changed user names

cluster_setup/README.md

@@ -4,6 +4,6 @@ This folder contains instructions and files for setting up the example cluster u
 
 # Cluster infrastructure
 
-The cluster we're using is running on the Heidelberg installation of the de.NBI cloud.  The current design is to create a 4 node cluster (1 controller, 3 compute nodes), with varying hardware specifications for each node so we can demonstrate resource managment.
+The cluster we're using is running on the Heidelberg installation of the [de.NBI cloud](https://www.denbi.de/cloud-overview/cloud-hd).  The current design is to create a 4 node cluster (1 controller, 3 compute nodes), with varying hardware specifications for each node so we can demonstrate resource managment.
 
-Job scheduling is doing using [https://slurm.schedmd.com/](SLURM) since it is (a) free and (b) mirrors the infrastructure we're currently using at EMBL.
+Job scheduling is doing using [SLURM](https://slurm.schedmd.com/) since it is (a) free and (b) mirrors the infrastructure we're currently using at EMBL.

cluster_setup/cloud_cluster_setup.md

 ## Generate _ubuntu_ user SSH keys
 
+We only need to do the is on the Master, since the home drive will be shared with the compute nodes
+
 ```
 ssh-keygen -t rsa -N "" -f $HOME/.ssh/id_rsa
 cat $HOME/.ssh/id_rsa.pub >> $HOME/.ssh/authorized_keys
@@ -21,7 +23,12 @@ sudo service nfs-kernel-server start
 ```
 sudo apt-get update
 sudo apt-get install nfs-common
+
+## add a line to automatically mount the shared home directory
 sudo cat '10.0.0.8:/home    /home   nfs auto,noatime,nolock,bg,nfsvers=4,intr,tcp,actimeo=1800 0 0' >> /etc/fstab
+
+## restart the machine
+sudo shutdown -r now
 ```
 
 
@@ -31,17 +38,34 @@ sudo cat '10.0.0.8:/home    /home   nfs auto,noatime,nolock,bg,nfsvers=4,intr,tc
 
 ```
 sudo apt-get install slurm-wlm
+
+## enable use of cgroups for process tracking and resource management
 sudo bash -c 'echo CgroupAutomount=yes >> /etc/slurm-llnl/cgroup.conf'
 sudo chown slurm:slurm /etc/slurm-llnl/cgroup.conf
+sudo sed -i 's/GRUB_CMDLINE_LINUX=""/GRUB_CMDLINE_LINUX="cgroup_enable=memory swapaccount=1"/g' /etc/default/grub
+sudo update-grub
+
+## put munge key in home directory so we can share it with the nodes
 sudo cp /etc/munge/munge.key $HOME/
+
+## download slurm.conf file (may require some editing of IP addresses etc)
+sudo wget https://raw.githubusercontent.com/grimbough/embl_swc_hpc/oct2017/cluster_setup/slurm.conf -O /etc/slurm-llnl/slurm.conf -o /dev/null
+sudo chown slurm:slurm /etc/slurm-llnl/slurm.conf
 ```
 
 ### Node
 
 ```
+## install slurm worker daemon
 sudo apt-get install slurmd
+
+## enable use of cgroups for process tracking and resource management
 sudo bash -c 'echo CgroupAutomount=yes >> /etc/slurm-llnl/cgroup.conf'
 sudo chown slurm:slurm /etc/slurm-llnl/cgroup.conf
+sudo sed -i 's/GRUB_CMDLINE_LINUX=""/GRUB_CMDLINE_LINUX="cgroup_enable=memory swapaccount=1"/g' /etc/default/grub
+sudo update-grub
+
+## copy the shared munge key and restart the service to start using it
 sudo cp /home/ubuntu/munge.key /etc/munge/munge.key
 sudo service munge restart
 ```

cluster_setup/user_delete.sh

@@ -5,5 +5,5 @@ n=40
 for i in `seq -w 1 ${n}`
 do
   echo $i;
-  userdel -rf test${i}
+  userdel -rf user${i}
 done;

cluster_setup/user_setup.sh

 #!/bin/bash
-## script to create 40 users called testXX with a default password
+## script to create 40 users called userXX with a default password
 ## and setup up ssh logins without asking for passwords & host checking
 
 n=40
@@ -7,20 +7,20 @@ for i in `seq -w 1 ${n}`
 do
   echo $i;
 
-  ## create n new user called testXX and create default password
-  adduser --gecos "" --disabled-password test${i}
-  echo test${i}:SoftwareC | chpasswd
+  ## create n new user called userXX and create default password
+  adduser --gecos "" --disabled-password user${i}
+  echo user${i}:SoftwareC | chpasswd
 
   ## create somewhere to store ssh configuration
-  mkdir -p /home/test${i}/.ssh
-  echo 'Host *\n  StrictHostKeyChecking no\n  ForwardX11 yes' > /home/test${i}/.ssh/config
+  mkdir -p /home/user${i}/.ssh
+  printf "Host *\n  StrictHostKeyChecking no\n  ForwardX11 yes\n" > /home/user${i}/.ssh/config
 
   ## generate a ssh key & copy to the list of authorized keys
-  ssh-keygen -f /home/test${i}/.ssh/id_rsa -t rsa -N ''
-  cp /home/test${i}/.ssh/id_rsa.pub /home/test${i}/.ssh/authorized_keys
+  ssh-keygen -f /home/user${i}/.ssh/id_rsa -t rsa -N ''
+  cp /home/user${i}/.ssh/id_rsa.pub /home/user${i}/.ssh/authorized_keys
 
   ## set new user as owner
-  chown -R test${i}:test${i} /home/test${i}/.ssh
-  chmod 600 /home/test${i}/.ssh/config
+  chown -R user${i}:user${i} /home/user${i}/.ssh
+  chmod 600 /home/user${i}/.ssh/config
 
 done