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CS402: High Performance Computing
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The HPSC Cluster
The HPSC Cluster – deepthought
Seminar Plan
• Week 1 - Introduction to C
• Week 2 - Memory Management
• Week 3 - Compiler Options and Debugging
• Week 4 - The Cluster
• Week 5 - Performance Modelling
• Week 6-9 - Coursework Troubleshooting
The HPSC Cluster
Outline
1. The Cluster
2. Logging In
3. Software
4. Running Jobs
The HPSC Cluster
The Cluster
The HPSC cluster deepthought:
• 42 dual processor nodes.
• Fibre-optic interconnect.
The HPSC Cluster
Outline
1. The Cluster
2. Logging In
3. Software
4. Running Jobs
The HPSC Cluster
Logging in
• You should all have a username: hpc<uni number>
• Log in with ssh:
ssh <user>@deepthought.dcs.warwick.ac.uk
The HPSC Cluster
Outline
1. The Cluster
2. Logging In
3. Software
4. Running Jobs
The HPSC Cluster
The Module System
• The cluster uses the modules system to manage software, this allows
us to easily install and manage compilers, MPI, and other tools.
• Use the module list command to see currently loaded software.
• Use the module avail command to see the software available to
load.
• Finally, use the module load command to load in some software.
The HPSC Cluster
Loading MPI
• To load the MPI libraries and compilers, we need to load the
gnu/openmpi-1.2.7 module.
• We use the command:
module load gnu/openmpi-1.2.7
The HPSC Cluster
Outline
1. The Cluster
2. Logging In
3. Software
4. Running Jobs
The HPSC Cluster
The Queue
• Don’t run jobs on the head node!
• We submit jobs to the queue, which are then run on the compute
nodes.
• To queue jobs we use the qsub command.
The HPSC Cluster
Job Types (1/2) – Interactive
• The first job type is the interactive job, this allows you to act as
though the job was just a normal shell session.
• qsub -V -I -l nodes=1:ppn=2
• Now you can use mpirun to run your MPI job.
The HPSC Cluster
Job Types (1/2) – Interactive
• The problem with interactive jobs is that you can’t get many cores,
not very good for testing your code!
• The solution . . .
The HPSC Cluster
Job Types (2/2) – Batch
• Batch jobs!
• These are put in the queue and run by the scheduler whenever it
decides.
• Batch jobs require a submission script, which will run your program
for you.
• There are examples in the lab, so let’s get going!
The HPSC Cluster