Project-MONAI / Project-MONAI/MONAILabel
Monailabel is ignoring arguments (issue with PYTHONPATH?)
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- Python
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Description
Describe the bug
Hi All,
I'm trying to set up an easy install of monailabel on a PBS-based computing cluster (AWS is unavailable on our computing environment).
The computing enviroment mainly loads packages by the creation and use of Tool Command Language (TCL) modules which typically contains a pip install e.g.
pip3 install -I --prefix="${APP_PATH}" monailabel==0.6.0 --no-warn-script-location
and then the required PATHs are adjusted accordingly:
mkdir -p ${APP_MODULE_PATH}
cat< ${APP_MODULE_PATH}/${APP_VERSION}
#%Module1.0
source /opt/Modules/extensions/extensions.tcl
soft-prereq python3/3.10.0
prepend-path PYTHONPATH /apps/python3.10.0/
prepend-path PYTHONPATH ${APP_PATH}/lib/python3.10/site-packages
prepend-path PATH ${APP_PATH}/bin
EOF
However, when I load the module and run the monailabel command line, the command is reached but there is no following output, I supect due to something missing PYTHONPATHS. Example runs are below:
Server logs
bash file used for qsubbing:
`[kd0793@gadi-login-05 0.6.0]$ cat bash_file.sh
#!/bin/bash
#PBS -P nm24
#PBS -q gpuvolta
#PBS -l walltime=48:00:00
#PBS -l mem=100GB
#PBS -l jobfs=200GB
#PBS -l ngpus=4
#PBS -l ncpus=48
#PBS -lstorage=gdata/if89
module unload LAMA python3
module load monailabel/0.6.0
python3 -c "import torch; print(torch.cuda.is_available())"
python -c 'import monai; monai.config.print_debug_info()'
monailabel --help
output (standard output)
True
Using PYTHONPATH=/g/data/if89/apps/monailabel:/g/data/if89/apps/monailabel/0.6.0/lib/python3.10/site-packages:/apps/python3.10.0/
Expected behavior
Should bring up the help arguments for monailabel
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with bash_file.sh and reproduce the module-loading and monailabel --help commands in the PBS environment described. Trace the monailabel CLI entry point and its Python path handling, then confirm that the command displays its help arguments when the reported environment is loaded.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python, pytorch
- Domain
- cli, devops
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100