Helpful Tips and Notes

Helpful Tips and Notes#

Working on and developing within a framework like GAME can come with a huge learning curve. Here are some tips and notes we compiled along the way.

File Permissions#

Note: You may need to change file permissions on your host machine before building the container. If you encounter permission errors during the build (specifically when copying files), try running chmod 755 file_name on your scripts/data before running the build command.

Data & Dependencies#

Data Formatting: Your data can be stored in any format in the evaluator_data/ folder.

  • If your data is already in the GAME API JSON format, you can use the generic evaluator API script directly.

  • If your data is in another format (e.g. FASTA, BED), you can refer to the pre-built GAME modules for examples of how to parse these custom formats.

Adding Dependencies: Additional dependencies (Python libraries, system tools) should be added to the .def files in the %post section.

Runtime & Isolation#

Binding Paths (-B): By default, Apptainer may not see files on your host system. The -B flag is used to “bind” (mount) local directories into the container so it can access them.

  • Example: -B /scratch/user/local_data:/data maps a folder on your host to /data inside the container.

  • Default Isolation: Our pre-built GAME containers include the environment variable APPTAINER_NO_MOUNT="home,tmp,proc,sys,dev". This provides a “safe default” by preventing these common host directories from being automatically mounted, keeping the container filesystem clean.

  • Full Isolation (--containall): While our default settings hide host files, the --containall flag provides complete isolation. It creates separate namespaces for processes (PID) and IPC, and fully cleans the environment. We recommend using this flag to guarantee the most reproducible runs.

GPU Support#

If your model requires a GPU, you must add the --nv flag to your run command to expose the host’s NVIDIA drivers to the container. For AMD GPUs, refer to Apptainer’s documentation.