developing and testing in a remote apptainer container

The conda environment proposed for development is not optimal. let's see whether we can develop and test new C++ gadgets in a remote apptainer container.

building container

first build the apptiner container appatainer build gadgetron.sif gadgetron.recipe

you might need ismrmrdviewer from mrdviewer.recipe for seeing the images.

Local container

need to test

remote container

setting up remote explorer in vscode

add the following lines to your ssh config file

Host RemoteGagetron
	RemoteCommand apptainer shell -B /ptmp /ptmp/pvalsala/MyContainers/gadgetron.sif
	RequestTTY yes
	User pvalsala
    HostName nyx.hpc.kyb.local
	ForwardX11 yes
	ForwardX11Trusted yes

RemoteGagetron should appear in your remote explorer

building the library

Now you can open this repo cloned on the remote. Opening terminal will give you a terminal inside the container.

mkcd build
cmake .. 
make

testing

simple testing

open another terminal in vscode and launch gadgetron.

testing in GPU

salloc-a-node --time 02:00:00 --partition gpu

keep that open another terminal and ssh into it with portforwarding and start gadgetron

ssh -Y -L 9004:localhost:9002 gpu-x
apptainer exec -B /ptmp  --nv /ptmp/pvalsala/MyContainers/gadgetron.sif bash
cd /so/file/location
gadgetron

now you can send data to gadgetron from login node to port 9004

gadgetron_ismrmrd_client -f testData/raw3D_R3.h5 -C config/piv_GadgetronSpiral_fast.xml -o im_2.h5 -p 9004

troubleshooting

• Ctrl+Shift+P : search for kill vs code server in vscode
• delete /home/user/.vscode-server folder
• ps aux | grep -E ${USER}.*.vscode-server | awk '{print $2}' |xargs kill -9 to kill all vscode-servers running with your user.

references

-https://code.visualstudio.com/docs/devcontainers/containers