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Prerequisites and Support Matrix for MSA Search NIM#

Sequence Databases and Search Types#

The MSA Search NIM includes pre-indexed databases optimized for GPU Server operation:

Database Name

Use Case

Paired Search

Template Search

Source

uniref30_2302

MSA and profile generation

Yes

Required

ColabFold Databases

colabfold_envdb_202108

MSA expansion

No

No

ColabFold Databases

pdb70_220313

Template search (70% cluster)

No

Yes

ColabFold Databases

pdb100_230517

Template search (100% cluster)

No

Yes

ColabFold Databases

pdb_20251028

mmCIF structure retrieval

No

Yes

RCSB PDB

Total size: 1660 GB

Note

Paired MSA search requires databases with taxonomy information. Only uniref30_2302 supports paired search among the default databases.

Note

Template search requires uniref30_2302 for profile generation plus at least one template database (PDB70 or PDB100). The profile generated from Uniref30 is used to search the template databases for structural homologs.

Tip

To reduce storage requirements, you can use task-specific database profiles that load only the databases needed for your use case. Refer to Task-Specific Profiles and Custom Databases for details.

Supported Hardware#

Minimum System Hardware Requirements#

CPU Cores

RAM (GB)

NVMe SSD Storage (GB)

GPU Count

24

64

1660

One or more NVIDIA GPU from the Supported NVIDIA GPUs

Supported NVIDIA GPUs#

The MSA Search NIM supports NVIDIA GPUs with at least 48 GB of GPU Memory. It has been tested on the following recommended configurations:

GPU

GPU Memory (GB)

GPU Count

A100

80

1-8

H100

80

1-8

B200

180

1-8

L40S

48

2-8

RTX 6000 Ada Generation

48

2-4

Note

Starting with version 2.0.0, GPUs with 48GB memory (L40S, RTX 6000 Ada) require a minimum of 2 GPUs when using GPU Server (enabled by default). This is because GPU Server holds databases in memory for optimal performance.

Software Prerequisites#

docker run --rm --runtime=nvidia --gpus all ubuntu nvidia-smi

Example output:

+-----------------------------------------------------------------------------+
| NVIDIA-SMI 580.82.07    Driver Version: 580.82.07    CUDA Version: 13.0     |
|-------------------------------+----------------------+----------------------+
| GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr. ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute M. |
|                               |                      |               MIG M. |
|===============================+======================+======================|
|   0  NVIDIA H100 ...     On  | 00000000:1B:00.0 Off |                    0 |
| N/A   33C    P0             75W /  700W |       1MiB /  81559MiB |      0%      Default |
|                               |                      |             Disabled |
+-------------------------------+----------------------+----------------------+

+-----------------------------------------------------------------------------+
| Processes:                                                                  |
|  GPU   GI   CI        PID   Type   Process name                  GPU Memory |
|        ID   ID                                                   Usage      |
|=============================================================================|
|  No running processes found                                                 |
+-----------------------------------------------------------------------------+

Note

For more information on enumerating multi-GPU systems, see the NVIDIA Container Toolkit’s GPU Enumeration Docs

Supported CPU architectures: x86_64 / amd64.

NGC (NVIDIA GPU Cloud) Account#

To download and run the MSA Search NIM, you need an NGC account and API key:

  1. Create an account on NGC if you don’t already have one

  2. Generate an API Key - ensure that NGC Catalog is selected from the “Services Included” dropdown

  3. Export the API key in your terminal:

export NGC_API_KEY=<your-api-key>

  1. Log in to Docker with your NGC API key:

echo "$NGC_API_KEY" | docker login nvcr.io --username '$oauthtoken' --password-stdin

Note

Personal keys allow you to configure an expiration date, revoke, or delete the key using an action button, and rotate the key as needed. For more information about key types, refer to the NGC User Guide.