How to get to Hamilton
Option 1 - the standard way
1. ssh to mira: ssh username@mira.dur.ac.uk
2. ssh to hamilton: ssh username@hamilton.dur.ac.uk
Option 2 - the recommended way
1. Follow the instruction here: http://www.ch.cam.ac.uk/computing/scp-over-ssh-tunnel.
Basically you need to adjust your ssh config file.
How to copy files from and to Hamilton
Option 1 - the standard way
1. copy the file from your local folder to mira: scp -r filename username@mira.dur.ac.uk:.
2. ssh to mira as above.
3. copy the file from mira to Hamilton: scp -r filename username@hamilton.dur.ac.uk:.
Option 2 - the recommended way; if you have modified your ssh config file as above
1. scp -r filename username@hamilton.dur.ac.uk:.
Copying files from Hamilton works more or less in the same way. You just have to reverse the copy direction.
Compiling the code
1. You need to load the right compiler module(s): https://www.dur.ac.uk/cis/local/hpc/hamilton/modules/ and https://www.dur.ac.uk/cis/local/hpc/hamilton/preparing_jobs/.
2i. If you are using the lattice Boltzmann code, there is a Makefile. Google how to use a Makefile. Ask Ciro, Subkhi or Halim if you are lost.
2ii. If you are using the energy landscapes code, ask Halim. This is a bit more complicated.
The slurm queuing system
1. You need to read: https://www.dur.ac.uk/cis/local/hpc/hamilton/slurm/.
2. Script template for a serial job: https://www.dur.ac.uk/cis/local/hpc/hamilton/slurm/slurm.serial/.
3. Script template for a parallel job: https://www.dur.ac.uk/cis/local/hpc/hamilton/slurm/mpi.slurm/.
Running out of space
1. Read: https://www.dur.ac.uk/cis/local/hpc/hamilton/basic_system_usage/
2. Can you use /scratch or /tmp to run your jobs? If yes, problem solved.
3. If no, you need to get your quota increased. Speak to Halim about it.