Servers at CCSE

The aim of this Wiki is to get you started with CCSE's servers. At this moment CCSE has one up and running server, BigFacet, and two servers under construction.

BigFacet

BigFacet is located on the 2nd floor, west wing of the Physics building. The server has 16 CPUs and 8 GPUs.

Get access to BigFacet

Send your UiO username to the administrator Alessandro Marin and ask to get access.

Log in to BigFacet

Once you have your credentials you can proceed with logging in to BigFacet.

Instructions for UNIX systems

The following will create a ProxyJump configuration, so that you can automatically connect to the remote server BigFacet through the uio bastion server. Create a file in ~/.ssh/config and paste the following text (replace username with your UiO username):

Host uio
    HostName login.uio.no
    User username

Host bigfacet
    HostName 193.157.210.121
    ProxyJump uio
    User username

Open a terminal and log in to the uio server:

ssh uio

Log in to BigFacet

ssh bigfacet

Please change your password the first time you log in (see instructions below)!

You can configure the ssh program on your local machine to remember your credentials so that you do not have to type in the passwords again:
ssh-keygen
ssh-copy-id uio
ssh-copy-id bigfacet
Instructions for Windows systems

Use WinSCP and plink (part of the PuTTY package). In the Login Dialog use fyslab-compphys:

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Next, the Advanced Site Settings dialog allows you to setup your session to tunnel through SSH connection through login.uio.no. The "Local proxy command" needs to be set to:

plink.exe -pw %pass %user@%proxyhost -nc %host:%port

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Finally, configure a second hop through motstand.uio.no on the Tunnel page of Advanced site settings dialog:

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Checking your configuration on BigFacet

If the login was successful, you should change your password.

username@bigfacet:~$ passwd username
username@bigfacet:~$ exit

You might want to check that you are in your home folder and that you have access to a personal folder in /datastorage/:

username@bigfacet:~$ pwd
/home/username
username@bigfacet:~$ ls /datastorage/username
job.sh

You probably want to use the bash shell on BigFacet. Check the shell in your session with:

$ echo ${SHELL}
/bin/sh    #NB: this is not the bash shell

If you need to change the default shell to bash:

$ chsh -s /bin/bash

After a new login the shell should be bash:

username@bigfacet:~$ echo ${SHELL}
/bin/bash

BigFacet/Slurm basics

The disk hosting BigFacet's OS has limited space, so store the least amount of files in your home directory (expecially not dump files!). For big files use your folder on the /datastorage directory. There you can find the sample script job.sh:

username@bigfacet:~$ cd /datastorage/username
username@bigfacet:~$ cat job.sh
#!/bin/bash
#SBATCH --partition=normal
#SBATCH --ntasks=1
#SBATCH --gres=gpu:1
#SBATCH --job-name=sphere
#SBATCH --cpus-per-task=2
  
echo $CUDA_VISIBLE_DEVICES
mpirun -n 1 lmp -k on g 1 -sf kk -pk kokkos newton on neigh half binsize 7.5 -in run.in

# Replace 1 everywhere with the number of GPUs.
# binsize 7.5 is for SiO2 Vashishta, remove or adjust otherwise.

which can be launched using the sbatch command.

Tags: BigFacet, Servers and operating services, CCSE, Molecular modelling, Molecular dynamics, quantum physics By Alessandro Marin
Published Aug. 18, 2020 11:51 AM - Last modified Mar. 11, 2021 2:18 PM