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. You can download CUDA here.
Please note that newer GPUs require later versions of CUDA.
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.
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.
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.
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.
ssh-keygen -t rsa -N "" -f $HOME/.ssh/id_rsa
This will create an RSA key-pair with no passphrase in the default location.
ssh-copy-id remote_username@remote_hostname
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.
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) |
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:
$ netstat -tuplen | grep :3900(Not all processes could be identified, non-owned process infowill not be shown, you would have to be root to see it all.)Proto Recv-Q Send-Q Local Address Foreign Address State User Inode PID/Program nametcp 0 0 0.0.0.0:39000 0.0.0.0:* LISTEN 3002 2088014397 -tcp 0 0 0.0.0.0:39001 0.0.0.0:* LISTEN 3002 2088031342 -tcp 0 0 0.0.0.0:39002 0.0.0.0:* LISTEN 3002 2088039523 -tcp 0 0 0.0.0.0:39003 0.0.0.0:* LISTEN 3002 2088044546 -tcp 0 0 0.0.0.0:39004 0.0.0.0:* LISTEN 3002 2088021927 -tcp 0 0 0.0.0.0:39005 0.0.0.0:* LISTEN 3002 2088020880 -tcp 0 0 0.0.0.0:39006 0.0.0.0:* LISTEN 3002 2088022457 -
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.
$ telnet cryosparc.server 39000Trying 192.168.64.49...Connected to cryoem5.slush.sandbox.Escape character is '^]'.$ ^CConnection closed by foreign host.
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.
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.