Difference between revisions of "Monai Usage"
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| Line 8: | Line 8: | ||
==MONAI label== | ==MONAI label== | ||
NGC container usage: | NGC container usage: | ||
| − | #Server: | + | #Server: to start the server as a slurm job: |
| − | + | #*<pre>ml purge</pre> | |
| − | # | + | #*<pre>ml ngc-monailabel/<version></pre> |
| − | # | + | #*Copy to your directory the file: |
| − | # | + | #**<pre>/apps/nvidia/containers/monai/start_monai_server_readonly.sh</pre> |
| − | # | + | #*Copy these directories to a place you own, e.g. |
| − | # | + | #**<pre>cp -r /apps/nvidia/containers/monai/apps/deepedit <my_place></pre> |
| − | # | + | #**<pre>cp -r /apps/nvidia/containers/monai/datasets/Task09_Spleen <my_place></pre> |
| − | # | + | #*Modify the start_monai_server_readonly.sh line to read: |
| − | # | + | #**<pre>singularity exec -B /apps/nvidia/containers/monai /apps/nvidia/containers/monai/monailabel/ monailabel start_server --app <my_place>/deepedit --studies <my_place>/Task09_Spleen/imagesTr</pre> |
| − | # | + | #*<pre>sbatch start_monai_server_readonly.sh</pre> |
| − | # | ||
#*Note server address from job output: used in next step | #*Note server address from job output: used in next step | ||
| − | |||
#3DSlicer client | #3DSlicer client | ||
#*Start Open On Demand (OOD) session | #*Start Open On Demand (OOD) session | ||
Revision as of 21:17, 1 August 2023
Back to Monai
MONAI core
NGC container usage:
ml purge ml ngc-monai/<version> python <your__python_script>
MONAI label
NGC container usage:
- Server: to start the server as a slurm job:
ml purge
ml ngc-monailabel/<version>
- Copy to your directory the file:
/apps/nvidia/containers/monai/start_monai_server_readonly.sh
- Copy these directories to a place you own, e.g.
cp -r /apps/nvidia/containers/monai/apps/deepedit <my_place>
cp -r /apps/nvidia/containers/monai/datasets/Task09_Spleen <my_place>
- Modify the start_monai_server_readonly.sh line to read:
singularity exec -B /apps/nvidia/containers/monai /apps/nvidia/containers/monai/monailabel/ monailabel start_server --app <my_place>/deepedit --studies <my_place>/Task09_Spleen/imagesTr
sbatch start_monai_server_readonly.sh
- Note server address from job output: used in next step
- 3DSlicer client
- Start Open On Demand (OOD) session
- Start Console in hwgui with 1 GPU: gpu:geforce:1
- In console: load & start Slicer
ml qt/5.15.4 slicer/4.13.0
vglrun -d :0.$CUDA_VISIBLE_DEVICES Slicer
- In Slicer GUI:
- Select module: Active Learning -> MONAILabel
- Fill in server address, e.g.: http://c1007a-s17:8000/
- Click on refresh button next to server address
- Load Next Sample
- You are good to go! Enjoy!