Cluster Notes

MSI

1. Jupyter Notebook
2. FileZilla to transfer data files.
3. Cuda and GPU number setting

Use the same configuration as in CSE Labs, configure ssh to login without password.

CSE Labs

SSH

1. Set ssh to login without password. Do this on the local machine. Run the following step by step exactly. Check the reference for more detail.
   • Don’t change id_rsa to other names. Don’t enter passphrase. Just press Enter for three times.

     1	ssh-keygen -t rsa

   • Even if there are .ssh in the cluster, run it.

     1	ssh x500@csecluster mkdir -p .ssh

   • 1	cat .ssh/id_rsa.pub | ssh x500@csecluster 'cat >> .ssh/authorized_keys'

   • Now I can log in without a password.

     1	ssh x500@csecluster

2. Set ssh to switch among the clusters without a password. Do this on the cluster machine.
   • Login to one cluster first.
   • Run the following code inside the cluster.

     1 2	ssh-keygen -t rsa -P "" cat ~/.ssh/id_rsa.pub > ~/.ssh/authorized_keys

3. Set ssh aliases. Do this on the local machine. Check the reference for more detail.
   • Edit the ~/.ssh/config file. Can also do for phixx and cudaxx account.

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     # CSElabs Lind account Host cse-lind HostName CSEcluster User x500 IdentityFile ~/.ssh/id_rsa UseKeychain yes

   • Then we can directly connect to the cluster using the following.

     1	ssh cse-lind

4. Set ssh aliases among the terminals. Do this on the cluster machine.
   • Create and edit the ~/.ssh/config file.

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     Host phi01 HostName phi01.cselabs.umn.edu User x500 IdentityFile ~/.ssh/id_rsa

   • Then we can switch among the clusters. For example, inside the lind machine, switch to phi01 machine.

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     ssh phi01

Modify the prompt format.

Copy git-completion.bash and git-prompt.sh files to the cluster machine. Then add the following to the .bashrc file.

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# Enable tab completion
source ~/git-completion.bash

# colors!
green="\[\033[0;32m\]"
blue="\[\033[0;34m\]"
purple="\[\033[0;35m\]"
reset="\[\033[0m\]"

# Change command prompt
source ~/git-prompt.sh
export GIT_PS1_SHOWDIRTYSTATE=1
# '\u' adds the name of the current user to the prompt
# '\$(__git_ps1)' adds git-related stuff
# '\W' adds the name of the current directory
export PS1="$purple\u@$green\h\$(__git_ps1)$blue \W $ $reset"

Module issues

My modules are obsolete, and could not load hpc/openmpi module. After asking Prof. Saad for help, I got the solution. Edit ~/.bashrc file. Change the MODULESINIT as the following.

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MODULESINIT="/soft/rko-modules/tcl/init/bash"

Google Cloud

Setup SSH

I found Connect To The Server Using SSH very helpful. Different from the other clusters, we need first add the public key to the Google Cloud settings (in Edit), then use private key to build the ssh tunnel. Suppose the private key you generate is id_rsa. Then,

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ssh-add id_rsa
ssh -A account-name@external-ip

And modify .ssh/config:

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Host gcloud
    HostName external-ip
    User account-name
    IdentityFile ~/.ssh/id_rsa