Using the Weizmann Cluster

Nov 162015

Overview

• Weizmann Cluster• Connection Basics• Getting a Desktop View• Working on cluster machines• GPU

• For many more details, please visit: http://math96-lx/

Cluster Structure

• The Weizmann cluster• Two types of machines:

– Workstations: Math-lx : for lightweight interactive sessions (math01-lx, math02-lx ,…, math13-lx)

– Cluster Machines: MCluster01 , MCluster03 : clusters of strong machines designed for the “heavy lifting” (multiple cores, lots of RAM)

– In MCluster01 we have some GPU machines (more on this later)

General Flow

1. Connect to a workstation2. get a GUI using VNC3. Connect to a cluster machine via the

workstation4. Do some work

Connecting to a Workstation:Putty

• SSH : a protocol enabling a secure connection to another host

• Putty is a windows SSH client. • To connect* to one of the math-lx

machines:– Launch Putty– In the session->Host name field, enter

e.g: math05-lx• In the terminal window, enter

user/password as required*Assuming you’re inside the Lab

Getting a Desktop GUI: > VNCserver

• VNC allows remote connection to a desktop• Install VNC on your windows machine. Available

clients: UltraVNC, TightVNC• On remote machine, start a VNC server, as follows:

> vncserver_:<display>_-geometry_<Width>x<Height>

• Example> vncserver :500 -geometry <1280>x<1024>

• Without the <display argument> a port will be chosen arbitrarily and VNC will output the chosen number

These are spaces!

VNC continued

• The <display> number allows concurrent vnc servers (e.g for different users).

• Once the VNC server is running, run UltraVNC on your PC.

• enter in the “vnc server” field : • <your_host>:N where

N=5900+DisplayNumber• Connect• Congratulations! You just started anInteractive session

Ending a session:> vncserver -kill

• Closing a VNC viewer will not end you session! • Instead, enter >vncserver –kill :N

Where N is the chosen display port.

Working on the Cluster

• The machines on the cluster are split into different queues, according to the memory, number of cores, etc. of the machines

• Usually you do not connect explicitly to a specific machine, but request a machine from one of the queues, depending on your needs

• To see the queue load and available queues, go to : http://math96-lx/?page_id=390

• To see load of all machines on a cluster

Connecting to a Cluster Machine

• To request a cluster machine, use:>ssh -X mcluster01 qsh -q amd64g.q -display HOST$DISPLAY

• This does the following:– Submits an interactive session request to be

fullfilled by a machine from the specified queue , in this case amd64g.q

– Forwards the graphics to your host and display• For a GPU machine the queue is gpu.q >ssh -X mcluster01 qsh -q gpu.q -display HOST$DISPLAY• If you need a specific node, add -l hostname=n82

GPU machines

• Currently 6 GPU machines:– node 82 - 2 x 12GB GPU – node 81 - 2 x 12GB GPU– node 80 - 2 x 12GB GPU– node 79 - 2 x 12GB GPU– node 78 - 1 x 6GB GPU– node 73 - 1 x 12GB GPU + 1 x 6GB GPU

512GB RAM

256GB RAM

Monitoring GPU memory• GPU memory is a shared• In principle, as long as there’s free memory, it

supports more concurrent users• nvidia-smi• To see continuously: use watch>watch –n .5 nvidia-smi(this will update the status every 0.5 seconds)

Summary

• Putty + VNC connect to math_-lx• Ssh+qsh : connect to cluster machine• Ssh+qsh+gpu.q : connect to GPU machine• No need to memorize! Helpful scripts on

course website – http://www.wisdom.weizmann.ac.il/~

vision/courses/2016_1/DNN/utils.html• http://math96-lx is your friend!