://andrew_satory/aum_ung_three_layer/aum-dataset:latest
Take your .sif file and place it into a new folder. Go to that folder in your terminal and run:
mkdir data
Note: if you are using the AUM dataset located in the AUM-UNG-HSI-Repository you will have to manually place the Datasets
folder into the data
folder you just created. Looking like /data/Datasets/AUM/
gt.mat dataset.mat
Now you should run the command:
singularity run --bind ./data:/mnt test.sif
If you are using a container made using the three-layer method for instance from 5MI7th3MI6’s or semihdinc’s repository, or aum-dataset.sif downloaded above.
singularity run --bind ./data:/mnt,./:/images aum-dataset.sif
Now you can run main.py as usual for example:
python main.py --model SVM --dataset IndianPines --training_sample 0.8