Accessing BlueBEAR

Prerequisites

To access BlueBEAR, you will need to:

1. be a member of a BEAR project that has the BlueBEAR facility (see BEAR Project Registration)
2. have an active BEAR Linux account (see activate BEAR Linux account)

For the security of the service, access is limited to machines on the campus network. The University provides a VPN, as part of the Remote Access Service, which allows you to be able to connect to BlueBEAR remotely.

Accessing BlueBEAR using BEAR Portal

BEAR Portal provides web-based access to a range of BlueBEAR services, such as JupyterLab, RStudio, and GUI applications. It also provides access to a BlueBEAR shell and a route for submitting BlueBEAR compute jobs.
BEAR Portal is only available from on-campus or through the University Remote Access Service.

Accessing BlueBEAR using the command line

Command-line access to BlueBEAR is via one of multiple login nodes, available from the address bluebear.bham.ac.uk.

Warning

The login nodes are provided for the following types of tasks:

• submitting batch jobs
• checking on the status of running or queuing jobs
• editing files
• file and directory operations such as copying, moving/renaming etc.

Login nodes must not be used for work requiring significant CPU resources, including analysis jobs running from a Graphical User Interface (GUI) such as those provided by some engineering or Computational Fluid Dynamics (CFD) codes.
Jobs requiring significant CPU/memory or multiple cores should be run in the batch system.
GUI applications should be run in BEAR Portal or through an interactive job.

Any work that is consuming significant CPU on a login node, or causing problems such as poor responsiveness of the login nodes for other users, may be stopped without warning.

How to connect to the BlueBEAR command line

Lower-case Usernames

All account usernames on BlueBEAR are lower-case; thus, abc123 is a valid username whereas ABC123 is not.

Linux or macOS Windows

To connect to BlueBEAR on Linux or macOS, run the following command in your terminal (replacing _username_ with your username):

ssh _username_@bluebear.bham.ac.uk

Known Hosts file

It might be necessary to add or remove keys from the known_hosts file.
The method for doing this varies depending on operating system and is beyond the scope of this documentation – please refer to online sources for further information.

To connect to a BlueBEAR shell using Windows we recommend the following methods in order of preference:

1. Using WSL (Windows Subsystem for Linux), if this is available on your system.
   • If WSL is installed then please refer to the Linux or macOS method for connecting.
2. Using the terminal client that is built-in to BEAR Portal
3. Using PuTTY (optionally with Exceed). Expand the section below for further information.

Using PuTTY and Exceed on Windows

Downloading and Installing PuTTY

From a University-owned machine:

Go to the Software Centre (see KB11882) and search for “putty” via the Application search field (at the top-right of the page). This will allow you to install PuTTY without requiring administrative privileges.

From your own computer (requires administrative privileges):

Obtain the PuTTY Windows installer (not the standalone putty.exe) from the PuTTY download site; the installer has the name putty-*version*-installer.exe, where version is the version number. Following installation, PuTTY will be available from the PuTTY program group.

Installing, Configuring and Running Exceed

If graphics is not required then this section may be skipped.

Exceed and Exceed3D are available on site license from Software Sales and can be downloaded by going to https://mysoftware.bham.ac.uk (N.B. you’ll need to log-in using your University credentials). When Exceed v14 or higher is installed it creates a program group Open Text Exceed version-number, for example Open Text Exceed 14. This will be referred to as the OpenText Program Group in this note. Earlier versions will have a different Program Group for Exceed, probably involving Hummingbird Connectivity.

We are aware of multiple users who have had issues using newer applications, especially those based on the GTK+ version 3 toolkit, with older versions of Exceed. Please make sure you are running the latest version before reporting a fault to us.

Exceed is configured using the Xconfig program, found in the OpenText Program Group/Exceed Tools group. The first step in configuring Exceed is to set the security options. Since PuTTY uses X tunnelling, described later, it should be set to disallow any direct calls from external hosts. To do this, go to the Security, Access Control and System Administration section from the Xconfig page and select the No Host Access radio button in the Security/Host Access Control List section. Select the large green tick (Validate and Apply Changes) from the Xconfig toolbar at the top of the Xconfig window. Next select the Network and Communication tabbed sheet and select the Passive mode. Select the large green tick (Validate and Apply Changes) from the Xconfig toolbar at the top of the Xconfig window.

Exceed3D is required for applications that use OpenGL graphics, and should always be installed since it has no adverse impact if it is not required. Exceed3D is installed after installing and configuring Exceed.

Run Exceed3D by clicking Exceed in the OpenText Program Group when an Exceed icon will appear in the taskbar; no other output apart from the splash screen at startup will be given. Exceed3D is now running, ready to provide graphical support to Unix applications when required.

Configuring PuTTY

Running PuTTY from the PuTTY program group will open a display similar to the following:

Specify bluebear.bham.ac.uk as the Host Name, specify bluebear in the Saved Sessions field and select Save. This will enable the session named bluebear to be loaded for subsequent uses of PuTTY for non-graphical use of the cluster.

PuTTY needs to be configured to expect the correct character set that is used on BlueBEAR; without this there may be problems with displaying non-alphanumeric characters, and some programs expect to find a particular character set. Open the Window/Translation page and select UTF-8 as the Remote Character Set:

Next open the Connection/Data page and under Environment Variables put LANG in the Variable box and en_GB.UTF-8 in the Value box:

then click Add.

Open the Session page, ensure that bluebear is still shown in the Saved Sessions box and select Save.

Some networks may drop the session if no data is transferred in either direction after a certain time interval. If sessions are closing unexpectedly (most often with a Connection reset by peer or similar message) after they have been idle for a while, it may be worth specifying an interval for PuTTY to send data through the session at regular intervals in a way that does not disrupt the actual terminal session. If there is not a problem with sessions closing unexpectedly then the following change should not be made, since it can introduce other problems depending on the type of network.

To send these keep-alive messages open up the Connection menu and specify a value in the Seconds between keepalives field; in this example an interval of 10 minutes (600 seconds) has been specified:

Open the Session page, ensure that bluebear is still shown in the Saved Sessions box and select Save.

If graphical applications are to used, PuTTY needs to be told to forward graphical commands to the X server. To do this, open the Connections/SSH/X11 page:

and select the Enable X11 forwarding check box. Re-open the Session tab, ensure that bluebear is still shown in the Saved Sessions box and select Save.

Open a connection to bluebear with the Open button at the bottom of the page, or by double-clicking on the session name (bluebear in this example). The first time that PuTTY is used to connect to a server from a PC a prompt asking if you want to save the key is given. Accept the key and the logon prompt is given - subsequent logons to bluebear from the same PC will lead directly to the logon prompt. After logging on to BlueBEAR, ensure that Exceed is running by observing the Exceed icon in the taskbar; if not, double-click OpenText Program Group/Exceed, and an Exceed icon will appear in the taskbar; no other output will be given.

Issue the xclock command and a clock should appear on the monitor. Note that sometimes the clock will appear under other windows, so you may need to minimise the active window before you see the clock.

Common Problems

When you run a graphical application you may encounter the following errors:

Error	Solution
Error: Can't open display:	This means you have not ticked Enable X11 forwarding checkbox in PuTTY.
PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connection refused Error: Can't open display: localhost: 27.0	This means Exceed is not running.
XDMCP has timed out, no response from XDMCP daemon.	If you see this error, follow this procedure: Launch Exceed, then right-click on its taskbar icon and launch Xconfig. Choose “Communication” and change the “Mode” to “Passive”. Click “Save”.
Xlib: extension "MIT-SHM" missing on display "localhost:21.0".	This means you need to enable MIT-SHM in Exceed. Launch Xconfig, navigate to X Protocol, Extensions and then place a checkmark beside MIT-SHM, and hit Save.

Troubleshooting

Fix Login

There are several files that are run by default when logging on or off. If these become corrupted or deleted a login session will be in an unpredictable state; a typical example of this happening is a non-standard command prompt.
If this happens the default files can be restored using the command

fixlogin

which will warn if any existing, and possibly corrupt, files are to be overwritten.
To restore the default files without being prompted use the command

fixlogin -y