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Single-cell RNA Sequencing
15 MIN
An end-to-end GPU-powered workflow for scRNA-seq using RAPIDS
| Symptom | Cause | Fix |
|---|---|---|
| Docker is not found. | Docker may have been uninstalled, as it is preinstalled on your DGX Spark | Please install Docker using their convenience script here: curl -fsSL https://get.docker.com -o get-docker.sh && sudo sh get-docker.sh. You will be prompted for your password. |
| Docker command unexpectedly exits with "permissions" error | Your user is not part of the docker group | Open Terminal and run these commands: sudo groupadd docker && sudo usermod -aG docker $USER. You will be prompted for your password. Then, close the Terminal, open a new one, and try again |
| Docker container download, environment build, or data download fails | There was either a connectivity issue or a resource may be temporarily unavailable. | You may need to try again later. If this persists, please post on the Spark user forum for support |
NOTE
DGX Spark uses a Unified Memory Architecture (UMA), which enables dynamic memory sharing between the GPU and CPU. With many applications still updating to take advantage of UMA, you may encounter memory issues even when within the memory capacity of DGX Spark. If that happens, manually flush the buffer cache with:
sudo sh -c 'sync; echo 3 > /proc/sys/vm/drop_caches'
For latest known issues, please review the DGX Spark User Guide.