The latest upgrade to this partition is in production as of Monday Jan 25, and consists of 6 nodes. Hardware details:
Interactive sessions on the Biowulf cluster are allocated using the
sinteractive command if they need a walltime shorter than 36h.
NIMH users who need interactive sessions with walltimes longer than 36h can
[user@local_computer]$ ssh biowulf.nih.gov ... [user@biowulf]$ spersist --cpus-per-task=4 --mem=16g salloc.exe: Pending job allocation 24833446 salloc.exe: job 24833446 queued and waiting for resources salloc.exe: job 24833446 has been allocated resources salloc.exe: Granted job allocation 24833446 salloc.exe: Waiting for resource configuration salloc.exe: Nodes cn1501 are ready for job [user@cn1501 ~]$
We recommend allocating no less than 4 CPUs and 16 GB of memory for spersist sessions which will be used for graphical applications.
Like sinteractive sessions, spersist sessions are terminated if their controlling terminal exits. This happens, for example, if you disconnect from the NIH network to go home with your laptop. To maintain the spersist sessions even when you disconnect, they have to be attached to a persistent session on the biowulf login node. There are two ways of creating such persistent sessions:
spersist makes it easy to set
up tunnels between compute nodes and the login node (also see our
tunneling documentation). Such
tunnels are necessary for applications that start a server you would
want to connect to from your local workstation. Examples include
Jupyter, Tensorboard, and Paraview amongst others. Example session:
user@biowulf:~$ spersist --tunnel salloc.exe: Pending job allocation 26710013 salloc.exe: job 26710013 queued and waiting for resources salloc.exe: job 26710013 has been allocated resources salloc.exe: Granted job allocation 26710013 salloc.exe: Waiting for resource configuration salloc.exe: Nodes cn1501 are ready for job Created 1 generic SSH tunnel(s) from this compute node to biowulf for your use at port numbers defined in the $PORTn ($PORT1, ...) environment variables. Please create a SSH tunnel from your workstation to these ports on biowulf. On Linux/MacOS, open a terminal and run: ssh -L 45000:localhost:45000 biowulf.nih.gov For Windows instructions, see https://hpc.nih.gov/docs/tunneling user@cn1501:~$ echo $PORT1 45000 user@cn1501:~$
While you have active spersist or sinteractive sessions with tunnels, the
reconnect_tunnels command will reconstruct an ssh command you can
use to connect all required tunnels from your local workstation to biowulf. See
our tunneling documentation
To run lightweight graphical applications such as RStudio, please use NoMachine to connect to the login node and start your spersist session from within the NX session. This is analogous to using graphical applications with sinteractive
For more demanding graphics applications, VNC servers are available on the 'spersist nodes'. Using VNC requires an extra step. In your Biowulf shell, run spersist as before with the --vnc flag, then create a tunnel to the biowulf login node from your workstation. You are now ready to start up a VNC client from your workstation and connect to the VNC session. Note that you will have to supply your NIH username and password when prompted by the VNC client.
Sample session (user input in bold):
[user@biowulf ~]$ spersist --cpus-per-task=4 --mem=16g --vnc salloc.exe: Pending job allocation 24833781 salloc.exe: job 24833781 queued and waiting for resources salloc.exe: job 24833781 has been allocated resources salloc.exe: Granted job allocation 24833781 salloc.exe: Waiting for resource configuration salloc.exe: Nodes cn1501 are ready for job [+] Loading TurboVNC Starting VNC server ... please be patient... VNC server started on display 1 port 5901 VNC configured with SSH forwarding. Please create a tunnel from your workstation to biowulf.nih.gov port 45001: On Linux/MacOS, open a terminal and run: ssh -L 45001:localhost:45001 biowulf.nih.gov For Windows instructions see https://hpc.nih.gov/docs/tunneling Then connect your VNC client to localhost port 45001 The VNC connection will terminate when this shell exits. [user@cn1501 ~]$
VNC based spersist sessions cannot be started from within an NX session.
The firefox browser is available on the spersist nodes, but not from within the desktop environment menu. Open a terminal within the desktop environment and run module load firefox to make it available, then run firefox to start the browser.
If Firefox opens with the error dialog saying "Firefox is already running, but is not responding...", this is likely due to your having Firefox open elsewhere on the HPC systems (like the Biowulf login node or another spersist session). Closing the other session or using a different Firefox profile will get around this issue.
Please send questions and comments to firstname.lastname@example.org