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To access a Linux workstation remotely, you can type the following command for command line access:
| Code Block |
|---|
ssh awf2130@spgpuawf2130@[spgpu or exxgpu][#].fitzpatrick.zi.columbia.edu |
Where "#" is the number associated with the workstation. You will be prompted for the credentials of the workstation user; these are different from UNI credentials used for other Columbia services (such as LionMail) and have been distributed to the Fitzpatrick lab.
You can also access the graphical user interface (GNOME) for the Fitzpatrick workstations remotely as well by using VNC. To use VNC, you will need a VNC client installed on your laptop/workstation. A list of VNC clients available for various platforms can be found here. Note that Mac OS X comes with a built-in VNC client, which is accessible from the Finder by navigating to Go → Connect to Server and then entering vnc://[spgpu or exxgpu][#].fitzpatrick.zi.columbia.edu:5901. VNC is accessible on port 5901, and requires authentication using credentials distributed to the Fitzpatrick lab. If these
If either the command line or VNC credentials are not working, please email rc@zi.columbia.edu for further assistance.
For security reasons, the Fitzpatrick workstations are only remotely accessible via SSH/VNC if you are on the Columbia campus or using the CUIT VPN.
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M will take in data produced by RELION as input as described in the pipeline outline here. Since RELION is not a native Windows application, this will require that you make heavy use of the Fitzpatrick lab Engram storage, which (as mentioned above) is mapped to the D drive. Roughly, you will need to perform the first steps of the pipeline (preprocessing, particle image/sub-tomogram export) on warp.fitzpatrick using Warp, then run classification and refinement on the cryoem cluster or a Linux-based workstation and save the results to Engram, and then perform the final steps of the pipeline on warp.fitzpatrick using M.
Remote Access
The Windows Warp/M workstation is remotely accessible using RDP. You can find a list of Microsoft-sanctioned RDP clients here. For Linux, we suggest using Remmina.