CryoSPARC Guide
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Setup, Configuration and Management
Deployment Guides
Processing Data in cryoSPARC
Real-time processing in cryoSPARC Live
Cryo-EM Data Processing Explained
cryoSPARC Installation Prerequisites
Before installing cryoSPARC, ensure these 5 requirements are met.
1. CUDA Toolkit
The cryoSPARC worker node requires CUDA to be installed alongside an NVIDIA GPU. CUDA is a parallel computing platform and programming model developed by NVIDIA for general computing on its own GPUs.
CryoSPARC supports CUDA Toolkit version ≥ 10 and ≤ 11.2. Some job types, such as Deep Picker, require CUDA 11. As of January 2022, we recommend CUDA minor version 11.2 for best cryoSPARC compatibility. You can download CUDA here.​
Please ensure you're running the latest NVIDIA Driver compatible with your GPU and CUDA Toolkit version. You can download the latest driver for your GPUs here. Visit Troubleshooting for common GPU errors.
2. Common Unix User Account
The cryoSPARC master and worker nodes must have the same Unix user available on each node.
You don't need to have a dedicated Unix user (e.g.,
cryosparcuser), to run and install cryoSPARC -- you can use your own user account. Using your own user account makes sense when you are installing cryoSPARC for yourself, and you don't plan on expanding to have any other users use the same instance.Create a dedicated user account (e.g.,
cryosparcuser) that will run the cryoSPARC application on the master node and each worker node that will be used for computation.In a master- worker setup, the cryoSPARC master node will use SSH to access the worker node and execute a bash script that will run the job a user has queued to that machine. Some lightweight job types queue directly to the master node, in which case the cryoSPARC master process will execute the job using a Python subprocess. If a user queues a job to a cluster, the cryoSPARC master process will submit a cluster job via the cluster workload scheduler's job submission system (for example via the
sbatch command on a SLURM cluster).For the purposes of this documentation, we will use the username
cryosparcuser to represent the user that owns the cryoSPARC processes.3. Password-less SSH Access
‌Set up SSH access between the master node and each standalone worker node. The
cryosparcuser account should be able to SSH without a password (using a SSH key-pair) into all non-cluster worker nodes.Setting up password-less SSH access to a remote workstation
Set up SSH keys for password-less access (only if you currently need to enter your password each time you ssh into the compute node).
If you do not already have SSH keys generated on your local machine, use
ssh-keygen to do so.Open a terminal prompt on your local machine, and enter:
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ssh-keygen -t rsa -N "" -f $HOME/.ssh/id_rsa
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This will create an RSA key-pair with no passphrase in the default location.‌
Copy the RSA public key to the remote compute node for password-less login:
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ssh-copy-id [email protected]_hostname
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remote_username and remote_hostname are your username and the hostname that you use to SSH into your compute node. This step will ask for your password.4. Open TCP Ports
Ensure ports
39000-39010 are accessible between every workstation node and the master node. The port range is configurable during install time. The following table details the purpose of each port.Port
Usage
39000
CryoSPARC web application
39001
MongoDB database
39002
Command Core (Master) server
39003
Command Visualization (Vis) server
39004
Command Proxy server (Not Used)
39005
CryoSPARC Live Command RTP server
39006
CryoSPARC Live web application
39007
Reserved (Not Used)
39008
Reserved (Not Used)
39009
Reserved (Not Used)
39010
Reserved (Not Used)
Identifying open ports
To see what ports are being used on your master node, run the command
netstat -tuplen. You can pipe the output to grep to search for specific ports. For example:1
$ netstat -tuplen | grep :3900
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(Not all processes could be identified, non-owned process info
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will not be shown, you would have to be root to see it all.)
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Proto Recv-Q Send-Q Local Address Foreign Address State User Inode PID/Program name
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tcp 0 0 0.0.0.0:39000 0.0.0.0:* LISTEN 3002 2088014397 -
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tcp 0 0 0.0.0.0:39001 0.0.0.0:* LISTEN 3002 2088031342 -
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tcp 0 0 0.0.0.0:39002 0.0.0.0:* LISTEN 3002 2088039523 -
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tcp 0 0 0.0.0.0:39003 0.0.0.0:* LISTEN 3002 2088044546 -
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tcp 0 0 0.0.0.0:39004 0.0.0.0:* LISTEN 3002 2088021927 -
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tcp 0 0 0.0.0.0:39005 0.0.0.0:* LISTEN 3002 2088020880 -
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tcp 0 0 0.0.0.0:39006 0.0.0.0:* LISTEN 3002 2088022457 -‌
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Testing open ports
To test if a TCP port is open (for example, to test if there is a firewall blocking the port), run a
telnet command from another computer inside the network. If you see any response other than the one below (e.g., a timeout or a denial), it may indicate that the port is not listening or is blocked.1
$ telnet cryosparc.server 39000
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Trying 192.168.64.49...
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Connected to cryoem5.slush.sandbox.
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Escape character is '^]'.
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$ ^C
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Connection closed by foreign host.
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5. Shared File System
The major requirement for installation is that all nodes (including the master) be able to access the same shared file system(s) at the same absolute path. These file systems (typically cluster file systems or NFS mounts) will be used for loading input raw data into jobs running on various nodes, as well as saving output data from jobs into projects.
Example of a Master-Worker setup where all nodes have access to the same shared filesystem
Each project created by a user is associated with a single project directory that all cryoSPARC nodes must be able to read from and write to.
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