For AI agents: a documentation index is available at the root level at /llms.txt. Append /llms.txt to any URL for a page-level index, or .md for the markdown version of any page.
This page is for MSA Search, version 2.2.0.
For other versions, use one of these documentation indexes:
- 2.6.0 (Latest) (default): https://docs.nvidia.com/nim/bionemo/msa-search/2.6.0/llms.txt
- 2.5.0: https://docs.nvidia.com/nim/bionemo/msa-search/2.5.0/llms.txt
- 2.4.0: https://docs.nvidia.com/nim/bionemo/msa-search/2.4.0/llms.txt
- 2.3.0: https://docs.nvidia.com/nim/bionemo/msa-search/2.3.0/llms.txt
- 2.2.0: https://docs.nvidia.com/nim/bionemo/msa-search/2.2.0/llms.txt
- 2.1.0: https://docs.nvidia.com/nim/bionemo/msa-search/2.1.0/llms.txt
- 2.0.0: https://docs.nvidia.com/nim/bionemo/msa-search/2.0.0/llms.txt
- 1.0.0: https://docs.nvidia.com/nim/bionemo/msa-search/1.0.0/llms.txt
This section describes how to configure the MSA Search NIM container using environment variables, GPU selection, and volume mounting.
GPU Selection
By default, Docker uses all available GPUs on the system when started with the NVIDIA Container Runtime:
docker run --runtime=nvidia ...
To expose only specific GPUs to the container, use the --gpus flag:
The following environment variables can be passed to the NIM using the -e flag with docker run:
ENV
Required?
Default
Notes
NGC_API_KEY
Yes
None
You must set this variable to the value of your personal NGC API key.
NIM_CACHE_PATH
No
/opt/nim/.cache
Location (in container) where the container caches model artifacts.
NIM_HTTP_API_PORT
No
8000
Port inside the container where the NIM service is published. When using the -p flag with docker run, ensure the right-hand side of the colon matches this value (e.g., -p 8000:8000).
NIM_DISABLE_GPU_SERVER
No
False
Controls the GPU Server for MMSeqs2. The GPU Server is enabled by default for optimal performance with the included ColabFold databases. Set to True to disable if using custom databases that do not support GPU Server.
NIM_GLOBAL_MAX_MSA_DEPTH
No
500
Sets the maximum number of MSA sequences returned. Must be set globally for all requests when GPU Server is enabled (default in version 2.0.0).
NIM_MSA_API_MAX_DATABASES
No
5
Maximum number of databases that can be specified in a single API request.
NIM_MSA_API_MAX_MSA_SEQUENCES
No
10001
Maximum value for the max_msa_sequences API parameter.
NIM_MSA_API_MAX_ITERATIONS
No
6
Maximum value for the iterations API parameter.
NIM_MSA_API_MAX_CHAINS
No
20
Maximum number of chains (sequences) allowed in a paired MSA search request.
NIM_MSA_API_MAX_SEQUENCE_LENGTH
No
4096
Maximum length of an input protein sequence.
NIM_MSA_API_DEFAULT_STRUCTURAL_TEMPLATE_DBS
No
PDB70_220313
Comma-separated list of databases to search for structural templates by default.
Comma-separated list of lowercase:DisplayName mappings for database names in API responses when using ["all"]. Used for backwards compatibility; will be removed in MSA 3.0 when all database names will resolve to lowercase.
NIM_LOG_LEVEL
No
INFO
Specifies the level of logging detail. Available options: DEBUG, INFO, WARNING, ERROR.
NIM_MODEL_NAME
No
None
Path to custom database directory inside the container. Use with volume mounts to load external or custom MMSeqs2 databases. See Task-Specific Profiles and Custom Databases for details.
NIM_MODEL_PROFILE
No
None
Select a specific database profile by ID. Profiles allow reduced storage by loading only the databases needed for a particular task. See Task-Specific Profiles and Custom Databases.
NIM_MSA_DB_INDEX_PATTERN
No
**/*.idx
Glob pattern for discovering sequence databases. The NIM scans for files matching this pattern under NIM_MODEL_NAME at startup. Database names are derived from the parent directory.
NIM_MSA_PDB_CIFS_ZIP
No
**/pdb*.zip
Glob pattern for discovering the PDB mmCIF structure archive. Used for retrieving 3D structures during structural template search.
NIM_TELEMETRY_MODE
No
0
Controls telemetry collection. Set to 0 to disable telemetry (default), set to 1 to enable telemetry. Telemetry helps NVIDIA improve performance, compatibility, and reliability while maintaining strict privacy protections. For more information, refer to NVIDIA’s Privacy Policy and NIM Telemetry Settings.
NIM_TELEMETRY_ENABLE_LOGGING
No
true
Enables logging for telemetry operations when set to true. Only applicable when NIM_TELEMETRY_MODE=1.
Volumes
The following container paths can be mounted to local directories for persistent storage.
Container Path
Required
Notes
Docker Argument Example
/opt/nim/.cache (or NIM_CACHE_PATH if set)
Recommended
Directory where model artifacts and databases are cached. If not mounted, the container will re-download on each startup. Ensure the local directory has read-write-execute permissions (chmod 0777). Example: mkdir -p ~/.cache/nim && chmod 0777 ~/.cache/nim
-v ~/.cache/nim:/opt/nim/.cache
Custom path (set via NIM_MODEL_NAME env variable)
Optional
Mount custom databases by setting NIM_MODEL_NAME to point to your database directory inside the container, then mount the host directory to that path. Useful for using external or custom MMSeqs2 databases. See Task-Specific Profiles and Custom Databases for detailed examples.
