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BioHPC Lab:
User Guide

 


Machine accounts and passwords

Your account used to access Lab machines can be managed online. All components use the same password, i.e. you use the same user id and password when login into the BioHPC Lab website as well as workstations. You can change your password online (you will need your old password) or reset it (in this case you don't need your old password, the new one will be e-mailed to you).

Access

The interactive workstations can be used directly in Rhodes 625 with advance online reservations. Access to the lab requires door code provided to users at their initial appointment and training.

All workstations can be accessed remotely via ssh or VNC (Linux) and Remote Desktop (Windows). The names of workstations are listed in the top row of the reservations table on reservations web page, fully qualified domain names are workstationname.tc.cornell.edu where workstationname is the name from the table. If you want to access the workstations from outside Cornell, and you are a Cornell user, you need to set up VPN through CIT (http://www.cit.cornell.edu/services/vpn/). Remote access is only allowed within the reserved time slot.

If you are an external user with no Cornell Netid, please refer to this document for instructions on how to connect from the outside. You still need to consult  remote access information for general information.

Please refer to the remote access information for step-by-step instructions on how to access our lab workstations from various types of client computers. This document also covers common means for data transfer between your local computer and workstations. It is also possible to use Globus to transfer data and share data with other users (even non-BioHPC Lab users) - please see Globus at BioHPC Lab and Using Globus to Share Data for details.

It is possible to access and exchange files between external file servers and the Lab workstations, as well as accessing files on dedicated BioHPC file servers. Please refer to this document for details. All users have full write access to their home directories, they are mounted on all Lab workstations.

Access with VNC

You can access your Linux workstations using VNC protocol and operate remotely in a graphical desktop environment. You need to go to "My Reservations" page, and click on "Connect VNC" for a workstation you want to connect to. It will initialize your VNC session. If your password is not yet stored in VNC you will be asked first to enter it before the next page loads.

The preferred method of connecting by VNC is to use an external VNC client. Windows users can use Real VNC VNC Viewer while Mac users can use Chicken of the VNC or Real VNC VNC Viewer. When your session is initialized the page will display further instructions, including port number to which you need to connect. Launch your VNC viewer, type machine name and port number into appropriate fields (often they are used together machinename:portno) and connect.

You can control the resolution of your VNC window using a pull-down just below the reservations table on �My Reservations� page.

It is also possible to use Java applet as VNC Viewer. However, very likely you will need to lower your Java security settings to do so. It will launch a new browser window that will load a VNC Java applet - your browser and computer must support Java. Sometime, you will see a brower window with "Redirecting to VNC connection" but redirection does not work. In  this case, you need to close this new browser window, and  click the "open VNC applet window" link in the previoud window to launch the VNC applet. The applet opens a Java application window, please click "OK" on "Connection Details" form and then type in your password in "VNC authentication form" (user name is blank, and it should be!). If your password is correct a Linux desktop will open in the Java applet window. If prompt for "Authenticate", igore it and click "Cancel".

VNC connections are persistent, i.e. when you close the VNC window your desktop continues to run as long as your reservation is active. You can reconnect at any time from any computer that supports Java. NOTE: If your VNC window is plain black after reconnecting just click anywhere inside, desktop locks out after some inactivity time (like screensaver). If by any reason you want to restart your VNC session (for example you killed your desktop and now cannot do anything) just click on "Reset VNC" for your reservation on "My Reservations" page. 

How to run graphical applications (soffice, gsAssembler, etc.) while working remotely

There are two ways to run graphical applications remotely: via a VNC connection or via an X-windows client. VNC connection (described above) opens a graphical desktop remotely where graphical application can be launched.

VNC is usually slower than X-windows, but it is persistent, i.e. it keeps running even when disconnected. If you expect your graphical software to run for many hours it is safer to use VNC, since a network outage will kill X-windows connected program, while it will continue running under VNC.

Using an X-windows client is a simple procedure:

1. Make sure that a suitable X-windows manager software is installed and running on your local computer (i.e., the one you are connecting from). If you are connecting from a Linux or Mac machine, the X-windows manager should be already there by default. If you are connecting from a Windows PC, we recommend that you install a free version of MobaXterm and start it before connecting to the lab machines.

2. While making the ssh connection to a lab machine, remember to enable the X11 forwarding. On Linux or Mac machines, this is done by supplying the "-X" option to the ssh command (e.g., ssh -X cbsuwrkst2.tc.cornell.edu). On Windows machines, ssh connection is accomplished using one of client programs, such as PuTTy. Such clients should be configured to enable X11 forwarding. Please refer to your client's documentation for specific instructions.

Step-by-step instructions for installation and configuration of client software and the access procedure can be found here.

Running Galaxy on workstations

An experimental version of Galaxy is now available on Linux workstations. This is a single-user local instance that runs on a local file system (in /workdir/XXXX/galaxy-dist where XXXX is your login name) on a workstation. You can start it by typing command "rungalaxy" (without quotation marks) in a terminal window. Graphical display connection is required, either local (working at a monitor of an interactive workstation) or remote (X-Windows, or full remote desktop with VNC).

 

 

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